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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM, Gibb K, Coventry K, Collignon P, Cassar S, Allerberger F, Begum A, Hossain ZZ, Worrell C, Vandenberg O, Pieters I, Victorien DT, Gutierrez ADS, Soria F, Grujić VR, Mazalica N, Rahube TO, Tagliati CA, Rodrigues D, Oliveira G, de Souza LCR, Ivanov I, Juste BI, Oumar T, Sopheak T, Vuthy Y, Ngandjio A, Nzouankeu A, Olivier ZAAJ, Yost CK, Kumar P, Brar SK, Tabo DA, Adell AD, Paredes-Osses E, Martinez MC, Cuadros-Orellana S, Ke C, Zheng H, Baisheng L, Lau LT, Chung T, Jiao X, Yu Y, JiaYong Z, Morales JFB, Valencia MF, Donado-Godoy P, Coulibaly KJ, Hrenovic J, Jergović M, Karpíšková R, Deogratias ZN, Elsborg B, Hansen LT, Jensen PE, Abouelnaga M, Salem MF, Koolmeister M, Legesse M, Eguale T, Heikinheimo A, Le Guyader S, Schaeffer J, Villacis JE, Sanneh B, Malania L, Nitsche A, Brinkmann A, Schubert S, Hesse S, Berendonk TU, Saba CKS, Mohammed J, Feglo PK, Banu RA, Kotzamanidis C, Lytras E, Lickes SA, Kocsis B, Solymosi N, Thorsteinsdottir TR, Hatha AM, Ballal M, Bangera SR, Fani F, Alebouyeh M, Morris D, O’Connor L, Cormican M, Moran-Gilad J, Battisti A, Diaconu EL, Corno G, Di Cesare A, Alba P, Hisatsune J, Yu L, Kuroda M, Sugai M, Kayama S, Shakenova Z, Kiiyukia C, Ng’eno E, Raka L, Jamil K, Fakhraldeen SA, Alaati T, Bērziņš A, Avsejenko J, Kokina K, Streikisa M, Bartkevics V, Matar GM, Daoud Z, Pereckienė A, Butrimaite-Ambrozeviciene C, Penny C, Bastaraud A, Rasolofoarison T, Collard JM, Samison LH, Andrianarivelo MR, Banda DL, Amin A, Rajandas H, Parimannan S, Spiteri D, Haber MV, Santchurn SJ, Vujacic A, Djurovic D, Bouchrif B, Karraouan B, Vubil DC, Pal P, Schmitt H, van Passel M, Jeunen GJ, Gemmell N, Chambers ST, Mendoza FP, Huete-Pιrez J, Vilchez S, Ahmed AO, Adisa IR, Odetokun IA, Fashae K, Sørgaard AM, Wester AL, Ryrfors P, Holmstad R, Mohsin M, Hasan R, Shakoor S, Gustafson NW, Schill CH, Rojas MLZ, Velasquez JE, Magtibay BB, Catangcatang K, Sibulo R, Yauce FC, Wasyl D, Manaia C, Rocha J, Martins J, Álvaro P, Di Yoong Wen D, Shin H, Hur HG, Yoon S, Bosevska G, Kochubovski M, Cojocaru R, Burduniuc O, Hong PY, Perry MR, Gassama A, Radosavljevic V, Tay MYF, Zuniga-Montanez R, Wuertz S, Gavačová D, Pastuchová K, Truska P, Trkov M, Keddy K, Esterhuyse K, Song MJ, Quintela-Baluja M, Lopez MG, Cerdà-Cuéllar M, Perera RRDP, Bandara NKBKRGW, Premasiri HI, Pathirage S, Charlemagne K, Rutgersson C, Norrgren L, Örn S, Boss R, Van der Heijden T, Hong YP, Kumburu HH, Mdegela RH, Hounmanou YMG, Chonsin K, Suthienkul O, Thamlikitkul V, de Roda Husman AM, Bidjada B, Njanpop-Lafourcade BM, Nikiema-Pessinaba SC, Levent B, Kurekci C, Ejobi F, Kalule JB, Thomsen J, Obaidi O, Jassim LM, Moore A, Leonard A, Graham DW, Bunce JT, Zhang L, Gaze WH, Lefor B, Capone D, Sozzi E, Brown J, Meschke JS, Sobsey MD, Davis M, Beck NK, Sukapanpatharam P, Truong P, Lilienthal R, Kang S, Wittum TE, Rigamonti N, Baklayan P, Van CD, Tran DMN, Do Phuc N, Kwenda G, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2023; 14:178. [PMID: 36635285 PMCID: PMC9837105 DOI: 10.1038/s41467-023-35890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick Munk
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christian Brinch
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N. Petersen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S. Hendriksen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S. Kjeldgaard
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M. Aarestrup
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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Gonçalves J, Koritnik T, Mioč V, Trkov M, Bolješič M, Berginc N, Prosenc K, Kotar T, Paragi M. Detection of SARS-CoV-2 RNA in hospital wastewater from a low COVID-19 disease prevalence area. Sci Total Environ 2021; 755:143226. [PMID: 33176933 PMCID: PMC7591869 DOI: 10.1016/j.scitotenv.2020.143226] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 05/18/2023]
Abstract
Previous studies on SARS-CoV and MERS-CoV reported the detection of viral RNA in the stool of both symptomatic and asymptomatic individuals. These clinical observations suggest that municipal and hospital wastewater from affected communities may contain SARS-CoV-2 RNA. Recent studies have also reported the presence of SARS-CoV-2 RNA in human feces. Wastewater-based epidemiology (WBE) is a promising approach to understand the prevalence of viruses in a given catchment population, as wastewater contains viruses from symptomatic and asymptomatic individuals. The current study reports the first detection of SARS-CoV-2 RNA in untreated wastewater in Slovenia. Two sizes of centrifugal filters were tested: 30 kDa and 10 kDA AMICON® Ultra-15 Centrifugal Filters, where 10 kDA resulted in a higher concentration factor and higher recovery efficiency. The results in hospital wastewater show that WBE can be used for monitoring COVID -19 and could be applied in municipal wastewater treatment plants as a potential complementary tool for public health monitoring at population level.
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Affiliation(s)
- José Gonçalves
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia.
| | - Tom Koritnik
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Verica Mioč
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Marija Trkov
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Maja Bolješič
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Nataša Berginc
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Katarina Prosenc
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
| | - Tadeja Kotar
- Department of Infectious Diseases, University Medical Center, Ljubljana, Slovenia
| | - Metka Paragi
- Department for Public Health Microbiology, National Laboratory for Health, Environment and Food, Ljubljana, Slovenia
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Krizman M, Avgustin JA, Zdovc I, Golob M, Trkov M, Ciglenecki UJ, Biasizzo M, Kirbis A. Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates. J Food Prot 2017; 80:113-120. [PMID: 28221881 DOI: 10.4315/0362-028x.jfp-16-214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibiotics have always appeared miraculous, saving innumerable lives. However, the unwise use of antimicrobial drugs has led to the appearance of resistant bacteria. The purpose of this study was to evaluate antimicrobial resistance in Escherichia coli (n =160) isolated from food of animal origin. The focus was on E. coli -producing extended-spectrum β-lactamases. E. coli was chosen because it is a part of the normal microbiota in mammals and can enter the food chain during slaughtering and food manipulation. Subsequently, its resistance genes can be transferred to pathogenic bacteria and human microbiota. Phenotypic and genotypic analyses of selected antimicrobial resistances were carried out together with a molecular analysis of virulence genes. E. coli isolates from food of animal origin were compared with clinical E. coli strains isolated from the human intestinal tract. Extended-spectrum β-lactamase-producing E. coli isolates were found in 9.4% of food isolates and in 1.8% of intestinal isolates. Phylogenetically, the majority of food (86.3%) and intestinal E. coli (58.1%) isolates were found to belong to the commensal phylogenetic groups A and B1. The distribution of 4 of 14 analyzed virulence factors was similar in the food and intestinal isolates. Strains isolated from food in Slovenia harbored resistance genes and virulence factors, which can constitute a problem for food safety if not handled properly.
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Affiliation(s)
- Manja Krizman
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Majda Golob
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marija Trkov
- Department for Public Health Microbiology, Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia
| | - Urska Jamnikar Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Majda Biasizzo
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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Kovač J, Čadež N, Stessl B, Stingl K, Gruntar I, Ocepek M, Trkov M, Wagner M, Smole Možina S. High genetic similarity of ciprofloxacin-resistant Campylobacter jejuni in central Europe. Front Microbiol 2015; 6:1169. [PMID: 26557112 PMCID: PMC4615952 DOI: 10.3389/fmicb.2015.01169] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/09/2015] [Indexed: 12/31/2022] Open
Abstract
Campylobacteriosis is the leading zoonosis in the European Union with the majority of cases attributed to Campylobacter jejuni. Although the disease is usually self-limiting, some severe cases need to be treated with antibiotics, primarily macrolides and quinolones. However, the resistance to the latter is reaching alarming levels in most of the EU countries. To shed light on the expansion of antibiotic resistance in central Europe, we have investigated genetic similarity across 178 ciprofloxacin-resistant C. jejuni mostly isolated in Slovenia, Austria and Germany. We performed comparative genetic similarity analyses using allelic types of seven multilocus sequence typing housekeeping genes, and single nucleotide polymorphisms of a quinolone resistance determining region located within the DNA gyrase subunit A gene. This analysis revealed high genetic similarity of isolates from clonal complex ST-21 that carry gyrA allelic type 1 in all three of these central-European countries, suggesting these ciprofloxacin resistant isolates arose from a recent common ancestor and are spread clonally.
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Affiliation(s)
- Jasna Kovač
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
| | - Beatrix Stessl
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary MedicineVienna, Austria
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
| | - Igor Gruntar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of LjubljanaLjubljana, Slovenia
| | - Matjaž Ocepek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of LjubljanaLjubljana, Slovenia
| | - Marija Trkov
- Department for Public Health Microbiology Ljubljana, Centre for Medical Microbiology, National Laboratory of Health, Environment and FoodLjubljana, Slovenia
| | - Martin Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary MedicineVienna, Austria
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
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Abstract
A molecular method for the detection of Salmonella enterica strains based on 16S rRNA sequence analysis was developed by a modification of the previously described PCR primer 16SFI [J. Appl. Bacteriol. 80 (1996) 659], which was combined with a newly developed primer annealing at the position 66-82. Only approximately two thirds of now determined Salmonella 16S rRNA sequences contained a region identical to the 16SFI primer sequence and the reverse primer 16SIII was also not specific. Combined, these two primers have been claimed to allow the specific detection of all Salmonella; however, in this study, they did not recognize S. bongori and 3 out of 78 tested S. enterica strains. They also identified some of the tested Enterobacter cloacae strains as Salmonella. On the contrary, the new primer pair, MINf and MINr, made it possible to recognize correctly all of the 78 tested S. enterica strains, representing 31 different Salmonella serovars. None of the 23 non-Salmonella strains from the related gamma-proteobacterial genera was incorrectly recognized as belonging to S. enterica.
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Affiliation(s)
- Marija Trkov
- Zootechnical Department, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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Trkov M, Accetto T, Kostanjsek R, Avgustin G. Preliminary characterization of a tentatively novel rumen bacterial species from the genus Treponema. Folia Microbiol (Praha) 2001; 46:91-3. [PMID: 11501488 DOI: 10.1007/bf02825896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A new spirochetal strain was isolated from the rumen of a black-and-white Holstein cow and preliminarily characterized. The sugar fermentation tests and morphological observations indicated this organism to be a member of a novel, as yet undescribed spirochetal rumen species. The small subunit ribosomal RNA genes were amplified and the PCR products were cut with the restriction endonucleases TaqI, DdeI, HhaI and Sau3AI. The comparison of the observed RFLP with the hypothetical fragment lengths of the computer analyzed 16S rRNA sequences from the type strains of the ruminal spirochetes Treponema bryantii and T. saccharophilum confirmed the tentative novel identification. Transmission electron microscopy showed that the bacterium has the typical spirochetal structures, i.e. the outer sheath, the protoplasmic cylinder and the axial filament (it is not yet clear how many flagella compose the filament). An additional extracellular structure was observed which appeared as an exocytoplasmic polar flagellum, approximately 2 microns long and protruding from one tip of the cell. The average size of the cells was 0.5 x 10-15 microns and the wavelengths and the amplitudes of the primary coils were 2.9 and 1.3 microns, respectively.
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Affiliation(s)
- M Trkov
- Zootechnical Department, Biotechnical Faculty, University of Ljubljana, 1230 Domzale, Slovenia
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