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Jarocki VM, Li D, Bogema DR, Yam J, Jenkins C, Hai FI, Djordjevic SP. Comparative genomic analysis of ESBL-selected and non-selected Escherichia coli in Australian wastewater: Elucidating differences in diversity, antimicrobial resistance, and virulence profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175079. [PMID: 39094658 DOI: 10.1016/j.scitotenv.2024.175079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/07/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Extended-spectrum β-lactamases (ESBLs)-producing E. coli have been proposed as an indicator bacterium for antimicrobial resistance (AMR) surveillance within a OneHealth framework. However, it is important to understand the effects and potential biases ESBL-selection has on E. coli populations. Utilising whole genome sequencing, this study compared 80 ESBL-selected E. coli isolates with 201 non-selected isolates from Australian wastewater. The findings revealed significant variations between these cohorts in genetic diversity, AMR profiles, and carriage of virulence-associated genes (VAGs), plasmids, and the transmissible Locus of Stress Tolerance (tLST), a genomic island that imparts resistance to extreme heat and chlorination. The study highlights the predominance of certain sequence types (STs), particularly ST131 (75 % clade A), in ESBL-selected isolates (40 % vs 2 %) and overall the ESBL-selected isolates were largely multidrug-resistant (MDR), predominantly carrying genes for resistance to aminoglycosides, extended-spectrum β-lactams, fluoroquinolone, macrolides, sulphonamides/trimethoprim, and tetracyclines. The ESBLs identified were almost exclusively blaCTX-M genes, most commonly blaCTX-M-15 > blaCTX-M-27 > blaCTX-M-14. These were predominately carried on IncF plasmids or chromosomally (always ISEcp1 associated), in equal numbers. In contrast, 80 % of non-selected isolates carried no acquired ARGs, and none carried blaCTX-M genes. In both cohorts, extraintestinal pathogenic E. coli (ExPEC) was the dominate pathotype (35 % total) with few (4 % total) intestinal pathogenic E. coli pathotypes identified (aEPEC > ETEC > EAEC). Nevertheless, some clinically important genes were only identified in the non-selected group, namely tigecycline-resistance gene tet(X4) and AmpC ESBL blaCMY-2. Additionally, the presence of tLST, associated with higher metal resistance gene carriage (Ag, As, Cu, Hg, Ni), in a substantial portion of non-selected isolates (20 % vs 0 %), underscores environmental pressures shaping bacterial populations in wastewater ecosystems. These insights are important for developing comprehensive, less biased genomic surveillance strategies to understand and manage public health threats posed by pathogenic E. coli and AMR.
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Affiliation(s)
- Veronica M Jarocki
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food and Environment (CRC SAAFE), South Australia, Australia.
| | - Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Daniel R Bogema
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Cheryl Jenkins
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Faisal I Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia.
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Yu D, Andersson-Li M, Maes S, Andersson-Li L, Neumann NF, Odlare M, Jonsson A. Development of a logic regression-based approach for the discovery of host- and niche-informative biomarkers in Escherichia coli and their application for microbial source tracking. Appl Environ Microbiol 2024; 90:e0022724. [PMID: 38940567 PMCID: PMC11267920 DOI: 10.1128/aem.00227-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
Microbial source tracking leverages a wide range of approaches designed to trace the origins of fecal contamination in aquatic environments. Although source tracking methods are typically employed within the laboratory setting, computational techniques can be leveraged to advance microbial source tracking methodology. Herein, we present a logic regression-based supervised learning approach for the discovery of source-informative genetic markers within intergenic regions across the Escherichia coli genome that can be used for source tracking. With just single intergenic loci, logic regression was able to identify highly source-specific (i.e., exceeding 97.00%) biomarkers for a wide range of host and niche sources, with sensitivities reaching as high as 30.00%-50.00% for certain source categories, including pig, sheep, mouse, and wastewater, depending on the specific intergenic locus analyzed. Restricting the source range to reflect the most prominent zoonotic sources of E. coli transmission (i.e., bovine, chicken, human, and pig) allowed for the generation of informative biomarkers for all host categories, with specificities of at least 90.00% and sensitivities between 12.50% and 70.00%, using the sequence data from key intergenic regions, including emrKY-evgAS, ibsB-(mdtABCD-baeSR), ompC-rcsDB, and yedS-yedR, that appear to be involved in antibiotic resistance. Remarkably, we were able to use this approach to classify 48 out of 113 river water E. coli isolates collected in Northwestern Sweden as either beaver, human, or reindeer in origin with a high degree of consensus-thus highlighting the potential of logic regression modeling as a novel approach for augmenting current source tracking efforts.IMPORTANCEThe presence of microbial contaminants, particularly from fecal sources, within water poses a serious risk to public health. The health and economic burden of waterborne pathogens can be substantial-as such, the ability to detect and identify the sources of fecal contamination in environmental waters is crucial for the control of waterborne diseases. This can be accomplished through microbial source tracking, which involves the use of various laboratory techniques to trace the origins of microbial pollution in the environment. Building on current source tracking methodology, we describe a novel workflow that uses logic regression, a supervised machine learning method, to discover genetic markers in Escherichia coli, a common fecal indicator bacterium, that can be used for source tracking efforts. Importantly, our research provides an example of how the rise in prominence of machine learning algorithms can be applied to improve upon current microbial source tracking methodology.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sharon Maes
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
| | - Lili Andersson-Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Norman F. Neumann
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Monica Odlare
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
| | - Anders Jonsson
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
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Yu D, Stothard P, Neumann NF. Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments. Sci Rep 2024; 14:13478. [PMID: 38866876 PMCID: PMC11169474 DOI: 10.1038/s41598-024-64241-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
The Escherichia coli species is comprised of several 'ecotypes' inhabiting a wide range of host and natural environmental niches. Recent studies have suggested that novel naturalized ecotypes have emerged across wastewater treatment plants and meat processing facilities. Phylogenetic and multilocus sequence typing analyses clustered naturalized wastewater and meat plant E. coli strains into two main monophyletic clusters corresponding to the ST635 and ST399 sequence types, with several serotypes identified by serotyping, potentially representing distinct lineages that have naturalized across wastewater treatment plants and meat processing facilities. This evidence, taken alongside ecotype prediction analyses that distinguished the naturalized strains from their host-associated counterparts, suggests these strains may collectively represent a novel ecotype that has recently emerged across food- and water-associated engineered environments. Interestingly, pan-genomic analyses revealed that the naturalized strains exhibited an abundance of biofilm formation, defense, and disinfection-related stress resistance genes, but lacked various virulence and colonization genes, indicating that their naturalization has come at the cost of fitness in the original host environment.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB, Canada.
- Antimicrobial Resistance-One Health Consortium, Calgary, AB, Canada.
| | - Paul Stothard
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance-One Health Consortium, Calgary, AB, Canada
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Moinet M, Collis RM, Rogers L, Devane ML, Biggs PJ, Stott R, Marshall J, Muirhead R, Cookson AL. Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples. J Microbiol Methods 2024; 220:106909. [PMID: 38432551 DOI: 10.1016/j.mimet.2024.106909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV). Reliable and specific techniques for their identification are required to avoid confounding microbial water quality assessments. To address this, a multiplex droplet digital PCR (ddPCR) assay targeting lipB (E. coli and E. ruysiae) and bglC (E. marmotae) was designed. The ddPCR performance was assessed using in silico analysis; genomic DNA from 40 local, international, and reference strains of target and non-target coliforms; and spiked water samples in a range relevant to water quality managers (1 to 1000 cells/100 mL). Results were compared to an analogous quantitative PCR (qPCR) and the Colilert method. Both PCR assays showed excellent sensitivity with a limit of detection of 0.05 pg/μL and 0.005 pg/μl for ddPCR and qPCR respectively, and of quantification of 0.5 pg/μL of genomic DNA. The ddPCR allowed differentiation and quantification of three Escherichia species per run by amplitude multiplexing and showed a high concordance with concentrations measured by Colilert once proportional bias was accounted for. In silico specificity testing underlined the possibility to further detect and distinguish Escherichia cryptic clade VI. Finally, the applicability of the ddPCR was successfully tested on environmental water samples where E. marmotae and E. ruysiae potentially confound E. coli counts based on the Most Probable Number method, highlighting the utility of this novel ddPCR as an efficient and rapid discriminatory test to improve water quality assessments.
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Affiliation(s)
- Marie Moinet
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Rose M Collis
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Lynn Rogers
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Megan L Devane
- Institute of Environmental Science and Research Ltd. (ESR), 27 Creyke Rd, Ilam, 8041 Christchurch, New Zealand.
| | - Patrick J Biggs
- Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, School of Natural Sciences, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Gate 10 Silverdale Road, Hillcrest, 3216 Hamilton, New Zealand.
| | - Jonathan Marshall
- Massey University, School of Mathematical and Computational Sciences, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Richard Muirhead
- AgResearch Ltd., Ethical Agriculture, Invermay, 176 Puddle Alley, 9092, Mosgiel, New Zealand.
| | - Adrian L Cookson
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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Puljko A, Babić I, Rozman SD, Barišić I, Jelić M, Maravić A, Parać M, Petrić I, Udiković-Kolić N. Treated municipal wastewater as a source of high-risk and emerging multidrug-resistant clones of E. coli and other Enterobacterales producing extended-spectrum β-lactamases. ENVIRONMENTAL RESEARCH 2024; 243:117792. [PMID: 38048868 DOI: 10.1016/j.envres.2023.117792] [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: 09/13/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a major public health problem, and wastewater from municipal wastewater treatment plants (WWTPs) is a potential means of spreading them into the environment and community. Our objective was to isolate ESBL-producing E. coli and other Enterobacterales from wastewater after treatment at Croatia's largest WWTP and to characterize these isolates by phenotypic and genotypic testing. Of the 200 bacterial isolates, 140 were confirmed as Enterobacterales by MALDI-TOF MS, with Escherichia coli and Klebsiella spp. predominating (69% and 7%, respectively). All 140 enterobacterial isolates were multidrug-resistant (MDR) and produced ESBLs. The most prevalent ESBL genes among the isolates tested were blaCTX-M-15 (60%), blaTEM-116 (44%), and blaCTX-M-3 (13%). Most isolates (94%) carried more than one ESBL gene in addition to blaCTX-M. Genes encoding plasmid-mediated AmpC, most notably blaEBC, were detected in 22% of isolates, whereas genes encoding carbapenemases (blaOXA-48, blaNDM-1, blaVIM-1) were less represented (10%). In E. coli, 9 different sequence types (ST) were found, with the emerging high-risk clones ST361 (serotype A-O9:H30) and pandemic ST131 (serotype B2-O25:H4) predominating (32% and 15%, respectively). Other high-risk E. coli clones included ST405 (3%), ST410 (3%), CC10 (3%), ST10 (3%), and ST38 (2%), and emerging clones included ST1193 (2%) and ST635 (2%). Whole-genome sequencing of three representative E. coli from two dominant clone groups (ST361 and ST131) and one extensively drug-resistant K. oxytoca revealed the presence of multiple plasmids and resistance genes to several other antibiotic classes, as well as association of the blaCTX-M-15 gene with transposons and insertion sequences. Our findings indicate that treated municipal wastewater contributes to the spread of emerging and pandemic MDR E. coli clones and other enterobacterial strains of clinical importance into the aquatic environment, with the risk of reintroduction into humans.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210, Vienna, Austria
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000, Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000, Split, Croatia
| | - Marija Parać
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia.
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Bazalar-Gonzales J, Silvestre-Espejo T, Rodríguez Cueva C, Carhuaricra Huamán D, Ignación León Y, Luna Espinoza L, Rosadio Alcántara R, Maturrano Hernández L. Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon. Front Vet Sci 2024; 10:1340428. [PMID: 38292135 PMCID: PMC10825005 DOI: 10.3389/fvets.2023.1340428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are on the WHO priority pathogens list because they are associated with high mortality, health-care burden, and antimicrobial resistance (AMR), a serious problem that threatens global public health and should be addressed through the One Health approach. Non-human primates (NHP) have a high risk of acquiring these antibiotic-resistant bacteria due to their close phylogenetic relationship with humans and increased anthropogenic activities in their natural environments. This study aimed to detect and analyze the genomes of ESBL-producing Escherichia coli (ESBL-producing E. coli) in NHP from the Peruvian Amazon. Materials and methods We collected a total of 119 fecal samples from semi-captive Saguinus labiatus, Saguinus mystax, and Saimiri boliviensis, and captive Ateles chamek, Cebus unicolor, Lagothrix lagothricha, and Sapajus apella in the Loreto and Ucayali regions, respectively. Subsequently, we isolated and identified E. coli strains by microbiological methods, detected ESBL-producing E. coli through antimicrobial susceptibility tests following CLSI guidelines, and analyzed their genomes using previously described genomic methods. Results We detected that 7.07% (7/99) of E. coli strains: 5.45% (3/55) from Loreto and 9.09% (4/44) from Ucayali, expressed ESBL phenotype. Genomic analysis revealed the presence of high-risk pandemic clones, such as ST10 and ST117, carrying a broad resistome to relevant antibiotics, including three blaCTX-M variants: blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenomic analysis confirmed the clonal relatedness of high-risk lineages circulating at the human-NHP interface. Additionally, two ESBL-producing E. coli strains were identified as EPEC (eae) and ExPEC according to their virulence profiles, and one more presented a hypermucoviscous phenotype. Discussion We report the detection and genomic analysis of seven ESBL-producing E. coli strains carrying broad resistome and virulence factors in NHP from two regions of the Peruvian Amazon. Some of these strains are closely related to high-risk pandemic lineages previously reported in humans and domestic animals, highlighting the negative impact of anthropogenic activities on Amazonian wildlife. To our knowledge, this is the first documentation of ESBL-producing E. coli in NHP from the Amazon, underscoring the importance of adopting the One Health approach to AMR surveillance and minimizing the potential transmission risk of antibiotic-resistant bacteria at the human-NHP interface.
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Affiliation(s)
- Jhonathan Bazalar-Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Asociación Equipo Primatológico del Perú (EPP), Iquitos, Peru
| | - Thalía Silvestre-Espejo
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carmen Rodríguez Cueva
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Dennis Carhuaricra Huamán
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Yennifer Ignación León
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Raúl Rosadio Alcántara
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Lenin Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
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Sudhakari PA, Ramisetty BCM. Resistome Diversity in Escherichia coli Isolates of Global Wastewaters. Microb Drug Resist 2024; 30:37-49. [PMID: 38150178 DOI: 10.1089/mdr.2022.0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health threat requiring urgent attention and effective strategies for containment. AMR is fueled by wastewater mismanagement and global mobility, disseminating multidrug-resistant (MDR) strains worldwide. While global estimates of AMR burden have been informative, community-level understanding has received little attention despite reports of high AMR prevalence in healthy communities. We assessed the "invasion" of antibiotic resistance genes (ARGs) into the normal human flora by characterizing AMR Escherichia coli in local wastewaters contributed by a healthy youth population. This study estimated 26% (out of 300 isolates) resistant and 59% plasmid-bearing E. coli in local wastewater. Of the 78 AMR isolates, the frequency of mono-resistance was higher against tetracycline (32%), followed by kanamycin (17%) and chloramphenicol (9%). Five isolates were potentially MDR. We further sequenced four MDRs and four sensitive strains to comprehend the genome and resistome diversity in comparison to the global wastewater E. coli (genomes from the PATRIC database). The whole-genome analysis revealed extensive genome similarity among global isolates, suggesting global dissemination and colonization of E. coli. Global wastewater resistome majorly comprised ARGs against aminoglycosides (26%), beta-lactam (17%), sulfonamide (11%), and trimethoprim (8%). Resistance to colistin, a last-resort antibiotic, was prevalent in MDRs of European and South Asian isolates. A systems approach is required to address the AMR crisis on a global scale, reduce antibiotic usage, and increase the efficiency of wastewater management and disinfection.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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Caetano S, Correia C, Vidal AFT, Matos A, Ferreira C, Cravo A. Fate of microbial contamination in a South European Coastal Lagoon (Ria Formosa) under the influence of treated effluents dispersal. J Appl Microbiol 2023; 134:lxad166. [PMID: 37516448 DOI: 10.1093/jambio/lxad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/17/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
AIM Assessment of the fate of microbial contamination driven from treated wastewater disposal at a highly productive zone on a South European coastal lagoon (Ria Formosa). METHODS AND RESULTS Microbial indicators of contamination (Total coliforms, Escherichia coli, and Enterococci) were evaluated monthly during September 2018-September 2020 at three study areas (Faro, Olhão, and Tavira) under different wastewater discharge flows and hydrodynamic conditions. Additional data on E. coli monitoring in bivalves, available from the national institution responsible for their surveillance was also considered. The maximum microbial contamination was found at Faro, the highest-load and less-flushed study area, contrasting the lowest contamination at Olhão, a lower-load and strongly flushed area. The wastewater impact decreased along the spatial dispersal gradients and during high water, particularly at Faro and Tavira study areas, due to a considerable dilution effect. Microbial contamination at Olhão increased during the summer, while at the other study areas seasonal evidence was not clear. Data also indicate that E. coli in bivalves from bivalve production zones next to the three study areas reflected the differentiated impact of the wastewater treatment plants effluents on the water quality of those areas. CONCLUSIONS Effluent loads together with local hydrodynamics, water temperature, solar radiation, precipitation, and land runoff as well as seabirds populations and environmentally adapted faecal or renaturelized bacterial communities, contributed to microbial contamination of the study areas.
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Affiliation(s)
- Sandra Caetano
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
- School of Health (ESS), University of Algarve, Escola Superior de Saúde da Universidade do Algarve, Campus de Gambelas, Edifício 1, Piso 3, 8005-139 Faro, Portugal
| | - Cátia Correia
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
| | - Ana Flor Torres Vidal
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
| | - André Matos
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
| | - Cristina Ferreira
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
| | - Alexandra Cravo
- CIMA, Centre of Marine and Environmental Research/ARNET-Infrastructure Network in Aquatic Research, University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
- Sciences and Technology Faculty (FCT), University of Algarve, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
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10
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Carlsen L, Büttner H, Christner M, Cordts L, Franke G, Hoffmann A, Knobling B, Lütgehetmann M, Nakel J, Werner T, Knobloch JK. Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany. J Infect Public Health 2023; 16:1142-1148. [PMID: 37267681 DOI: 10.1016/j.jiph.2023.05.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages. METHODS In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n = 59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n = 240). RESULTS Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum β-lactamases decreased over time. CONCLUSIONS This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.
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Affiliation(s)
- Laura Carlsen
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henning Büttner
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Lukas Cordts
- HAMBURG WASSER, Billhorner Deich 2, 20539 Hamburg, Germany
| | - Gefion Franke
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Armin Hoffmann
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Birte Knobling
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jacqueline Nakel
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Biology, Martinistraße 52, 20251 Hamburg, Germany
| | - Thomas Werner
- HAMBURG WASSER, Billhorner Deich 2, 20539 Hamburg, Germany
| | - Johannes K Knobloch
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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11
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Gomi R, Haramoto E, Wada H, Sugie Y, Ma CY, Raya S, Malla B, Nishimura F, Tanaka H, Ihara M. Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:160952. [PMID: 36549531 DOI: 10.1016/j.scitotenv.2022.160952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Escherichia coli has been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identify E. coli microbial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewater E. coli genomes sequenced by us (n = 50) and RefSeq animal E. coli genomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewater E. coli genomes and 3318 RefSeq animal E. coli genomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associated E. coli isolates. These two markers showed higher performance than the previously developed human wastewater-associated E. coli markers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9 % and sensitivity of 25.7 %. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detecting E. coli isolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.
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Affiliation(s)
- Ryota Gomi
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540 Kyoto, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, 400-8511 Yamanashi, Japan
| | - Hiroyuki Wada
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Yoshinori Sugie
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Chih-Yu Ma
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, Kofu, 400-8511 Yamanashi, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, 400-8511 Yamanashi, Japan
| | - Fumitake Nishimura
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan; Faculty of Agriculture and Marine Science, Kochi University, Nankoku 783-8502, Kochi, Japan.
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12
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Behruznia M, Gordon DM. Molecular and metabolic characteristics of wastewater associated Escherichia coli strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:646-654. [PMID: 35638456 PMCID: PMC9543349 DOI: 10.1111/1758-2229.13076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/04/2023]
Abstract
We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP-types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E. coli strains were selected for whole-genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E. coli genomes with a collection of 433 E. coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 (n = 15) and 399 (n = 10) along with sequence type (ST) 401 (n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche-specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient-limited conditions. The results of this study characterized the adaptive mechanisms allowing E. coli to persist in wastewater.
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Affiliation(s)
- Mahboobeh Behruznia
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - David M. Gordon
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
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13
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Yu D, Ryu K, Zhi S, Otto SJG, Neumann NF. Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics. Front Microbiol 2022; 13:810312. [PMID: 35707173 PMCID: PMC9189398 DOI: 10.3389/fmicb.2022.810312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
| | - Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Simon J. G. Otto
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
- Human-Environment-Animal Transdisciplinary Antimicrobial Resistance Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments, Centre for Health Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Norman F. Neumann
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance – One Health Consortium, Calgary, AB, Canada
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14
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Kvesić M, Šamanić I, Novak A, Fredotović Ž, Dželalija M, Kamenjarin J, Goić Barišić I, Tonkić M, Maravić A. Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment. Front Microbiol 2022; 13:858821. [PMID: 35602062 PMCID: PMC9121779 DOI: 10.3389/fmicb.2022.858821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.
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Affiliation(s)
- Marija Kvesić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region, University of Split, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Anita Novak
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Kamenjarin
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goić Barišić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
- *Correspondence: Ana Maravić,
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15
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Carlsen L, Büttner H, Christner M, Franke G, Indenbirken D, Knobling B, Lütgehetmann M, Knobloch J. High burden and diversity of carbapenemase-producing Enterobacterales observed in wastewater of a tertiary care hospital in Germany. Int J Hyg Environ Health 2022; 242:113968. [PMID: 35390565 DOI: 10.1016/j.ijheh.2022.113968] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
Hospitals are one of the main reservoirs of multi-resistant Enterobacterales (MRE). As MRE are resistant to the most frequently used antibiotics, therapy for patients with MRE infections is challenging. It has been previously described that MRE from hospital wastewater can pass into municipal wastewater and even surface water. In this study, we investigated the diversity and epidemiology of MRE in the wastewater of a large tertiary care hospital. Wastewater samples were collected for a four-day period and tested for the presence of Enterobacterales resistant to 3rd gen. cephalosporins. Representative isolates were further characterized by whole genome sequencing. In 120 β-glucuronidase-producing isolates, 68 Escherichia coli and, interestingly, also 52 Citrobacter freundii were identified. In 120 β-glucosidase-producing isolates 45 Serratia marcescens, 34 Klebsiella oxytoca, 32 Enterobacter cloacae and 9 Klebsiella pneumoniae were observed. For all species various MLST sequence types and different clusters of resistance genes were determined, showing a great diversity within the different Enterobacterales, further corroborated by clonal analysis performed by cgMLST. The most prominent clone was wastewater associated E. coli ST635, which accounted for 47.1% of all E. coli isolates. Interestingly, 45.6% of E. coli, 88.5% of C. freundii, 95.6% of S. marcescens, 91.2% of K. oxytoca, 96.9% of E. cloacae and 88.9% of K. pneumoniae isolates carried a carbapenemase gene, indicating a high burden with carbapenemase-producing Enterobacterales. Comparison with clinical isolates from the same hospital displayed few clonal matches. One wastewater isolate of K. pneumoniae was identified to be closely related compared to a clone that had been introduced into the hospital during an outbreak four years earlier. One E. coli isolate was identified as identical to an isolate from a patient, with inpatient stay during the sampling period. The data obtained in this study highlight the problem of antibiotic resistance of Enterobacterales in hospital wastewater. In particular, the clustered occurrence of carbapenemase genes is of great concern and underscores the problem of increasingly scarce antibiotic options against these bacteria.
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Affiliation(s)
- Laura Carlsen
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Henning Büttner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Gefion Franke
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Biology, Martinistraße 52, 20251, Hamburg, Germany
| | - Birte Knobling
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Johannes Knobloch
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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16
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Zhi S, Banting G, Neumann NF. Development of a qPCR assay for the detection of naturalized wastewater E. coli strains. JOURNAL OF WATER AND HEALTH 2022; 20:727-736. [PMID: 35482388 DOI: 10.2166/wh.2022.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We recently demonstrated the presence of naturalized populations of Escherichia coli in municipal sewage. We wanted to develop a quantitative polymerase chain reaction (qPCR) assay targeting the uspC-IS30-flhDC marker of naturalized wastewater E. coli and assess the prevalence of these naturalized strains in wastewater. The limit of detection for the qPCR assay was 3.0 × 10-8 ng of plasmid DNA template with 100% specificity. This strain was detected throughout the wastewater treatment process, including treated effluents. We evaluated the potential of this marker for detecting municipal sewage/wastewater contamination in water by comparing it to other human and animal markers of fecal pollution. Strong correlations were observed between the uspC-IS30-flhDC marker and the human fecal markers Bacteroides HF183 and HumM2, but not animal fecal markers, in surface and stormwater samples. The uspC-IS30-flhDC marker appears to be a potential E. coli-based marker for human wastewater contamination.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315200, China E-mail: ; School of Medicine, Ningbo University, Ningbo 315211, China
| | - Graham Banting
- School of Public Health, University of Alberta, Room 3-57, South Academic Building, Edmonton, Alberta T6G 2G7, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Room 3-57, South Academic Building, Edmonton, Alberta T6G 2G7, Canada
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17
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Behruznia M, O'Brien CL, Gordon DM. Prevalence, diversity and genetic structure of Escherichia coli isolates from septic tanks. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:138-146. [PMID: 34918455 DOI: 10.1111/1758-2229.13035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
The present study investigated the diversity and genetic structure of Escherichia coli isolates from 100 septic tanks in the Canberra region, Australia. The physicochemical characteristics of the septic tanks were determined to examine the extent to which environmental factors might influence E. coli prevalence, diversity and population structure. The results of this study indicated that the temperature of the septic tank could explain some of the variation observed in the number of E. coli isolates recovered per septic tank, whereas pH was an important driver of E. coli diversity. Conductivity, pH and household size had a significant impact on E. coli population structure, and household size significantly affected the probability of detecting human-associated E. coli lineages [sequence types (STs) 69, 73, 95 and 131] in septic tanks. Phylogroup A and B1 strains were not randomly distributed among septic tanks, and the strong negative association between them may indicate intraspecific competition. The findings of this study suggest that the combination of environmental factors and intraspecific interactions may influence the distribution and genetic structure of E. coli in the environment.
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Affiliation(s)
- Mahboobeh Behruznia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Claire L O'Brien
- Faculty of Science and Technology, University of Canberra, Bruce, ACT, 2617, Australia
| | - David M Gordon
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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18
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Emerging Ecotone and Microbial Community of a Sulfidic Spring in the Reka River near Škocjanske Jame, Slovenia. DIVERSITY 2021. [DOI: 10.3390/d13120655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During long periods with no precipitation, a sulfidic spring (Smrdljivec) appears in the dry bed of the Reka River before sinking into the karst underground. The study characterizes the area’s geological setting, development of microbial communities and an ecotone, and impact on the vulnerable karst ecosystem. Geological mapping of the area, stable isotopic analyses, field measurements, and physico-chemical and toxicity analyses were applied to elucidate the environmental conditions. The spring’s microbial diversity was assessed using cultivation methods, microscopy, and metagenomics. Sulfur compounds in the spring probably originate from coal layers in the vicinity. Metagenomic analyses revealed 175 distinct operational taxonomic units in spring water and biofilms. Proteobacteria predominated in developed biofilms, and a “core” microbiome was represented by methylotrophs, including Methylobacter, Methylomonas, and Methylotenera. Diatoms represented an important component of biofilm biomass. A combination of environmental factors and climatic conditions allows the formation and accessibility of emerging biodiversity hotspots and ecotones. Details of their dynamic nature, global impact, and distribution should be highlighted further and given more protection.
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19
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McCubbin KD, Anholt RM, de Jong E, Ida JA, Nóbrega DB, Kastelic JP, Conly JM, Götte M, McAllister TA, Orsel K, Lewis I, Jackson L, Plastow G, Wieden HJ, McCoy K, Leslie M, Robinson JL, Hardcastle L, Hollis A, Ashbolt NJ, Checkley S, Tyrrell GJ, Buret AG, Rennert-May E, Goddard E, Otto SJG, Barkema HW. Knowledge Gaps in the Understanding of Antimicrobial Resistance in Canada. Front Public Health 2021; 9:726484. [PMID: 34778169 PMCID: PMC8582488 DOI: 10.3389/fpubh.2021.726484] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 01/21/2023] Open
Abstract
Current limitations in the understanding and control of antimicrobial resistance (AMR) in Canada are described through a comprehensive review focusing on: (1) treatment optimization; (2) surveillance of antimicrobial use and AMR; and (3) prevention of transmission of AMR. Without addressing gaps in identified areas, sustained progress in AMR mitigation is unlikely. Expert opinions and perspectives contributed to prioritizing identified gaps. Using Canada as an example, this review emphasizes the importance and necessity of a One Health approach for understanding and mitigating AMR. Specifically, antimicrobial use in human, animal, crop, and environmental sectors cannot be regarded as independent; therefore, a One Health approach is needed in AMR research and understanding, current surveillance efforts, and policy. Discussions regarding addressing described knowledge gaps are separated into four categories: (1) further research; (2) increased capacity/resources; (3) increased prescriber/end-user knowledge; and (4) policy development/enforcement. This review highlights the research and increased capacity and resources to generate new knowledge and implement recommendations needed to address all identified gaps, including economic, social, and environmental considerations. More prescriber/end-user knowledge and policy development/enforcement are needed, but must be informed by realistic recommendations, with input from all relevant stakeholders. For most knowledge gaps, important next steps are uncertain. In conclusion, identified knowledge gaps underlined the need for AMR policy decisions to be considered in a One Health framework, while highlighting critical needs to achieve realistic and meaningful progress.
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Affiliation(s)
- Kayley D. McCubbin
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | | | - Ellen de Jong
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | - Jennifer A. Ida
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Diego B. Nóbrega
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John P. Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John M. Conly
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | - Ian Lewis
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Leland Jackson
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Kathy McCoy
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Myles Leslie
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- School of Public Policy, University of Calgary, Calgary, AB, Canada
| | - Joan L. Robinson
- Department of Pediatrics, Faculty of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Lorian Hardcastle
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Law, University of Calgary, Calgary, AB, Canada
| | - Aidan Hollis
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Economics, Faculty of Arts, University of Calgary, Calgary, AB, Canada
| | - Nicholas J. Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Sylvia Checkley
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Gregory J. Tyrrell
- Alberta Precision Laboratories, Alberta Health Services, Calgary, AB, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Calgary, AB, Canada
| | - André G. Buret
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Elissa Rennert-May
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ellen Goddard
- Department of Resource Economics and Environmental Sociology, Faculty of Agriculture, Life and Environmental Science, University of Alberta, Edmonton, AB, Canada
| | - Simon J. G. Otto
- HEAT-AMR Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Thematic Area Lead, Healthy Environments, Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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20
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Bojar B, Sheridan J, Beattie R, Cahak C, Liedhegner E, Munoz-Price LS, Hristova KR, Skwor T. Antibiotic resistance patterns of Escherichia coli isolates from the clinic through the wastewater pathway. Int J Hyg Environ Health 2021; 238:113863. [PMID: 34662851 DOI: 10.1016/j.ijheh.2021.113863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance (AMR) remains one of the leading global health threats. This study compared antimicrobial resistance patterns among E. coli isolates from clinical uropathogenic Escherichia coli (UPEC) to hospital wastewater populations and throughout an urban wastewater treatment facility - influent, pre- and post-chlorinated effluents. Antibiotic susceptibility of 201 isolates were analyzed against eleven different antibiotics, and the presence of twelve antibiotic resistant genes and type 1 integrase were identified. AMR exhibited the following pattern: UPEC (46.8%) > hospital wastewater (37.8%) > urban post-chlorinated effluent (27.6%) > pre-chlorinated effluent (21.4%) > urban influent wastewater (13.3%). However, multi-drug resistance against three or more antimicrobial classes was more prevalent among hospital wastewater populations (29.7%) compared to other sources. E. coli from wastewaters disinfected with chlorine were significantly correlated with increased trimethoprim-sulfamethoxazole resistance in E. coli compared to raw and treated wastewater populations. blaCTX-M-1 group was the most common extended spectrum beta-lactamase in E. coli from hospital wastewater (90%), although UPEC strains also encoded blaCTX-M-1 group (50%) and blaTEM (100%) genes. Among tetracycline-resistant populations, tetA and tetB were the only resistance genes identified throughout wastewater populations that were associated with increased phenotypic resistance. Further characterization of the E. coli populations identified phylogroup B2 predominating among clinical UPEC populations and correlated with the highest AMR, whereas the elevated rate of multi-drug resistance among hospital wastewater was mostly phylogroup A. Together, our findings highlight hospital wastewater as a rich source of AMR and multi-drug resistant bacterial populations.
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Affiliation(s)
- Brandon Bojar
- Department of Biomedical Sciences, College of Health Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, 53211, USA
| | - Jennifer Sheridan
- Department of Biomedical Sciences, College of Health Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, 53211, USA
| | - Rachelle Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53233, USA
| | - Caitlin Cahak
- Wisconsin Diagnostic Laboratories, Milwaukee, WI, 53226, USA
| | - Elizabeth Liedhegner
- Department of Biomedical Sciences, College of Health Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, 53211, USA
| | | | | | - Troy Skwor
- Department of Biomedical Sciences, College of Health Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, 53211, USA.
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21
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Graham JP, Amato H, Mendizabal-Cabrera R, Alvarez D, Ramay B. Waterborne Urinary Tract Infections: Have We Overlooked an Important Source of Exposure? Am J Trop Med Hyg 2021; 105:12-17. [PMID: 33939640 DOI: 10.4269/ajtmh.20-1271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/16/2021] [Indexed: 11/07/2022] Open
Abstract
The presence of intestinal pathogenic Escherichia coli in drinking water is well recognized as a risk for diarrhea. The role of drinking water in extraintestinal infections caused by E. coli-such as urinary tract infections (UTIs)-remains poorly understood. Urinary tract infections are a leading cause of outpatient infections globally, with a lifetime incidence of 50-60% in adult women. We reviewed the scientific literature on the occurrence of uropathogenic E. coli (UPEC) in water supplies to determine whether the waterborne route may be an important, overlooked, source of UPEC. A limited number of studies have assessed whether UPEC isolates are present in drinking water supplies, but no studies have measured whether their presence in water may increase UPEC colonization or the risk of UTIs in humans. Given the prevalence of drinking water supplies contaminated with E. coli across the globe, efforts should be made to characterize UTI-related risks associated with drinking water, as well as other pathways of exposure.
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Affiliation(s)
- Jay P Graham
- 1Berkeley School of Public Health, University of California Berkeley, Berkeley, California
| | - Heather Amato
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | | | - Danilo Alvarez
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Brooke Ramay
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala.,3Paul G. Allen School for Global Animal Health, Washington State University Pullman, Guatemala City, Guatemala
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22
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Miryala S, Nair VG, Chandramohan S, Srinandan CS. Matrix inhibition by Salmonella excludes uropathogenic E. coli from biofilm. FEMS Microbiol Ecol 2021; 97:5924450. [PMID: 33059364 DOI: 10.1093/femsec/fiaa214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/13/2020] [Indexed: 11/15/2022] Open
Abstract
Biofilm is a predominant lifestyle of bacteria that comprises of cells as collectives enmeshed in a polymeric matrix. Biofilm formation is vital for bacterial species as it provides access to nutrients and protects the cells from environmental stresses. Here we show that interference in biofilm matrix production is a strategy by the competing bacterial species to reduce the ability of the other species to colonize a surface. Escherichia coli colonies that differ in matrix production display different morphologies on Congo red agar media, which we exploited for screening bacterial isolates capable of inhibiting the matrix. The cell-free supernatants from growth culture of the screened isolates impaired uropathogenic E. coli (UPEC) UTI89 strain's biofilm. A physicochemical analysis suggested that the compound could be a glycopeptide or a polysaccharide. Isolates that inhibited matrix production belonged to species of the family Enterobacteriaceae such as Shigella, Escherichia, Enterobacter and Salmonella. Competition experiments between the isolates and the UPEC strain resulted in mutual inhibition, particularly during biofilm formation causing significant reduction in productivity and fitness. Furthermore, we show that Salmonella strains competitively excluded the UPEC strain in the biofilm by inhibiting its matrix production, highlighting the role of interference competition.
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Affiliation(s)
- Sandeep Miryala
- Biofilm Biology Lab, Centre for Research in Infectious Diseases, School of Chemical and Biotechnology,Thanjavur, Tamil Nadu, India
| | - Veena G Nair
- Biofilm Biology Lab, Centre for Research in Infectious Diseases, School of Chemical and Biotechnology,Thanjavur, Tamil Nadu, India
| | - S Chandramohan
- Biofilm Biology Lab, Centre for Research in Infectious Diseases, School of Chemical and Biotechnology,Thanjavur, Tamil Nadu, India
| | - C S Srinandan
- Biofilm Biology Lab, Centre for Research in Infectious Diseases, School of Chemical and Biotechnology,Thanjavur, Tamil Nadu, India
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23
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Yu D, Banting G, Neumann NF. A review of the taxonomy, genetics, and biology of the genus Escherichia and the type species Escherichia coli. Can J Microbiol 2021; 67:553-571. [PMID: 33789061 DOI: 10.1139/cjm-2020-0508] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
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24
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Nowicki S, deLaurent ZR, de Villiers EP, Githinji G, Charles KJ. The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing. PLoS One 2021; 16:e0245910. [PMID: 33481909 PMCID: PMC7822521 DOI: 10.1371/journal.pone.0245910] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.
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Affiliation(s)
- Saskia Nowicki
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Zaydah R. deLaurent
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Etienne P. de Villiers
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katrina J. Charles
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
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25
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Eshrati B, Baradaran HR, Motevalian SA, Majidpour A, Boustanshenas M, Soleymanzadeh Moghadam S, Moradi Y. Investigating the relationship between extended spectrum β-lactamase producing Escherichia coli in the environment and food chains with the presence of this infection in people suspected of septicemia: Using the fuzzy set qualitative comparative analysis. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:1509-1520. [PMID: 33312657 PMCID: PMC7721934 DOI: 10.1007/s40201-020-00567-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/08/2020] [Indexed: 06/01/2023]
Abstract
PROPOSE Among antibiotic resistance cases, resistance to β-lactam antibiotics is a major concern for the treatment of microbial infections. Furthermore, the prevalence of extended-spectrum β-lactamases (ESBL) Escherichia coli (E. coli) in environment, food, and human resources of Iran has increased over the past few years. This study aimed to predict the relationship between the prevalence of ESBL E. coli in the environment and the food chains with the presence of this infection in people suspected of septicemia using fuzzy set qualitative comparative analysis model. METHODS In this analytical cross sectional study samples were collected from the environment (hospital sewage, downstream and upstream urban sewage, and slaughterhouse sewage), food (chicken), and human chains (people suspected of septicemia) in Tehran province, Iran. This study was conducted from September to February 2019 and the prevalence of ESBL E. coli was calculated in each resource. Then, the relationship between the prevalence of ESBL E. coli in the environment and food chains and its prevalence in the human chain was predicted using the fuzzy set qualitative comparative analysis. RESULTS The results showed the prevalence of ESBL E. coli in those suspected of septicemia in September, October, November, December, January and February was 58.1%, 60%, 33.3%, 100%, 43%, and 57.8%, respectively. Also, the results of the fuzzy set qualitative comparative analysis indicated hospital wastewater and chicken contamination with ESBL E. coli were the main causes of contamination with ESBL E. coli in people suspected of septicemia. CONCLUSIONS According to the results of this study, if there is a contamination of hospital wastewater and chickens in an area, it can be claimed that people suspected of septicemia are infected with ESBL E. coli, and the percentage of this contamination can be high. On the other hand, controlling ESBL E. coli in hospital wastewater (environmental chain) and chickens (food chain) can prevent contamination in people with suspected septicemia.
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Affiliation(s)
- Babak Eshrati
- Preventive Medicine and Public Health Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Baradaran
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | - Seyed Abbas Motevalian
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | - Ali Majidpour
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mina Boustanshenas
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Soleymanzadeh Moghadam
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Yousef Moradi
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
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26
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Ogura Y, Ueda T, Nukazawa K, Hiroki H, Xie H, Arimizu Y, Hayashi T, Suzuki Y. The level of antimicrobial resistance of sewage isolates is higher than that of river isolates in different Escherichia coli lineages. Sci Rep 2020; 10:17880. [PMID: 33087784 PMCID: PMC7578040 DOI: 10.1038/s41598-020-75065-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/09/2020] [Indexed: 01/14/2023] Open
Abstract
The dissemination of antimicrobial-resistant bacteria in environmental water is an emerging concern in medical and industrial settings. Here, we analysed the antimicrobial resistance of Escherichia coli isolates from river water and sewage by the use of a combined experimental phenotypic and whole-genome-based genetic approach. Among the 283 tested strains, 52 were phenotypically resistant to one or more antimicrobial agents. The E. coli isolates from the river and sewage samples were phylogenetically indistinguishable, and the antimicrobial-resistant strains were dispersedly distributed in a whole-genome-based phylogenetic tree. The prevalence of antimicrobial-resistant strains as well as the number of antimicrobials to which they were resistant were higher in sewage samples than in river samples. Antimicrobial resistance genes were more frequently detected in strains from sewage samples than in those from river samples. We also found that 16 river isolates that were classified as Escherichia cryptic clade V were susceptible to all the antimicrobials tested and were negative for antimicrobial resistance genes. Our results suggest that E. coli strains may acquire antimicrobial resistance genes more frequently and/or antimicrobial-resistant E. coli strains may have higher rates of accumulation and positive selection in sewage than in rivers, irrespective of their phylogenetic distribution.
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Affiliation(s)
- Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan. .,Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Takuya Ueda
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Kei Nukazawa
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hayate Hiroki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hui Xie
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.,Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan.
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27
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Devane ML, Moriarty E, Weaver L, Cookson A, Gilpin B. Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring. WATER RESEARCH 2020; 185:116204. [PMID: 32745743 DOI: 10.1016/j.watres.2020.116204] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.
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Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand.
| | - Elaine Moriarty
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Adrian Cookson
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Brent Gilpin
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
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28
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Zhi S, Stothard P, Banting G, Scott C, Huntley K, Ryu K, Otto S, Ashbolt N, Checkley S, Dong T, Ruecker NJ, Neumann NF. Characterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater. WATER RESEARCH 2020; 182:115827. [PMID: 32580076 DOI: 10.1016/j.watres.2020.115827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 05/29/2023]
Abstract
A growing body of evidence has demonstrated that extraintestinal pathogenic E. coli (ExPEC), such as the urinary pathogenic E. coli (UPEC), are common constituents of treated wastewater, and therefore represent a potential public health risk. However, no single virulence gene, or set of virulence genes, can be used to conclusively identify this genetically diverse pathotype. As such we sought to identify and characterize the public health relevance of potential UPEC found in treated sewage/wastewater using a comparative genomics approach. Presumptive wastewater UPEC (W-UPEC) were initially identified by virulence gene screening against 5 virulence genes, and for which isolates containing ≥3 virulence genes were whole genome sequenced (n = 24). Single nucleotide polymorphic (SNP) spanning tree analysis demonstrated that many of these wastewater UPEC (WUPEC) were virtually identical at the core genome (0.4 Mbp) when compared to clinical UPEC (C-UPEC) sequences obtained from NCBI, varying by as little as 1 SNP. Remarkably, at the whole genome level, W-UPEC isolates displayed >96% whole genome similarity to C-UPEC counterparts in NCBI, with one strain demonstrating 99.5% genome similarity to a particular C-UPEC strain. The W-UPEC populations were represented by sequence types (ST) known to be clinically important, including ST131, ST95, ST127 and ST640. Many of the W-UPEC carried the exact same complement of virulence genes as their most closely related C-UPEC strains. For example, O25b-ST131 W-UPEC strains possessed the same 80 virulence genes as their most closely related C-UPEC counterparts. Concerningly, W-UPEC strains also carried a plethora of antibiotic resistance genes, and O25b-ST131strains were designated as extended spectrum beta-lactamase (ESBL) producing E. coli by both genome profiling and phenotypic resistance testing. W-UPEC ST131 strains were found in the effluents of a single treatment plant at different times, as well as different wastewater treatment plants, suggesting a differentially ability to survive wastewater treatment. Indeed, in sewage samples treated with chlorine doses sufficient for inducing a ∼99.99% reduction in total E. coli levels, UPEC represented a significant proportion of the chlorine-resistant population. By contrast, no Shiga toxin-producing E. coli were observed in these chlorinated sewage libraries. Our results suggest that clinically-relevant UPEC exist in treated wastewater effluents and that they appear to be specifically adapted to survive wastewater treatment processes.
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Affiliation(s)
- Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
| | - Paul Stothard
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Candis Scott
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kristin Huntley
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Simon Otto
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sylvia Checkley
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tao Dong
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Norma J Ruecker
- City of Calgary, Water Quality Services, Calgary, Alberta, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada.
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29
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Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Gweon HS, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers AJ, Crook DW, Peto TE, Walker AS, Stoesser N. Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microb Genom 2020; 6:mgen000391. [PMID: 32553019 PMCID: PMC7478627 DOI: 10.1099/mgen.0.000391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/24/2020] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05-11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.
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Affiliation(s)
- Bede Constantinides
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Kevin K. Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - T. Phuong Quan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Monique I. Andersson
- Department of Infectious diseases/Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Katie Jeffery
- Department of Infectious diseases/Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sam Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hyun S. Gweon
- Harborne Building, School of Biological Sciences, University of Reading, Reading, UK
| | - Andy Peniket
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Graham Pike
- Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Julian Millo
- Adult Intensive Care Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mary Byukusenge
- Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Matt Holdaway
- Adult Intensive Care Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Cat Gibbons
- Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Amy J. Mathers
- Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
- Department of Infectious diseases/Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E.A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
- Department of Infectious diseases/Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
- Department of Infectious diseases/Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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30
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Wyrsch ER, Chowdhury PR, Jarocki VM, Brandis KJ, Djordjevic SP. Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58. Microb Genom 2020; 6:e000387. [PMID: 32519937 PMCID: PMC7371111 DOI: 10.1099/mgen.0.000387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
The AB5 cytotoxins are important virulence factors in Escherichia coli. The most notable members of the AB5 toxin families include Shiga toxin families 1 (Stx1) and 2 (Stx2), which are associated with enterohaemorrhagic E. coli infections causing haemolytic uraemic syndrome and haemorrhagic colitis. The subAB toxins are the newest and least well understood members of the AB5 toxin gene family. The subtilase toxin genes are divided into a plasmid-based variant, subAB1, originally described in enterohaemorrhagic E. coli O113:H21, and distinct chromosomal variants, subAB2, that reside in pathogenicity islands encoding additional virulence effectors. Previously we identified a chromosomal subAB2 operon within an E. coli ST58 strain IBS28 (ONT:H25) taken from a wild ibis nest at an inland wetland in New South Wales, Australia. Here we show the subAB2 toxin operon comprised part of a 140 kb tRNA-Phe chromosomal island that co-hosted tia, encoding an outer-membrane protein that confers an adherence and invasion phenotype and additional virulence and accessory genetic content that potentially originated from known virulence island SE-PAI. This island shared a common evolutionary history with a secondary 90 kb tRNA-Phe pathogenicity island that was presumably generated via a duplication event. IBS28 is closely related [200 single-nucleotide polymorphisms (SNPs)] to four North American ST58 strains. The close relationship between North American isolates of ST58 and IBS28 was further supported by the identification of the only copy of a unique variant of IS26 within the O-antigen gene cluster. Strain ISB28 may be a historically important E. coli ST58 genome sequence hosting a progenitor pathogenicity island encoding subAB.
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Affiliation(s)
- Ethan R. Wyrsch
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Veronica M. Jarocki
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kate J. Brandis
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
| | - Steven P. Djordjevic
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
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31
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The Locus of Heat Resistance Confers Resistance to Chlorine and Other Oxidizing Chemicals in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.02123-19. [PMID: 31811037 DOI: 10.1128/aem.02123-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Some chlorine-resistant Escherichia coli isolates harbor the locus of heat resistance (LHR), a genomic island conferring heat resistance. In this study, the protective effect of the LHR for cells challenged by chlorine and oxidative stress was quantified. Cloning of the LHR protected against NaClO (32 mM; 5 min), H2O2 (120 mM; 5 min), and peroxyacetic acid (105 mg/liter; 5 min) but not against 5.8 mM KIO4, 10 mM acrolein, or 75 mg/liter allyl isothiocyanate. The lethality of oxidizing treatments for LHR-negative strains of E. coli was about 2 log10 CFU/ml higher than that for LHR-positive strains of E. coli The oxidation of cytoplasmic proteins and membrane lipids was quantified with the fusion probe roGFP2-Orp1 and the fluorescent probe BODIPY581/591, respectively. The fragment of the LHR coding for heat shock proteins protected cytoplasmic proteins but not membrane lipids against oxidation. The middle fragment of the LHR protected against the oxidation of membrane lipids but not of cytoplasmic proteins. The addition of H2O2, NaClO, and peroxyacetic acid also induced green fluorescent protein (GFP) expression in the oxidation-sensitive reporter strain E. coli O104:H4 Δstx 2::gfp::amp Cloning of pLHR reduced phage induction in E. coli O104:H4 Δstx 2::gfp::amp after treatment with oxidizing chemicals. Screening of 160 strains of Shiga toxin-producing E. coli (STEC) revealed that none of them harbors the LHR, additionally suggesting that the LHR and Stx prophages are mutually exclusive. Taking our findings together, the contribution of the LHR to resistance to chlorine and oxidative stress is based on the protection of multiple cellular targets by different proteins encoded by the genetic island.IMPORTANCE Chlorine treatments are used in water and wastewater sanitation; the resistance of Escherichia coli to chlorine is thus of concern to public health. We show that a genetic island termed the locus of heat resistance (LHR) protects E. coli not only against heat but also against chlorine and other oxidizing chemicals, adding to our knowledge of the tools used by E. coli to resist stress. Specific detection of the oxidation of different cellular targets in combination with the cloning of fragments of the LHR provided insight into mechanisms of protection and demonstrated that different fragments of the LHR protect different cellular targets. In E. coli, the presence of the LHR virtually always excluded other virulence factors. It is tempting to speculate that the LHR is maintained by strains of E. coli with an environmental lifestyle but is excluded by pathogenic strains that adapted to interact with vertebrate hosts.
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32
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Maestre‐Carballa L, Lluesma Gomez M, Angla Navarro A, Garcia‐Heredia I, Martinez‐Hernandez F, Martinez‐Garcia M. Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter. Environ Microbiol 2019; 21:4582-4596. [DOI: 10.1111/1462-2920.14758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/21/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Lucia Maestre‐Carballa
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Andrea Angla Navarro
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Inmaculada Garcia‐Heredia
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Francisco Martinez‐Hernandez
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Manuel Martinez‐Garcia
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
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