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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] [MESH Headings] [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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Cookson AL, Devane M, Marshall JC, Moinet M, Gardner A, Collis RM, Rogers L, Biggs PJ, Pita AB, Cornelius AJ, Haysom I, Hayman DTS, Gilpin BJ, Leonard M. Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13319. [PMID: 39096033 PMCID: PMC11297283 DOI: 10.1111/1758-2229.13319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024]
Abstract
Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli-associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non-recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land-use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non-recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent.
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Affiliation(s)
- Adrian L. Cookson
- AgResearch LimitedHopkirk Research InstitutePalmerston NorthNew Zealand
- mEpiLab, School of Veterinary SciencesMassey UniversityPalmerston NorthNew Zealand
- Institute of Environmental Science and ResearchKenepuru Science CentrePoriruaNew Zealand
| | - Meg Devane
- Institute of Environmental Science and ResearchChristchurchNew Zealand
| | - Jonathan C. Marshall
- School of Mathematical and Computational SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Marie Moinet
- AgResearch LimitedHopkirk Research InstitutePalmerston NorthNew Zealand
- Institute of Environmental Science and ResearchChristchurchNew Zealand
| | - Amanda Gardner
- AgResearch LimitedHopkirk Research InstitutePalmerston NorthNew Zealand
| | - Rose M. Collis
- AgResearch LimitedHopkirk Research InstitutePalmerston NorthNew Zealand
| | - Lynn Rogers
- AgResearch LimitedHopkirk Research InstitutePalmerston NorthNew Zealand
| | - Patrick J. Biggs
- mEpiLab, School of Veterinary SciencesMassey UniversityPalmerston NorthNew Zealand
- School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Anthony B. Pita
- mEpiLab, School of Veterinary SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Iain Haysom
- Institute of Environmental Science and ResearchChristchurchNew Zealand
| | - David T. S. Hayman
- mEpiLab, School of Veterinary SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Brent J. Gilpin
- Institute of Environmental Science and ResearchChristchurchNew Zealand
| | - Margaret Leonard
- Institute of Environmental Science and ResearchChristchurchNew Zealand
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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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Bydalek F, Webster G, Barden R, Weightman AJ, Kasprzyk-Hordern B, Wenk J. Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland. WATER RESEARCH 2024; 254:121408. [PMID: 38442607 DOI: 10.1016/j.watres.2024.121408] [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: 06/06/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.
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Affiliation(s)
- Franciszek Bydalek
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; GW4 NERC CDT in Freshwater Biosciences and Sustainability, Cardiff University, Cardiff CF10 3AX, UK; Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Gordon Webster
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Andrew J Weightman
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Barbara Kasprzyk-Hordern
- Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK.
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Heljanko V, Tyni O, Johansson V, Virtanen JP, Räisänen K, Lehto KM, Lipponen A, Oikarinen S, Pitkänen T, Heikinheimo A. Clinically relevant sequence types of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae detected in Finnish wastewater in 2021-2022. Antimicrob Resist Infect Control 2024; 13:14. [PMID: 38291521 PMCID: PMC10829384 DOI: 10.1186/s13756-024-01370-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a critical threat to human health. Escherichia coli and Klebsiella pneumoniae are clinically the most important species associated with AMR and are the most common carbapenemase-producing (CP) Enterobacterales detected in human specimens in Finland. Wastewater surveillance has emerged as a potential approach for population-level surveillance of AMR, as wastewater could offer a reflection from a larger population with one sample and minimal recognized ethical issues. In this study, we investigated the potential of wastewater surveillance to detect CP E. coli and K. pneumoniae strains similar to those detected in human specimens. METHODS Altogether, 89 composite samples of untreated community wastewater were collected from 10 wastewater treatment plants across Finland in 2021-2022. CP E. coli and K. pneumoniae were isolated using selective culture media and identified using MALDI-TOF MS. Antimicrobial susceptibility testing was performed using disk diffusion test and broth microdilution method, and a subset of isolates was characterized using whole-genome sequencing. RESULTS CP E. coli was detected in 26 (29.2%) and K. pneumoniae in 25 (28.1%) samples. Among E. coli, the most common sequence type (ST) was ST410 (n = 7/26, 26.9%), while ST359 (n = 4/25, 16.0%) predominated among K. pneumoniae. Globally successful STs were detected in both E. coli (ST410, ST1284, ST167, and ST405) and K. pneumoniae (ST512, ST101, and ST307). K. pneumoniae carbapenemases (KPC) were the most common carbapenemases in both E. coli (n = 11/26, 42.3%) and K. pneumoniae (n = 13/25, 52.0%), yet also other carbapenemases, such as blaNDM-5, blaOXA-48, and blaOXA-181, were detected. We detected isolates harboring similar ST and enzyme type combinations previously linked to clusters in Finland, such as E. coli ST410 with blaKPC-2 and K. pneumoniae ST512 with blaKPC-3. CONCLUSIONS Our study highlights the presence of clinically relevant strains of CP E. coli and K. pneumoniae in community wastewater. The results indicate that wastewater surveillance could serve as a monitoring tool for CP Enterobacterales. However, the specificity and sensitivity of the methods should be improved, and technologies, like advanced sequencing methods, should be utilized to distinguish data with public health relevance, harness the full potential of wastewater surveillance, and implement the data in public health surveillance.
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Affiliation(s)
- Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
| | - Olga Tyni
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Venla Johansson
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Kati Räisänen
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anssi Lipponen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tarja Pitkänen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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6
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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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