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Li W, Wang Y, Gao J, Wang A. Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116699. [PMID: 38981389 DOI: 10.1016/j.ecoenv.2024.116699] [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: 04/26/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/11/2024]
Abstract
Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Weiwei Li
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Yanfang Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Jianxin Gao
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Ailan Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China.
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2
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Farrell ML, Chueiri A, Maguire M, Kovářová A, Miliotis G, O'Connor L, McDonagh F, Duane S, Cormican M, Devane G, Tuohy A, DeLappe N, De Bock F, Burke LP, Morris D. Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167100. [PMID: 37717747 DOI: 10.1016/j.scitotenv.2023.167100] [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: 07/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.
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Affiliation(s)
- Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland.
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Mark Maguire
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Aneta Kovářová
- Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Sinead Duane
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland; J.E. Cairnes School of Business and Economics, University of Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland; National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Genevieve Devane
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Alma Tuohy
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Niall DeLappe
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Florence De Bock
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Liam P Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
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OXA-48-Like β-Lactamases: Global Epidemiology, Treatment Options, and Development Pipeline. Antimicrob Agents Chemother 2022; 66:e0021622. [PMID: 35856662 PMCID: PMC9380527 DOI: 10.1128/aac.00216-22] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Modern medicine is threatened by the rising tide of antimicrobial resistance, especially among Gram-negative bacteria, where resistance to β-lactams is most often mediated by β-lactamases. The penicillin and cephalosporin ascendancies were, in their turn, ended by the proliferation of TEM penicillinases and CTX-M extended-spectrum β-lactamases. These class A β-lactamases have long been considered the most important. For carbapenems, however, the threat is increasingly from the insidious rise of a class D carbapenemase, OXA-48, and its close relatives. Over the past 20 years, OXA-48 and "OXA-48-like" enzymes have proliferated to become the most prevalent enterobacterial carbapenemases across much of Europe, Northern Africa, and the Middle East. OXA-48-like enzymes are notoriously difficult to detect because they often cause only low-level in vitro resistance to carbapenems, meaning that the true burden is likely underestimated. Despite this, they are associated with carbapenem treatment failures. A highly conserved incompatibility complex IncL plasmid scaffold often carries blaOXA-48 and may carry other antimicrobial resistance genes, leaving limited treatment options. High conjugation efficiency means that this plasmid is sometimes carried by multiple Enterobacterales in a single patient. Producers evade most β-lactam-β-lactamase inhibitor combinations, though promising agents have recently been licensed, notably ceftazidime-avibactam and cefiderocol. The molecular machinery enabling global spread, current treatment options, and the development pipeline of potential new therapies for Enterobacterales that produce OXA-48-like β-lactamases form the focus of this review.
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Teixeira P, Tacão M, Henriques I. Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118958. [PMID: 35131334 DOI: 10.1016/j.envpol.2022.118958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (blaNDM, blaKPC, tetA, blaCTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried blaKPC while Enterobacter harbored blaNDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between blaCTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.
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Affiliation(s)
- Pedro Teixeira
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal.
| | - Isabel Henriques
- University of Coimbra, Centre for Functional Ecology and Department of Life Sciences, Faculty of Science and Technology, Coimbra, Portugal
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Ledda A, Cummins M, Shaw LP, Jauneikaite E, Cole K, Lasalle F, Barry D, Turton J, Rosmarin C, Anaraki S, Wareham D, Stoesser N, Paul J, Manuel R, Cherian BP, Didelot X. Hospital outbreak of carbapenem-resistant Enterobacterales associated with a blaOXA-48 plasmid carried mostly by Escherichia coli ST399. Microb Genom 2022; 8:000675. [PMID: 35442183 PMCID: PMC9453065 DOI: 10.1099/mgen.0.000675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A hospital outbreak of carbapenem-resistant Enterobacterales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous blaOXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacterales were involved in the outbreak. Escherichia coli ST399 accounted for 35 of all the 55 isolates. Comparative genomics analysis using publicly available E. coli ST399 genomes showed that the outbreak E. coli ST399 isolates formed a unique clade. We developed a mathematical model of pOXA-48-like plasmid transmission between host lineages and used it to estimate its conjugation rate, giving a lower bound of 0.23 conjugation events per lineage per year. Our analysis suggests that co-evolution between the pOXA-48-like plasmid and E. coli ST399 could have played a role in the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying blaOXA-48 as the main cause of a plasmid-borne outbreak within a hospital setting. Our findings suggest complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.
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Affiliation(s)
- Alice Ledda
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
- *Correspondence: Alice Ledda,
| | - Martina Cummins
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Liam P. Shaw
- Department of Zoology, University of Oxford, Oxford, UK
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- NHIR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious disease, Imperial College London, Hammersmith Campus, London, UK
| | | | - Florent Lasalle
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- Microbes and Pathogens Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Deborah Barry
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Jane Turton
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Caryn Rosmarin
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Sudy Anaraki
- North East and North Central London Health Protection Team, Public Health England, London, UK
| | - David Wareham
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - John Paul
- Brighton and Sussex Medical school, Department of Global health and Infection, University of Sussex, Falmer, Brighton, UK
| | - Rohini Manuel
- Public Health Laboratory London, National Infection Service, Public Health England, London, UK
| | - Benny P. Cherian
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
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6
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Leonard AF, Morris D, Schmitt H, Gaze WH. Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health. Curr Opin Microbiol 2022; 65:40-46. [PMID: 34739925 DOI: 10.1016/j.mib.2021.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/15/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.
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Affiliation(s)
- Anne Fc Leonard
- University of Exeter Medical School, Environment and Sustainability Institute, University of Exeter, Cornwall TR10 9FE, UK.
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland
| | - Heike Schmitt
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology - Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - William H Gaze
- University of Exeter Medical School, Environment and Sustainability Institute, University of Exeter, Cornwall TR10 9FE, UK.
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Campos-Madueno EI, Moser AI, Jost G, Maffioli C, Bodmer T, Perreten V, Endimiani A. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones. J Glob Antimicrob Resist 2022; 28:206-215. [DOI: 10.1016/j.jgar.2022.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
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Li D, Wyrsch ER, Elankumaran P, Dolejska M, Marenda MS, Browning GF, Bushell RN, McKinnon J, Chowdhury PR, Hitchick N, Miller N, Donner E, Drigo B, Baker D, Charles IG, Kudinha T, Jarocki VM, Djordjevic SP. Genomic comparisons of Escherichia coli ST131 from Australia. Microb Genom 2021; 7:000721. [PMID: 34910614 PMCID: PMC8767332 DOI: 10.1099/mgen.0.000721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically blaCTX-M-15 and blaCTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
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Affiliation(s)
- Dmitriy Li
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ethan R. Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic,Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic,Biomedical Center, Charles University, Czech Republic,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
| | - Marc S. Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Glenn F. Browning
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Rhys N. Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Jessica McKinnon
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Nola Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Natalie Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | | | | | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Veronica M. Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Veronica M. Jarocki,
| | - Steven Philip Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Steven Philip Djordjevic,
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9
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Li Y, Tang M, Dai X, Zhou Y, Zhang Z, Qiu Y, Li C, Zhang L. Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China. Infect Drug Resist 2021; 14:4427-4440. [PMID: 34737583 PMCID: PMC8559237 DOI: 10.2147/idr.s330787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis. Methods In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of blaNDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the blaNDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome. Results Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, blaNDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these blaNDM-5-haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates. Conclusion This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene blaNDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the “One-Health” perspective.
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Affiliation(s)
- Ying Li
- Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Min Tang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xiaoyi Dai
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Yichuan Qiu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Chengwen Li
- Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Luhua Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
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10
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Farrell ML, Joyce A, Duane S, Fitzhenry K, Hooban B, Burke LP, Morris D. Evaluating the potential for exposure to organisms of public health concern in naturally occurring bathing waters in Europe: A scoping review. WATER RESEARCH 2021; 206:117711. [PMID: 34637971 DOI: 10.1016/j.watres.2021.117711] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Globally, water-based bathing pastimes are important for both mental and physical health. However, exposure to waterborne organisms could present a substantial public health issue. Bathing waters are shown to contribute to the transmission of illness and disease and represent a reservoir and pathway for the dissemination of antimicrobial resistant (AMR) organisms. Current bathing water quality regulations focus on enumeration of faecal indicator organisms and are not designed for detection of specific waterborne organisms of public health concern (WOPHC), such as antimicrobial resistant (AMR)/pathogenic bacteria, or viruses. This investigation presents the first scoping review of the occurrence of waterborne organisms of public health concern (WOPHC) in identified natural bathing waters across the European Union (EU), which aimed to critically evaluate the potential risk of human exposure and to assess the appropriateness of the current EU bathing water regulations for the protection of public health. Accordingly, this review sought to identify and synthesise all literature pertaining to a selection of bacterial (Campylobacter spp., Escherichia coli, Salmonella spp., Shigella spp., Vibrio spp., Pseudomonas spp., AMR bacteria), viral (Hepatitis spp., enteroviruses, rotavirus, adenovirus, norovirus), and protozoan (Giardia spp., and Cryptosporidium spp.) contaminants in EU bathing waters. Sixty investigations were identified as eligible for inclusion and data was extracted. Peer-reviewed investigations included were from 18 countries across the EU, totalling 87 investigations across a period of 35 years, with 30% published between 2011 and 2015. A variety of water bodies were identified, with 27 investigations exclusively assessing coastal waters. Waterborne organisms were classified into three categories; bacteria, viruses, and protozoa; amounting to 58%, 36% and 17% of the total investigations, respectively. The total number of samples across all investigations was 8,118, with detection of one or more organisms in 2,449 (30%) of these. Viruses were detected in 1281 (52%) of all samples where WOPHC were found, followed by bacteria (865(35%)) and protozoa (303(12%)). Where assessed (442 samples), AMR bacteria had a 47% detection rate, emphasising their widespread occurrence in bathing waters. Results of this scoping review highlight the potential public health risk of exposure to WOPHC in bathing waters that normally remain undetected within the current monitoring parameters.
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Affiliation(s)
- Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland.
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Sinead Duane
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland; Whitaker Institute, National University of Ireland Galway, Ireland
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Liam P Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
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Dewi DAR, Thomas T, Ahmad Mokhtar AM, Mat Nanyan NS, Zulfigar SB, Salikin NH. Carbapenem Resistance among Marine Bacteria-An Emerging Threat to the Global Health Sector. Microorganisms 2021; 9:microorganisms9102147. [PMID: 34683467 PMCID: PMC8537846 DOI: 10.3390/microorganisms9102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/24/2023] Open
Abstract
The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.
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Affiliation(s)
- Dewa A.P. Rasmika Dewi
- School of Medicine, International University of Health and Welfare, Narita 286-8686, Japan;
- Faculty of Medicine and Health Sciences, Udayana University, Bali 80232, Indonesia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Ana Masara Ahmad Mokhtar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Noreen Suliani Mat Nanyan
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Siti Balqis Zulfigar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Nor Hawani Salikin
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
- Correspondence: ; Tel.: +60-4-653-2241
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12
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Hooban B, Fitzhenry K, Cahill N, Joyce A, O' Connor L, Bray JE, Brisse S, Passet V, Abbas Syed R, Cormican M, Morris D. A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019. ENVIRONMENT INTERNATIONAL 2021; 152:106466. [PMID: 33706038 DOI: 10.1016/j.envint.2021.106466] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with blaCTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was blaOXA-48 (n=6), followed by blaNDM-5 (n=2) and blaKPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters. The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.
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Affiliation(s)
- Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway.
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - Louise O' Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Raza Abbas Syed
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway; Health Service Executive, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway; Centre for One Health, Ryan Institute, National University of Ireland, Galway
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13
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Monahan C, Nag R, Morris D, Cummins E. Antibiotic residues in the aquatic environment - current perspective and risk considerations. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:733-751. [PMID: 33979269 DOI: 10.1080/10934529.2021.1923311] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance is a major concern for human and animal health, projected to deteriorate with time and given current trends of antimicrobial usage. Antimicrobial use, particularly in healthcare and agriculture, can result in the release of antimicrobials into surface waters, promoting the development of antibiotic resistance in the environment, and potentially leading to human health risks. This study reviews relevant literature, and investigates current European and Irish antimicrobial usage trends in humans and animals, as well as potential pathways that antibiotics can take into surface waters following use. Reported levels in the aquatic environment are summarized, with particular focus on Ireland. There are relatively few studies examining Irish water bodies or sewage effluent for antibiotic residues, however, five antibiotics, namely azithromycin, ciprofloxacin, clarithromycin, metronidazole, and trimethoprim, have been measured in Irish waters, in concentrations predicted to select for resistance. Numerous isolates of multi-drug resistant bacteria have also been found in water bodies throughout Ireland and Europe. The value of risk assessment methodologies in understanding risks posed by antibiotic residues is reviewed including the advantages and disadvantages of specific approaches. Hazard quotient and bespoke Monte Carlo approaches are predominant risk assessment tools used to examine antimicrobial release and their complex pathways. This study highlights the need for monitoring of antimicrobial releases and the potential for resistance development, persistence and transmission while highlighting the role of risk assessment methodologies in assessing potential human and environmental health impacts.
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Affiliation(s)
- Ciaran Monahan
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Rajat Nag
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Dearbháile Morris
- Galway School of Medicine, National University of Ireland, Galway, Ireland
| | - Enda Cummins
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
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14
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Cherak Z, Loucif L, Moussi A, Rolain JM. Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review. J Glob Antimicrob Resist 2021; 25:287-309. [PMID: 33895415 DOI: 10.1016/j.jgar.2021.03.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.
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Affiliation(s)
- Zineb Cherak
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna, Algeria.
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; and Assistance Publique des Hôpitaux de Marseille, Marseille, France
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15
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Multidrug-resistant enterobacteriaceae in coastal water: an emerging threat. Antimicrob Resist Infect Control 2020; 9:169. [PMID: 33126924 PMCID: PMC7602311 DOI: 10.1186/s13756-020-00826-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background The environmental role of carbapenemase-producing Enterobacteriaceae (CPE) acquisition and infection in human disease has been described but not thoroughly investigated. We aimed to assess the occurrence of CPE in nearshore aquatic bodies. Methods Enterobacteriaceae were cultured from coastal and estuary water near Netanya, Israel in June and July of 2018. Bacteria were identified by VITEK2® and their antimicrobial susceptibility was tested according to the CLSI guidelines. Enterobacteriaceae genomes were sequenced to elucidate their resistome and carbapenemase types. Results Among other clinically relevant bacteria, four CPE (three Enterobacter spp and one Escherichia coli isolate) were isolated from two river estuaries (Poleg and Alexander Rivers) and coastal water at a popular recreational beach (Beit Yanai). Molecular analysis and genome sequencing revealed the persistent presence of rare beta-lactamase resistance genes, including blaIMI-2 and a previously unknown blaIMI-20 allele, which were not found among the local epidemiological strains. Genome comparisons revealed the high identity of riverine and marine CPE that were cultivated one month apart. Conclusions We show that CPE contamination was widespread in nearshore marine and riverine habitats. The high genome-level similarity of riverine and marine CPEs, isolated one month apart, hints at the common source of infection. We discuss the clinical implications of these findings and stress the urgent need to assess the role of the aquatic environment in CPE epidemiology.
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16
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Paschoal RP, Campana EH, de S Castro L, Picão RC. Predictors of carbapenemase-producing bacteria occurrence in polluted coastal waters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114776. [PMID: 32417584 DOI: 10.1016/j.envpol.2020.114776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
The spread of carbapenemase-producing bacteria is a worldwide concern as it challenges healthcare, especially considering the insufficient development of antimicrobials. These microorganisms have been described not only in hospitals, but also in several environmental settings including recreational waters. Community exposure to antimicrobial-resistant bacteria through recreation might be relevant for human health, but risk assessment studies are lacking. Absence of effective and feasible monitoring in recreational aquatic matrices contributes to such a knowledge gap. Here, we aimed at assessing predictors of occurrence of medically relevant carbapenemase-producing bacteria in coastal waters. We quantitatively assessed recovery of carbapenemase-producing Enterobacteriaceae, Pseudomonas spp., Acinetobacter spp. and Aeromonas spp. in superficial coastal waters showing distinct pollution history across one year, and registered data regarding tide regimen, 7-days pluviosity, salinity, pH, water temperature. We analyzed data using General Estimating Equation (GEE) to assess predictors of such occurrence. Our results suggest that the sampling site had the strongest effect over concentration of these antimicrobial-resistant microorganisms, followed by pollution indexes and tide regimen. Increased salinity, advanced sampling time, water temperature, rainfall and decrease of pH were related to decrease concentrations. We provide a list of factors that could be easily monitored and further included in models aiming at predicting occurrence of carbapenemase producers in coastal waters. Our study may encourage researchers to further improve this list and validate the model proposed, so that monitoring and future public policies can be developed to control the spread of antimicrobial resistance in the environment.
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Affiliation(s)
- Raphael P Paschoal
- LIMM, Laboratório de Investigação em Microbiologia Médica, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eloiza H Campana
- LIMM, Laboratório de Investigação em Microbiologia Médica, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; LMC, Laboratório de Microbiologia Clínica (LMC), Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Laura de S Castro
- Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata C Picão
- LIMM, Laboratório de Investigação em Microbiologia Médica, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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17
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Zagui GS, de Andrade LN, Moreira NC, Silva TV, Machado GP, da Costa Darini AL, Segura-Muñoz SI. Gram-negative bacteria carrying β-lactamase encoding genes in hospital and urban wastewater in Brazil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:376. [PMID: 32417981 DOI: 10.1007/s10661-020-08319-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Multidrug resistance mediated by β-lactamase in Gram-negative bacilli is a serious public health problem. Sewers are considered reservoirs of multiresistant bacteria due to presence of antibiotics that select them and favor their dissemination. The present study evaluated the antibiotic resistance profile and β-lactamases production in Gram-negative bacilli isolates from hospital sewage and urban wastewater treatment plants (UWWTP) in Brazil. Bacteria were isolated and identified with biochemical tests. Antibiotic susceptibility testing was performed by the disk-diffusion method and detection of extended-spectrum β-lactamase and carbapenemases by enzymatic inhibitor and conventional PCR. Differences in resistance to amoxicillin clavulanic, aztreonam, cefepime, and cefotaxime were observed in hospital sewage compared with urban sewage (p < 0.05). The multidrug-resistant phenotype was observed in 33.3% of hospital sewage isolates (p = 0.0025). β-lactamases genes were found in 35.6% of isolates, with the most frequent being blaKPC and blaTEM (17.8%), and blaSHV and blaCTX-M (13.3% and 8.9%, respectively). The data obtained are relevant, since the bacteria detected are on the priority pathogens list from the World Health Organization and hospital sewage could be released untreated into the municipal collection system, which may favor the spread of resistance. Changes in hospital sewage discharge practices, as well as additional technologies regarding effluent disinfection in the UWWTP, can prevent the spread of these bacteria into the environment and negative impact on water resources.
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Affiliation(s)
| | | | | | - Thaís Vilela Silva
- College of Nursing of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | | | | | - Susana Inés Segura-Muñoz
- College of Nursing of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
- Laboratory of Ecotoxicology and Environmental Parasitology, Department of Maternal-Infant Nursing and Public Health, College of Nursing of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
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18
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Surleac M, Czobor Barbu I, Paraschiv S, Popa LI, Gheorghe I, Marutescu L, Popa M, Sarbu I, Talapan D, Nita M, Iancu AV, Arbune M, Manole A, Nicolescu S, Sandulescu O, Streinu-Cercel A, Otelea D, Chifiriuc MC. Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania. PLoS One 2020; 15:e0228079. [PMID: 31999747 PMCID: PMC6992004 DOI: 10.1371/journal.pone.0228079] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
We report on the genomic characterization of 47 multi-drug resistant, carbapenem resistant and ESBL-producing K. pneumoniae isolates from the influent (I) and effluent (E) of three wastewater treatment plants (WWTPs) and from Romanian hospital units which are discharging the wastewater in the sampled WWTPs. The K. pneumoniae whole genome sequences were analyzed for antibiotic resistance genes (ARGs), virulence genes and sequence types (STs) in order to compare their distribution in C, I and E samples. Both clinical and environmental samples harbored prevalent and widely distributed ESBL genes, i.e. blaSHV, blaOXA, blaTEM and blaCTX M. The most prevalent carbapenemase genes were blaNDM-1, blaOXA-48 and blaKPC-2. They were found in all types of isolates, while blaOXA-162, a rare blaOXA-48 variant, was found exclusively in water samples. A higher diversity of carbapenemases genes was seen in wastewater isolates. The aminoglycoside modifying enzymes (AME) genes found in all types of samples were aac(6’), ant(2'')Ia, aph(3'), aaD, aac(3) and aph(6). Quinolone resistance gene qnrS1 and the multi-drug resistance oqxA/B pump gene were found in all samples, while qnrD and qnrB were associated to aquatic isolates. The antiseptics resistance gene qacEdelta1 was found in all samples, while qacE was detected exclusively in the clinical ones. Trimethroprim-sulfamethoxazole (dfrA, sul1 and sul2), tetracyclines (tetA and tetD) and fosfomycin (fosA6, known to be located on a transpozon) resistance genes were found in all samples, while for choramphenicol and macrolides some ARGs were detected in all samples (catA1 and catB3 / mphA), while other (catA2, cmIA5 and aac(6’)Ib / mphE and msrE) only in wastewater samples. The rifampin resistance genes arr2 and 3 (both carried by class I integrons) were detected only in water samples. The highly prevalent ARGs preferentially associating with aquatic versus clinical samples could ascribe potential markers for the aquatic (blaSHV-145, qacEdelta1, sul1, aadA1, aadA2) and clinical (blaOXA-1, blaSHV-106,blaTEM-150, aac(3)Iia, dfrA14, oqxA10; oqxB17,catB3, tetD) reservoirs of AR. Moreover, some ARGs (oqxA10; blaSHV-145; blaSHV-100, aac(6')Il, aph(3')VI, armA, arr2, cmlA5, blaCMY-4, mphE, msrE, oqxB13, blaOXA-10) showing decreased prevalence in influent versus effluent wastewater samples could be used as markers for the efficiency of the WWTPs in eliminating AR bacteria and ARGs. The highest number of virulence genes (75) was recorded for the I samples, while for E and C samples it was reduced to half. The most prevalent belong to three functional groups: adherence (fim genes), iron acquisition (ent, fep, fyu, irp and ybt genes) and the secretion system (omp genes). However, none of the genes associated with hypervirulent K. pneumoniae have been found. A total of 14 STs were identified. The most prevalent clones were ST101, ST219 in clinical samples and ST258, ST395 in aquatic isolates. These STs were also the most frequently associated with integrons. ST45 and ST485 were exclusively associated with I samples, ST11, ST35, ST364 with E and ST1564 with C samples. The less frequent ST17 and ST307 aquatic isolates harbored blaOXA-162, which was co-expressed in our strains with blaCTX-M-15 and blaOXA-1.
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Affiliation(s)
- Marius Surleac
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- Institute of Biochemistry, Romanian Academy, Bucharest, Romania
| | - Ilda Czobor Barbu
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Simona Paraschiv
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Laura Ioana Popa
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Irina Gheorghe
- The Research Institute of the University of Bucharest, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Luminita Marutescu
- The Research Institute of the University of Bucharest, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Marcela Popa
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Ionela Sarbu
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Daniela Talapan
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Mihai Nita
- National Institute for R & D in Industrial Ecology (ECOIND), Bucharest, Romania
| | - Alina Viorica Iancu
- Infectious Diseases Hospital Galati, Galati, Romania
- Faculty of Medicine and Pharmacy “Dunarea de Jos”, University of Galati, Galati, Romania
| | - Manuela Arbune
- Infectious Diseases Hospital Galati, Galati, Romania
- Faculty of Medicine and Pharmacy “Dunarea de Jos”, University of Galati, Galati, Romania
| | - Alina Manole
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | - Oana Sandulescu
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Adrian Streinu-Cercel
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Dan Otelea
- National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- * E-mail:
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
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Decano AG, Downing T. An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates. Sci Rep 2019; 9:17394. [PMID: 31758048 PMCID: PMC6874702 DOI: 10.1038/s41598-019-54004-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131's origin, adaptation and spread is essential. E. coli ST131's ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131's population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.
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Affiliation(s)
- Arun Gonzales Decano
- School of Biotechnology, Dublin City University, Dublin, Ireland
- School of Medicine, University of, St. Andrews, UK
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland.
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