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Kerkvliet JJ, Bossers A, Kers JG, Meneses R, Willems R, Schürch AC. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements. PeerJ 2024; 12:e16695. [PMID: 38188174 PMCID: PMC10771768 DOI: 10.7717/peerj.16695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.
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Affiliation(s)
- Jesse J. Kerkvliet
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Alex Bossers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
- Wageningen University, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jannigje G. Kers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Rob Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
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Heydari A, Kim ND, Biggs PJ, Horswell J, Gielen GJHP, Siggins A, Taylor MD, Bromhead C, Palmer BR. Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms. Antibiotics (Basel) 2023; 12:antibiotics12040772. [PMID: 37107134 PMCID: PMC10135173 DOI: 10.3390/antibiotics12040772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.
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Affiliation(s)
- Ali Heydari
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Nick D Kim
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North 4410, New Zealand
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Jacqui Horswell
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | | | - Alma Siggins
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, H91 TK33 Galway, Ireland
| | | | - Collette Bromhead
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Barry R Palmer
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
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3
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Despotovic M, de Nies L, Busi SB, Wilmes P. Reservoirs of antimicrobial resistance in the context of One Health. Curr Opin Microbiol 2023; 73:102291. [PMID: 36913905 DOI: 10.1016/j.mib.2023.102291] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023]
Abstract
The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.
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Affiliation(s)
- Milena Despotovic
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, avenue du Swing, Belvaux, L-4367, Luxembourg.
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4
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Busi SB, de Nies L, Pramateftaki P, Bourquin M, Kohler TJ, Ezzat L, Fodelianakis S, Michoud G, Peter H, Styllas M, Tolosano M, De Staercke V, Schön M, Galata V, Wilmes P, Battin T. Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters. Microbiol Spectr 2023; 11:e0406922. [PMID: 36688698 PMCID: PMC9927545 DOI: 10.1128/spectrum.04069-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michail Styllas
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Tolosano
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vincent De Staercke
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martina Schön
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tom Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Abstract
The alarming rise of microbial resistance to antibiotics has severely limited the efficacy of current treatment options. The prevalence of β-lactamase enzymes is a significant contributor to the emergence of antibiotic resistance. There are four classes of β-lactamases: A, B, C, and D. Class B is the metallo-β-lactamase, while the rest are serine β-lactamases. The clinical use of β-lactamase inhibitors began as an attempt to combat β-lactamase-mediated resistance. Although β-lactamase inhibitors alone are ineffective against bacteria, research has shown that combining inhibitors with antibiotics is a safe and effective treatment that not only prevents β-lactamase formation but also broadens the range of activity. These inhibitors may cause either temporary or permanent inhibition. The development of new β-lactamase inhibitors will be a primary focus of future research. This study discusses recent advances in our knowledge of the biochemistry behind β-lactam breakdown, with special emphasis on the mechanism of inhibitors for β-lactam complexes with β-lactamase. The study also focuses on the pharmacokinetic and pharmacodynamic properties of all inhibitors and then applies them in clinical settings. Our analysis and discussion of the challenges that exist in designing inhibitors might help pharmaceutical researchers address root issues and develop more effective inhibitors.
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Olorunleke SO, Kirchner M, Duggett N, AbuOun M, Okorie-Kanu OJ, Stevens K, Card RM, Chah KF, Nwanta JA, Brunton LA, Anjum MF. Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria. Front Microbiol 2022; 13:937968. [PMID: 35935201 PMCID: PMC9354541 DOI: 10.3389/fmicb.2022.937968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with blaCTX-M present in all but others in a subset [blaTEM (62.8%) and blaSHV (0.5%)] of isolates; none harboured transferable carbapenemase genes. Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying blaCTX-M-55 was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant blaCTX-M variant was blaCTX-M-15 (87.9%), although blaCTX-M-55, blaCTX-M-64, and blaCTX-M-65 were present; it was notable that blaCTX-M-1, common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, blaTEM-1b, tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A blaCTX-M-15 harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E. coli; they were likely to be MDR with several harbouring blaCTX-M-15. Surprisingly, human isolates had highest numbers of AMR genes and pigs the least.
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Affiliation(s)
- Solomon O. Olorunleke
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
- Department of Animal Science, Ebonyi State University, Abakaliki, Nigeria
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- School of Health and Life Science, Teesside University, Middlesbrough, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Onyinye J. Okorie-Kanu
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Kim Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Roderick M. Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Kennedy Foinkfu Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, Nigeria
| | - John A. Nwanta
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Lucy A. Brunton
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- *Correspondence: Muna F. Anjum
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Amankwah FKD, Gbedema SY, Boakye YD, Bayor MT, Boamah VE. Antimicrobial Potential of Extract from a Pseudomonas aeruginosa Isolate. Scientifica (Cairo) 2022; 2022:4230397. [PMID: 35812345 PMCID: PMC9259217 DOI: 10.1155/2022/4230397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are one of the main sources of antimicrobial agents and over 50% of antibiotics currently used in hospitals are metabolites from microbes. This study aimed to isolate microorganisms from the Dompoase landfill site, Kwame Nkrumah University Physics Garden, Kosiko River, and Ada Foah seashore of Ghana and screen their metabolites for antimicrobial activity. Forty-eight (48) microorganisms were isolated and their metabolites were screened against Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, Vibrio cholerae, Salmonella typhi, Pseudomonas aeruginosa, Streptococcus pyogenes, Proteus mirabilis, and Candida albicans using the agar well diffusion method. Ten (10) of the isolates exhibited antimicrobial activity. Isolate DO5, identified as P. aeruginosa isolate, from the Dompoase landfill site was selected for fermentation because it exhibited the highest activity against all the test organisms. DO5 produced optimum antimicrobial activity when fermented for 11 days at 30°C. In the agar diffusion method, the extract of isolate DO5 recorded zones of inhibition ranging between 11.67 ± 0.23 and 21.50 ± 0.71 mm. The MIC and MBC recorded for the DO5 extract ranged from 3.13-25.0 mg/mL and from 6.25-50.0 mg/mL, respectively. Column chromatography analysis yielded eight (8) subfractions from the DO5 extract. IR analysis revealed the presence of functional groups such as alcohols, esters, and hydrocarbons in the fractions. GC-MS analysis identified nine compounds that have been reported to have antimicrobial agents. The DO5 metabolites stand the chance to be developed into potent antibiotics for infection treatment.
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Affiliation(s)
- Francis Kwaku Dzideh Amankwah
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Stephen Yao Gbedema
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Yaw Duah Boakye
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Marcel Tunkumgmen Bayor
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Vivian Etsiapah Boamah
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
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Ghaznavi-Rad E, Komijani M, Moradabadi A, Rezaei M, Shaykh-Baygloo N. Isolation of a lytic bacteriophage against extensively drug-resistant Acinetobacter baumannii infections and its dramatic effect in rat model of burn infection. J Clin Lab Anal 2022; 36:e24497. [PMID: 35708005 PMCID: PMC9279972 DOI: 10.1002/jcla.24497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022] Open
Abstract
Objectives Acinetobacter Baumannii is an opportunistic nosocomial pathogen belonging to the Moraxellaceae family. The emergence of multidrug resistant strains of this pathogen caused many problems for hospitals and patients. The aim of the current study was to isolate, identify, and morphologically, physiologically, and in vivo analyze a new lytic bacteriophage targeting extensively drug‐resistant (XDR) A. baumannii. Materials and Methods Different wastewater samples were tested for isolation of lytic bacteriophage against 19 A. baumannii isolates obtained from patients hospitalized in a hospital in Arak, Iran, from January 2019 to March 2019. The phenotypic and genotypic characteristics of A. baumannii strains (resistance genes including: adeA, adeB, adeC, adeR, adeS, ISAba1, blaOXA‐23, blaOXA‐24) were analyzed. The isolated phage characteristics including adsorption time, pH and thermal stability, host range, one‐step growth rate, electron microscopy examination, and therapeutic efficacy of the phage were also investigated. Therapeutic efficacy of the phage was evaluated in a rat model with burn infection of XDR A. baumannii. The lesion image was taken on different days after burning and infection induction and was compared with phage untreated lesions. Results The results showed unique characteristics of the isolated phage (vB‐AbauM‐Arak1) including high specificity for Acinetobacter baumannii, stability at a relatively wide range of temperatures and pH values, short adsorption time, short latent period, and large burst size. In relation to the therapeutic efficacy of the phage, the lesion area decreased in phage‐treated groups over 14 days than in those untreated, significantly (p < 0.05). Conclusion Our findings demonstrated that isolated lytic phage was able to eliminate burn infections caused by XDR A. baumannii in a rat model. So, it may be recommended as alternative options toward to developing a treatment for extensively drug resistant Acinetobacter infections.
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Affiliation(s)
- Ehsanollah Ghaznavi-Rad
- Department of Medical Laboratory Science, Faculty of Paramedicine, Arak University of Medical Sciences, Arak, Iran.,Molecular Research Center, Faculty of Medicine, Arak University of medical sciences, Arak, Iran
| | - Majid Komijani
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | - Alireza Moradabadi
- Molecular and medicine research center, Khomein University of Medical Sciences, Khomein, Iran
| | - Marzieh Rezaei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Biotechnology, University of Isfahan, Isfahan, Iran
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9
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Pattis I, Weaver L, Burgess S, Ussher JE, Dyet K. Antimicrobial Resistance in New Zealand-A One Health Perspective. Antibiotics (Basel) 2022; 11:antibiotics11060778. [PMID: 35740184 PMCID: PMC9220317 DOI: 10.3390/antibiotics11060778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is an increasing global threat that affects human, animal and, often less acknowledged, environmental health. This complex issue requires a multisectoral One Health approach to address the interconnectedness of humans, animals and the natural environment. The prevalence of AMR in these reservoirs varies widely among countries and thus often requires a country-specific approach. In New Zealand (NZ), AMR and antimicrobial usage in humans are relatively well-monitored and -understood, with high human use of antimicrobials and the frequency of resistant pathogens increasing in hospitals and the community. In contrast, on average, NZ is a low user of antimicrobials in animal husbandry systems with low rates of AMR in food-producing animals. AMR in New Zealand’s environment is little understood, and the role of the natural environment in AMR transmission is unclear. Here, we aimed to provide a summary of the current knowledge on AMR in NZ, addressing all three components of the One Health triad with a particular focus on environmental AMR. We aimed to identify knowledge gaps to help develop research strategies, especially towards mitigating AMR in the environment, the often-neglected part of the One Health triad.
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Affiliation(s)
- Isabelle Pattis
- Institute of Environmental Science and Research Ltd., Christchurch 8041, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch 8041, New Zealand
| | - Sara Burgess
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Kristin Dyet
- Institute of Environmental Science and Research Ltd., Porirua 5022, New Zealand
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Stenholm Å, Hedeland M, Pettersson CE. Neomycin removal using the white rot fungus Trametes versicolor. J Environ Sci Health A Tox Hazard Subst Environ Eng 2022; 57:436-447. [PMID: 35583106 DOI: 10.1080/10934529.2022.2072644] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The presence of antibiotic resistance genes in wastewater treatment plants (WWTPs), and in river and lake recipients show the need to develop new antibiotic removal strategies. The aminoglycoside antibiotic class is of special concern since the chemical structure of these compounds limits the choices of removal technologies. The experimental design included fungal mediated in vivo and in vitro experiments. The experiments were performed in Erlenmeyer flasks under non-sterile conditions. In the study, the role of the laccase redox mediator 4-hydroxy benzoic acid (HBA) in the removal of neomycin was investigated. The specific objective of the study was to conclude whether it is possible to use the white rot fungus (WRF) Trametes versicolor to biodegrade neomycin. It was shown that it is feasible to remove 34% neomycin in vitro (excluding living fungal cells) by laccase-HBA mediated extracellular biodegradation. In the in vivo experiments, polyurethane foam (PUF) was used as supporting material to immobilize fungal mycelia on. The presence of living fungal cells facilitated a removal of approximately 80% neomycin in the absence of HBA. Using liquid chromatography-high resolution-mass spectrometry, it was possible to tentatively identify oxidation products of neomycin hydrolysates. The results in this study open up the possibility to implement a pretreatment plant (PTP) aimed for neomycin removal.
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Affiliation(s)
- Åke Stenholm
- Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
- Cytiva AB, Uppsala, Sweden
| | - Mikael Hedeland
- Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
| | - Curt E Pettersson
- Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
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Ghordouei Milan E, Mahvi AH, Nabizadeh R, Alimohammadi M. What is the effect on antibiotic resistant genes of chlorine disinfection in drinking water supply systems? A systematic review protocol. Environ Evid 2022. [DOI: 10.1186/s13750-022-00266-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Background
Antibiotic-resistant bacteria (ARB) usually enter water sources in different ways, such as via municipal and hospital wastewaters. Because conventional technologies used to treat water inefficient in removing these contaminants (especially antibiotic-resistant genes; ARGs), these contaminants easily enter drinking water distribution networks and pose serious threats to consumers’ health. This study’s main purpose is to systematically investigate the effect of chlorine disinfection on ARGs in drinking water supply systems. This study could play an important role in elucidating the effect of chlorine disinfection on ARGs.
Methods
The systematic review outlining this protocol will be performed according to the Collaboration for Environmental Evidence (CEE) guidelines. The main question is, “what is the effect of chlorine disinfection on ARGs in drinking water supply systems?” For this purpose, the articles will be considered, in which chlorine’s effect on ARGs is investigated. The search includes electronic resources, grey literature, and related websites. Electronic resources include Scopus, PubMed, Embase, Web of Science Core Collection, and Science Direct. After the final search, the obtained articles will be collected in the reference management software (Endnote X8). Upon removing the duplicate articles, the first stage of article screening will be performed based on the title and abstract the articles. In the second stage, the articles obtained from the first screening stage will be screened based on the full text of the articles based on the eligibility criteria. Then, two members of the expert team extract the data. To assess the validity of the articles, bias sources will be determined by an expert team. Biases will be defined according to the criteria designed by Bilotta et al. Finally, a narrative synthesis will be performed for the extracted data; if appropriate data are available, quantitative analysis will also be performed.
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13
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Stanton IC, Bethel A, Leonard AFC, Gaze WH, Garside R. Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map. Environ Evid 2022; 11:8. [PMID: 35308196 PMCID: PMC8917330 DOI: 10.1186/s13750-022-00262-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/24/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom. METHODS Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs. RESULTS For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments. CONCLUSIONS Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s13750-022-00262-2.
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Affiliation(s)
- Isobel Catherine Stanton
- European Centre for Environment and Human Health, College of Medicine and Health, Penryn Campus, University of Exeter, Penryn, TR10 9FE UK
| | - Alison Bethel
- College of Medicine and Health, St Luke’s Campus, University of Exeter, Exeter, EX1 1TX UK
| | - Anne Frances Clare Leonard
- European Centre for Environment and Human Health, College of Medicine and Health, Penryn Campus, University of Exeter, Penryn, TR10 9FE UK
| | - William Hugo Gaze
- European Centre for Environment and Human Health, College of Medicine and Health, Penryn Campus, University of Exeter, Penryn, TR10 9FE UK
| | - Ruth Garside
- European Centre for Environment and Human Health, College of Medicine and Health, Knowledge Spa, University of Exeter, Truro, TR1 3HD UK
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Matviichuk O, Mondamert L, Geffroy C, Gaschet M, Dagot C, Labanowski J. River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics. Front Microbiol 2022; 13:795206. [PMID: 35222329 PMCID: PMC8863943 DOI: 10.3389/fmicb.2022.795206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.
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Affiliation(s)
- Olha Matviichuk
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France.,UMR INSERM 1092, Limoges, France
| | - Leslie Mondamert
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | - Claude Geffroy
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | | | | | - Jérôme Labanowski
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
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15
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Holm M, Zellweger RM, Poudyal N, Smith KHT, Joh HS, Marks F. Measuring the Link Between Vaccines and Antimicrobial Resistance in Low Resource Settings – Limitations and Opportunities in Direct and Indirect Assessments and Implications for Impact Studies. Front Trop Dis 2022. [DOI: 10.3389/fitd.2022.805833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The importance of vaccines in combatting antimicrobial resistance (AMR) is commonly accepted. Although scientific reasoning supports the putative connection between vaccines and reduction of AMR, reliably measuring the magnitude and effect of vaccines on antimicrobial resistance is inherently challenging, especially in low resource settings. We review the intrinsic challenges in estimating the effect of vaccines on AMR and discuss the limitations and opportunities in current methods from the host, pathogen, and environment perspectives. We highlight advantages and pitfalls in different epidemiological study designs with a specific focus on impact studies in low resource settings and suggest how these perspectives could be considered in future research.
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16
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Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat Microbiol 2022; 7:2054-2067. [PMID: 36411354 PMCID: PMC9712112 DOI: 10.1038/s41564-022-01263-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/10/2022] [Indexed: 11/22/2022]
Abstract
The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.
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Affiliation(s)
- Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ross Booton
- grid.5337.20000 0004 1936 7603Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Teemu Kallonen
- grid.410552.70000 0004 0628 215XDepartment of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Marjorie J. Gibbon
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Natacha Couto
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Virginie Passet
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sebastián López-Fernández
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Carla Rodrigues
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Louise Matthews
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sonia Mitchell
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Reeve
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophia David
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Cristina Merla
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Marta Corbella
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Carolina Ferrari
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Francesco Comandatore
- grid.4708.b0000 0004 1757 2822Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, Milan, Italy
| | - Piero Marone
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Sylvain Brisse
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology, Università di Pavia, Pavia, Italy
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.7737.40000 0004 0410 2071Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Edward J. Feil
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
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Mayne J, Zhang X, Butcher J, Walker K, Ning Z, Wójcik E, Dastych J, Stintzi A, Figeys D. Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL ®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach. Viruses 2021; 13:1734. [PMID: 34578313 DOI: 10.3390/v13091734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022] Open
Abstract
Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.
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Mbanga J, Amoako DG, Abia ALK, Allam M, Ismail A, Essack SY. Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa. Front Vet Sci 2021; 8:636715. [PMID: 33718473 PMCID: PMC7952442 DOI: 10.3389/fvets.2021.636715] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 01/09/2023] Open
Abstract
There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the bla TEM1B gene and a single isolate the blaCTX-M-14 and blaCTX-M-55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
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19
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Pieri A, Aschbacher R, Fasani G, Mariella J, Brusetti L, Pagani E, Sartelli M, Pagani L. Country Income Is Only One of the Tiles: The Global Journey of Antimicrobial Resistance among Humans, Animals, and Environment. Antibiotics (Basel) 2020; 9:E473. [PMID: 32752276 DOI: 10.3390/antibiotics9080473] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/25/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most complex global health challenges today: decades of overuse and misuse in human medicine, animal health, agriculture, and dispersion into the environment have produced the dire consequence of infections to become progressively untreatable. Infection control and prevention (IPC) procedures, the reduction of overuse, and the misuse of antimicrobials in human and veterinary medicine are the cornerstones required to prevent the spreading of resistant bacteria. Purified drinking water and strongly improved sanitation even in remote areas would prevent the pollution from inadequate treatment of industrial, residential, and farm waste, as all these situations are expanding the resistome in the environment. The One Health concept addresses the interconnected relationships between human, animal, and environmental health as a whole: several countries and international agencies have now included a One Health Approach within their action plans to address AMR. Improved antimicrobial usage, coupled with regulation and policy, as well as integrated surveillance, infection control and prevention, along with antimicrobial stewardship, sanitation, and animal husbandry should all be integrated parts of any new action plan targeted to tackle AMR on the Earth. Since AMR is found in bacteria from humans, animals, and in the environment, we briefly summarize herein the current concepts of One Health as a global challenge to enable the continued use of antibiotics.
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