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Chen Z, Ding Q, Ning X, Song Z, Gu J, Wang X, Sun W, Qian X, Hu T, Wei S, Xu L, Li Y, Zhou Z, Wei Y. Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133921. [PMID: 38452670 DOI: 10.1016/j.jhazmat.2024.133921] [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: 11/21/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.
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Affiliation(s)
- Zhihui Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingling Ding
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xing Ning
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shumei Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liang Xu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuexuan Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhipeng Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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Morgado S, Fonseca É, Freitas F, Caldart R, Vicente AC. In-depth analysis of Klebsiella aerogenes resistome, virulome and plasmidome worldwide. Sci Rep 2024; 14:6538. [PMID: 38503805 PMCID: PMC10951357 DOI: 10.1038/s41598-024-57245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/15/2024] [Indexed: 03/21/2024] Open
Abstract
Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. aerogenes have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and plasmidome of this species based on 561 genomes, spanning all continents. Furthermore, we sequenced four new strains from Brazil (mostly from the Amazon region). Dozens of STs occur worldwide, but the pandemic clones ST93 and ST4 have prevailed in several countries. Almost all genomes were clinical, however, most of them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations (omp36, ampD, ampG, ampR) associated with resistance to β-lactams. Integrons were also identified, presenting gene cassettes not yet reported in this species (blaIMP, blaVIM, blaGES). Considering the virulence loci, the yersiniabactin and colibactin operons were found in the ICEKp10 element, which is disseminated in genomes of several STs, as well as an incomplete salmochelin cluster. In contrast, the aerobactin hypervirulence trait was observed only in one ST432 genome. Plasmids were common, mainly from the ColRNAI replicon, with some carrying resistance genes (mcr, blaTEM, blaNDM, blaIMP, blaKPC, blaVIM) and virulence genes (EAST1, senB). Interestingly, 172 genomes of different STs presented putative plasmids containing the colicin gene.
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Affiliation(s)
- Sergio Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil.
| | - Érica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Raquel Caldart
- Centro de Ciências da Saúde, Universidade Federal de Roraima, Boa Vista, RR, 69300-000, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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Teixeira M, Pillay S, Urhan A, Abeel T. SHIP: identifying antimicrobial resistance gene transfer between plasmids. Bioinformatics 2023; 39:btad612. [PMID: 37796811 PMCID: PMC10598575 DOI: 10.1093/bioinformatics/btad612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/29/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
MOTIVATION Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR. RESULTS We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis. AVAILABILITY AND IMPLEMENTATION The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.
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Affiliation(s)
- Marco Teixeira
- Faculty of Engineering, University of Porto, Porto 4200-465, Portugal
- INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, Porto 4200-465, Portugal
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, The Netherlands
| | - Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, The Netherlands
| | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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Sánchez-Urtaza S, Ocampo-Sosa A, Molins-Bengoetxea A, Rodríguez-Grande J, El-Kholy MA, Hernandez M, Abad D, Shawky SM, Alkorta I, Gallego L. Co-Existence of blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57 in a Clinical Isolate of Acinetobacter baumannii from Alexandria, Egypt. Int J Mol Sci 2023; 24:12515. [PMID: 37569889 PMCID: PMC10419532 DOI: 10.3390/ijms241512515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
The increasing rates of antimicrobial resistance among carbapenem-resistant Acinetobacter baumannii in the Middle East and North Africa are one of the major concerns for healthcare settings. We characterised the first A. baumannii isolate harbouring five β-lactamases identified in Egypt. The isolate Ale25 was obtained from an ICU patient of a hospital from Alexandria. The isolate was phenotypically and genotypically screened for carbapenemase genes. The isolate was resistant to carbapenems, aminoglycosides, fluoroquinolones and cefiderocol. Whole-Genome Sequencing identified five β-lactamase genes, blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57, together with other antibiotic resistance genes, conferring resistance to sulfonamides, macrolides, tetracyclines, rifamycin and chloramphenicol. Virulome analysis showed the presence of genes involved in adhesion and biofilm production, type II and VI secretion systems, exotoxins, etc. Multi-Locus Sequence Typing analysis identified the isolate as Sequence Types 113Pas and 2246Oxf, belonging to International Clone 7. Sequencing experiments revealed the presence of four plasmids of 2.7, 22.3, 70.4 and 240.8 Kb. All the β-lactamase genes were located in the chromosome, except the blaPER-7, gene which was found within the plasmid of 240.8 Kb. This study highlights the threat of the emergence and dissemination of these types of isolates.
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Affiliation(s)
- Sandra Sánchez-Urtaza
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
| | - Alain Ocampo-Sosa
- Microbiology Service, Health Research Institute (IDIVAL), University Hospital Marqués de Valdecilla, 39008 Santander, Spain;
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ainhoa Molins-Bengoetxea
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
| | - Jorge Rodríguez-Grande
- Microbiology Service, Health Research Institute (IDIVAL), University Hospital Marqués de Valdecilla, 39008 Santander, Spain;
| | - Mohammed A. El-Kholy
- Division of Clinical and Biological Sciences, Department of Microbiology and Biotechnology, College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport (AASTMT), Alexandria P.O. Box 1029, Egypt;
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, One Health, Agrarian Technological Institute of Castile and Leon (ITACyL), 47009 Valladolid, Spain; (M.H.); (D.A.)
| | - David Abad
- Laboratory of Molecular Biology and Microbiology, One Health, Agrarian Technological Institute of Castile and Leon (ITACyL), 47009 Valladolid, Spain; (M.H.); (D.A.)
| | - Sherine M. Shawky
- Medical Research Institute, Alexandria University, Alexandria 5422031, Egypt;
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain;
| | - Lucia Gallego
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
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Sánchez-Urtaza S, Ocampo-Sosa A, Molins-Bengoetxea A, El-Kholy MA, Hernandez M, Abad D, Shawky SM, Alkorta I, Gallego L. Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt. Front Cell Infect Microbiol 2023; 13:1208046. [PMID: 37545857 PMCID: PMC10399577 DOI: 10.3389/fcimb.2023.1208046] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Carbapenem resistant Acinetobacter baumannii is a major global concern, especially in countries of the Middle East and North Africa, where the antibiotic resistance rates are on the rise. The aim of this study was to study the genomic characteristics and antimicrobial susceptibility profile of thirty-six multidrug resistant A. baumannii clinical isolates obtained in hospitals from Alexandria, Egypt. Antibiotic resistance rates were estimated by determination of Minimum Inhibitory Concentrations. Carbapenemase genes, other antibiotic resistance genes and virulence factors were then screened by the use of Whole Genome Sequencing. Isolates were also subjected to Multi Locus Sequence Typing (MLST) using the Pasteur Scheme and to core genome MLST to study their clonal relatedness. In addition, plasmid analysis was performed by the use of a commercial kit and S1- Pulsed Field Gel Electrophoresis, and Hybridization experiments with DIG-labeled DNA probes for bla NDM-1, blaPER-7 and bla GES-like were performed to locate these genes. The majority of isolates were resistant to β-lactams (including carbapenems), fluoroquinolones, aminoglycosides and trimethoprim; and some showed resistance to cefiderocol and minocycline. We identified 8 different bla OXA-51-like variants including bla OXA-51, bla OXA-64, bla OXA-65, bla OXA-66, bla OXA-68, bla OXA-91, bla OXA-94 and bla OXA-336; bla OXA-23, bla NDM-1, bla PER-7, bla GES-like and bla ADC-like and other antibiotic resistance genes, some of these genes were within transposons or class 1 integrons. Multiple virulence factors responsible for adherence, biofilm production, type II and type VI secretion systems, exotoxins, exoenzymes, immune modulation and iron uptake were observed and 34 out of 36 isolates showed motility. Thirty-five out of 36 isolates clustered with International Clones 2, 4, 5, 7, 8 and 9; and 9 STs were identified including ST570, ST2, ST600, ST15, ST113, ST613, ST85, ST158, ST164. Plasmids ranging in size from 1.7 to 70 kb were found; bla NDM-1 and blaPER-7 genes were located in the chromosome and bla GES-like genes were simultaneously located in the chromosome and in a plasmid of 70kb. In conclusion, this study revealed a wide spectrum of antibiotic resistance genes and a variety of lineages among A. baumannii isolated in hospitals from Alexandria, and highlights the importance of investigating the molecular epidemiology to control the spread of multi-drug resistant isolates.
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Affiliation(s)
- Sandra Sánchez-Urtaza
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
| | - Alain Ocampo-Sosa
- Microbiology Service, University Hospital Marqués de Valdecilla, Health Research Institute (Instituto de Investigación Valdecilla), Santander, Spain and CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Ainhoa Molins-Bengoetxea
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
| | - Mohammed A. El-Kholy
- Department of Microbiology and Biotechnology, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport (AASTMT), Alexandria, Egypt
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, One Health, Agricultural Technological, Institute of Castile and Leon (ITACyL), Valladolid, Spain
| | - David Abad
- Laboratory of Molecular Biology and Microbiology, One Health, Agricultural Technological, Institute of Castile and Leon (ITACyL), Valladolid, Spain
| | - Sherine M. Shawky
- Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
| | - Lucia Gallego
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
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Noel HR, Petrey JR, Palmer LD. Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination. Ann N Y Acad Sci 2022; 1518:166-182. [PMID: 36316792 PMCID: PMC9771954 DOI: 10.1111/nyas.14918] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Jessica R. Petrey
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
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Hao J, Zhang B, Deng J, Wei Y, Xiao X, Liu J. Emergence of a Hypervirulent Tigecycline-Resistant Klebsiella pneumoniae Strain Co-producing blaNDM–1 and blaKPC–2 With an Uncommon Sequence Type ST464 in Southwestern China. Front Microbiol 2022; 13:868705. [PMID: 35572689 PMCID: PMC9100695 DOI: 10.3389/fmicb.2022.868705] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Emergence of blaNDM–1 and blaKPC–2 co-producing Klebsiella pneumoniae strains is currently attracting widespread attention, but little information is available about their tigecycline resistance, virulence, and prevalence in Southwest China. In July 2021, an extensively drug-resistant K. pneumoniae strain AHSWKP25 whose genome contained both blaNDM–1 and blaKPC–2 genes was isolated from the blood of a patient with the malignant hematological disease in Luzhou, China. We investigated the resistance profiles of AHSWKP25 using microbroth dilution, agar dilution, modified carbapenemase inactivation (mCIM), and EDTA-modified carbapenemase inactivation methods (eCIM). The virulence of AHSWKP25 was assessed through string tests, serum killing assays, and a Galleria mellonella larval infection model. Conjugation and plasmid stability experiments were conducted to determine the horizontal transfer capacity of plasmids. And efflux pump phenotype test and real-time quantitative reverse transcription-PCR (RT-PCR) were used to determine its efflux pump activity. Sequencing of AHSWKP25 determined that AHSWKP25 belonged to ST464, which is resistant to antibiotics such as carbapenems, tetracycline, fluoroquinolones, tigecycline, and fosfomycin. The efflux pump phenotype tests and RT-PCR results demonstrated that efflux pumps were overexpressed in the AHSWKP25, which promoted the tigecycline resistance of the bacteria. AHSWKP25 also showed hypervirulence and serum resistance in vitro model. AHSWKP25 carried several different plasmids that contained blaNDM–1, blaKPC–2, and mutated tet(A) genes. Sequence alignment revealed that the plasmids carrying blaNDM–1 and blaKPC–2 underwent recombination and insertion events, respectively. We demonstrated that an X3 plasmid carrying blaNDM–1 was transferred from pSW25NDM1 to E. coli J53. We also identified missense mutations in the ramR, rcsA, lon, and csrD genes of AHSWKP25. Our results highlighted the potential of blaNDM–1 and blaKPC–2 co-producing K. pneumoniae strains to further develop antimicrobial resistance and hypervirulent phenotypes, but measures should be taken to closely monitor and control the spread of superbugs with multidrug-resistant phenotypes and hypervirulence.
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Affiliation(s)
- Jingchen Hao
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Bangqin Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jiamin Deng
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yueshuai Wei
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xue Xiao
- Department of Laboratory Medicine, Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Jinbo Liu,
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Yuan W, Zhang Y, Riaz L, Yang Q, Du B, Wang R. Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123822. [PMID: 33254807 DOI: 10.1016/j.jhazmat.2020.123822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/26/2020] [Accepted: 08/24/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.
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Affiliation(s)
- Wei Yuan
- School of Environment, Henan Normal University, Xinxiang 453007, China; School of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450046, Henan, China
| | - Yongli Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Luqman Riaz
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China.
| | - Bingbing Du
- School of Environment, Henan Normal University, Xinxiang 453007, China
| | - Ruifei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
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Characterization of a novel class 1 integron InSW39 and a novel transposon Tn5393k identified in an imipenem-nonsusceptible Salmonella Typhimurium strain in Sichuan, China. Diagn Microbiol Infect Dis 2020; 99:115263. [PMID: 33248418 DOI: 10.1016/j.diagmicrobio.2020.115263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/30/2020] [Accepted: 11/08/2020] [Indexed: 11/22/2022]
Abstract
This study aimed to characterize molecular mechanism of 3 Salmonella enterica strains and novel mobile genetic elements identified in them. The strains, designated SW1, SW39, and SW109084, were obtained from diarrhea patients. The results of susceptibility testing showed SW39 was nonsusceptible to imipenem and cefotaxime. Whole genome sequencing was performed on Illumina HiSeq platform. Multilocus-sequence typing revealed SW1 belonged to ST2529 which was first confirmed in S. enterica, SW109084 was ST34 which was first reported in Enteritidis and SW39 was ST19. Resistome analysis showed SW1, SW109084, and SW39 carried 14, 19, and 17 antibiotic resistance genes. Seven transposons and 4 integrons were confirmed in these strains. Notably, a novel In6- and In7-like class 1 integron designated InSW39 and a novel transposon Tn5393k were identified in plasmid pSW39. The study of genomics and resistance in S. enterica plays a significant role in prevention and treatment of Salmonella infections.
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Zou H, Jia X, Liu H, Li S, Wu X, Huang S. Emergence of NDM-5-Producing Escherichia coli in a Teaching Hospital in Chongqing, China: IncF-Type Plasmids May Contribute to the Prevalence of bla NDM- 5. Front Microbiol 2020; 11:334. [PMID: 32210935 PMCID: PMC7069339 DOI: 10.3389/fmicb.2020.00334] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/17/2020] [Indexed: 11/24/2022] Open
Abstract
The newly emerging NDM-5 confers increased antibiotic resistance and attracts extensive global attention, but the prevalence, dissemination mechanism, and clinical significance of NDM-5 among clinical Escherichia coli (E. coli) infections have not been thoroughly characterized to date. In the present study, 109 unique carbapenem-resistant E. coli (CR-EC) isolates were collected in Southwest China, from 2013 to 2017, among which 41 (37.61%) CR-EC isolates were identified as NDM-5-producers, with most isolates carrying the IncF-type plasmids. Molecular epidemiological studies revealed ST167 being the most common sequence type (ST). Moreover, we described the first report of a clinical CR-EC isolate co-harboring blaKPC–2 and blaNDM–5, which showed a higher level of resistance to carbapenems. In addition, blaNDM–5 plasmid transformation and conjugation indicated that blaNDM–5 itself did confer resistance to carbapenems. Complete sequencing of the blaNDM–5-harboring IncF plasmid revealed highly conserved regions (bleMBL-trpF-tat) and some transposons around blaNDM–5. Our findings revealed a new potential threat of NDM-5-postive CR-EC in mainland China and emphasized an urgent need to control their further spread.
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Affiliation(s)
- Hua Zou
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hang Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianan Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shifeng Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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11
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Characterization of Integrons and Antimicrobial Resistance in Escherichia coli Sequence Type 131 Isolates. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:3826186. [PMID: 32184909 PMCID: PMC7060437 DOI: 10.1155/2020/3826186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/05/2020] [Accepted: 01/14/2020] [Indexed: 01/17/2023]
Abstract
Background Escherichia coli sequence type 131 (ST131) is an important multidrug-resistant extraintestinal pathogen, which can cause many kinds of infections. Integrons may play a crucial role in the dissemination of antibiotic resistance genes. The purpose of this study was to characterize the prevelance of integrons among E. coli ST131 strains in China. Methods Eighty-three E. coli ST131 strains in China. E. coli ST131 strains in China. Results Overall, 26.5% (22/83) of the E. coli ST131 strains in China. dfrA17-aadA5 and aac(6')-Ib-cr-cmlA5. Only one type of Pc promoter variant was detected among 22 integron-positive isolates (PcW). In vivo transfer of integron was successful for 9 of integron-positive E. coli ST131 strains in China. E. coli ST131 strains in China. Conclusions Our study showed a low prevalence of integrons was detected in E. coli ST131. Continued surveillance of this mobile genetic element should be performed to study the evolution of antibiotic resistance among E. coli ST131.E. coli ST131 strains in China. E. coli ST131 strains in China.
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12
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Wang H, Wang J, Li S, Li J, Jing C. Prevalence of antibiotic resistance genes in cell culture liquid waste and the virulence assess for isolated resistant strains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:32040-32049. [PMID: 31493078 DOI: 10.1007/s11356-019-06299-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Cell culture liquid waste containing antibiotic resistance genes (ARGs) and microbial community were still not received enough recognition, which pose potential risks to human health. Sixty-eight resistance genes and intl1 were detected in eight samples by Quantitative real-time PCR, while intl1 was only detected in hospital group. Meanwhile, the bacterial community was complex and diverse in each sample by 16S rRNA gene high-throughput sequencing, in addition, Morganella and Enterococcus presented a significant difference between two groups. Whole genome shotgun sequencing revealed that Morganella morganii had more resistance genes and virulence factors in hospital group, and three extended-spectrum beta-lactamase (ESBL) genotypes were found to be blaDHA-5, blaOXA-1, and blaTEM-1. This study provided a preliminary report on ARGs and resistant strains, which reminded people attention to the health risks of potential pathogens in this waste.
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Affiliation(s)
- Haichao Wang
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China
| | - Jin Wang
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China.
| | - Shuming Li
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China
| | - Jinzhao Li
- China Shenhua Overseas Development & Investment Co., Limited, Beijing, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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13
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Reid CJ, Wyrsch ER, Roy Chowdhury P, Zingali T, Liu M, Darling AE, Chapman TA, Djordjevic SP. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microb Genom 2019; 3. [PMID: 29306352 PMCID: PMC5761274 DOI: 10.1099/mgen.0.000143] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
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Affiliation(s)
- Cameron J Reid
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ethan R Wyrsch
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tiziana Zingali
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Michael Liu
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Aaron E Darling
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Toni A Chapman
- 2NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Steven P Djordjevic
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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14
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Khalifa HO, Soliman AM, Ahmed AM, Shimamoto T, Nariya H, Matsumoto T, Shimamoto T. High Prevalence of Antimicrobial Resistance in Gram-Negative Bacteria Isolated from Clinical Settings in Egypt: Recalling for Judicious Use of Conventional Antimicrobials in Developing Nations. Microb Drug Resist 2019; 25:371-385. [PMID: 30681401 DOI: 10.1089/mdr.2018.0380] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study was designed to investigate, at the molecular level, the antimicrobial resistance mechanisms of different antimicrobial resistance genes, including, extended-spectrum β-lactamases, AmpC β-lactamases, class 1 and 2 integrons, and plasmid-mediated quinolone resistance genes of Gram-negative bacteria isolated from clinical settings in Egypt. A total of 126 nonduplicate Gram-negative isolates were recovered from different clinical samples taken from hospitalized patients in Egypt in 2014. Antimicrobial susceptibility testing showed that, 93.6% (118/126) of the isolates had a multidrug-resistant phenotype. Interestingly, we reported a high level of antimicrobial resistance nearly for all tested antibiotics; to our knowledge, this is the first report from Egypt indicating very high level of antibiotic resistance in Egypt. Polymerase chain reaction screening and DNA sequencing revealed that, 75.4% (95/126) of the isolates harbored at least one extended-spectrum β-lactamase-encoding gene, with blaCTX-M being the most prevalent (65.9%), followed by blaSHV (46.8%). The AmpC β-lactamase, blaCMY, was detected in 7.1% (9/126) of bacterial isolates, with blaCMY-42 being the most prevalent. Class 1 integrons were detected in 50.8% (64/126) of the isolates, and class 2 integrons were detected in 2.4% (3/126) of the isolates. The plasmid-mediated quinolone resistance gene, qnr, was detected in 58.7% (74/126) of the tested isolates, with qnrS being the most prevalent. Several antimicrobial resistance determinants were identified in Egypt for the first time, such as SHV-27, SHV-28, SHV-33, SHV-63, SHV-71, SHV-82, SHV-142, CMY-42, CMY-6, and the new CMY-72 like. This study highlights the importance of the conscious use of conventional antimicrobials to overcome the multidrug resistance problem.
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Affiliation(s)
- Hazim O Khalifa
- 1 Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita, Japan.,2 Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Ahmed M Soliman
- 3 Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,4 Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Ashraf M Ahmed
- 5 Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Toshi Shimamoto
- 3 Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hirofumi Nariya
- 3 Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tetsuya Matsumoto
- 1 Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Tadashi Shimamoto
- 3 Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
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15
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Wang M, Liu H, Cheng X, Zhang B, Cai C, Wang J. Hydrothermal treatment of lincomycin mycelial residues: Antibiotic resistance genes reduction and heavy metals immobilization. BIORESOURCE TECHNOLOGY 2019; 271:143-149. [PMID: 30268008 DOI: 10.1016/j.biortech.2018.09.106] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
In this study, fate of antibiotic resistance genes (ARGs - lmrA, lmrB, ermB, lnuA, lnuB and vgaC) and species distribution of heavy metals during lincomycin mycelial residues hydrothermal treatment (HT) process were investigated. The results showed that HT could reduce both ARGs and mobile genetic elements effectively by 1.02 to 4.14 logs. Total bacterial biomass reflecting by 16S rRNA decreased from 1.27 × 109 to 4.47 × 105 copies g-1 dry weight. Moreover, half-lives of these targets varied from 2.4 min (ermB) to 8.9 min (lmrB) in the first 30 min of treatment based on a biphasic first-order kinetic model. After the first 30 min, however, half-lives ranged between 15.4 min (lmrA) and 247.6 min (ISCR1). Complexation and precipitation resulted in the transformation of heavy metals from weakly bounded to relatively stable fraction in HT process. Simultaneously, their environmental risk level decreased by at least one grade.
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Affiliation(s)
- Mengmeng Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Huiling Liu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Xiangming Cheng
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bo Zhang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen Cai
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jing Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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16
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Rui Y, Lu W, Li S, Cheng C, Sun J, Yang Q. Integrons and insertion sequence common region 1 (ISCR1) of carbapenem-non-susceptible Gram-negative bacilli in fecal specimens from 5000 patients in southern China. Int J Antimicrob Agents 2018; 52:571-576. [DOI: 10.1016/j.ijantimicag.2018.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 05/22/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
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17
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Prevalence of Integrons and Insertion Sequences in ESBL-Producing E. coli Isolated from Different Sources in Navarra, Spain. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102308. [PMID: 30347800 PMCID: PMC6209886 DOI: 10.3390/ijerph15102308] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 11/17/2022]
Abstract
Mobile genetic elements play an important role in the dissemination of antibiotic resistant bacteria among human and environmental sources. Therefore, the aim of this study was to determine the occurrence and patterns of integrons and insertion sequences of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from different sources in Navarra, northern Spain. A total of 150 isolates coming from food products, farms and feeds, aquatic environments, and humans (healthy people and hospital inpatients), were analyzed. PCRs were applied for the study of class 1, 2, and 3 integrons (intI1, intI2, and intI3), as well as for the determination of insertion sequences (IS26, ISEcp1, ISCR1, and IS903). Results show the wide presence and dissemination of intI1 (92%), while intI3 was not detected. It is remarkable, the prevalence of intI2 among food isolates, as well as the co-existence of class 1 and class 2 (8% of isolates). The majority of isolates have two or three IS elements, with the most common being IS26 (99.4%). The genetic pattern IS26⁻ISEcp1 (related with the pathogen clone ST131) was present in the 22% of isolates (including human isolates). In addition, the combination ISEcp1⁻IS26⁻IS903⁻ISCR1 was detected in 11 isolates being, to our knowledge, the first study that describes this genetic complex. Due to the wide variability observed, no relationship was determined among these mobile genetic elements and β-lactam resistance. More investigations regarding the genetic composition of these elements are needed to understand the role of multiple types of integrons and insertion sequences on the dissemination of antimicrobial resistance genes among different environments.
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18
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Rui Y, Lu W, Li S, Cheng C, Sun J, Yang Q. Detection of common mobile genetic elements and genotyping of multidrug-resistant Gram-negative bacilli in blood specimens from septicemia patients in southern China. Infect Drug Resist 2018; 11:1741-1750. [PMID: 30349331 PMCID: PMC6190624 DOI: 10.2147/idr.s165513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background Integron, ISCR1 and complex class 1 integrons lead bacteria to become resistant to antibiotic regimens. The aim of this study was to detect common mobile genetic elements of multidrug-resistant Gram-negative bacilli and evaluate the genotyping of these bacilli in blood specimens from septicemia patients in southern China. Methods A total of 837 Gram-negative bacilli including 578 strains containing Enterobacteriaceae and 259 strains containing non-fermentative bacilli were investigated in blood samples collected from septicemia patients between 2011 and 2014 in southern China. Mobile genetic elements, such as class 1 integrons, the insertion sequence common region 1 (ISCR1), and complex class 1 integrons, were detected from the 837 strains. Results Twenty-seven types of gene cassette arrays were found among 837 strains in which 492 (58.8%) class 1 integron-positive isolates and 254 (51.6%) gene cassette-positive isolates were found, including the first description of two types, aacA4-blaIMP-1-blaOXA-30-catB3 and aac(6′)-II-aadA13-cmlA8-blaOXA-10, in the corresponding species and two gene cassettes, putative helicase and aadA-like, originally detected in integrons. Twelve types of ISCR1-linked resistance gene regions in 196 ISCR1-positive bacilli and seven different types of complex class 1 integron-positive strains were obtained including four distinct complex class 1 integrons that have never been described in any species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fngerprinting showed that isolates with identical gene profles were clonally unrelated. Conclusion Our results indicated that we should pay more attention to enhance the quality of infection control measures and prevent hospital infection, so as to avoid the outbreak of multidrug-resistant Gram-negative bacilli.
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Affiliation(s)
- Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Wengting Lu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Si Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Cancan Cheng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Jingjing Sun
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
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19
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Hennequin C, Chlilek A, Beyrouthy R, Bonnet R, Robin F. Diversity of DHA-1-encoding plasmids in Klebsiella pneumoniae isolates from 16 French hospitals. J Antimicrob Chemother 2018; 73:2981-2989. [DOI: 10.1093/jac/dky285] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/20/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Claire Hennequin
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
| | - Alexandre Chlilek
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Laboratoire de microbiologie, CHU Nîmes, Nîmes, France
| | - Racha Beyrouthy
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Université Clermont Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Richard Bonnet
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Université Clermont Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Frédéric Robin
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Université Clermont Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
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20
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Hennequin C, Ravet V, Robin F. Plasmids carrying DHA-1 β-lactamases. Eur J Clin Microbiol Infect Dis 2018; 37:1197-1209. [PMID: 29663096 DOI: 10.1007/s10096-018-3231-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/12/2018] [Indexed: 01/22/2023]
Abstract
The aim of this review is to provide an update on the plasmids mediating DHA-1 cephalosporinase in Klebsiella pneumoniae. These plasmids have been mainly found in this bacterium but not only. The first was isolated from Salmonella sp. in France in the early 1990s. They are currently reported worldwide. BlaDHA-1 beta-lactamase gene is usually co-expressed with many other antibiotic resistance genes such as extended-spectrum β-lactamases (blaCTX-M-, bla SHV -types), oxacillinases (blaOXA-1, blaOXA-30), penicillinases (bla TEM -type), carbapenemases (bla OXA48 , blaKPC-2), aminoglycosides (aacA, aadA, armA), fluoroquinolones (qnrB4, aac6'-1b-cr), and sulfonamide (sul1) resistance genes. Plasmids carrying DHA-1 cephalosporinase have different sizes (22 to 313 kb), belong to diverse groups of incompatibility (R, L/M, FII(k), FIB, A/C2, HI2, HIB), and are self-transferable or not. The multidrug resistance region consists of a mosaic structure composed of resistance genes, insertion sequences, composite transposon, and integrons.
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Affiliation(s)
- Claire Hennequin
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France. .,Laboratoire de Bactériologie, CHU Clermont-Ferrand, 58, rue Montalembert, 63003, Clermont-Ferrand, France.
| | - Viviane Ravet
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
| | - Frédéric Robin
- Laboratoire de Bactériologie, CHU Clermont-Ferrand, 58, rue Montalembert, 63003, Clermont-Ferrand, France.,Université Clermont Auvergne, UMR INSERM 1071, USC INRA2018, Clermont-Ferrand, France.,Laboratoire associé Résistance des Entérobactéries BLSE/Céphalosporinases, Centre National de Référence Résistance aux Antibiotiques, Clermont-Ferrand, France
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21
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Integrons in Enterobacteriaceae: diversity, distribution and epidemiology. Int J Antimicrob Agents 2017; 51:167-176. [PMID: 29038087 DOI: 10.1016/j.ijantimicag.2017.10.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/29/2017] [Accepted: 10/07/2017] [Indexed: 01/03/2023]
Abstract
Integrons are versatile gene acquisition systems that allow efficient capturing of exogenous genes and ensure their expression. Various classes of integrons possessing a wide variety of gene cassettes are ubiquitously distributed in enteric bacteria worldwide. The epidemiology of integrons associated multidrug resistance in Enterobacteriaceae is rapidly evolving. In the past two decades, the incidence of integrons in enteric bacteria has increased drastically with evolution of multiple gene cassettes, novel gene arrangements and complex chromosomal integrons such as Salmonella genomic islands. This review focuses on the distribution, versatility, spread and global trends of integrons among important members of the Enterobacteriaceae, including Escherichia coli, Klebsiella, Shigella and Salmonella, which are known to cause infections globally. Such a comprehensive understanding of integron-associated antibiotic resistance, their role in the spread of such resistance traits and their clinical relevance especially with regard to each genus individually is paramount to contain the global spread of antibiotic resistance.
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22
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Gillings MR. Class 1 integrons as invasive species. Curr Opin Microbiol 2017; 38:10-15. [DOI: 10.1016/j.mib.2017.03.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 02/05/2023]
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23
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Tong J, Lu X, Zhang J, Sui Q, Wang R, Chen M, Wei Y. Occurrence of antibiotic resistance genes and mobile genetic elements in enterococci and genomic DNA during anaerobic digestion of pharmaceutical waste sludge with different pretreatments. BIORESOURCE TECHNOLOGY 2017; 235:316-324. [PMID: 28371770 DOI: 10.1016/j.biortech.2017.03.104] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 05/16/2023]
Abstract
Pharmaceutical waste sludge harbors large amounts of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and it is necessary to study the reduction of ARGs and MGEs during sludge treatment. Therefore, the antibiotic resistance phenotypes and genotypes of enterococci, and the ARGs and MGEs in genomic DNA were investigated during anaerobic digestion (AD) with microwave (MW), thermal hydrolysis (TH) and ozone pretreatment. Results showed that sludge pretreatment increased the occurrence of the resistance phenotypes and genotypes of enterococci. During AD, the resistance of enterococci to macrolides decreased, except for in the MW-pretreated sludge. Horizontal gene transfer and co-occurrence of ermB and tetM in enterococci resulted in increased tetracycline resistance of enterococci throughout the sludge treatment. MGEs such as intI1, ISCR1 and Tn916/1545 had a significant effect on the distribution of ARGs. AD with pretreatment, especially TH pretreatment, resulted in greater ARGs and MGEs reduction and improved methane production.
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Affiliation(s)
- Juan Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - XueTing Lu
- Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - JunYa Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qianwen Sui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Rui Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meixue Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01225-16. [PMID: 27811104 PMCID: PMC5095474 DOI: 10.1128/genomea.01225-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate.
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