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Gager C, Flores-Mireles AL. Blunted blades: new CRISPR-derived technologies to dissect microbial multi-drug resistance and biofilm formation. mSphere 2024; 9:e0064223. [PMID: 38511958 PMCID: PMC11036814 DOI: 10.1128/msphere.00642-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
The spread of multi-drug-resistant (MDR) pathogens has rapidly outpaced the development of effective treatments. Diverse resistance mechanisms further limit the effectiveness of our best treatments, including multi-drug regimens and last line-of-defense antimicrobials. Biofilm formation is a powerful component of microbial pathogenesis, providing a scaffold for efficient colonization and shielding against anti-microbials, which further complicates drug resistance studies. Early genetic knockout tools didn't allow the study of essential genes, but clustered regularly interspaced palindromic repeat inference (CRISPRi) technologies have overcome this challenge via genetic silencing. These tools rapidly evolved to meet new demands and exploit native CRISPR systems. Modern tools range from the creation of massive CRISPRi libraries to tunable modulation of gene expression with CRISPR activation (CRISPRa). This review discusses the rapid expansion of CRISPRi/a-based technologies, their use in investigating MDR and biofilm formation, and how this drives further development of a potent tool to comprehensively examine multi-drug resistance.
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Affiliation(s)
- Christopher Gager
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Ana L. Flores-Mireles
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana, USA
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2
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Whelan S, Lucey B, Finn K. Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment. Microorganisms 2023; 11:2169. [PMID: 37764013 PMCID: PMC10537683 DOI: 10.3390/microorganisms11092169] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.
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Affiliation(s)
- Shane Whelan
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Karen Finn
- Department of Analytical, Biopharmaceutical and Medical Sciences, Atlantic Technological University Galway City, Dublin Road, H91 T8NW Galway, Ireland
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3
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Liu L, Zou X, Gao Y, Li H, Cheng Y, Zhang X, Yuan Q. Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115070. [PMID: 37257347 DOI: 10.1016/j.ecoenv.2023.115070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Although antibiotics are one of the most significant factors contributing to the propagation of antibiotic resistance genes (ARGs), studies on the dose-response relationship at sub-lethal concentrations of antibiotics remain scarce, despite their importance for assessing the risks of antibiotics in the environment. In this study, we constructed a series of microcosms to investigate the propagation of intracellular (iARGs) and extracellular (eARGs) ARGs in both water and biofilms when exposed to antibiotics at various concentrations (1-100 μg/L) and frequencies. Results showed that eARGs were more abundant than iARGs in water, while iARGs were the dominant ARGs form in biofilms. eARGs showed differentiated dose-response relationships from iARGs. The abundance of iARGs increased with the concentration of antibiotics as enhanced selective pressure overcame the metabolic burden of antibiotic-resistant bacteria carrying ARGs. However, the abundance of eARGs decreased with increasing antibiotic concentrations because less ARGs were secreted from bacterial hosts at higher concentrations (100 μg/L). Furthermore, combined exposure to two antibiotics (tetracycline & imipenem) showed a synergistic effect on the propagation of iARGs, but an antagonistic effect on the propagation of eARGs compared to exposure to a single antibiotic. When exposed to antibiotic at a fixed total dose, one-time dosing (1 time/10 d) favored the propagation of iARGs, while fractional dosing (5 times /10 d) favored the propagation of eARGs. This study sheds light on the propagation of antibiotic resistance in the environment and can help in assessing the risks associated with the use of antibiotics.
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Affiliation(s)
- Lele Liu
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xinyi Zou
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yifan Gao
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Huihui Li
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yuan Cheng
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xueying Zhang
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Qingbin Yuan
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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4
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Chia-Wei L, Cheng JF, Tung KC, Hong YK, Lin JH, Lin YH, Tsai CA, Lin SP, Chen YC, Shi ZY, Huang YT, Liu PY. Evolution of trimethoprim/sulfamethoxazole resistance in Shewanella algae from the perspective of comparative genomics and global phylogenic analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1195-1202. [PMID: 34732312 DOI: 10.1016/j.jmii.2021.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/22/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Shewanella algae is a zoonotic marine bacterium that causes a variety of infections in immunocompromised patients or those who have been exposed to seawater. The development of trimethoprim/sulfamethoxazole (TMP/SMX) resistance in S. algae are found in human and environment isolates during the past ten years, and thus the treatment options are decreasing. METHODOLOGY In the study, we conduct a comparative genomic study to identify the resistant mechanism of TMP/SMX-resistance in S. algae. RESULTS We found the resistance of TMP/SMX in S. algae is associated with the existence of sul1 and dfrA12 within the class 1 integron. The gene cassette dfra12-aadA2-qacEΔ1/sul1 within the class 1 integron is highly conserved. In addition, the class 1 integron and encapsulated sul1 are significantly enriched in Enterobacteriaceae in NCBI and UniProt databases. CONCLUSION Our study suggests that the horizontal transfer of TMP/SMX resistance via class 1 integron is most frequently occurred within Enterobacteriaceae and has spread to a wide range of sources including soil, poultry, and marine water.
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Affiliation(s)
- Liu Chia-Wei
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Kai Hong
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yu-Hui Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Che-An Tsai
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shih-Ping Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yung-Chun Chen
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Zhi-Yuan Shi
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
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5
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Wang Y, Dong J, Wang J, Chi W, Zhou W, Tian Q, Hong Y, Zhou X, Ye H, Tian X, Hu R, Wong A. Assessing the drug resistance profiles of oral probiotic lozenges. J Oral Microbiol 2022; 14:2019992. [PMID: 35024089 PMCID: PMC8745366 DOI: 10.1080/20002297.2021.2019992] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria. Aim To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro. Results Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments. Conclusion Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.
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Affiliation(s)
- Yi Wang
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Jingya Dong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Qiwen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Yue Hong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Xuan Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
| | - Rongdang Hu
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
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6
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Kurittu P, Khakipoor B, Jalava J, Karhukorpi J, Heikinheimo A. Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources. Front Microbiol 2022; 12:789280. [PMID: 35058905 PMCID: PMC8764355 DOI: 10.3389/fmicb.2021.789280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing Escherichia coli clinical samples from Finland to the genomic level and investigation of possible zoonotic transmission routes are scarce. This study characterizes ESBL-producing E. coli from clinical samples in Finland using whole genome sequencing (WGS). Comparison is made between animal, food, and environmental sources in Finland to gain insight into potential zoonotic transmission routes and to recognize successful AMR genes, bacterial sequence types (STs), and plasmids. ESBL-producing E. coli isolates (n = 30) obtained from the Eastern Finland healthcare district between 2018 and 2020 underwent WGS and were compared to sequences from non-human and healthy human sources (n = 67) isolated in Finland between 2012 and 2018. A majority of the clinical isolates belonged to ST131 (n = 21; 70%), of which 19 represented O25:H4 and fimH30 allele, and 2 O16:H5 and fimH41 allele. Multidrug resistance was common, and the most common bla gene identified was bla CTX-M-27 (n = 14; 47%) followed by bla CTX-M-15 (n = 10; 33%). bla CTX-M-27 was identified in 13 out of 21 isolates representing ST131, with 12 isolates belonging to a recently discovered international E. coli ST131 C1-M27 subclade. Isolates were found to be genetically distinct from non-human sources with core genome multilocus sequence typing based analysis. Most isolates (n = 26; 87%) possessed multiple replicons, with IncF family plasmids appearing in 27 (90%) and IncI1 in 5 (17%) isolates. IncF[F1:A2:B20] replicon was identified in 11, and IncF[F-:A2:B20] in 4 isolates. The results indicate the ST131-C1-M27 clade gaining prevalence in Europe and provide further evidence of the concerning spread of this globally successful pathogenic clonal group. This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBL-producing E. coli belonging to the C1-M27 subclade. The results will help guide public health actions and guide future research.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Jalava
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jari Karhukorpi
- Eastern Finland Laboratory Centre Joint Authority Enterprise (ISLAB), Joensuu, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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7
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Turner AK, Yasir M, Bastkowski S, Telatin A, Page A, Webber M, Charles I. Chemical biology-whole genome engineering datasets predict new antibacterial combinations. Microb Genom 2021; 7. [PMID: 34874820 PMCID: PMC8767339 DOI: 10.1099/mgen.0.000718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Trimethoprim and sulfamethoxazole are used commonly together as cotrimoxazole for the treatment of urinary tract and other infections. The evolution of resistance to these and other antibacterials threatens therapeutic options for clinicians. We generated and analysed a chemical-biology-whole-genome data set to predict new targets for antibacterial combinations with trimethoprim and sulfamethoxazole. For this we used a large transposon mutant library in Escherichia coli BW25113 where an outward-transcribing inducible promoter was engineered into one end of the transposon. This approach allows regulated expression of adjacent genes in addition to gene inactivation at transposon insertion sites, a methodology that has been called TraDIS-Xpress. These chemical genomic data sets identified mechanisms for both reduced and increased susceptibility to trimethoprim and sulfamethoxazole. The data identified that over-expression of FolA reduced trimethoprim susceptibility, a known mechanism for reduced susceptibility. In addition, transposon insertions into the genes tdk, deoR, ybbC, hha, ldcA, wbbK and waaS increased susceptibility to trimethoprim and likewise for rsmH, fadR, ddlB, nlpI and prc with sulfamethoxazole, while insertions in ispD, uspC, minC, minD, yebK, truD and umpG increased susceptibility to both these antibiotics. Two of these genes’ products, Tdk and IspD, are inhibited by AZT and fosmidomycin respectively, antibiotics that are known to synergise with trimethoprim. Thus, the data identified two known targets and several new target candidates for the development of co-drugs that synergise with trimethoprim, sulfamethoxazole or cotrimoxazole. We demonstrate that the TraDIS-Xpress technology can be used to generate information-rich chemical-genomic data sets that can be used for antibacterial development.
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Affiliation(s)
- Arthur K Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Sarah Bastkowski
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrew Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.,University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Mark Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.,University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ian Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.,University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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8
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Buta M, Korzeniewska E, Harnisz M, Hubeny J, Zieliński W, Rolbiecki D, Bajkacz S, Felis E, Kokoszka K. Microbial and chemical pollutants on the manure-crops pathway in the perspective of "One Health" holistic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147411. [PMID: 33957582 DOI: 10.1016/j.scitotenv.2021.147411] [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: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/24/2021] [Indexed: 05/23/2023]
Abstract
This study determined the impact of poultry and bovine manure fertilization on the content of antibiotics, heavy metals (HMs), and the quantitative and qualitative composition of integrase and antibiotic resistance genes in soil, groundwater, and crops cultivated on manure-amended plots. Antibiotic concentration levels were analyzed using the HPLC-MS/MS, heavy metal concentration level were measured by HGAAS and ICP-OES, while the integrase genes and ARGs were quantified using Real-Time PCR (qPCR) method. Manure, soil, and crops samples contained the highest concentration of Zn (104-105 ng gdm-1) and Cu (103-105 ng gdm-1) of all HMs tested. Manure-supplemented soil was characterised by a high concentration of doxycycline and enrofloxacin. A high abundance of integrase genes was noted in samples of manure (109-1010 copies gdm-1) and soil (107-108 copies gdm-1). Among all the analyzed genes, sul1, sul2, blaTEM, and integrase genes were the most common. Results of the study demonstrate the selective character of ARGs transfer from poultry and bovine manure to plants. The only gene to occur in all studied environmental compartments was sul1 (from 102 - groundwater to 1011 - poultry manure). It was also found that animal manure may cause an increase in the HMs concentration in soil and their accumulation in crops, which may influence the health of humans and animals consuming crops grown on manure-amended soil. The high abundance of integrase genes and ARGs and their reciprocal correlations with HMs pose a serious risk of the rapid spread of antibiotic resistance in the environment. Moreover, unusual dependencies between integrase genes and selected ARGs indicate the possibility of changes in the mobility nature of genetic elements.
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Affiliation(s)
- Martyna Buta
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Jakub Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Damian Rolbiecki
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Sylwia Bajkacz
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland
| | - Ewa Felis
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Environmental Biotechnology Department, Faculty of Energy and Environmental Engineering, Silesian University of Technology, Akademicka 2 Str., 44-100 Gliwice, Poland
| | - Klaudia Kokoszka
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland
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9
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Antibiotic resistance in bacterial isolates from freshwater samples in Fildes Peninsula, King George Island, Antarctica. Sci Rep 2020; 10:3145. [PMID: 32081909 PMCID: PMC7035346 DOI: 10.1038/s41598-020-60035-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/04/2020] [Indexed: 11/08/2022] Open
Abstract
Anthropic activity in Antarctica has been increasing considerably in recent years, which could have an important impact on the local microbiota affecting multiple features, including the bacterial resistome. As such, our study focused on determining the antibiotic-resistance patterns and antibiotic-resistance genes of bacteria recovered from freshwater samples collected in areas of Antarctica under different degrees of human influence. Aerobic heterotrophic bacteria were subjected to antibiotic susceptibility testing and PCR. The isolates collected from regions of high human intervention were resistant to several antibiotic groups, and were mainly associated with the presence of genes encoding aminoglycosides-modifying enzymes (AMEs) and extended-spectrum β-lactamases (ESBLs). Moreover, these isolates were resistant to synthetic and semi-synthetic drugs, in contrast with those recovered from zones with low human intervention, which resulted highly susceptible to antibiotics. On the other hand, we observed that zone A, under human influence, presented a higher richness and diversity of antibiotic-resistance genes (ARGs) in comparison with zones B and C, which have low human activity. Our results suggest that human activity has an impact on the local microbiota, in which strains recovered from zones under anthropic influence were considerably more resistant than those collected from remote regions.
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10
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Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors. J Antibiot (Tokyo) 2019; 73:5-27. [PMID: 31578455 PMCID: PMC7102388 DOI: 10.1038/s41429-019-0240-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 12/17/2022]
Abstract
The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.
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11
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Chen J, Su Z, Dai T, Huang B, Mu Q, Zhang Y, Wen D. Occurrence and distribution of antibiotic resistance genes in the sediments of the East China Sea bays. J Environ Sci (China) 2019; 81:156-167. [PMID: 30975318 DOI: 10.1016/j.jes.2019.01.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980s, resulting in severe pollution of its environments. Antibiotic resistance genes (ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay (HB), Xiangshan Bay (XB), and Taizhou Bay (TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron-integrase gene (intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB (based on both the absolute and relative abundances) and dfrA13 was higher in HB (based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and blaPSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and blaPSE-1. In addition, the joint effect of heavy metals and nutrients & organic pollutants might be crucial for the fate of ARGs in the coastal sediments.
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Affiliation(s)
- Jiayu Chen
- School of Environmental and Geography Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Qinglin Mu
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Yongming Zhang
- School of Environmental and Geography Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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12
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Domínguez M, Miranda CD, Fuentes O, de la Fuente M, Godoy FA, Bello-Toledo H, González-Rocha G. Occurrence of Transferable Integrons and sul and dfr Genes Among Sulfonamide-and/or Trimethoprim-Resistant Bacteria Isolated From Chilean Salmonid Farms. Front Microbiol 2019; 10:748. [PMID: 31031727 PMCID: PMC6474311 DOI: 10.3389/fmicb.2019.00748] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/25/2019] [Indexed: 11/17/2022] Open
Abstract
Salmon farming industry in Chile currently uses a significant quantity of antimicrobials to control bacterial pathologies. The main aims of this study were to investigate the presence of transferable sulfonamide- and trimethoprim-resistance genes, sul and dfr, and their association with integrons among bacteria associated to Chilean salmon farming. For this purpose, 91 Gram-negative strains resistant to sulfisoxazole and/or trimethoprim recovered from various sources of seven Chilean salmonid farms and mainly identified as belonging to the Pseudomonas genus (81.0%) were studied. Patterns of antimicrobial resistance of strains showed a high incidence of resistance to florfenicol (98.9%), erythromycin (95.6%), furazolidone (90.1%) and amoxicillin (98.0%), whereas strains exhibited minimum inhibitory concentrations (MIC90) values of sulfisoxazole and trimethoprim of >4,096 and >2,048 μg mL−1, respectively. Strains were studied for their carriage of these genes by polymerase chain reaction, using specific primers, and 28 strains (30.8%) were found to carry at least one type of sul gene, mainly associated to a class 1 integron (17 strains), and identified by 16S rRNA gene sequencing as mainly belonging to the Pseudomonas genus (21 strains). Of these, 22 strains carried the sul1 gene, 3 strains carried the sul2 gene, and 3 strains carried both the sul1 and sul2 genes. Among these, 19 strains also carried the class 1 integron-integrase gene intI1, whereas the dfrA1, dfrA12 and dfrA14 genes were detected, mostly not inserted in the class 1 integron. Otherwise, the sul3 and intI2 genes were not found. In addition, the capability to transfer by conjugation these resistance determinants was evaluated in 22 selected strains, and sul and dfr genes were successfully transferred by 10 assayed strains, mainly mediated by a 10 kb plasmid, with a frequency of transfer of 1.4 × 10−5 to 8.4 × 10−3 transconjugant per recipient cell, and exhibiting a co-transference of resistance to florfenicol and oxytetracycline, currently the most used in Chilean salmon industry, suggesting an antibacterial co-selection phenomenon. This is the first report of the characterization and transferability of integrons as well as sul and dfr genes among bacteria associated to Chilean salmon farms, evidencing a relevant role of this environment as a reservoir of these genes.
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Affiliation(s)
- Mariana Domínguez
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | - Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile.,Centro AquaPacífico, Coquimbo, Chile
| | - Oliver Fuentes
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile.,Facultad de Medicina Veterinaria, Universidad San Sebastián, Concepción, Chile
| | - Mery de la Fuente
- Facultad de Medicina Veterinaria, Universidad San Sebastián, Concepción, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Talcahuano, Chile
| | - Félix A Godoy
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
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13
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Hossain S, Dahanayake P, De Silva B, Wickramanayake M, Wimalasena S, Heo G. Multidrug resistantAeromonasspp. isolated from zebrafish (Danio rerio): antibiogram, antimicrobial resistance genes and class 1 integron gene cassettes. Lett Appl Microbiol 2019; 68:370-377. [DOI: 10.1111/lam.13138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Affiliation(s)
- S. Hossain
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - P.S. Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - B.C.J. De Silva
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - M.V.K.S. Wickramanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - S.H.M.P. Wimalasena
- Bio‐Safety Research Institute and College of Veterinary Medicine Chonbuk National University Jeonju Korea
| | - G.‐J. Heo
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
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14
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Pathogenic Nocardia cyriacigeorgica and Nocardia nova Evolve To Resist Trimethoprim-Sulfamethoxazole by both Expected and Unexpected Pathways. Antimicrob Agents Chemother 2018; 62:AAC.00364-18. [PMID: 29686152 DOI: 10.1128/aac.00364-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/15/2018] [Indexed: 12/12/2022] Open
Abstract
Nocardia spp. are Gram-positive opportunistic pathogens that affect largely immunocompromised patients, leading to serious pulmonary or systemic infections. Combination therapy using the folate biosynthesis pathway inhibitors trimethoprim (TMP) and sulfamethoxazole (SMX) is commonly used as an antimicrobial therapy. Not surprisingly, as antibiotic therapies for nocardiosis can extend for many months, resistance to TMP-SMX has emerged. Using experimental evolution, we surveyed the genetic basis of adaptation to TMP-SMX across 8 strains of Nocardia nova and 2 strains of Nocardia cyriacigeorgica By employing both continuous experimental evolution to provide longitudinal information on the order of changes and characterization of resistant endpoint isolates, we observe changes that are consistent with modifications of two enzymes of the folate biosynthesis pathway: dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) (FolP), with the mutations often being clustered near the active site of the enzymes. While changes to DHFR and DHPS might be expected, we also noted that mutations in a previously undescribed homolog of DHPS (DHPS2 or FolP2) that was annotated as being "nonfunctional" were also sufficient to generate TMP-SMX resistance, which serves as a cautionary tale for the use of automated annotation by investigators and for the future discovery of drugs against this genus. Additionally, folP2 overlapped glucosyl-3-phosphoglycerate synthase. Remarkably, an adaptive frameshift mutation within the overlapping region resulted in a new in-frame fusion to the downstream gene to produce a potentially new bifunctional enzyme. How a single potentially bifunctional DHPS2 enzyme might confer resistance is unclear. However, it highlights the unexpected ways in which adaptive evolution finds novel solutions for selection.
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Yi X, Tran NH, Yin T, He Y, Gin KYH. Removal of selected PPCPs, EDCs, and antibiotic resistance genes in landfill leachate by a full-scale constructed wetlands system. WATER RESEARCH 2017; 121:46-60. [PMID: 28511040 DOI: 10.1016/j.watres.2017.05.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/27/2017] [Accepted: 05/04/2017] [Indexed: 05/22/2023]
Abstract
Landfill leachate could be a significant source of emerging contaminants (ECs) and antibiotic resistance genes (ARGs) into the environment. This study provides the first information on the occurrence of selected ECs and ARGs in raw leachate from 16-year old closed landfill site in Singapore. Among the investigated ECs, acetaminophen (ACT), bisphenol A (BPA), clofibric acid (CA), caffeine (CF), crotamiton (CTMT), diclofenac (DCF), N,N-diethyl-m-toluamide (DEET), gemfibrozil (GFZ), lincomycin (LIN), salicylic acid (SA), and sulfamethazine (SMZ) were the most frequently detected compounds in raw landfill leachate. The concentrations of detected ECs in raw landfill leachate varied significantly, from below quantification limit to 473,977 ng/L, depending on the compound. In this study, Class I integron (intl1) gene and ten ARGs were detected in raw landfill leachate. Sulfonamide resistance (sul1, sul2, and dfrA), aminoglycoside resistance (aac6), tetracycline resistance (tetO), quinolone resistance (qnrA), and intl1 were ubiquitously present in raw landfill leachate. Other resistance genes, such as beta-lactam resistance (blaNMD1, blaKPC, and blaCTX) and macrolide-lincosamide resistance (ermB) were also detected, detection frequency of <50%. The removal of target ECs and ARGs by a full-scale hybrid constructed wetland (CW) was also evaluated. The vast majority of ECs exhibited excellent removal efficiencies (>90%) in the investigated hybrid CW system. This hybrid CW system was also found to be effective in the reduction of several ARGs (intl1, sul1, sul2, and qnrA). Aeration lagoons and reed beds appeared to be the most important treatment units of the hybrid CW for removing the majority of ECs from the leachate.
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Affiliation(s)
- Xinzhu Yi
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Ngoc Han Tran
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore.
| | - Tingru Yin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore.
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Umpiérrez A, Bado I, Oliver M, Acquistapace S, Etcheverría A, Padola NL, Vignoli R, Zunino P. Zoonotic Potential and Antibiotic Resistance of Escherichia coli in Neonatal Calves in Uruguay. Microbes Environ 2017; 32:275-282. [PMID: 28904264 PMCID: PMC5606698 DOI: 10.1264/jsme2.me17046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli is one of the main etiological agents of neonatal calf diarrhea (NCD). The objective of this study was to assess the presence of virulence genes, genetic diversity, and antibiotic resistance mechanisms in E. coli associated with NCD in Uruguay. PCR was used to assess the presence of intimin, Shiga-like toxin, and stable and labile enterotoxin genes. Resistance to fluoroquinolones and oxyimino-cephalosporins was estimated on Müller-Hinton agar plates. Further antibiotic disc-diffusion tests were performed to assess bacterial multi-resistance. The presence of PMQR, ESBL, MCR-1, and integron genes was evaluated. Isolates were typed using ERIC-PCR, and 20 were selected for MLST, adhesion to Hep-2 cells, in vitro biofilm formation, and eukaryotic cytotoxicity. The prevalence of ETEC genes was lower than 3% in each case (estA and elt). Six isolates were EPEC (eae+) and 2 were EHEC/STEC (eae+/stx1+). The results of a diversity analysis showed high genetic heterogenicity among isolates. Additionally, different sequence types, including ST10, ST21, and ST69, were assigned to selected isolates. Thirty-six percent (96/264) of the isolates were fluoroquinolone-resistant, with 61/96 (63.5%) being multidrug-resistant. Additionally, 6 were oxyimino-cephalosporin-resistant. The qnrB, qnrS1, and blaCTX-M-14 genes were detected, whereas no isolates carried the mcr-1 gene. Isolates had the ability to adhere to Hep-2 cells and form biofilms. Only 1 isolate expressed toxins in vitro. E. coli from NCD cases in Uruguay are very diverse, potentially virulent, and may interact with eukaryotic cells. Zoonotic potential, together with resistance traits and the presence of horizontal transfer mechanisms, may play a significant role in infections caused by these microorganisms.
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Affiliation(s)
- Ana Umpiérrez
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable
| | - Inés Bado
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República
| | - Martín Oliver
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable
| | - Sofía Acquistapace
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable
| | - Analía Etcheverría
- Laboratorio de Inmunoquímica y Biotecnología, CIVETAN-Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires
| | - Nora Lía Padola
- Laboratorio de Inmunoquímica y Biotecnología, CIVETAN-Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República
| | - Pablo Zunino
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable
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17
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Odetoyin BW, Labar AS, Lamikanra A, Aboderin AO, Okeke IN. Classes 1 and 2 integrons in faecal Escherichia coli strains isolated from mother-child pairs in Nigeria. PLoS One 2017; 12:e0183383. [PMID: 28829804 PMCID: PMC5568733 DOI: 10.1371/journal.pone.0183383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antimicrobial resistance among enteric bacteria in Africa is increasingly mediated by integrons on horizontally acquired genetic elements. There have been recent reports of such elements in invasive pathogens across Africa, but very little is known about the faecal reservoir of integron-borne genes. METHODS AND FINDINGS We screened 1098 faecal Escherichia coli isolates from 134 mother-child pairs for integron cassettes by PCR using primers that anneal to the 5' and 3' conserved ends of the cassette regions and for plasmid replicons. Genetic relatedness of isolates was determined by flagellin and multi-locus sequence typing. Integron cassettes were amplified in 410 (37.5%) isolates and were significantly associated with resistance to trimethoprim and multiple resistance. Ten cassette combinations were found in class 1 and two in class 2 integrons. The most common class 1 cassette configurations were single aadA1 (23.4%), dfrA7 (18.3%) and dfrA5 (14.4%). Class 2 cassette configurations were all either dfrA1-satI-aadA1 (n = 31, 7.6%) or dfrA1-satI (n = 13, 3.2%). A dfr cassette was detected in 294 (31.1%) of trimethoprim resistant strains and an aadA cassette in 242 (23%) of streptomycin resistant strains. Strains bearing integrons carried a wide range of plasmid replicons of which FIB/Y (n = 169; 41.2%) was the most frequently detected. Nine isolates from five different individuals carried the dfrA17-aadA5-bearing ST69 clonal group A (CGA). The same integron cassette combination was identified from multiple distinct isolates within the same host and between four mother-child pairs. CONCLUSIONS Integrons are important determinants of resistance in faecal E. coli. Plasmids in integron-containing strains may contribute to dispersing resistance genes. There is a need for improved surveillance for resistance and its mechanisms of dissemination and persistence and mobility of resistance genes in the community and clinical settings.
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Affiliation(s)
- Babatunde W. Odetoyin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
- * E-mail:
| | - Amy S. Labar
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Adebayo Lamikanra
- Department of Pharmaceutics, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Iruka N. Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
- Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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Paraoan CEM, Rivera WL, Vital PG. Detection of Class I and II integrons for the assessment of antibiotic and multidrug resistance among Escherichia coli isolates from agricultural irrigation waters in Bulacan, Philippines. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2017; 52:306-313. [PMID: 28277085 DOI: 10.1080/03601234.2017.1281647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Contaminated irrigation water may greatly affect not only the quality of produce but also the people exposed to it. In this study, agricultural irrigation waters in Bulacan, Philippines were assessed and found to be contaminated with Escherichia coli (E. coli) ranging from 0.58 to 4.51 log10 CFU/mL. A total of 79 isolates of E. coli were confirmed through polymerase chain reaction (PCR) amplifying the uidA gene and were tested for phenotypic resistance using 10 antimicrobials through the Kirby-Bauer disc diffusion method. Forty-six isolates (58.22%) were noted to be multidrug resistant (MDR) with high resistance rate to cephalothin, tetracycline, streptomycin, ampicillin, trimethoprim, nalidixic acid, and chloramphenicol. Moreover, this study also examined the prevalence of Class I and II integrons accounting to 67.39% and 17.39%, respectively, of the MDR E. coli strains using multiplex PCR. The results imply that the agricultural water used in Bulacan is contaminated with the fecal material of man or other animals present in the area, and the presence of MDR bacteria, which pose a potential threat to individuals in these areas, is alarming. In addition, detection of integrons could be a good marker for the identification of MDR isolates. Lastly, this study could develop strategies for the proper management of farming sites leading to the detection of food-borne pathogens and prevention of infectious diseases.
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Affiliation(s)
- Cielo Emar M Paraoan
- a Institute of Biology, College of Science, University of the Philippines , Diliman, Quezon City , Philippines
| | - Windell L Rivera
- a Institute of Biology, College of Science, University of the Philippines , Diliman, Quezon City , Philippines
- b Natural Sciences Research Institute, University of the Philippines , Diliman, Quezon City , Philippines
| | - Pierangeli G Vital
- a Institute of Biology, College of Science, University of the Philippines , Diliman, Quezon City , Philippines
- b Natural Sciences Research Institute, University of the Philippines , Diliman, Quezon City , Philippines
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Chung YS, Song JW, Kim DH, Shin S, Park YK, Yang SJ, Lim SK, Park KT, Park YH. Isolation and characterization of antimicrobial-resistant Escherichia coli from national horse racetracks and private horse-riding courses in Korea. J Vet Sci 2017; 17:199-206. [PMID: 26645344 PMCID: PMC4921668 DOI: 10.4142/jvs.2016.17.2.199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/10/2015] [Accepted: 10/07/2015] [Indexed: 01/08/2023] Open
Abstract
Limited information is available regarding horse-associated antimicrobial resistant (AR) Escherichia (E.) coli. This study was designed to evaluate the frequency and characterize the pattern of AR E. coli from healthy horse-associated samples. A total of 143 E. coli (4.6%) were isolated from 3,078 samples collected from three national racetracks and 14 private horse-riding courses in Korea. Thirty of the E. coli isolates (21%) showed antimicrobial resistance to at least one antimicrobial agent, and four of the AR E. coli (13.3%) were defined as multi-drug resistance. Most of the AR E. coli harbored AR genes corresponding to their antimicrobial resistance phenotypes. Four of the AR E. coli carried class 1 integrase gene (intI1), a gene associated with multi-drug resistance. Pulsed-field gel electrophoretic analysis showed no genetic relatedness among AR E. coli isolated from different facilities; however, cross-transmissions between horses or horses and environments were detected in two facilities. Although cross-transmission of AR E. coli in horses and their environments was generally low, our study suggests a risk of transmission of AR bacteria between horses and humans. Further studies are needed to evaluate the risk of possible transmission of horse-associated AR bacteria to human communities through horse riders and horse-care workers.
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Affiliation(s)
- Yeon Soo Chung
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Jae Won Song
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Dae Ho Kim
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Sook Shin
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Young Kyung Park
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Soo Jin Yang
- Department of Animal Science and Technology, College of Biotechnology and Natural Resource, Chung-Ang University 2nd Campus, Anseong 17546, Korea
| | - Suk Kyung Lim
- Animal and Plant Quarantine Agency, Anyang 14086, Korea
| | - Kun Taek Park
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
| | - Yong Ho Park
- Department of Veterinary Microbiology, BK21 PLUS Program for Creative Veterinary Science Research, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Koreaivers
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A putative multi-replicon plasmid co-harboring beta-lactamase genes blaKPC-2, blaCTX-M-14 and blaTEM-1 and trimethoprim resistance gene dfrA25 from a Klebsiella pneumoniae sequence type (ST) 11 strain in China. PLoS One 2017; 12:e0171339. [PMID: 28152085 PMCID: PMC5289562 DOI: 10.1371/journal.pone.0171339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/19/2017] [Indexed: 11/19/2022] Open
Abstract
The global emergence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae poses a major public health threat requiring immediate and aggressive action. Some older generation antibiotics, such as trimethoprim, serve as alternatives for treatment of infections. Here, we determined the complete nucleotide sequence of plasmid pHS091147, which co-harbored the carbapenemase (blaKPC-2) and trimethoprim resistance genes (dfrA25) from a Klebsiella pneumoniae sequence type (ST) 11 clone recovered in Shanghai, China. pHS091147 had three replication genes, several plasmid-stability genes and an intact type IV secretion system gene cluster. Besides blaKPC-2 and dfrA25, pHS091147 carried several other resistance genes, including β-lactamase genes blaTEM-1 and blaCTX-M-14, sulphonamide resistance gene sul1, a quinolone resistance gene remnant (ΔqnrB2), and virulence associated gene iroN. Notably, the multidrug-resistance region was a chimeric structure composed of three subregions, which shared strong sequence homology with several plasmids previously assigned in Genbank. To our knowledge, this is the first report of the co-localization of blaKPC-2 and dfrA25 on a novel putative multi-replicon plasmid in a Klebsiella pneumoniae ST11 clone.
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Occurrences and Characterization of Antibiotic-Resistant Bacteria and Genetic Determinants of Hospital Wastewater in a Tropical Country. Antimicrob Agents Chemother 2016; 60:7449-7456. [PMID: 27736769 DOI: 10.1128/aac.01556-16] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
Wastewater discharged from clinical isolation and general wards at two hospitals in Singapore was examined to determine the emerging trends of antibiotic resistance (AR). We quantified the concentrations of 12 antibiotic compounds by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS), antibiotic-resistant bacteria (ARB), the class 1 integrase gene (intI1), and 16 antibiotic resistance genes (ARGs) that confer resistance to 10 different clinically relevant antibiotics. A subset of 119 antibiotic-resistant isolates were phylogenetically classified and tested for the presence of ARGs encoding resistance to β-lactam antibiotics (blaNDM, blaKPC, blaSHV, blaCTX-M), amikacin [aac(6')-Ib], co-trimoxazole (sul1, sul2, dfrA), ciprofloxacin (qnrA, qnrB), and the intI1 gene. Among these resistant isolates, 80.7% were detected with intI1 and 66.4% were found to carry at least 1 of the tested ARGs. Among 3 sampled locations, the clinical isolation ward had the highest concentrations of ARB and the highest levels of ARGs linked to resistance to β-lactam (blaKPC), co-trimoxazole (sul1, sul2, dfrA), amikacin [aac(6')-Ib], ciprofloxacin (qnrA), and intI1 We found strong positive correlations (P < 0.05) between concentrations of bacteria resistant to meropenem, ceftazidime, amikacin, co-trimoxazole, and ciprofloxacin and abundances of blaKPC, aac(6')-Ib, sul1, sul2, dfrA, qnrA, and intI1 genes.
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Manyahi J, Tellevik MG, Ndugulile F, Moyo SJ, Langeland N, Blomberg B. Molecular Characterization of Cotrimoxazole Resistance Genes and Their Associated Integrons in Clinical Isolates of Gram-Negative Bacteria from Tanzania. Microb Drug Resist 2016; 23:37-43. [PMID: 27533639 DOI: 10.1089/mdr.2016.0074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cotrimoxazole is widely used, particularly as a prophylactic drug in HIV patients. We assessed resistance mechanisms among cotrimoxazole resistant-Gram negative bacterial isolates (n = 123) obtained from blood (n = 69) and urine (n = 54) from Tanzanian patients. sul genes were detected in 98% (121/123) of the isolates. Coexistence of sul1 and sul2 was common (49/123). The dfr genes were found in 63% (77/123) of all isolates. sul1, dfrA15, and dfrA5 genes predominated among Klebsiella pneumoniae, while sul2 and dfrA1 genes were frequent in Escherichia coli isolates. Two isolates, both K. pneumoniae, carried sul3. Integrons were detected in 81.3% (100/123) of all isolates. Class 1 integrons were found in 95% (42/44), 53% (23/43), and 80.6% (25/31) of K. pneumoniae, E. coli, and other Enterobacteriaceae isolates, respectively. Class 2 integrons were found in 14% of E. coli, but not in K. pneumoniae. All sul1 genes in K. pneumoniae were carried in class 1 integrons. Gene cassette arrays dfrA5 and dfrA15-aadA1 were most frequently associated with class 1 integrons, while class 2 integrons contained only dfrA1-sat2-aadA1 gene cassettes. This is the first report of sul3 gene in K. pneumoniae from human sources. The finding that mechanisms differ between E. coli and K. pneumoniae may broaden our understanding of cotrimoxazole resistance.
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Affiliation(s)
- Joel Manyahi
- 1 Department of Clinical Science, University of Bergen , Bergen, Norway .,2 Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS) , Dar es Salaam, Tanzania
| | - Marit Gjerde Tellevik
- 3 Department of Medicine, National Centre for Tropical Infectious Diseases, Haukeland University Hospital , Bergen, Norway
| | - Faustine Ndugulile
- 2 Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS) , Dar es Salaam, Tanzania .,4 Parliament of Tanzania, United Republic of Tanzania , Dodoma, Tanzania
| | - Sabrina J Moyo
- 1 Department of Clinical Science, University of Bergen , Bergen, Norway .,2 Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS) , Dar es Salaam, Tanzania
| | - Nina Langeland
- 1 Department of Clinical Science, University of Bergen , Bergen, Norway .,3 Department of Medicine, National Centre for Tropical Infectious Diseases, Haukeland University Hospital , Bergen, Norway
| | - Bjørn Blomberg
- 1 Department of Clinical Science, University of Bergen , Bergen, Norway .,3 Department of Medicine, National Centre for Tropical Infectious Diseases, Haukeland University Hospital , Bergen, Norway
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Singha P, Chanda DD, Maurya AP, Paul D, Chakravarty A, Bhattacharjee A. Distribution of Class II integrons and their contribution to antibiotic resistance within Enterobacteriaceae family in India. Indian J Med Microbiol 2016; 34:303-7. [DOI: 10.4103/0255-0857.188319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lombardo MN, G-Dayanandan N, Wright DL, Anderson AC. Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates. ACS Infect Dis 2016; 2:149-56. [PMID: 27624966 DOI: 10.1021/acsinfecdis.5b00129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Multidrug-resistant Enterobacteriaceae, notably Escherichia coli and Klebsiella pneumoniae, have become major health concerns worldwide. Resistance to effective therapeutics is often carried by class I and II integrons that can confer insensitivity to carbapenems, extended spectrum β-lactamases, the antifolate trimethoprim, fluoroquinolones, and aminoglycosides. Specifically of interest to the study here, a prevalent gene (dfrA1) coding for an insensitive dihydrofolate reductase (DHFR) confers 190- or 1000-fold resistance to trimethoprim for K. pneumoniae and E. coli, respectively. Attaining inhibition of both the wild-type and resistant forms of the enzyme is critical for new antifolates. For several years, we have been developing the propargyl-linked antifolates (PLAs) as effective inhibitors against trimethoprim-resistant DHFR enzymes. Here, we show that the PLAs are active against both the wild-type and DfrA1 DHFR proteins. We report two high-resolution crystal structures of DfrA1 bound to potent PLAs. The structure-activity relationships and crystal structures will be critical in driving the design of broadly active inhibitors against wild-type and resistant DHFR.
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Affiliation(s)
- Michael N. Lombardo
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Narendran G-Dayanandan
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Dennis L. Wright
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Amy C. Anderson
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
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Ng C, Le TH, Goh SG, Liang L, Kim Y, Rose JB, Yew-Hoong KG. A Comparison of Microbial Water Quality and Diversity for Ballast and Tropical Harbor Waters. PLoS One 2015; 10:e0143123. [PMID: 26575481 PMCID: PMC4648578 DOI: 10.1371/journal.pone.0143123] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/31/2015] [Indexed: 11/19/2022] Open
Abstract
Indicator organisms and antibiotic resistance were used as a proxy to measure microbial water quality of ballast tanks of ships, and surface waters in a tropical harbor. The survival of marine bacteria in ballast tanks appeared to diminish over longer water retention time, with a reduction of cell viability observed after a week based on heterotrophic plate counts. Pyrosequencing of 16S rRNA genes showed distinct differences in microbial composition of ballast and harbor waters. The harbor waters had a higher abundance of operational taxonomic units (OTUs) assigned to Cyanobacteria (Synechococcus spp.) and α-proteobacteria (SAR11 members), while marine hydrocarbon degraders such as γ-proteobacteria (Ocenspirillaes spp., Thiotrchales spp.) and Bacteroidetes (Flavobacteriales spp.) dominated the ballast water samples. Screening of indicator organisms found Escherichia coli (E. coli), Enterococcus and Pseudomonas aeruginosa (P. aeruginosa) in two or more of the ballast and harbor water samples tested. Vibrio spp. and Salmonella spp. were detected exclusively in harbor water samples. Using quantitative PCR (qPCR), we screened for 13 antibiotic resistant gene (ARG) targets and found higher abundances of sul1 (4.13-3.44 x 102 copies/mL), dfrA (0.77-1.80 x10 copies/mL) and cfr (2.00-5.21 copies/mL) genes compared to the other ARG targets selected for this survey. These genes encode for resistance to sulfonamides, trimethoprim and chloramphenicol-florfenicol antibiotics, which are also known to persist in sediments of aquaculture farms and coastal environments. Among the ARGs screened, we found significant correlations (P<0.05) between ereA, ermG, cfr and tetO genes to one or more of the indicator organisms detected in this study, which may suggest that these members contribute to the environmental resistome. This study provides a baseline water quality survey, quantitatively assessing indicators of antibiotic resistance, potentially pathogenic organisms and a broad-brush description of difference in microbial composition and diversity between open oceans and tropical coastal environments through the use of next generation sequencing technology.
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Affiliation(s)
- Charmaine Ng
- National University of Singapore, Department of Civil and Environmental Engineering, Singapore, Singapore
| | - Thai-Hoang Le
- National University of Singapore, Department of Civil and Environmental Engineering, Singapore, Singapore
| | - Shin Giek Goh
- National University of Singapore, Department of Civil and Environmental Engineering, Singapore, Singapore
| | - Liang Liang
- National University of Singapore, Department of Civil and Environmental Engineering, Singapore, Singapore
| | - Yiseul Kim
- Michigan State University, Department of Microbiology and Molecular Genetics, East Lansing, Michigan, United States of America
| | - Joan B. Rose
- Michigan State University, Department of Microbiology and Molecular Genetics, East Lansing, Michigan, United States of America
| | - Karina Gin Yew-Hoong
- National University of Singapore, Department of Civil and Environmental Engineering, Singapore, Singapore
- National University of Singapore Environmental Research Institute (NERI), Singapore, Singapore
- * E-mail:
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Alizadeh-Hesar M, Bakhshi B, Najar-Peerayeh S. Clonal dissemination of a single Shigella sonnei strain among Iranian children during Fall 2012 in Tehran, I.R. Iran. INFECTION GENETICS AND EVOLUTION 2015; 34:260-6. [DOI: 10.1016/j.meegid.2015.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 11/30/2022]
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Structural Diversity of Class 1 Integrons in Multiresistant Strains of Escherichia coli Isolated from Patients in a Hospital in Mexico City. Curr Microbiol 2015. [DOI: 10.1007/s00284-015-0876-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Adel El-Sokkary MM, Abdelmegeed ES. Characterisation of Class 1 Integron among <i>Escherichia coli</i> Isolated from Mansoura University Hospitals in Egypt. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/aim.2015.54025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Eftekhari N, Bakhshi B, Pourshafie MR, Zarbakhsh B, Rahbar M, Hajia M, Ghazvini K. Genetic diversity of Shigella spp. and their integron content. Foodborne Pathog Dis 2013; 10:237-42. [PMID: 23489046 DOI: 10.1089/fpd.2012.1250] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The aim of this study was to investigate the occurrence and resistance gene content of class 1 and 2 integrons among Shigella spp. and to study the genetic diversity of isolates using the pulsed-field gel electrophoresis (PFGE) method. METHODS AND RESULTS A total of 32 Shigella spp. were identified from 700 stool samples of patients with diarrhea from two provinces in Iran. S. sonnei (70.8%) and S. flexneri (62.5%) were the most frequent serogroups in Tehran and Razavi Khorasan provinces, respectively. Class 2 integrons were more frequent among Shigella spp. in comparison with class 1 integrons. Three different resistance gene arrays were identified among class 1 integrons. Dihydrofolate reductase (dfrA) gene cassette was detected in 78.9% of total integrons (class 1 and 2). PFGE analysis revealed clonal dissemination (62.5%) of a single clone with identical class 2 resistance gene content in Tehran province. Comparison of our Shigella pulsotypes with those published from other countries showed similar pulsotypes in India and Korea, with identical resistance profiles, which suggests dissemination of this (these) clone(s) in Asian countries. CONCLUSIONS Class 2 integrons were found to be predominant among our Shigella spp. This reflects the need to monitor the acquisition and dissemination of different resistant gene cassettes among integrons. Comparison of PFGE pattern through standard procedures promoted the molecular epidemiological surveys and identification of clonal isolates in Iran and other Asian countries.
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Affiliation(s)
- Nazanin Eftekhari
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Puah SM, Puthucheary S, Liew FY, Chua KH. Aeromonas aquariorum clinical isolates: antimicrobial profiles, plasmids and genetic determinants. Int J Antimicrob Agents 2013; 41:281-4. [DOI: 10.1016/j.ijantimicag.2012.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/20/2012] [Accepted: 11/23/2012] [Indexed: 11/29/2022]
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Oteo J, Domingo-García D, Fernández-Romero S, Saez D, Guiu A, Cuevas O, Lopez-Brea M, Campos J. Abdominal abscess due to NDM-1-producing Klebsiella pneumoniae in Spain. J Med Microbiol 2012; 61:864-867. [PMID: 22383442 DOI: 10.1099/jmm.0.043190-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
We describe a clinical case of an abdominal abscess due to NDM-1-producing Klebsiella pneumoniae in a 35-year-old Spanish patient after hospitalization in India for perforated appendicitis and peritonitis. The strain belonged to the MLST type 231 and had multiple additional antibiotic resistance genes such as bla(CTX-M-15), armA methylase, aac(6')-Ib-cr, dfrA12, sul1 and qnrB and lack of porin genes ompK35 and ompK36. The patient was cured after abscess drainage.
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Affiliation(s)
- Jesús Oteo
- Spanish Network in Infectious Pathology (REIPI), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Antibiotic Laboratory, Bacteriology, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Sara Fernández-Romero
- Antibiotic Laboratory, Bacteriology, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - David Saez
- Antibiotic Laboratory, Bacteriology, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Alba Guiu
- Microbiology Department, Hospital Universitario de La Princesa, Madrid, Spain
| | - Oscar Cuevas
- Antibiotic Laboratory, Bacteriology, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Manuel Lopez-Brea
- Microbiology Department, Hospital Universitario de La Princesa, Madrid, Spain
| | - José Campos
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Spanish Network in Infectious Pathology (REIPI), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Antibiotic Laboratory, Bacteriology, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Labar AS, Millman JS, Ruebush E, Opintan JA, Bishar RA, Aboderin AO, Newman MJ, Lamikanra A, Okeke IN. Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS One 2012; 7:e38142. [PMID: 22666464 PMCID: PMC3364232 DOI: 10.1371/journal.pone.0038142] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 04/30/2012] [Indexed: 02/04/2023] Open
Abstract
Background Antimicrobial resistance is a growing international problem. We observed a 50% increase in the prevalence of trimethoprim resistance among fecal Escherichia coli from healthy Nigerian students between 1998 and 2005, a trend to increase that continued in 2009. Methods and Findings A PCR-based screen revealed that 131 (43.1%) of isolates obtained in Nigeria in 2005 and 2009 carried integron-borne dfrA cassettes. In the case of 67 (51.1%) of these isolates, the cassette was a class 1-integron-borne dfrA7 gene, which has been reported at high prevalence from E. coli isolates from other parts of Africa. Complete sequencing of a 27 Kb dfrA7-bearing plasmid from one isolate located the dfrA7 gene within a Tn21-type transposon. The transposon also contained an IS26-derived bla/sul/str element, encoding resistance to β-lactams, sulphonamides and streptomycin, and mercury resistance genes. Although the plasmid backbone was only found in 12 (5.8%) of trimethoprim-resistant isolates, dfrA7 and other transposon-borne genes were detected in 14 (16.3%) and 32 (26.3%) of trimethoprim resistant isolates collected in Nigeria in 2005 and 2009, respectively. Additionally, 37 (19.3%) of trimethoprim-resistant E. coli isolates collected between 2006 and 2008 from Ghana were positive for the dfrA7 and a transposon marker, but only 4 (2.1%) harbored the plasmid backbone. Conclusions Our data point to transposition as a principal mechanism for disseminating dfrA7 among E. coli from Nigeria and Ghana. On-going intensive use of the affordable broad-spectrum antibacterials is likely to promote selective success of a highly prevalent transposable element in West Africa.
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Affiliation(s)
- Amy S. Labar
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Jennifer S. Millman
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Ellen Ruebush
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Japheth A. Opintan
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Rima A. Bishar
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Mercy J. Newman
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Adebayo Lamikanra
- Department of Pharmaceutics, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Iruka N. Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail:
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Muhammad I, Uzma M, Yasmin B, Mehmood Q, Habib B. Prevalence of antimicrobial resistance and integrons in Escherichia coli from Punjab, Pakistan. Braz J Microbiol 2011; 42:462-6. [PMID: 24031655 PMCID: PMC3769832 DOI: 10.1590/s1517-83822011000200008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 10/06/2010] [Accepted: 01/13/2011] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance was studied in Escherichia coli strains isolated from urine samples of 457 patients suffering from urinary tract infection. High prevalence of class 1 integrons (43.56%), sulfamethoxazole resistance genes sul1 (45.54%) and sul2 (51.48%) along with occurrence of quinolone resistance genes was detected in multi drug resistance isolates.
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Affiliation(s)
- Idrees Muhammad
- Department of Biosciences, COMSATS Institute of Information Technology , Park Road, Chak Shahzad, Islamabad , Pakistan
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Wedley AL, Maddox TW, Westgarth C, Coyne KP, Pinchbeck GL, Williams NJ, Dawson S. Prevalence of antimicrobial-resistant Escherichia coli in dogs in a cross-sectional, community-based study. Vet Rec 2011; 168:354. [PMID: 21498238 DOI: 10.1136/vr.d1540] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The prevalence of carriage of antimicrobial-resistant (AMR) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli was determined in 183 healthy dogs from a semi-rural community in Cheshire. Isolates were tested against a panel of antimicrobials and by PCR to detect resistance genes. In the suspected ESBL-producing isolates, the presence of bla(SHV), bla(TEM), bla(CTX-M) and bla(AmpC) genes was determined by PCR and sequencing. A total of 53 (29 per cent, 95 per cent confidence interval [CI] 22.4 to 35.5 per cent) dogs carried at least one AMR E coli isolate. Twenty-four per cent (95 per cent CI 17.9 to 30.2 per cent) of dogs carried isolates resistant to ampicillin, 19.7 per cent (95 per cent CI 13.9 to 25.4 per cent) to tetracycline and 16.9 per cent (95 per cent CI 11.5 to 22.4 per cent) to trimethoprim. A bla(TEM) gene was detected in 39 of 54 ampicillin-resistant isolates, a tet(B) gene in 12 of 45 tetracycline-resistant isolates, and a dfr gene in 22 of 33 trimethoprim-resistant isolates. Multidrug-resistant isolates were demonstrated in 15 per cent (28 of 183; 95 per cent CI 10.1 to 20.5 per cent) of dogs. Nine suspected ESBL-producing E coli were isolated, of which only one was confirmed by double disc diffusion testing. Two of these isolates carried the bla(TEM-1) gene and seven carried the bla(CMY-2) gene.
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Affiliation(s)
- A L Wedley
- Department of Epidemiology and Population Health Research, University of Liverpool, Leahurst Campus, Neston, Cheshire CH64 7TE.
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Jin YH, Oh YH, Jung JH, Kim SJ, Kim JA, Han KY, Kim MY, Park SG, Lee YK. Antimicrobial resistance patterns and characterization of integrons of Shigella sonnei isolates in Seoul, 1999-2008. J Microbiol 2010; 48:236-42. [PMID: 20437157 DOI: 10.1007/s12275-010-9220-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 11/08/2009] [Indexed: 11/30/2022]
Abstract
A total of 66 Shigella sonnei isolates from 1999 to 2008 in Seoul was analyzed for their antimicrobial resistance, carriage of integron, and the patterns of Pulsed-field gel electrophoresis (PFGE). A high level of antimicrobial resistance to streptomycin (100%), trimethoprim/sulfamethoxazole (95%), tetracycline (94%), nalidixic acid (65%), and ampicillin (41%) was observed among S. sonnei isolates. Fourteen profiles of antimicrobial resistance were identified with the most common resistance profile being nalidixic acid, streptomycin, tetracycline, and trimethoprim/sulfamethoxazole (35%). PCR and DNA sequencing analysis revealed the presence of class 2 integron in all isolates, and class 1 and 2 integrons in 7 isolates. The class 2 integron carried two types of gene cassettes. One cassette array was dfrI, sat2, and aadA1 (91%), and the other was dfr1 and sat1 (8%). dfrA12 and aadA2 gene cassette was found in one isolate containing class 1 integron. PFGE was carried out to examine the genetic relatedness among isolates. All isolates except for one showed similar PFGE patterns (similarity of 80.1%). These results suggest that the S. sonnei isolated during 1999-2008 in Seoul have similar lineages that have not undergone evolutionary changes with time.
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Affiliation(s)
- Young-hee Jin
- Division of Epidemiology, Seoul Metropolitan Government Research Institute of Public Health and Environment, Seoul, 137-134, Republic of Korea
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Ahmed MO, Clegg PD, Williams NJ, Baptiste KE, Bennett M. Antimicrobial resistance in equine faecal Escherichia coli isolates from North West England. Ann Clin Microbiol Antimicrob 2010; 9:12. [PMID: 20374640 PMCID: PMC2867969 DOI: 10.1186/1476-0711-9-12] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 04/07/2010] [Indexed: 11/24/2022] Open
Abstract
Background Escherichia coli isolates of equine faecal origin were investigated for antibiotic resistance, resistance genes and their ability to perform horizontal transfer. Methods In total, 264 faecal samples were collected from 138 horses in hospital and community livery premises in northwest England, yielding 296 resistant E. coli isolates. Isolates were tested for susceptibility to antimicrobial drugs by disc diffusion and agar dilution methods in order to determine minimum inhibitory concentrations (MIC). PCR amplification was used to detect genes conferring resistance to: ampicillin (TEM and SHV beta-lactamase), chloramphenicol (catI, catII, catIII and cml), tetracycline (tetA, tetB, tetC, tetD, tet E and tetG), and trimethoprim (dfrA1, dfrA9, dfrA12, dfrA13, dfr7, and dfr17). Results The proportion of antibiotic resistant isolates, and multidrug resistant isolates (MDR) was significantly higher in hospital samples compared to livery samples (MDR: 48% of hospital isolates; 12% of livery isolates, p < 0.001). Resistance to ciprofloxacin and florfenicol were identified mostly within the MDR phenotypes. Resistance genes included dfr, TEM beta-lactamase, tet and cat, conferring resistance to trimethoprim, ampicillin, tetracycline and chloramphenicol, respectively. Within each antimicrobial resistance group, these genes occurred at frequencies of 93% (260/279), 91%, 86.8% and 73.5%, respectively; with 115/296 (38.8%) found to be MDR isolates. Conjugation experiments were performed on selected isolates and MDR phenotypes were readily transferred. Conclusions Our findings demonstrate that E. coli of equine faecal origin are commonly resistant to antibiotics used in human and veterinary medicine. Furthermore, our results suggest that most antibiotic resistance observed in equine E. coli is encoded by well-known and well-characterized resistant genes common to E. coli from man and domestic animals. These data support the ongoing concern about antimicrobial resistance, MDR, antimicrobial use in veterinary medicine and the zoonotic risk that horses could potentially pose to public health.
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Affiliation(s)
- Mohamed O Ahmed
- Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, Al Fateh University, Tripoli, P.O. Box 13662, Libya.
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Brolund A, Sundqvist M, Kahlmeter G, Grape M. Molecular characterisation of trimethoprim resistance in Escherichia coli and Klebsiella pneumoniae during a two year intervention on trimethoprim use. PLoS One 2010; 5:e9233. [PMID: 20169085 PMCID: PMC2821933 DOI: 10.1371/journal.pone.0009233] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 01/28/2010] [Indexed: 11/26/2022] Open
Abstract
Background Trimethoprim resistance is increasing in Enterobacteriaceae. In 2004-2006 an intervention on trimethoprim use was conducted in Kronoberg County, Sweden, resulting in 85% reduction in trimethoprim prescriptions. We investigated the distribution of dihydrofolate reductase (dfr)-genes and integrons in Escherichia coli and Klebsiella pneumoniae and the effect of the intervention on this distribution. Methodology/Principal Findings Consecutively isolated E. coli (n = 320) and K. pneumoniae (n = 54) isolates phenotypicaly resistant to trimethoprim were studied. All were investigated for the presence of dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA14, dfrA17 and integrons class I and II. Isolates negative for the seven dfr-genes (n = 12) were also screened for dfr2d, dfrA3, dfrA9, dfrA10, dfrA24 and dfrA26. These genes accounted for 96% of trimethoprim resistance in E. coli and 69% in K. pneumoniae. The most prevalent was dfrA1 in both species. This was followed by dfrA17 in E. coli which was only found in one K. pneumoniae isolate. Class I and II Integrons were more common in E. coli (85%) than in K. pneumoniae (57%). The distribution of dfr-genes did not change during the course of the 2-year intervention. Conclusions/Significance The differences observed between the studied species in terms of dfr-gene and integron prevalence indicated a low rate of dfr-gene transfer between these two species and highlighted the possible role of narrow host range plasmids in the spread of trimethoprim resistance. The stability of dfr-genes, despite large changes in the selective pressure, indirectly suggests a low fitness cost of dfr-gene carriage.
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Affiliation(s)
- Alma Brolund
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden.
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Šeputienė V, Povilonis J, Ružauskas M, Pavilonis A, Sužiedėlienė E. Prevalence of trimethoprim resistance genes in Escherichia coli isolates of human and animal origin in Lithuania. J Med Microbiol 2009; 59:315-322. [PMID: 20007760 DOI: 10.1099/jmm.0.015008-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 456 non-repetitive Escherichia coli isolates from human clinical specimens (urinary, n=134; cervix, vagina and prostate, n=52; blood, pus and wounds, n=45), healthy animals (cattle, n=45; poultry, n=20) and diseased animals (cattle, n=53; swine, n=64; poultry, n=43) obtained in Lithuania during the period 2005-2008 were studied for trimethoprim (TMP) resistance and the prevalence of dfr genes. A TMP resistance rate in the range of 18-26 % respective to the origin was found in clinical isolates, 23-40 % in isolates from diseased animals and 9-20 % in isolates from healthy animals. Of 112 TMP-resistant isolates, 103 carried at least one of the six dfrA genes (dfrA1, dfrA5, dfrA8, dfrA12, dfrA14 and dfrA17) as determined by multiplex PCR and RFLP. The dfrA1 and dfrA17 genes were found most frequently in clinical isolates (17 and 19 isolates, respectively), whilst dfrA1 and dfrA14 genes dominated in isolates of animal origin (25 and 13 isolates, respectively). The dfrA5, dfrA12 and dfrA8 genes were detected at lower frequencies. The association with class 1/class 2 integrons was confirmed for 73-100 % of dfr genes found in most groups of isolates, except for the isolates from diseased swine. In this group, the majority of dfr-positive isolates (67 %, 8/12) carried dfrA8 (6/12) or dfrA14 genes (2/12) that were not associated with integrons. Non-integron location was also confirmed for the remaining dfrA8 genes (six clinical isolates and one isolate from diseased cattle) and for dfrA14 genes (two isolates from diseased cattle and swine each). All cassette-independent dfrA14 genes were found to be located within the strA gene. This study on the prevalence and distribution of TMP resistance genes among E. coli isolates of human and animal origin in Lithuania demonstrates that dfr genes are carried most frequently as gene cassettes within class 1 and/or class 2 integrons. However, TMP resistance in some of the isolates was found to be mediated by non-integron-associated dfrA8 and dfrA14 genes, indicating the existence of alternative sources for the spread of resistance.
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Affiliation(s)
- Vaida Šeputienė
- Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionio 21, LT-03101 Vilnius, Lithuania
| | - Justas Povilonis
- Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionio 21, LT-03101 Vilnius, Lithuania
| | - Modestas Ružauskas
- Veterinary Institute of Lithuania Veterinary Academy, Instituto 2, LT-56115 Kaišiadorys, Lithuania
| | - Alvydas Pavilonis
- Department of Microbiology, Kaunas University of Medicine, A. Mickevičiaus 9, LT-44307 Kaunas, Lithuania
| | - Edita Sužiedėlienė
- Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionio 21, LT-03101 Vilnius, Lithuania
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Hilbert DW, Paulish TE, Mordechai E, Adelson ME, Gygax SE, Trama JP. Antimicrobial non-susceptibility of cervico-vaginal and rectal Escherichia coli isolates is associated with phylogeny and plasmid carriage. Eur J Clin Microbiol Infect Dis 2009; 28:1399-403. [DOI: 10.1007/s10096-009-0788-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 07/12/2009] [Indexed: 10/20/2022]
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40
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Baudry PJ, Nichol K, DeCorby M, Lagacé-Wiens P, Olivier E, Boyd D, Mulvey MR, Hoban DJ, Zhanel GG. Mechanisms of resistance and mobility among multidrug-resistant CTX-M–producing Escherichia coli from Canadian intensive care units: the 1st report of QepA in North America. Diagn Microbiol Infect Dis 2009; 63:319-26. [DOI: 10.1016/j.diagmicrobio.2008.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 11/27/2008] [Accepted: 12/02/2008] [Indexed: 11/30/2022]
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Chang YC, Shih DYC, Wang JY, Yang SS. Molecular characterization of class 1 integrons and antimicrobial resistance in Aeromonas strains from foodborne outbreak-suspect samples and environmental sources in Taiwan. Diagn Microbiol Infect Dis 2007; 59:191-7. [PMID: 17908616 DOI: 10.1016/j.diagmicrobio.2007.04.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 04/09/2007] [Accepted: 04/18/2007] [Indexed: 10/22/2022]
Abstract
One hundred thirty-three Aeromonas spp. isolates were examined for multiple antibiotic resistance phenotypes and prevalence of class 1 integron sequences. Twenty-four (18.0%) of these isolates contained class 1 integron. Seven different class 1 integrons were found among 24strains, with a total of 10 different gene cassettes encoding for resistance to trimethoprim (dfr12 and dfr2d), aminoglycosides (aadA1 and aadA2), beta-lactam antibiotics (oxa2), chloramphenicol (catB3 and catB8), quaternary ammonium amines (qacE2), and 2 ORFs (orfD and orfF) with unknown function. Rate of antibiotic resistance was different between integron-positive and integron-negative strains. Trimethoprim and trimethoprim-sulphamethoxazole resistances were commonly associated with integron, and all of integron-positive isolates were multiple resistant to more than 3 agents. Resistance to as many as 10 antimicrobial agents were observed in integron-positive strains. Several cassette arrays of class 1 integrons identified in this study were not previously reported in Aeromonas strains. This study demonstrates the wide distribution of class 1 integron in Aeromonas spp. isolated from foodborne outbreak-suspect samples and environmental sources in Taiwan.
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Affiliation(s)
- Yu-Chang Chang
- Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 106, Taiwan
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42
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Grape M, Motakefi A, Pavuluri S, Kahlmeter G. Standard and real-time multiplex PCR methods for detection of trimethoprim resistance dfr genes in large collections of bacteria. Clin Microbiol Infect 2007; 13:1112-8. [PMID: 17725650 DOI: 10.1111/j.1469-0691.2007.01807.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two multiplex PCR (mPCR) methods were developed to screen large collections of trimethoprim-resistant Escherichia coli isolates for the most prevalent resistance determinants. Five common integron-carried genes (dfrA1, dfrA5, dfrA7, dfrA12 and dfrA17) were selected as PCR targets. Primers and conditions for standard mPCRs and real-time mPCRs were selected and tested. Two protocols using essentially the same primer pairs were established. The standard mPCR protocol also included an internal control targeting the E. coli 16S rRNA gene. Both protocols proved to be sensitive and specific for detection of the five selected genes. Screening of three different collections of clinical urinary and blood isolates (n = 368) with the two multiplex methods revealed that the five dfr genes accounted for 75-86% of trimethoprim resistance. The standard mPCR is useful and accessible for most laboratories, while the real-time mPCR requires additional equipment and expensive reagents, but is very convenient for high-throughput screening of large collections of bacterial isolates.
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Affiliation(s)
- M Grape
- Department of Microbiology, Tumor and Cell Biology (MTC), Division of Clinical Microbiology, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden
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43
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Yao F, Qian Y, Chen S, Wang P, Huang Y. Incidence of extended-spectrum beta-lactamases and characterization of integrons in extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolated in Shantou, China. Acta Biochim Biophys Sin (Shanghai) 2007; 39:527-32. [PMID: 17622472 DOI: 10.1111/j.1745-7270.2007.00304.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study is concerned with the level of antibiotic resistance of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae, isolated in Shantou, China, and its mechanism. Seventy-four non-repetitive clinical isolates of K. pneumoniae producing ESBLs were isolated over a period of 2 years. Antibiotic susceptibility, carried out by Epsilometer test, showed that most of the isolates were multiresistant. Polymerase chain reaction showed that, among the several types of beta-lactamases, SHV was the most prevalent, TEM was the second most prevalent, and CTX-M was the least prevalent. Sixty-nine isolates were positive for integrase gene IntI1, but no IntI2 or IntI3 genes were found. The variable region of class 1 integrons were amplified and further identified by sequencing. Thirteen different gene cassettes and 11 different cassette combinations were detected. Dfr and aadA cassettes were predominant and cassette combinations dfrA12, orfF and aadA2 were most frequently found. No gene cassettes encoding ESBLs were found. Integrons were prevalent and played an important role in multidrug resistance in ESBL-producing K. pneumoniae.
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Affiliation(s)
- Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China.
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44
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Pallecchi L, Lucchetti C, Bartoloni A, Bartalesi F, Mantella A, Gamboa H, Carattoli A, Paradisi F, Rossolini GM. Population structure and resistance genes in antibiotic-resistant bacteria from a remote community with minimal antibiotic exposure. Antimicrob Agents Chemother 2007; 51:1179-84. [PMID: 17220407 PMCID: PMC1855465 DOI: 10.1128/aac.01101-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study, we detected unexpectedly high levels of acquired antibiotic resistance in commensal Escherichia coli isolates from a remote Guaraní Indian (Bolivia) community with very low levels of antibiotic exposure and limited exchanges with the exterior. Here we analyzed the structure of the resistant E. coli population from that community and the resistance mechanisms. The E. coli population (113 isolates from 72 inhabitants) showed a high degree of genetic heterogeneity, as evidenced by phylogenetic grouping (77% group A, 10% group B1, 8% group D, 5% group B2) and genotyping by randomly amplified polymorphic DNA (RAPD) analysis (44 different RAPD types). The acquired resistance genes were always of the same types as those found in antibiotic-exposed settings [blaTEM, blaPSE-1, catI, cmlA6, tet(A), tet(B), dfrA1, dfrA7, dfrA8, dfrA17, sul1, sul2, aphA1, aadA1, aadA2, aadA5, aadB, and sat-1]. Class 1 and class 2 integrons were found in 12% and 4% of the isolates, respectively, and harbored arrays of gene cassettes similar to those already described. The cotransferability of multiple-resistance traits was observed from selected isolates and was found to be associated with resistance conjugative plasmids of the F, P, and N types. Overall, these data suggest that the resistance observed in this remote community is likely the consequence of the dissemination of resistant bacteria and resistance genes from antibiotic-exposed settings (rather than of an independent in situ selection) which involved both the clonal expansion of resistant strains and the horizontal transfer/recombination of mobile genetic elements harboring resistance genes.
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Affiliation(s)
- Lucia Pallecchi
- Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Policlinico Santa Maria alle Scotte, 53100 Siena, Italy
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45
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Oteo J, Navarro C, Cercenado E, Delgado-Iribarren A, Wilhelmi I, Orden B, García C, Miguelañez S, Pérez-Vázquez M, García-Cobos S, Aracil B, Bautista V, Campos J. Spread of Escherichia coli strains with high-level cefotaxime and ceftazidime resistance between the community, long-term care facilities, and hospital institutions. J Clin Microbiol 2006; 44:2359-66. [PMID: 16825350 PMCID: PMC1489527 DOI: 10.1128/jcm.00447-06] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 151 Escherichia coli strains resistant to cefotaxime and ceftazidime were isolated during a prospective surveillance study. These strains were characterized by clinical, microbiological, and molecular analyses and were distributed into four clusters of 103, 11, 6, and 5 isolates, along with 25 unrelated strains. The principal cluster was isolated from urine, wound, blood, and other samples in three hospitals, eight nursing homes, and a community healthcare center. This cluster was associated with both nosocomial (65%) and community-acquired (35%) infections. Most strains were resistant to ciprofloxacin, gentamicin, tobramycin, cefepime, amoxicillin-clavulanic acid, and trimethoprim-sulfamethoxazole but were susceptible to imipenem. All isolates from the four clusters expressed the extended-spectrum beta-lactamase (ESBL) CTX-M-15. This enzyme was also present in 8 (30.8%) of the 26 unrelated isolates. The other ESBLs, CTX-M-14 and CTX-M-32, were detected in five and seven cases, respectively, but they were detected in individual E. coli isolates only. In three clusters, blaCTX-M-15 alleles were linked to an ISEcp1-like element, while in eight strains of cluster II an IS26 element preceded the blaCTX-M-15 allele. An additional pool of resistance genes included tetA, drfA14 or dfrA17, sul1 or sul2, aac(6')Ib, and aac(3)IIb. All except one of the 27 isolates tested for genetic virulence markers harbored the same three virulence genes: iutA and fyuA (siderophores), and traT (serum survival factor). Epidemic or occasional isolates of cefotaxime- and ceftazidime-resistant E. coli can spread between distinct health facilities including hospitals, community health centers, and long-term care centers.
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Affiliation(s)
- Jesús Oteo
- Antibiotic Laboratory, Bacteriology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Pozuelo a Majadahonda, 28220 Majadahonda, Madrid, Spain
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46
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Seol SY, Kim YT, Jeong YS, Oh JY, Kang HY, Moon DC, Kim J, Lee YC, Cho DT, Lee JC. Molecular characterization of antimicrobial resistance in Shigella sonnei isolates in Korea. J Med Microbiol 2006; 55:871-877. [PMID: 16772414 DOI: 10.1099/jmm.0.46441-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The antimicrobial resistance of 122 Shigella sonnei isolates obtained in Korea during the period 1991-2000 was characterized. These isolates were highly resistant to traditional antibiotics such as trimethoprim (100 %), streptomycin (100 %), sulfamethoxazole (94 %), tetracycline (93 %) and nalidixic acid (90 %). All S. sonnei isolates carried Tn7 in their chromosomes. The 8.4 kb non-transferable resistance (R) plasmid carrying tetA, strA-strB and sul1 was found in 93 % of the S. sonnei isolates. Resistance to nalidixic acid first appeared in a S. sonnei isolate in 1997, and then in all S. sonnei isolates from 1998 and 1999. Resistance to commonly prescribed antibiotics such as ampicillin was increased in S. sonnei isolates during the outbreak period 1998-2000. Resistance to ampicillin was mediated by the conjugative R plasmids carrying blaTEM-1. In conclusion, S. sonnei acquired antimicrobial resistance to commonly prescribed antibiotics through the horizontal transfer of conjugative R plasmids, while the genetic stability of transposon and non-transferable R plasmids was responsible for resistance to traditional antibiotics.
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MESH Headings
- Blotting, Southern
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Disease Outbreaks
- Drug Resistance, Multiple, Bacterial/genetics
- Dysentery, Bacillary/epidemiology
- Dysentery, Bacillary/microbiology
- Electrophoresis, Gel, Pulsed-Field
- Humans
- Korea/epidemiology
- Microbial Sensitivity Tests
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- R Factors/chemistry
- R Factors/genetics
- Retrospective Studies
- Shigella sonnei/drug effects
- Shigella sonnei/genetics
- Shigella sonnei/growth & development
- Shigella sonnei/isolation & purification
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Affiliation(s)
- Sung Yong Seol
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Yong Tae Kim
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Young Sook Jeong
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Jae Young Oh
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Hee Young Kang
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Dong Chan Moon
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Jungmin Kim
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Yoo Chul Lee
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Dong Taek Cho
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
| | - Je Chul Lee
- Department of Microbiology, Kyungpook National University School of Medicine, 101, Dongin-dong, Jung-gu, Daegu, 700-422, Korea
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Bartoloni A, Pallecchi L, Benedetti M, Fernandez C, Vallejos Y, Guzman E, Villagran AL, Mantella A, Lucchetti C, Bartalesi F, Strohmeyer M, Bechini A, Gamboa H, Rodríguez H, Falkenberg T, Kronvall G, Gotuzzo E, Paradisi F, Rossolini GM. Multidrug-resistant commensal Escherichia coli in children, Peru and Bolivia. Emerg Infect Dis 2006; 12:907-13. [PMID: 16707045 PMCID: PMC3373029 DOI: 10.3201/eid1206.051258] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Healthy children in urban areas have a high prevalence of fecal carriage of drug-resistant E. coli. Using a rapid screening method, we investigated the prevalence of fecal carriage of antimicrobial drug–resistant Escherichia coli in 3,174 healthy children from 4 urban settings in Peru and Bolivia. High resistance rates were observed for ampicillin (95%), trimethoprim-sulfamethoxazole (94%), tetracycline (93%), streptomycin (82%), and chloramphenicol (70%). Lower resistance rates were observed for nalidixic acid (35%), kanamycin (28%), gentamicin (21%), and ciprofloxacin (18%); resistance to ceftriaxone and amikacin was uncommon (<0.5%). In a random sample of 1,080 resistant E. coli isolates, 90% exhibited a multidrug-resistance (MDR) phenotype. The 2 most common MDR phenotypes (ampicillin/tetracycline/trimethoprim-sulfamethoxazole and ampicillin/tetracycline/trimethoprim-sulfamethoxazole/chloramphenicol) could be transferred en bloc in conjugation experiments. The most common acquired resistance genes were blaTEM, tet(A), tet(B), drfA8, sul1, sul2, and catI. These findings underscore the magnitude of the problem of antimicrobial drug resistance in low-resource settings and the urgent need for surveillance and control of this phenomenon.
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Affiliation(s)
- Alessandro Bartoloni
- Clinica Malattie Infettive, Dipartimento Area Critica Medico Chirurgica, Universitá di Firenze, Florence, Italy.
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48
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Fonseca EL, Vieira VV, Cipriano R, Vicente ACP. Emergence of dhfrXVb and blaCARB-4 gene cassettes in class 1 integrons from clinical Pseudomonas aeruginosa isolated in Amazon region. Mem Inst Oswaldo Cruz 2006; 101:81-4. [PMID: 16699713 DOI: 10.1590/s0074-02762006000100015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Integrons play a role in horizontal acquisition and expression of genes, as well as gene reservoir, contributing for the resistance phenotype, particularly relevant to bacteria of clinical importance. We aimed to determine the composition and the organization of the class 1 integron variable region present in Pseudomonas aeruginosa clinical isolates from Brazil. Strains carrying class 1 integrons were resistant to the majority of antibiotics tested, except to imipenem and ceftazidime. Sequence analysis of the integron variable region revealed the presence of the blaCARB-4 gene into two distinct cassette arrays: aacA4-dhfrXVb-blaCARB-4 and aadB-aacA4-blaCARB-4. dhfrXVb gene cassette, which is rare in Brazil and in P. aeruginosa species, was found in one isolate. PFGE analysis showed the spread of blaCARB-4 among P. aeruginosa clones. The occurrence of blaCARB-4 and dhfrXVb in Brazil may contribute for developing resistance to clinically important antibiotics, and shows a diversified scenarium of these elements occurring in Amazon clinical settings, where no study about integron dynamics was performed to date.
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Affiliation(s)
- Erica L Fonseca
- Departamento de Genética, Instituto Oswaldo Cruz-Fiocruz, 21040-900 Rio de Janeiro, RJ, Brazil.
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Harada K, Asai T, Kojima A, Ishihara K, Takahashi T. Role of coresistance in the development of resistance to chloramphenicol inEscherichia coliisolated from sick cattle and pigs. Am J Vet Res 2006; 67:230-5. [PMID: 16454626 DOI: 10.2460/ajvr.67.2.230] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the cause of persistent resistance to chloramphenicol (CP) after the ban on its use in food-producing animals in several countries. SAMPLE POPULATION 71 CP-resistant and 104 CP-susceptible Escherichia coli strains isolated from sick cattle and pigs in Japan. PROCEDURE Susceptibility of all bacterial strains to thiamphenicol (TP) and florfenicol (FFC) was tested by use of an agar dilution method. The CP-resistance genes and variable region within class 1 integrons in CP-resistant strains were identified by use of a PCR assay. RESULTS The CP acetyltransferase gene (ie, cat1) was identified as the predominant CP-resistance gene in strains isolated from cattle, and the cat1and nonenzymatic CP-resistance gene (ie, cmlA) were the predominant CP-resistance genes in strains isolated from pigs. Additionally, strains with cat1 isolated from cattle often were resistant to ampicillin, dihydrostreptomycin (DSM), oxytetracycline, and trimethoprim (TMP), whereas strains with cat1 or cmlA isolated from pigs often were resistant to DSM and TMP. Class 1 integrons were significantly more prevalent in strains with CP-resistance genes, compared with prevalence in strains without CP-resistance genes. All gene cassettes within the integrons were involved in resistance to DSM, TMP, or both. CONCLUSIONS AND CLINICAL RELEVANCE Coresistance that develops because of the use of DSM and TMP in cattle and pigs apparently contributes to the selection of CP-resistant strains of E coli. Thus, it is possible that bacterial resistance to CP in animals would persist despite a ban on the use of CP in cattle and pigs.
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Affiliation(s)
- Kazuki Harada
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
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50
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Kang HY, Jeong YS, Oh JY, Tae SH, Choi CH, Moon DC, Lee WK, Lee YC, Seol SY, Cho DT, Lee JC. Characterization of antimicrobial resistance and class 1 integrons found in Escherichia coli isolates from humans and animals in Korea. J Antimicrob Chemother 2005; 55:639-44. [PMID: 15761064 DOI: 10.1093/jac/dki076] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Antimicrobial resistance and class 1 integrons found in Escherichia coli isolates from humans and animals in Korea were characterized. METHODS E. coli isolates were examined for susceptibility to antimicrobial agents. Integrase genes were amplified. Gene cassette regions for classes 1 and 2 integrons were amplified and sequenced. Conjugal transfer and Southern hybridization were performed to determine the genetic localization of class 1 integrons. The clonal relationship of E. coli isolates carrying an identical cassette array was analysed by PFGE. RESULTS Commensal E. coli isolates from animals were highly resistant to commonly used antimicrobial agents such as tetracycline, sulfamethoxazole, streptomycin, ampicillin and carbenicillin. Integrons were most prevalent in commensal E. coli isolates from poultry (44%), followed by clinical isolates from humans (33%), commensal isolates from swine (23%) and humans (13%). dfrA17-aadA5, dfrA12-orfF-aadA2 and aadA1 were found most frequently in E. coli isolates from humans, poultry and swine, respectively. Class 1 integrons were mostly located in conjugative plasmids. E. coli isolates carrying an identical cassette array were phylogenetically unrelated. CONCLUSIONS The use of antibiotics is strongly associated with antimicrobial resistance. E. coli isolates from different sources may select a specific gene cassette by antibiotic selective pressure, which results in differences in class 1 integrons. The horizontal transfer of class 1 integrons through conjugative plasmids seems to be responsible for wide dissemination of a particular type of class 1 integron.
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Affiliation(s)
- Hee Young Kang
- Department of Microbiology, Kyungpook National University School of Medicine, 101 Dongin-dong, Jung-gu, Daegu 700-422, Korea
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