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Shindoh S, Kadoya A, Kanechi R, Watanabe K, Suzuki S. Marine bacteria harbor the sulfonamide resistance gene sul4 without mobile genetic elements. Front Microbiol 2023; 14:1230548. [PMID: 37779713 PMCID: PMC10539471 DOI: 10.3389/fmicb.2023.1230548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Marine bacteria are possible reservoirs of antibiotic-resistance genes (ARGs) originating not only from clinical and terrestrial hot spots but also from the marine environment. We report here for the first time a higher rate of the sulfonamide-resistance gene sul4 in marine bacterial isolates compared with other sul genes. Among four sulfonamide-resistance genes (sul1, sul2, sul3, and sul4), sul4 was most abundant (45%) in 74 sulfonamide-resistant marine isolates by PCR screening. The order of abundance was sul4 (33 isolates) >sul2 (6 isolates) >sul3 (5 isolates) >sul1 (1 isolate). Whole-genome sequencing of 23 isolates of sul4-expressing α- and γ-proteobacteria and bacilli revealed that sul4 was not accompanied by known mobile genetic elements. This suggests that sul4 in these marine isolates is clonally transferred and not horizontally transferable. Folate metabolism genes formed a cluster with sul4, suggesting that the cluster area plays a role in folate metabolism, at which sul4 functions as a dihydropteroate synthase. Thus, sul4 might be expressed in marine species and function in folate synthesis, but it is not a transferable ARG.
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Affiliation(s)
- Suzune Shindoh
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Aya Kadoya
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Reo Kanechi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Satoru Suzuki
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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2
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Tran TQ, Park M, Lee JE, Kim SH, Jeong JH, Choy HE. Analysis of antibiotic resistance gene cassettes in a newly identified Salmonella enterica serovar Gallinarum strain in Korea. Mob DNA 2023; 14:4. [PMID: 37095552 PMCID: PMC10124037 DOI: 10.1186/s13100-023-00292-8] [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] [Received: 11/02/2022] [Accepted: 03/20/2023] [Indexed: 04/26/2023] Open
Abstract
Antimicrobial resistant pathogens are a global health threat driven by the indiscriminate use of antimicrobials. Antimicrobial resistance can be acquired by resistance genes encoded by mobile genetic elements. In this study, we identified a strain of Salmonella enterica serovar Gallinarum (SG4021) from an infected chicken in Korea and characterized the presence of resistance genes in its plasmid by whole genome sequencing. The sequence was then compared with that of a plasmid (P2) from strain SG_07Q015, the only other strain of S. Gallinarum isolated in Korea for which a genome sequence is available. The results revealed that both strains harbored nearly identical DNA carrying antibiotic resistance gene cassettes inserted into integron In2 of the transposable element Tn21, namely an aadA1 resistance gene conferring resistance to aminoglycosides and a sul1 resistance gene conferring resistance to sulfonamide. Interestingly, despite the presence of sul1 in SG4021, an antibiotic sensitivity test revealed that it was sensitive to sulfonamides. Further analysis revealed that this disparity was due to the insertion of a ~ 5 kb ISCR16 sequence downstream of the promoter driving sul1 expression in SG4021. Using various mutants, we showed that the insertion of ISCR16 blocked the expression of the sul1 gene from the upstream promoter. Therefore, the functionality of antimicrobial resistance genes determines phenotypic antimicrobial resistance.
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Affiliation(s)
- Thanh Quang Tran
- Departments of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, 322 Seoyangro, Hwansun, Jeonnam, 519-763, South Korea
| | - Minyoung Park
- DNA Link, Inc, Seodaemun-Gu Bugahyeon-Ro 150, Industry Coop Bldg. 2Nd Fl, Seoul, 120-140, South Korea
| | - Jong Eun Lee
- DNA Link, Inc, Seodaemun-Gu Bugahyeon-Ro 150, Industry Coop Bldg. 2Nd Fl, Seoul, 120-140, South Korea
| | - Soo Hyun Kim
- Departments of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, 322 Seoyangro, Hwansun, Jeonnam, 519-763, South Korea
| | - Jae-Ho Jeong
- Departments of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, 322 Seoyangro, Hwansun, Jeonnam, 519-763, South Korea.
- Department of Microbiology, Chonnam National University Medical School, Hwasun, 58128, Jeollanam-Do, Republic of Korea.
| | - Hyon E Choy
- Departments of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, 322 Seoyangro, Hwansun, Jeonnam, 519-763, South Korea.
- Department of Microbiology, Chonnam National University Medical School, Hwasun, 58128, Jeollanam-Do, Republic of Korea.
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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Li Q, Li Z, Wang Y, Chen Y, Sun J, Yang Y, Si H. Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province. Animals (Basel) 2022; 12:ani12080976. [PMID: 35454223 PMCID: PMC9025041 DOI: 10.3390/ani12080976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/27/2023] Open
Abstract
Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.
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Vásquez-Ponce F, Higuera-Llantén S, Parás-Silva J, Gamboa-Acuña N, Cortés J, Opazo-Capurro A, Ugalde JA, Alcalde-Rico M, Olivares-Pacheco J. Genetic characterization of clinically relevant class 1 integrons carried by multi-drug resistant bacteria (MDRB) isolated from the gut microbiota of highly antibiotic treated Salmo salar. J Glob Antimicrob Resist 2022; 29:55-62. [DOI: 10.1016/j.jgar.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/08/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
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Fauzi NNFNM, Hamdan RH, Mohamed M, Ismail A, Mat Zin AA, Mohamad NFA. Prevalence, antibiotic susceptibility, and presence of drug resistance genes in Aeromonas spp. isolated from freshwater fish in Kelantan and Terengganu states, Malaysia. Vet World 2021; 14:2064-2072. [PMID: 34566322 PMCID: PMC8448652 DOI: 10.14202/vetworld.2021.2064-2072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 12/03/2022] Open
Abstract
Background and Aim: The emergence of antibiotic-resistant bacterial pathogens has been increasingly reported, which has resulted in a decreasing ability to treat bacterial infections. Therefore, this study investigated the presence of Aeromonas spp., including its antibiotic resistance in various fish samples, Oreochromis spp., Clarias gariepinus, and Pangasius hypophthalmus, obtained from Kelantan and Terengganu, Malaysia. Materials and Methods: In this study, 221 fish samples, of which 108 (Oreochromis spp., n=38; C. gariepinus, n=35; and P. hypophthalmus, n=35) were from Kelantan and 113 (Oreochromis spp., n=38; C. gariepinus, n=35; and P. hypophthalmus, n=40) were from Terengganu, were caught using cast nets. Then, samples from their kidneys were cultured on a Rimler Shott agar to isolate Aeromonas spp. Polymerase chain reaction (PCR) was used to confirm this isolation using specific gene primers for species identification. Subsequently, the isolates were tested for their sensitivity to 14 antibiotics using the Kirby–Bauer method, after which the PCR was conducted again to detect resistance genes: sul1, strA-strB, aadA, blaTEM, blaSHV, tetA-tetE, and tetM. Results: From the results, 61 isolates were identified as being from the genus Aeromonas using PCR, of which 28 were Aeromonas jandaei, 19 were Aeromonas veronii, seven were Aeromonas hydrophila, and seven were Aeromonas sobria. Moreover, 8, 12, and 8 of A. jandaei; 4, 3, and 12 of A. veronii; 6, 0, and 1 of A. hydrophila; and 3, 3, and 1 of A. sobria were obtained from Oreochromis spp., C. gariepinus, and P. hypophthalmus, respectively. In addition, the isolates showed the highest level of resistance to ampicillin (100%), followed by streptomycin (59.0%), each kanamycin and nalidixic acid (41.0%), neomycin (36.1%), tetracycline (19.7%), sulfamethoxazole (14.8%), and oxytetracycline (13.1%). Resistance to gentamicin and ciprofloxacin both had the same percentage (9.8%), whereas isolates showed the lowest resistance to norfloxacin (8.2%) and doxycycline (1.6%). Notably, all Aeromonas isolates were susceptible to chloramphenicol and nitrofurantoin. Results also revealed that the multiple antibiotic resistances index of the isolates ranged from 0.07 to 0.64, suggesting that the farmed fish in these areas were introduced to the logged antibiotics indiscriminately and constantly during their cultivation stages. Results also revealed that the sul1 gene was detected in 19.7% of the Aeromonas isolates, whereas the tetracycline resistance genes, tetA and tetE, were detected in 27.9% and 4.9% of the isolates, respectively. However, β-lactam resistance genes, blaTEM and blaSHV, were found in 44.3% and 13.1% of Aeromonas isolates, respectively, whereas strA-strB and aadA genes were found in 3.3% and 13.1% of the isolates, respectively. Conclusion: This study, therefore, calls for continuous surveillance of antibiotic-resistant Aeromonas spp. in cultured freshwater fish to aid disease management and better understand their implications to public health.
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Affiliation(s)
- Nik Nur Fazlina Nik Mohd Fauzi
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Ruhil Hayati Hamdan
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Maizan Mohamed
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Aziana Ismail
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Ain Auzureen Mat Zin
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Nora Faten Afifah Mohamad
- Department of Paraclinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
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Zhou Y, Fang J, Davood Z, Han J, Qu D. Fitness cost and compensation mechanism of sulfonamide resistance genes (sul1, sul2, and sul3) in Escherichia coli. Environ Microbiol 2021; 23:7538-7549. [PMID: 34554624 DOI: 10.1111/1462-2920.15783] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/24/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022]
Abstract
The fitness cost of antibiotic resistance is a crucial factor to determine the evolutionary and transmission success of resistant bacteria. Exploring the fitness cost and compensation mechanism of antibiotic resistance genes (ARGs) in bacteria may effectively reduce the transmission of drug-resistant genes in the environment. Engineered bacteria with the same genetic background that carry sulfonamide resistance gene were generated to explore the fitness cost of sulfonamide resistance gene in Escherichia coli. There were significant differences in the protein expression of the two-component system pathway (fliZ, fliA, fliC and lrhA), folate biosynthesis pathway (sul1, sul2 and sul3), ABC transporter system (ugpC, rbsA and gsiA), and outer membrane pore protein OmpD through the comparative analysis of differential proteins compared to sensitive bacteria. Thus, we could speculate the possible fitness compensation mechanism. Finally, quantitative Real-time PCR (qRT-PCR) was used to verify the functions of some differential proteins at the transcriptional level. The fitness cost and compensatory evolution of antibiotic resistance are an essential part of bacterial evolution.
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Affiliation(s)
- Yuqiao Zhou
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Jiehong Fang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Zaeim Davood
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Jianzhong Han
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Daofeng Qu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China
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Ambrose SJ, Hall RM. dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering. J Antimicrob Chemother 2021; 76:2748-2756. [PMID: 34180526 DOI: 10.1093/jac/dkab212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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Souque C, Escudero JA, MacLean RC. Integron activity accelerates the evolution of antibiotic resistance. eLife 2021; 10:62474. [PMID: 33634790 PMCID: PMC8024014 DOI: 10.7554/elife.62474] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to 'evolve on demand' in response to antibiotic pressure. To test this hypothesis, we inserted a custom three-cassette integron into Pseudomonas aeruginosa and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.
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Affiliation(s)
- Célia Souque
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - José Antonio Escudero
- University of Oxford, Department of Zoology, Oxford, United Kingdom.,Universidad Complutense de Madrid, Departamento de Sanidad Animal and VISAVET, Madrid, Spain
| | - R Craig MacLean
- University of Oxford, Department of Zoology, Oxford, United Kingdom
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10
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Roy PH, Partridge SR, Hall RM. Comment on "Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection" by A.N. Zhang et al. MICROBIOME 2021; 9:3. [PMID: 33397505 PMCID: PMC7784347 DOI: 10.1186/s40168-020-00950-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/06/2020] [Indexed: 05/31/2023]
Abstract
An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.
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Affiliation(s)
- Paul H Roy
- Centre de Recherche en Infectiologie, CHU de Québec, Québec, QC, Canada.
- Department de Biochimie, de Microbiologie, et de Bio-informatique, Université Laval, Québec, QC, Canada.
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, 2145, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, 2006, Australia
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He J, Li C, Cui P, Wang H. Detection of Tn 7-Like Transposons and Antibiotic Resistance in Enterobacterales From Animals Used for Food Production With Identification of Three Novel Transposons Tn 6813, Tn 6814, and Tn 6765. Front Microbiol 2020; 11:2049. [PMID: 33013752 PMCID: PMC7500258 DOI: 10.3389/fmicb.2020.02049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/04/2020] [Indexed: 12/04/2022] Open
Abstract
Enterobacterales are widely distributed in the gastro-intestinal system of animals and may cause opportunistic infections. Worse still, multidrug-resistant Enterobacterales also poses a serious threat to public health. Tn7-like transposons have been found in several species of the Enterobacterales order and play an important role in dissemination of antibiotic resistance. This study aimed to investigate the distribution and genetic characterization of Tn7-like transposons in Enterobacterales isolates from food animals and their association with antibiotic resistance. Enterobacterales isolated from the samples were identified and classified according to the 16S rDNA sequence. Tn7-like transposons and associated integrons were detected by polymerase chain reaction (PCR) and sequencing. The antibiotic resistance of each Tn7-like transposon positive isolate was detected according to the Kirby-Bauer disk diffusion method. Then, six representative strains were selected to study the genetic environment by whole-genome sequencing (WGS). In total, we isolated 377 Tn7-like transposons positive strains of Enterobacterales. Class 2 integrons were detected in 99.5% of the isolates, and there were high frequency mutation sites especially in base 535, a stop mutation. Many isolates (54.9%) were multidrug-resistant and observed high resistance rates to trimethoprim/sulfamethoxazole and streptomycin. Among these strains, we found three new types of Tn7-like transposons, named Tn6813, Tn6814, and Tn6765. This is the first comprehensive survey that shows Tn7-like transposons in Enterobacterales from animals used for food production in different regions of China. This study also provides an insight into the horizontal transfer of resistance genes associated with Tn7-like transposons.
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Affiliation(s)
- Juan He
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Pengfei Cui
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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12
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Preena PG, Swaminathan TR, Rejish Kumar VJ, Bright Singh IS. Unravelling the menace: detection of antimicrobial resistance in aquaculture. Lett Appl Microbiol 2020; 71:26-38. [PMID: 32248555 DOI: 10.1111/lam.13292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
One of the major problems to be addressed in aquaculture is the prominence of antimicrobial resistance (AMR). The occurrence of bacterial infections in cultured fishes promotes the continuous use of antibiotics in aquaculture, which results in the selection of proliferated antibiotic-resistant bacteria and increases the possibility of transfer to the whole environment through horizontal gene transfer. Hence, the accurate cultivation-dependent and cultivation-independent detection methods are very much crucial for the immediate and proper management of this menace. Antimicrobial resistance determinants carrying mobile genetic transfer elements such as transposons, plasmids, integrons and gene cassettes need to be specifically analysed through molecular detection techniques. The susceptibility of microbes to antibiotics should be tested at regular intervals along with various biochemical assays and conjugation studies so as to determine the extent of spread of AMR. Advanced omic-based and bioinformatic tools can also be incorporated for understanding of genetic diversity. The present review focuses on different detection methods to unearth the complexity of AMR in aquaculture. This monitoring helps the authorities to curb the use of antibiotics, commencement of appropriate management measures and adequate substitute strategies in aquaculture. The long battle of AMR could be overcome by the sincere implementation of One Health approach. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of antibiotics and increased antimicrobial resistance (AMR) are of major concerns in aquaculture industry. This could result in global health risks through direct consumption of cultured fishes and dissemination of AMR to natural environment through horizontal gene transfer. Hence, timely detection of the antimicrobial-resistant pathogens and continuous monitoring programmes are inevitable. Advanced microbiological, molecular biological and omic-based tools can unravel the menace to a great extent. This will help the authorities to curb the use of antibiotics and implement appropriate management measures to overcome the threat.
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Affiliation(s)
- P G Preena
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, India
| | - T Raja Swaminathan
- Peninsular and Marine Fish Genetic Resources Centre of ICAR-NBFGR, CMFRI Campus, Kochi, India
| | - V J Rejish Kumar
- Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - I S Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, India
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Ducey TF, Durso LM, Ibekwe AM, Dungan RS, Jackson CR, Frye JG, Castleberry BL, Rashash DMC, Rothrock MJ, Boykin D, Whitehead TR, Ramos Z, McManus M, Cook KL. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:120991. [PMID: 31446353 DOI: 10.1016/j.jhazmat.2019.120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.
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Affiliation(s)
- Thomas F Ducey
- Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, Department of Agriculture, Florence, SC, United States.
| | - Lisa M Durso
- Agroecosystem Management Research Unit, Agricultural Research Service, Department of Agriculture, Lincoln, NE, United States
| | - Abasiofiok M Ibekwe
- U.S. Salinity Laboratory, Agricultural Research Service, Department of Agriculture, Riverside, CA, United States
| | - Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, Department of Agriculture, Kimberly, ID, United States
| | - Charlene R Jackson
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - B Lana Castleberry
- Livestock Nutrient Management Research Unit, Agricultural Research Service, Department of Agriculture, Bushland, TX, United States
| | - Diana M C Rashash
- North Carolina Cooperative Extension Service, Jacksonville, NC, United States
| | - Michael J Rothrock
- Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Debbie Boykin
- Jamie Whitten Delta States Research Center, Agricultural Research Service, Department of Agriculture, Stoneville, MS, United States
| | - Terence R Whitehead
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Department of Agriculture, Peoria, IL, United States
| | - Zeanmarj Ramos
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Morgan McManus
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Kimberly L Cook
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
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Abstract
During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.
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Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E. The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis. Microb Genom 2018; 4. [PMID: 30461373 PMCID: PMC6321870 DOI: 10.1099/mgen.0.000233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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Affiliation(s)
- Anna Johnning
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Nahid Karami
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erika Tång Hallbäck
- 3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Vilhelm Müller
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena Nyberg
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mariana Buongermino Pereira
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Callum Stewart
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Tobias Ambjörnsson
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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Gong J, Zhuang L, Zhang D, Zhang P, Dou X, Wang C. Establishment of a Multiplex Loop-Mediated Isothermal Amplification Method for Rapid Detection of Sulfonamide Resistance Genes (sul1, sul2, sul3) in Clinical Enterobacteriaceae Isolates from Poultry. Foodborne Pathog Dis 2018; 15:413-419. [PMID: 29708802 DOI: 10.1089/fpd.2017.2410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial resistance genes play an important role in mediating resistance to sulfonamide in Gram-negative bacteria. While PCR is the current method to detect sulfonamide resistance genes (sul1, sul2, sul3), it is time-consuming and costly and there is an urgent need to develop a more convenient, simpler and rapid test for the sul. In this study, we describe a multiplex loop-mediated isothermal amplification (m-LAMP) assay we developed for the rapid and simultaneous detection of three sul. This m-LAMP assay successfully detected seven reference strains with different sul genotypes, but was negative for nine sul-negative reference strains. The m-LAMP products were verified by HinfI restriction enzyme digestion and the detection limit of the test was 0.5 pg genomic DNA per reaction. Testing 307 sulfonamide-resistant Enterobacteriaceae clinical isolates with the m-LAMP revealed all were positive for the sul with sul2 (79.5%) and sul1 (64.5%) being most prevalent, and sul3 the least (12.1%). Of the Enterobacteriaceae isolates tested, the Salmonella Indiana, a newly emerging serovar resistant to numerous antimicrobials, were most commonly positive with 33% having sul3.
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Affiliation(s)
- Jiansen Gong
- 1 Poultry Institute , Chinese Academy of Agricultural Sciences, Yangzhou, China
- 2 Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, Jiangsu, China
| | - Linlin Zhuang
- 3 State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University , Nanjing, China
| | - Di Zhang
- 1 Poultry Institute , Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Ping Zhang
- 1 Poultry Institute , Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Xinhong Dou
- 1 Poultry Institute , Chinese Academy of Agricultural Sciences, Yangzhou, China
- 2 Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, Jiangsu, China
| | - Chengming Wang
- 4 College of Veterinary Medicine, Auburn University , Auburn, Alabama
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18
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Zhou Y, Niu L, Zhu S, Lu H, Liu W. Occurrence, abundance, and distribution of sulfonamide and tetracycline resistance genes in agricultural soils across China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:1977-1983. [PMID: 28558428 DOI: 10.1016/j.scitotenv.2017.05.152] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/16/2017] [Accepted: 05/16/2017] [Indexed: 05/26/2023]
Abstract
The prevalence and proliferation of antibiotic resistance genes (ARGs) have been identified as an emerging contaminant of concern and a crucial threat to public health worldwide. In this study, we carried out a nation-wide sampling campaign across China to investigate the distribution and abundances of 8 major ARGs in agricultural soils. The levels of sulfonamide (sul) and tetracycline (tet) resistance genes in China's agricultural soils ranged from 10-6-10-2 to 10-8-10-2 gene copies/16S rRNA gene copies, respectively. Northeast China is the hot-spot of ARGs, likely due to long-term wastewater irrigation in the area. Redundancy analysis was further performed to assess the influences of environmental variables on ARG abundances. Sulfonamide resistance genes displayed strong correlations with meteorological parameters (mean annual precipitation and temperature), and decreased from north to south. In comparison, tetracycline resistance genes were more closely related to soil organic matter and pH. Co-selection between heavy metals and ARGs was significant among Cu, Hg and sulfonamide resistance genes. This study highlighted the current status of ARG contamination and their influencing factors in China's agricultural soils. Findings are valuable to identify effective management options for reducing the release of antibiotics and control ARG spread in the agriculture sector across the world.
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Affiliation(s)
- Yuting Zhou
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lili Niu
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Siyu Zhu
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijie Lu
- Institute of Eco-environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Department of Civil and Environment Engineering, University of Vermont Burlington, VT 05405, United States.
| | - Weiping Liu
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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19
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Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains. Antimicrob Agents Chemother 2017; 61:AAC.00995-17. [PMID: 28674052 DOI: 10.1128/aac.00995-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a leading cause of severe infantile diarrhea in developing countries. Previous research has focused on the diversity of the EPEC virulence plasmid, whereas less is known regarding the genetic content and distribution of antibiotic resistance plasmids carried by EPEC. A previous study demonstrated that in addition to the virulence plasmid, reference EPEC strain B171 harbors a second, larger plasmid that confers antibiotic resistance. To further understand the genetic diversity and dissemination of antibiotic resistance plasmids among EPEC strains, we describe the complete sequence of an antibiotic resistance plasmid from EPEC strain B171. The resistance plasmid, pB171_90, has a completed sequence length of 90,229 bp, a GC content of 54.55%, and carries protein-encoding genes involved in conjugative transfer, resistance to tetracycline (tetA), sulfonamides (sulI), and mercury, as well as several virulence-associated genes, including the transcriptional regulator hha and the putative calcium sequestration inhibitor (csi). In silico detection of the pB171_90 genes among 4,798 publicly available E. coli genome assemblies indicates that the unique genes of pB171_90 (csi and traI) are primarily restricted to genomes identified as EPEC or enterotoxigenic E. coli However, conserved regions of the pB171_90 plasmid containing genes involved in replication, stability, and antibiotic resistance were identified among diverse E. coli pathotypes. Interestingly, pB171_90 also exhibited significant similarity with a sequenced plasmid from Shigella dysenteriae type I. Our findings demonstrate the mosaic nature of EPEC antibiotic resistance plasmids and highlight the need for additional sequence-based characterization of antibiotic resistance plasmids harbored by pathogenic E. coli.
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20
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Guo X, Pang W, Dou C, Yin D. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors. CHEMOSPHERE 2017; 175:21-27. [PMID: 28211331 DOI: 10.1016/j.chemosphere.2017.01.134] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.
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Affiliation(s)
- Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Weihai Pang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Chunling Dou
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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21
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Knowles M, Stinson S, Lambert D, Carrillo C, Koziol A, Gauthier M, Blais B. Genomic Tools for Customized Recovery and Detection of Foodborne Shiga Toxigenic Escherichia coli. J Food Prot 2016; 79:2066-2077. [PMID: 28221970 DOI: 10.4315/0362-028x.jfp-16-220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e.g., Antimicrobial Resistance Marker Identifier), or publicly available tools based on clinically relevant acquired AMR gene databases (e.g., ResFinder). In combination with a previously reported pipeline (SigSeekr) designed to identify specific DNA sequences associated with a particular strain for its rapid identification by PCR, it should be possible to deploy custom recovery and identification tools for the efficient detection of priority pathogens such as Shiga toxigenic Escherichia coli (STEC) outbreak strains within the time frame of an active investigation. Using a laboratory STEC strain as a model, trimethoprim resistance identified by both Antimicrobial Resistance Marker Identifier and ResFinder was used as the basis for its selective recovery against a background of commensal E. coli bacteria in ground beef samples. Enrichment in modified tryptic soy broth containing trimethoprim greatly enhanced the recovery of low numbers of model strain cells inoculated in ground beef samples, as verified by the enumeration of colonies on plating media using a strain-specific PCR method to determine the recovery efficiency for the target strain. We discuss the relative merits of different AMR marker prediction tools for this purpose and describe how such tools can be utilized to good effect in a typical outbreak investigation scenario.
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Affiliation(s)
- Michael Knowles
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Sara Stinson
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Dominic Lambert
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Catherine Carrillo
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Adam Koziol
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Martine Gauthier
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Burton Blais
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
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22
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Affiliation(s)
- C.J. Thomson
- Department of Medical Microbiology Medical School -University of Edinburgh Teviot Place Edinburgh EH8 9AG
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23
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Folate Biosynthesis, Reduction, and Polyglutamylation and the Interconversion of Folate Derivatives. EcoSal Plus 2015; 2. [PMID: 26443588 DOI: 10.1128/ecosalplus.3.6.3.6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many microorganisms and plants possess the ability to synthesize folic acid derivatives de novo, initially forming dihydrofolate. All the folic acid derivatives that serve as recipients and donors of one-carbon units are derivatives of tetrahydrofolate, which is formed from dihydrofolate by an NADPH-dependent reduction catalyzed by dihydrofolate reductase (FolA). This review discusses the biosynthesis of dihydrofolate monoglutamate, its reduction to tetrahydrofolate monoglutamate, and the addition of glutamyl residues to form folylpolyglutamates. Escherichia coli and Salmonella, like many microorganisms that can synthesize folate de novo, appear to lack the ability to transport folate into the cell and are thus highly susceptible to inhibitors of folate biosynthesis. The review includes a brief discussion of the inhibition of folate biosynthesis by sulfa drugs. The folate biosynthetic pathway can be divided into two sections. First, the aromatic precursor chorismate is converted to paminobenzoic acid (PABA) by the action of three proteins. Second, the pteridine portion of folate is made from GTP and coupled to PABA to generate dihydropteroate, and the bifunctional protein specified by folC, dihydrofolate synthetase, or folylpolyglutamate synthetase, adds the initial glutamate molecule to form dihydrofolate (H2PteGlu1, or dihydropteroylmonoglutamate). Bacteriophage T4 infection of E. coli has been shown to cause alterations in the metabolism of folate derivatives. Infection is associated with an increase in the chain lengths in folylpolyglutamates and particularly the accumulation of hexaglutamate derivatives.
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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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25
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Mondal S, Mandal SM, Mondal TK, Sinha C. Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:268-279. [PMID: 26056977 DOI: 10.1016/j.saa.2015.05.049] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/17/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 μg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 μg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters.
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Affiliation(s)
- Sudipa Mondal
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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26
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Capasso C, Supuran CT. Sulfa and trimethoprim-like drugs – antimetabolites acting as carbonic anhydrase, dihydropteroate synthase and dihydrofolate reductase inhibitors. J Enzyme Inhib Med Chem 2013; 29:379-87. [DOI: 10.3109/14756366.2013.787422] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Claudiu T. Supuran
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Firenze
Polo Scientifico, Sesto Fiorentino (Florence)Italy
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Tariq A, Haque A, Ali A, Bashir S, Habeeb MA, Salman M, Sarwar Y. Molecular profiling of antimicrobial resistance and integron association of multidrug-resistant clinical isolates of Shigella species from Faisalabad, Pakistan. Can J Microbiol 2012; 58:1047-54. [DOI: 10.1139/w2012-085] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillary dysentery, common in developing countries, is usually caused by Shigella species. A major problem in shigellosis is the rapid emergence of multidrug-resistant strains. This is the first detailed molecular study on drug resistance of Shigella isolates from the Faisalabad region of Pakistan. Ninety-five Shigella isolates obtained after screening of 2500 stool samples were evaluated for in vitro resistance to commonly used antimicrobial agents; the presence or absence of 20 of the most relevant drug resistance genes; and the prevalence of integrons 1, 2, and 3. Shigella flexneri was found to be the most prevalent and most resistant species. Collectively, high resistance was found towards ampicillin (96.84%), tetracycline (93.68%), streptomycin (77.89%), and chloramphenicol (72.63%). Significant emerging resistance was detected towards the modern frontline drugs ciprofloxacin (12.63%), cefradine (17.89%), ceftriaxone (20.00%), cefoperazone (22.10%), and cefixime (28.42%). Prevalence rates for blaTEM, blaCTX-M, gyrA, gyrB, qnrS, aadA1, strAB, tetA, tetB, catA, and catP were 78.94%, 12.63%, 20.00%, 21.05%, 21.05%, 67.36%, 42.10%, 12.63%, 53.68%, 33.68%, and 25.26%, respectively. Class 2 integrons (42.10%) were more common in the local isolates. Simultaneous detection of class 1 and 2 integrons in some isolates and a rapidly emerging resistance to modern frontline drugs are the major findings of this study.
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Affiliation(s)
- Aaysha Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Abdul Haque
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Saira Bashir
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Asif Habeeb
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Salman
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Yasra Sarwar
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
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Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso ML, Prévost MC, Mazel D, Carniel E. A natural system of chromosome transfer in Yersinia pseudotuberculosis. PLoS Genet 2012; 8:e1002529. [PMID: 22412380 PMCID: PMC3297565 DOI: 10.1371/journal.pgen.1002529] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/23/2011] [Indexed: 01/21/2023] Open
Abstract
The High Pathogenicity Island of Yersinia pseudotuberculosis IP32637 was previously shown to be horizontally transferable as part of a large chromosomal segment. We demonstrate here that at low temperature other chromosomal loci, as well as a non-mobilizable plasmid (pUC4K), are also transferable. This transfer, designated GDT4 (Generalized DNA Transfer at 4°C), required the presence of an IP32637 endogenous plasmid (pGDT4) that carries several mobile genetic elements and a conjugation machinery. We established that cure of this plasmid or inactivation of its sex pilus fully abrogates this process. Analysis of the mobilized pUC4K recovered from transconjugants revealed the insertion of one of the pGDT4-borne ISs, designated ISYps1, at different sites on the transferred plasmid molecules. This IS belongs to the IS6 family, which moves by replicative transposition, and thus could drive the formation of cointegrates between pGDT4 and the host chromosome and could mediate the transfer of chromosomal regions in an Hfr-like manner. In support of this model, we show that a suicide plasmid carrying ISYps1 is able to integrate itself, flanked by ISYps1 copies, at multiple locations into the Escherichia coli chromosome. Furthermore, we demonstrate the formation of RecA-independent cointegrates between the ISYps1-harboring plasmid and an ISYps1-free replicon, leading to the passive transfer of the non-conjugative plasmid. We thus demonstrate here a natural mechanism of horizontal gene exchange, which is less constrained and more powerful than the classical Hfr mechanism, as it only requires the presence of an IS6-type element on a conjugative replicon to drive the horizontal transfer of any large block of plasmid or chromosomal DNA. This natural mechanism of chromosome transfer, which occurs under conditions mimicking those found in the environment, may thus play a significant role in bacterial evolution, pathogenesis, and adaptation to new ecological niches.
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Affiliation(s)
- Biliana Lesic
- Yersinia Research Unit, Institut Pasteur, Paris, France
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29
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van Hoek AHAM, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJM. Acquired antibiotic resistance genes: an overview. Front Microbiol 2011; 2:203. [PMID: 22046172 PMCID: PMC3202223 DOI: 10.3389/fmicb.2011.00203] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/08/2011] [Indexed: 01/18/2023] Open
Abstract
In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
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Affiliation(s)
- Angela H. A. M. van Hoek
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
| | - Dik Mevius
- Central Veterinary Institute of Wageningen URLelystad, Netherlands
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Beatriz Guerra
- National Salmonella Reference Laboratory, Federal Institute for Risk AssessmentBerlin, Germany
| | - Peter Mullany
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Adam Paul Roberts
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Henk J. M. Aarts
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
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30
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Ndi OL, Barton MD. Incidence of class 1 integron and other antibiotic resistance determinants in Aeromonas spp. from rainbow trout farms in Australia. JOURNAL OF FISH DISEASES 2011; 34:589-99. [PMID: 21762170 DOI: 10.1111/j.1365-2761.2011.01272.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
There is limited information on antibiotic resistance determinants present in bacteria of aquaculture origin in Australia. The presence of integron and other resistance determinants was investigated in 90 Aeromonas isolates derived from nine freshwater trout farms in Victoria (Australia). Polymerase chain reaction was carried out for the detection of integrase genes Int1, Int2 and Int3, gene cassette array, integron-associated aadA, sul1 and qac1 genes, streptomycin resistance genes strA-strB, β-lactamase resistance genes bla(TEM) and bla(SHV) , and tetracycline resistance genes tetA-E and tetM. Clonal analysis was performed by pulsed-field gel electrophoresis (PFGE). Class 1 integrons were detected in 28/90 (31%) and class 2 and class 3 in none of the strains, aadA gene in 19/27 (70%) streptomycin-resistant strains, sul1 in 13/15 (86.7%) sulphonamide-resistant strains and qac1 gene in 8/28 (28.6%) integron-bearing strains. Five strains from two different farms carried gene cassettes of 1000 bp each containing the aadA2 gene and PFGE analysis revealed genetic relatedness. tetC was detected in all and tetA in 9/18 (50%) tetracycline-resistant strains. The strA-strB, bla(TEM) or bla(SHV) genes were not detected in any of the strains. Aeromonas spp. carrying integrons and other resistance genes are present in farm-raised fish and sediments even though no antibiotics were licensed for use in Australian aquaculture at the time of the study.
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Affiliation(s)
- O L Ndi
- Sansom Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.
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31
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Stokes HW, Gillings MR. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 2011; 35:790-819. [PMID: 21517914 DOI: 10.1111/j.1574-6976.2011.00273.x] [Citation(s) in RCA: 369] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.
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Affiliation(s)
- Hatch W Stokes
- The i3 Institute, University of Technology, Broadway 2007, Sydney, NSW, Australia.
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Okeke IN, Wallace-Gadsden F, Simons HR, Matthews N, Labar AS, Hwang J, Wain J. Multi-locus sequence typing of enteroaggregative Escherichia coli isolates from Nigerian children uncovers multiple lineages. PLoS One 2010; 5:e14093. [PMID: 21124856 PMCID: PMC2990770 DOI: 10.1371/journal.pone.0014093] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 11/04/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Enteroaggregative Escherichia coli (EAEC) are defined by their stacked-brick adherence pattern to human epithelial cells. There is no all-encompassing genetic marker for EAEC. The category is commonly implicated in diarrhea but research is hampered by perplexing heterogeneity. METHODOLOGY/PRINCIPAL FINDINGS To identify key EAEC lineages, we applied multilocus sequence typing to 126 E. coli isolates from a Nigerian case-control study that showed aggregative adherence in the HEp-2 adherence assay, and 24 other EAEC strains from diverse locations. EAEC largely belonged to the A, B1 and D phylogenetic groups and only 7 (4.6%) isolates were in the B2 cluster. As many as 96 sequence types (STs) were identified but 60 (40%) of the EAEC strains belong to or are double locus variants of STs 10, 31, and 394. The remainder did not belong to predominant complexes. The most common ST complex, with predicted ancestor ST10, included 32 (21.3%) of the isolates. Significant age-related distribution suggests that weaned children in Nigeria are at risk for diarrhea from of ST10-complex EAEC. Phylogenetic group D EAEC strains, predominantly from ST31- and ST394 complexes, represented 38 (25.3%) of all isolates, include genome-sequenced strain 042, and possessed conserved chromosomal loci. CONCLUSIONS/SIGNIFICANCE We have developed a molecular phylogenetic framework, which demonstrates that although grouped by a shared phenotype, the category of 'EAEC' encompasses multiple pathogenic lineages. Principal among isolates from Nigeria were ST10-complex EAEC that were associated with diarrhea in children over one year and ECOR D strains that share horizontally acquired loci.
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Affiliation(s)
- Iruka N Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA.
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33
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Dawes FE, Kuzevski A, Bettelheim KA, Hornitzky MA, Djordjevic SP, Walker MJ. Distribution of class 1 integrons with IS26-mediated deletions in their 3'-conserved segments in Escherichia coli of human and animal origin. PLoS One 2010; 5:e12754. [PMID: 20856797 PMCID: PMC2939871 DOI: 10.1371/journal.pone.0012754] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 08/17/2010] [Indexed: 11/18/2022] Open
Abstract
Class 1 integrons play a role in the emergence of multi-resistant bacteria by facilitating the recruitment of gene cassettes encoding antibiotic resistance genes. 512 E. coli strains sourced from humans (n = 202), animals (n = 304) and the environment (n = 6) were screened for the presence of the intI1 gene. In 31/79 integron positive E. coli strains, the gene cassette regions could not be PCR amplified using standard primers. DNA sequence analysis of 6 serologically diverse strains revealed atypical integrons harboured the dfrA5 cassette gene and only 24 bp of the integron 3′-conserved segment (CS) remained, due to the insertion of IS26. PCR targeting intI1 and IS26 followed by restriction fragment length polymorphism (RFLP) analysis identified the integron-dfrA5-IS26 element in 27 E. coli strains of bovine origin and 4 strains of human origin. Southern hybridization and transformation studies revealed the integron-dfrA5-IS26 gene arrangement was either chromosomally located or plasmid borne. Plasmid location in 4/9 E. coli strains and PCR linkage of Tn21 transposition genes with the intI1 gene in 20/31 strains, suggests this element is readily disseminated by horizontal transfer.
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Affiliation(s)
- Fay E. Dawes
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Alexander Kuzevski
- Microbiological Diagnostic Unit, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Karl A. Bettelheim
- Microbiological Diagnostic Unit, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael A. Hornitzky
- Microbiology and Immunology Section, Industry and Investment NSW, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Steven P. Djordjevic
- Microbiology and Immunology Section, Industry and Investment NSW, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
- The ithree Institute, University of Technology, Sydney, New South Wales, Australia
| | - Mark J. Walker
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Léon G, Quiroga C, Centrón D, Roy PH. Diversity and strength of internal outward-oriented promoters in group IIC-attC introns. Nucleic Acids Res 2010; 38:8196-207. [PMID: 20716518 PMCID: PMC3001079 DOI: 10.1093/nar/gkq709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Integrons are genetic elements that incorporate mobile gene cassettes by site-specific recombination and express them as an operon from a promoter (Pc) located upstream of the cassette insertion site. Most gene cassettes found in integrons contain only one gene followed by an attC recombination site. We have recently shown that a specific lineage of group IIC introns, named group IIC-attC introns, inserts into the bottom strand sequence of attC sites. Here, we show that S.ma.I2, a group IIC-attC intron inserted in an integron cassette array of Serratia marcescens, impedes transcription from Pc while allowing expression of the following antibiotic resistance cassette using an internal outward-oriented promoter (Pout). Bioinformatic analyses indicate that one or two putative Pout, which have sequence similarities with the Escherichia coli consensus promoters, are conserved in most group IIC-attC intron sequences. We show that Pout with different versions of the −35 and −10 sequences are functionally active in expressing a promoterless chloramphenicol acetyltransferase (cat) reporter gene in E. coli. Pout in group IIC-attC introns may therefore play a role in the expression of one or more gene cassettes whose transcription from Pc would otherwise be impeded by insertion of the intron.
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Affiliation(s)
- Grégory Léon
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Québec, Canada
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35
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Johansson C, Boukharta L, Eriksson J, Aqvist J, Sundström L. Mutagenesis and homology modeling of the Tn21 integron integrase IntI1. Biochemistry 2010; 48:1743-53. [PMID: 19199791 DOI: 10.1021/bi8020235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horizontal DNA transfer between bacteria is widespread and a major cause of antibiotic resistance. For logistic reasons, single or combined genes are shuttled between vectors such as plasmids and bacterial chromosomes. Special elements termed integrons operate in such shuttling and are therefore vital for horizontal gene transfer. Shorter elements carrying genes, cassettes, are integrated in the integrons, or excised from them, by virtue of a recombination site, attC, positioned in the 3' end of each unit. It is a remarkable and possibly restricting elementary feature of attC that it must be single-stranded while the partner target site, attI, may be double-stranded. The integron integrases belong to the tyrosine recombinase family, and this work reports mutations of the integrase IntI1 from transposon Tn21, chosen within a well-conserved region characteristic of the integron integrases. The mutated proteins were tested for binding to a bottom strand of an attC substrate, by using an electrophoresis mobility shift assay. To aid in interpreting the results, a homology model was constructed on the basis of the crystal structure of integron integrase VchIntIA from Vibrio cholerae bound to its cognate attC substrate VCRbs. The local stability and hydrogen bonding network of key domains of the modeled structure were further examined using molecular dynamics simulations. The homology model allowed us to interpret the roles of several amino acid residues, four of which were clearly binding assay responsive upon mutagenesis. Notably, we also observed features indicating that IntI1 may be more prone to base-specific contacts with VCRbs than VchIntIA.
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Affiliation(s)
- Carolina Johansson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 751 23 Uppsala, Sweden
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Philip DS, Sarovich DS, Pemberton JM. Complete sequence and analysis of the stability functions of pPSX, a vector that allows stable cloning and expression of Streptomycete genes in Escherichia coli K12. Plasmid 2009; 62:39-43. [PMID: 19303899 DOI: 10.1016/j.plasmid.2009.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 03/05/2009] [Accepted: 03/11/2009] [Indexed: 10/21/2022]
Abstract
The broad host range, cloning and expression vector pPSX has been completely sequenced and analysed. pPSX is 14.7kb in length and contains the fusion of two continuous segments of the parental 34kb, IncW plasmid pR388. pPSX appears to have retained at least three sets of gene/s which contribute in different ways to plasmid stability. The first of these parB, is a known participant in the partitioning of low-copy number plasmids. While the adjoining gene, orf35, has high homology with kfrA, a putative plasmid nucleoid organiser that is often associated with the ParAB family of proteins. The second set of genes; orfs18, 19, 20, whose exact functions are not clear, have homology to the stability operons of both IncW and IncN plasmids. The third is the resolvase, resP, which may resolve plasmid multimers that can lead to plasmid instability. pPSX is a small, stable cloning vector good for cloning and expression of a wide range of genes, including those from streptomycetes.
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Affiliation(s)
- Daniel S Philip
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
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Labbate M, Case RJ, Stokes HW. The integron/gene cassette system: an active player in bacterial adaptation. Methods Mol Biol 2009; 532:103-25. [PMID: 19271181 DOI: 10.1007/978-1-60327-853-9_6] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high, suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.
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Affiliation(s)
- Maurizio Labbate
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrob Agents Chemother 2008; 53:696-702. [PMID: 19064898 DOI: 10.1128/aac.00652-07] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalences of three sulfonamide resistance genes, sul1, sul2, and sul3 and sulfachloropyridazine (SCP) resistance were determined in bacteria isolated from manured agricultural clay soils and slurry samples in the United Kingdom over a 2-year period. Slurry from tylosin-fed pigs amended with SCP and oxytetracycline was used for manuring. Isolates positive for sul genes were further screened for the presence of class 1 and 2 integrons. Phenotypic resistance to SCP was significantly higher in isolates from pig slurry and postapplication soil than in those from preapplication soil. Of 531 isolates, 23% carried sul1, 18% sul2, and 9% sul3 only. Two percent of isolates contained all three sul genes. Class 1 and class 2 integrons were identified in 5% and 11.7%, respectively, of sul-positive isolates. In previous reports, sul1 was linked to class 1 integrons, but in this study only 8% of sul1-positive isolates carried the intI1 gene. Sulfonamide-resistant pathogens, including Shigella flexneri, Aerococcus spp., and Acinetobacter baumannii, were identified in slurry-amended soil and soil leachate, suggesting a potential environmental reservoir. Sulfonamide resistance in Psychrobacter, Enterococcus, and Bacillus spp. is reported for the first time, and this study also provides the first description of the genotypes sul1, sul2, and sul3 outside the Enterobacteriaceae and in the soil environment.
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Bay DC, Rommens KL, Turner RJ. Small multidrug resistance proteins: A multidrug transporter family that continues to grow. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1814-38. [DOI: 10.1016/j.bbamem.2007.08.015] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 08/07/2007] [Accepted: 08/14/2007] [Indexed: 11/17/2022]
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40
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Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother 2008; 52:1472-80. [PMID: 18268088 PMCID: PMC2292564 DOI: 10.1128/aac.00982-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA sequence analysis of five IncW plasmids (R388, pSa, R7K, pIE321, and pIE522) demonstrated that they share a considerable portion of their genomes and allowed us to define the IncW backbone. Among these plasmids, the backbone is stable and seems to have diverged recently, since the overall identity among its members is higher than 95%. The only gene in which significant variation was observed was trwA; the changes in the coding sequence correlated with parallel changes in the corresponding TrwA binding sites at oriT, suggesting a functional connection between both sets of changes. The present IncW plasmid diversity is shaped by the acquisition of antibiotic resistance genes as a consequence of the pressure exerted by antibiotic usage. Sequence comparisons pinpointed the insertion events that differentiated the five plasmids analyzed. Of greatest interest is that a single acquisition of a class I integron platform, into which different gene cassettes were later incorporated, gave rise to plasmids R388, pIE522, and pSa, while plasmids R7K and pIE321 do not contain the integron platform and arose in the antibiotic world because of the insertion of several antibiotic resistance transposons.
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Navon-Venezia S, Chmelnitsky I, Leavitt A, Carmeli Y. Dissemination of the CTX-M-25 family -lactamases among Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae and identification of the novel enzyme CTX-M-41 in Proteus mirabilis in Israel. J Antimicrob Chemother 2008; 62:289-95. [DOI: 10.1093/jac/dkn182] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Valderas MW, Bourne PC, Barrow WW. Genetic basis for sulfonamide resistance in Bacillus anthracis. Microb Drug Resist 2007; 13:11-20. [PMID: 17536929 DOI: 10.1089/mdr.2006.9992] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural resistance of field strains of Bacillus anthracis to drugs from the sulfonamide class of antimicrobials that act by inhibiting dihydropteroate synthase (DHPS) has been reported. Though the structure of B. anthracis DHPS has been determined, its connection to the apparent intrinsic sulfonamide resistance of the bacterium has not been established. The aim of this study was to determine if a connection exists between DHPS and the observed sulfonamide resistance of B. anthracis. Microdilution broth assays verified that B. anthracis Sterne is highly resistant to a variety of sulfonamides with minimum inhibitory concentrations (MICs) exceeding 1250 microg/ml. A putative gene encoding DHPS (folP) was amplified from B. anthracis Sterne chromosomal DNA by polymerase chain reaction (PCR) and cloned. Sequence comparisons showed 100% identity with DHPSs from published genome sequences for various strains of B. anthracis. Additionally, expression of folP in B. anthracis Sterne was confirmed. Functionality of the B. anthracis DHPS was confirmed by complementation of an Escherichia coli folP deletion mutant as well as a standard enzyme assay. Concomitant transfer of high level sulfonamide resistance to this mutant along with increased sulfonamide IC(50)values for purified B. anthracis DHPS links DHPS to sulfonamide resistance in B. anthracis. These findings lay the groundwork that will aid future development of antimicrobics that target DHPS to treat anthrax infections.
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Affiliation(s)
- Michelle Wright Valderas
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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Hall RM, Collis CM. Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons. Drug Resist Updat 2007; 1:109-19. [PMID: 16904397 DOI: 10.1016/s1368-7646(98)80026-5] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/1998] [Revised: 02/10/1998] [Accepted: 02/20/1998] [Indexed: 11/24/2022]
Abstract
Resistance of gram-negative organisms to antibiotics such as beta-lactams, aminoglycosides, trimethoprim and chloramphenicol is caused by many different acquired genes, and a substantial proportion of these are part of small mobile elements known as gene cassettes. A gene cassette consists of the gene and a downstream sequence, known as a 59-base element (59-be), that acts as a specific recombination site. Gene cassettes can move into or out of a specific receptor site (attl site) in a companion element called an integron, and integration or excision of the cassettes is catalysed by a site-specific recombinase (Intl) that is encoded by the integron. At present count there are 40 different cassette-associated resistance genes and three distinct classes of integron, each encoding a distinct Intl integrase. The same cassettes are found in all three classes of integron, indicating that cassettes can move freely between different integrons. Integrons belonging to class I often contain a further antibiotic resistance gene, sull, conferring resistance to sulphonamides. The sull gene is found in a conserved region (3'-CS) that is not present in all members of this class. Class I integrons of the sull type are most prevalent in clinical isolates and have been found in many different organisms. Even though most of them are defective transposon derivatives, having lost at least one of the transposition genes, they are none the less translocatable and consequently found in many different locations. The transposon Tn7 is the best known representative of class 2 integrons, and Tn7 and relatives are also found in many different species.
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Affiliation(s)
- R M Hall
- CSIRO Molecular Science, Sydney Laboratory, New South Wales, Australia.
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44
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O'Mahony R, Quinn T, Drudy D, Walsh C, Whyte P, Mattar S, Fanning S. Antimicrobial resistance in nontyphoidal Salmonella from food sources in Colombia: evidence for an unusual plasmid-localized class 1 integron in serotypes Typhimurium and Anatum. Microb Drug Resist 2007; 12:269-77. [PMID: 17227213 DOI: 10.1089/mdr.2006.12.269] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seventy-two isolates representing 18 serotypes recovered from various food samples collected in Colombia were tested for antimicrobial susceptibilities. The collection was further characterized for extended-spectrum cephalosporin, aminoglycoside, and tetracycline resistance markers. Multidrug resistant (MDR) isolates were further investigated for class 1 integrons and were evaluated for the presence of conjugative plasmids along with a determination of the incompatibility group by polymerase chain reaction (PCR). Antibiogram analysis showed that the incidence rate of ceftiofur resistance was moderately high (15%). A similar level of resistance to neomycin and oxytetracycline (11% and 10%, respectively) was also observed. There was a high prevalence of gene cassettes as part of one or more class 1 integrons (61%), many of which contained determinants that contributed to the resistance profile. Class 1 integrons identified in MDR Salmonella enterica serotypes Typhimurium and Anatum isolates were characterized. Sequencing identified several incomplete open reading frames (ORFs) as part of a gene cassette (bla-( imp-13 ), dfr7, blr1088, and aac8) along with a complete gene cassette (bla-(oxa2)) in each case. A mosaic of gene cassettes was identical in the two Salmonella serotypes. These integrons were located to a conjugative replicon. Plasmid profiling and incompatibility typing identified three plasmids belonging to Inc groups A/C, P, and W. Our study highlights the role of integrons, contributing to a MDR phenotype that is capable of dissemination to other bacteria.
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Affiliation(s)
- Rebecca O'Mahony
- Centre for Food Safety, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland
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Johansson C, Samskog J, Sundström L, Wadensten H, Björkesten L, Flensburg J. Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics 2006; 6:4475-85. [PMID: 16858737 DOI: 10.1002/pmic.200500921] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The study of changes in protein levels between samples derived from cells representing different biological conditions is a key to the understanding of cellular function. There are two main methods available that allow both for global scanning for significantly varying proteins and targeted profiling of proteins of interest. One method is based on 2-D gel electrophoresis and image analysis of labelled proteins. The other method is based on LC-MS/MS analysis of either unlabelled peptides or peptides derived from isotopically labelled proteins or peptides. In this study, the non-labelling approach was used involving a new software, DeCyder MS Differential Analysis Software (DeCyder MS) intended for automated detection and relative quantitation of unlabelled peptides in LC-MS/MS data. Total protein extracts of E. coli strains expressing varying levels of dihydrofolate reductase and integron integrase were digested with trypsin and analyzed using a nanoscale liquid chromatography system, Ettan MDLC, online connected to an LTQTM linear ion-trap mass spectrometer fitted with a nanospray interface. Acquired MS data were subjected to DeCyder MS analysis where 2-D representations of the peptide patterns from individual LC-MS/MS analyses were matched and compared. This approach to unlabelled quantitative analysis of the E. coli proteome resulted in relative protein abundances that were in good agreement with results obtained from traditional methods for measuring protein levels.
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Affiliation(s)
- Carolina Johansson
- Uppsala University, Department of Medical Biochemistry and Microbiology (IMBlm), and GE Healthcare, Biosciences AB, Sweden
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Walsh C, Duffy G, O'Mahony R, Fanning S, Blair IS, McDowell DA. Antimicrobial resistance in Irish isolates of verocytotoxigenic Escherichia coli (E. coli)—VTEC. Int J Food Microbiol 2006; 109:173-8. [PMID: 16626832 DOI: 10.1016/j.ijfoodmicro.2006.01.023] [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] [Received: 07/18/2005] [Revised: 11/24/2005] [Accepted: 01/03/2006] [Indexed: 11/19/2022]
Abstract
This study compared the antimicrobial resistance profiles of Escherichia coli O157:H7 isolates (n=257) recovered from bovine hides, minced beef and human clinical samples in Ireland, to those profiles of a range of Irish non-O157 E. coli (O111 and O26) isolates (n=31) from a variety of clinical and veterinary sources. Four multi-drug resistant (MDR) E. coli O157:H7 food isolates were identified, with resistance to 10 (1 isolate), 6 (1 isolate) and 4 (2 isolates) antimicrobial agents, respectively. Two of these isolates (resistant to 7 and 4 antimicrobial classes) were characterised further by molecular methods and found to contain class 1 integrons along with a beta-lactamase-encoding tem-1 gene. Transfer of antimicrobial resistance (ampicillin, streptomycin and sulphonamides), the tem-1 gene and markers (int1, qacEDelta1, sul1) characteristic of class 1 integrons were evident in one MDR isolate (resistant to 4 antimicrobial classes) when conjugation and transformation experiments were performed. A clinical isolate and a veterinary isolate of the O111 serotype were MDR and resistant to 4 and 3 antimicrobial classes, respectively. These data suggest that the prevalence of antimicrobial resistance among the three VTEC serotypes examined in this study is low. However, these organisms may become a public health risk should they enter the food chain.
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Affiliation(s)
- C Walsh
- The National Food Centre, Teagasc, Dunsinea, Ashtown, Dublin 15, Ireland
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Fonseca EL, Vieira VV, Cipriano R, Vicente ACP. Class 1 integrons in Pseudomonas aeruginosa isolates from clinical settings in Amazon region, Brazil. ACTA ACUST UNITED AC 2006; 44:303-9. [PMID: 15907453 DOI: 10.1016/j.femsim.2005.01.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 12/23/2004] [Accepted: 01/03/2005] [Indexed: 10/25/2022]
Abstract
A hundred and six Pseudomonas aeruginosa isolates from clinical cases were screened using PCR for the presence of integrons and associated resistance gene cassettes. Forty-four isolates harboured class 1 integrons (41.5%), of which 29 isolates (66%) also carried gene cassettes. The aacA gene was most frequently found within class 1 integrons (69%), followed by blaOXA family genes (52%). From class 1 integron-positive strains, we detected a total of 15 isolates (34%) carrying no gene cassettes. Restriction fragment-length polymorphism analysis of the integrons variable region revealed some identical structures, as well as distinct profiles indicating heterogeneity among these cassette regions. Multiresistance was observed in 71% of isolates, nevertheless no strong correlation was observed between integron presence and multiresistance. This is the first report showing class 1 integron prevalence and gene cassette content in P. aeruginosa isolates from clinical settings in the Brazilian Amazon.
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Affiliation(s)
- Erica L Fonseca
- Department of Genetics, Instituto Oswaldo Cruz, FIOCRUZ, Avenida Brazil 4365, P.O. Box 926, CEP 21045-100, Rio de Janeiro, Brazil
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Jones LA, McIver CJ, Kim MJ, Rawlinson WD, White PA. The aadB gene cassette is associated with blaSHV genes in Klebsiella species producing extended-spectrum beta-lactamases. Antimicrob Agents Chemother 2005; 49:794-7. [PMID: 15673771 PMCID: PMC547205 DOI: 10.1128/aac.49.2.794-797.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons were detected in 37 (72.5%) of 51 Klebsiella spp. producing extended-spectrum beta-lactamases by PCR with primers that targeted integrase genes and cassette regions. PCR and amplicon sequencing of the cassette regions revealed aadB and aadA2 gene cassettes that confer resistance to a range of aminoglycosides. aadB was associated with a class 1 integron on a 28-kb plasmid, pES1, that also contained bla(SHV-12) and IS26.
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Affiliation(s)
- Louisa A Jones
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney 2052, Australia
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Johansson C, Kamali-Moghaddam M, Sundström L. Integron integrase binds to bulged hairpin DNA. Nucleic Acids Res 2004; 32:4033-43. [PMID: 15289577 PMCID: PMC506814 DOI: 10.1093/nar/gkh730] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene cassettes are short, monogenic DNA elements that translocate between integrons through site-specific excision and integration. These events require that an integron-coded tyrosine recombinase forms a reactive complex with two sites, at least one of which belongs to the attC class. An attC site can be divided into two pairs of short repeats flanking a palindromic central region. The nucleotide sequence of attC among different cassettes varies extensively, implying that the site contains a structural recognition determinant with low sequence constraints. Oligonucleotides representing many different sequence modifications in either strand of the site were examined for integrase binding by using an electrophoresis mobility shift assay. The inner repeats, a central triplet and two single-nucleotide asymmetries in the site had the strongest influence on binding strength and strand choice. Our data show that the recombinase binds to a bulged hairpin in attC and that the hairpin distortion due to bulging could define the appropriate orientation of the otherwise symmetrical site. This is consistent with the strong bias for binding of recombinase to the bottom-strand oligonucleotides in vitro. Moreover, it was observed that the mobility-shifted complexes persisted under protein-denaturing assay conditions, indicating that a covalent link is indeed formed between integrase and DNA. Upon substitution of the presumed DNA-attacking residue, Y312, with a phenylalanine, DNA binding remained but there was no covalent linkage.
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Affiliation(s)
- Carolina Johansson
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, Box 582, Biomedical Center, S-751 23 Uppsala, Sweden
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Iversen J, Sandvang D, Srijan A, Cam PD, Dalsgaard A. Characterization of antimicrobial resistance, plasmids, and gene cassettes in Shigella spp. from patients in vietnam. Microb Drug Resist 2004; 9 Suppl 1:S17-24. [PMID: 14633363 DOI: 10.1089/107662903322541856] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The objective of the study was to investigate antimicrobial resistance, plasmids and class 1 integrons in 150 Shigella strains isolated from patients with diarrhea in Vietnam. Most isolates were resistant to the majority of antimicrobial agents used for treatment in the isolation areas and 90% were resistant to three or more antibiotics. A total of 20 strains yielded class 1 integrons, which harbored oxa1, dfrA, orfF, and aadA gene cassettes. The most common gene cassette, aadA2, was always located closest to the 3' conserved segment of the integrons and oxa1 and dfrA closest to the 5' end. Plasmid profiles of the 20 class 1 integron-positive strains all contained more than one plasmid, and 14 different profiles were found. No correlation was found between species, antibiograms, plasmid profiles, or presence of class 1 integrons. Conjugation resulted in 25 transconjugants, which all were resistant to four or more antimicrobial agents and all harbored at least one plasmid (>60 kb). Class 1 integrons were detected in 64% of the transconjugants. Phenotypic resistance pattern and plasmid profiles of the transconjugants seemed independent of the presence of an integron. Class 1 integrons seemed of less importance in phenotypic antibiograms and in transfer of resistance genes than conjugative plasmids.
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Affiliation(s)
- J Iversen
- Department of Veterinary Microbiology, Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Copenhagen, Denmark.
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