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Pan H, Guo X, Pan Z, Wang R, Tian B, Li H. Fork PCR: a universal and efficient genome-walking tool. Front Microbiol 2023; 14:1265580. [PMID: 37808312 PMCID: PMC10556450 DOI: 10.3389/fmicb.2023.1265580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
The reported genome-walking methods still suffer from some deficiencies, such as cumbersome experimental steps, short target amplicon, or deep background. Here, a simple and practical fork PCR was proposed for genome-walking. The fork PCR employs a fork primer set of three random oligomers to implement walking task. In primary fork PCR, the low-stringency amplification cycle mediates the random binding of primary fork primer to some places on genome, producing a batch of single-stranded DNAs. In the subsequent high-stringency amplification, the target single-strand is processed into double-strand by the site-specific primer, but a non-target single-stranded DNA cannot be processed by any primer. As a result, only the target DNA can be exponentially amplified in the remaining high-stringency cycles. Secondary/tertiary nested fork PCR(s) further magnifies the amplification difference between the both DNAs by selectively enriching target DNA. The applicability of fork PCR was validated by walking several gene loci. The fork PCR could be a perspective substitution for the existing genome-walking schemes.
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Affiliation(s)
- Hao Pan
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Rongrong Wang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Bingkun Tian
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Haixing Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
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Fadare FT, Fadare TO, Okoh AI. Prevalence, molecular characterization of integrons and its associated gene cassettes in Klebsiella pneumoniae and K. oxytoca recovered from diverse environmental matrices. Sci Rep 2023; 13:14373. [PMID: 37658232 PMCID: PMC10474106 DOI: 10.1038/s41598-023-41591-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
The high prevalence of infections arising from Klebsiella species is related to their ability to acquire and disseminate exogenous genes associated with mobile genetic elements such as integrons. We assessed the prevalence, diversity, and associated gene cassettes (GCs) of integrons in Klebsiella species. The isolates recovered from wastewater and hospital effluents, rivers, and animal droppings were identified using the conventional Polymerase Chain Reaction (PCR) with primers targeting the gryA, pehX, and 16S-23S genes. The antimicrobial resistance profile and the Extended-Spectrum and Metallo β-lactamases production were carried out using standard microbiological techniques. PCR, DNA sequencing analyses, and Restriction Fragment Length Polymorphism were used to characterize the integrons and their associated GCs. Furthermore, the genotypic relationships between the different isolated K. pneumoniae were determined using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR. About 98% (51/52) of the confirmed isolates harboured an integrase gene, with 80% intI1, while the remaining 20% concurrently harboured intI1 and intI2, with no intI3 observed. About 78% (40/51) of the bacterial strains were positive for a promoter, the P2R2, investigated, while 80% (41/51) harboured at least one of the qacEΔ1 and sul1. Three different GCs arrangements identified were aac(6')-Ib, aadA1-dfrA1, and dfrA1-sat2. At a similarity index of 60%, the ERIC-PCR fingerprints generated were categorized into nine clusters. Our study is the first to reveal the features of integrons in Klebsiella spp. recovered from environmental sources in the Eastern Cape Province, South Africa. We conclude that the organisms' sources are repositories of integrons harbouring various gene cassettes, which can be readily mobilized to other microorganisms in similar or varied niches.
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Affiliation(s)
- Folake Temitope Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa.
| | - Taiwo Olawole Fadare
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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Mohamed SA, Ardiyati T, Rifa'i M, Widodo. Detection of class 1 integron-associated gene cassettes and tetracycline resistance genes in Escherichia coli isolated from ready to eat vegetables. Ann Med Surg (Lond) 2020; 55:327-331. [PMID: 32566218 PMCID: PMC7296334 DOI: 10.1016/j.amsu.2020.04.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/26/2020] [Accepted: 04/30/2020] [Indexed: 11/03/2022] Open
Abstract
Background Ready to eat (RTE) vegetables are easily accessible healthy foods that are commonly consumed globally, including in Indonesia. However, these RTE vegetables contain potential contamination from pathogens and multi-drug resistant bacteria. Therefore, in the present study, we examined the presence of tetracycline-resistant E. coli (TRE) isolates from RTE vegetables. Methods Susceptibility to antimicrobial agents was determined using the Kirby-Bauer disc diffusion method. Characterisation of antibiotic resistant genes was performed using PCR and sequencing of tetracycline resistant gene, integron and gene cassette from the TRE isolates. Results The isolates collected in this study were resistant not only to tetracycline, but also to streptomycin. Some isolates also displayed resistance to kanamycin (77.8%), chloramphenicol (11.1%), and ciprofloxacin (5.6%). All of the isolates contained integrons (intI1) and the tetA gene; tetB was not detected in our study. Further analysis showed that some isolates (38.8%) contained the dfrA7 gene cassette, which encodes dihydrofolate reductase, which is responsible for resistance to trimethoprim. Of all the isolates that presented integrons, 11 isolates (61.1%) did not carry gene cassettes. These empty integrons have the potential to convert themselves rapidly into multigraviton strains. Conclusions TRE isolates contain the tetA gene and integron 1. Only 38.8% of the isolates that have been identified contain the dfrA7 gene cassette, which is responsible for trimethoprim antibiotic resistance. Further identification of genes conferring resistance to other antibiotics is necessary to better characterise antibiotic resistance. This study was obtained Tetracycline Resistant E. coli (TRE) isolate. The isolate was also resistant to streptomycin. The isolate contains integrons (intI1) and the tetA gene.
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Affiliation(s)
- Saad A Mohamed
- Biology Department, Faculty of Sciences, Bani Walid University, Libya.,Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Tri Ardiyati
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Muhaimin Rifa'i
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Widodo
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
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Kaushik M, Kumar S, Kapoor RK, Gulati P. Integrons and antibiotic resistance genes in water-borne pathogens: threat detection and risk assessment. J Med Microbiol 2019; 68:679-692. [DOI: 10.1099/jmm.0.000972] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Megha Kaushik
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Rajeev Kr. Kapoor
- Enzyme Biotechnology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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Mazurek J, Bok E, Baldy-Chudzik K. Complexity of Antibiotic Resistance in Commensal Escherichia coli Derived from Pigs from an Intensive-Production Farm. Microbes Environ 2018; 33:242-248. [PMID: 30210140 PMCID: PMC6167118 DOI: 10.1264/jsme2.me17041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antibiotics in animal husbandry are used to maintain welfare, but lead to the generation of resistant strains. We analyzed commensal multidrug-resistant Escherichia coli from pigs at the beginning and end of the production cycle in a farm with a farrow-to-finish system in order to investigate whether clonal spread or horizontal gene transfer constitutes the main factor responsible for the prevalence of resistance in this environment. Among 380 isolates, 56 multidrug-resistant E. coli with a similar resistant phenotype were selected for more detailed investigations including a genomic similarity analysis and the detection of mobile elements. Isolates carried blaTEM-1, aadA1, strA/B, tetA, tetB, tetC, dfrA1, dfrA5, dfrA7, dfrA12, sul1, sul2, sul3, and qnrS resistance genes, with the common co-occurrence of genes encoding the same resistance phenotype. A pulse-field gel electrophoresis analysis of the genomic similarity of multidrug-resistant E. coli showed ≤65% similarity of most of the tested strains and did not reveal a dominant clone responsible for the prevalence of resistance. Class 1 and 2 integrons and transposons 7 and 21 were detected among mobile elements; however, some were truncated. Plasmids were represented by 11 different incompatibility groups (K, FIB, I1, FIIA, FIC, FIA, Y, P, HI1, B/O, and T). Genetic resistance traits were unevenly spread in the clonal groups and suggested the major rearrangement of genetic material by horizontal gene transfer. The present results revealed that in commensal E. coli from pigs in a homogeneous farm environment, there was no dominant clone responsible for the spread of resistance and persistence in the population.
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Affiliation(s)
- Justyna Mazurek
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra
| | - Ewa Bok
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra
| | - Katarzyna Baldy-Chudzik
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra
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Yu T, Jiang X, Liang Y, Zhu Y, Tian J, Ying H, Wang X, Shi L. Characterization and Horizontal Transfer of Antimicrobial Resistance Genes and Integrons in Bacteria Isolated from Cooked Meat Products in China. J Food Prot 2017; 80:2048-2055. [PMID: 29148877 DOI: 10.4315/0362-028x.jfp-17-119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this study was to investigate antimicrobial resistance and the presence and transferability of corresponding resistance genes and integrons in bacteria isolated from cooked meat samples in the People's Republic of China. A total of 150 isolates (22 species belonging to 15 genera) were isolated from 49 samples. Resistance of these isolates to antimicrobials was commonly observed; 42.7, 36.0, and 25.3% of the isolates were resistant to tetracycline, streptomycin, and ampicillin, respectively. Multidrug resistance was observed in 41 (27.3%) of the isolates. Sixteen resistance genes, i.e., blaTEM-1 and blaCTX-M-14 (β-lactams), aac(3)-IIa (gentamicin), strA and strB (streptomycin), qnrB and qnrS (fluoroquinolone), sul1, sul2, and sul3 (sulfamethoxazole), cat1 and cat2 (chloramphenicol), and tetM, tetA, tetS, and tetB (tetracycline), were found in 54 isolates. One isolate of Pseudomonas putida carried qnrB, and sequence analysis of the PCR product revealed 96% identity to qnrB2. The qnr genes were found coresiding and were cotransferred with bla genes in two isolates. Twelve isolates were positive for the class 1 integrase gene, and four isolates carried the class 2 integrase gene. However, no class 3 integrase gene was detected. One isolate of Proteus mirabilis carried dfrA32-ereA-aadA2, and this unusual array could be transferred to Escherichia coli. Nonclassic class 1 integrons lacking qacEΔ1 and sul1 genes were found in 2 of the 12 intI1-positive isolates. Our results revealed the presence of multidrug-resistant bacteria in cooked meats and the presence and transferability of resistance genes in some isolates, suggesting that cooked meat products may act as reservoirs of drug-resistant bacteria and may facilitate the spread of resistance genes.
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Affiliation(s)
- Tao Yu
- 1 College of Life Science and Technology and
| | - Xiaobing Jiang
- 2 College of Life Sciences, Henan Normal University, Xinxiang 453007, People's Republic of China; and
| | - Yu Liang
- 3 College of Chemistry and Chemical Engineering, Xinxiang University, Xinxiang 453003, People's Republic of China
| | - Yanping Zhu
- 1 College of Life Science and Technology and
| | - Jinhe Tian
- 1 College of Life Science and Technology and
| | - Hao Ying
- 1 College of Life Science and Technology and
| | | | - Lei Shi
- 4 Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, People's Republic of China
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Luk-In S, Pulsrikarn C, Bangtrakulnonth A, Chatsuwan T, Kulwichit W. Occurrence of a novel class 1 integron harboring qnrVC4 in Salmonella Rissen. Diagn Microbiol Infect Dis 2017; 88:282-286. [PMID: 28427794 DOI: 10.1016/j.diagmicrobio.2017.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 11/18/2022]
Abstract
We described qnrVC4 in S. Rissen 166ANSS50, a swine isolate, which was detected in the study on quinolone resistance mechanisms of nontyphoidal Salmonella in Thailand. The isolate was found to harbor a ̴17-kb non-conjugative plasmid carrying qnrVC4 within 8.91kb of a novel In4-like class 1 integron (In805). It contained the multi-drug resistance gene cassettes of qnrVC4-qacH4-aacA4-cmlA7-blaOXA-10-aadA1-dfrA14 and unusual 3'-CS of mobC-IS6100. This 1014-bp qnrVC4 cassette included with promoter (PqnrVC4: -35 TTGAGA and -10 TAGTCT) showed high homology with qnrVC4 in superintegron of V. cholerae O1 El Tor. The qnrVC4 recombinant plasmid resulted in 4-, 8-, and 16-fold increase in the MICs of nalidixic acid (2-8μg/mL), ciprofloxacin (0.015-0.125μg/mL), and norfloxacin (0.03-0.5μg/mL), respectively. In addition, the backbone plasmid revealed a novel replicon belonging to the MOBQ1 group from the broad-host-range mobilisable IncQ1 plasmid RFS1010 based on relaxase sequences. This is the first known report of qnrVC in Salmonella enterica. The qnrVC4 gene was co-transferred with other resistance genes via a novel plasmid-borne In805. This allowed the spread of this resistance gene to Enterobacteriaceae.
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Affiliation(s)
- Sirirat Luk-In
- Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Chaiwat Pulsrikarn
- World Health Organization National Salmonella and Shigella Centre, Nonthaburi, Thailand
| | - Aroon Bangtrakulnonth
- World Health Organization National Salmonella and Shigella Centre, Nonthaburi, Thailand
| | | | - Wanla Kulwichit
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Increase in the Prevalence of Resistance Determinants to Trimethoprim/Sulfamethoxazole in Clinical Stenotrophomonas maltophilia Isolates in China. PLoS One 2016; 11:e0157693. [PMID: 27310255 PMCID: PMC4911037 DOI: 10.1371/journal.pone.0157693] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/02/2016] [Indexed: 12/17/2022] Open
Abstract
Aims This study was carried to reveal the genetic mechanisms of trimethoprim/sulfamethoxazole (SXT) resistance. Methods Among 300 clinical Stenotrophomonas maltophilia isolates from China, resistance determinants such as sul and dfrA genes, integrons and transposase were examined using PCR, DNA sequencing and thermal asymmetric interlaced PCR (TAIL-PCR). Data were analyzed using SPSS 20.0. Results Of the 300 isolates, 116 (38.7%) were resistant to SXT. An alarming trend of increased resistance to SXT were found over the 10-year period. The positive rates of sul and class 1 integrase (intI1) increased gradually with the development of SXT resistance over the 10-year period. Multiple logistic regression analyses indicated that the genes of qacEΔ1-sul1 (81% vs 46.2%, p = 0.000), sul2 (50.9% vs 9.8%, p = 0.000), intI1 (83.6% vs 65.8%, p = 0.000), dfrA12 (25% vs 3.3%, p = 0.000), dfrA17 (15.5% vs 3.8%, p = 0.000) and dfrA27 (4.3% vs 1.6%, p = 0.01) were more prevalent in SXT-resistant isolates than SXT-susceptible isolates except dfrA1(p = 0.83) and dfrA5(p = 0.18). Sequencing data revealed 12 types of resistance gene cassettes (aar-3-dfrA27, dfrA12–aadA2, dfrA17–aadA5, cmlA1, aacA4, aadA5, arr-3-aacA4, aadA1, aadB–aadA4, aacA4–catB8–aadA1, aadB–aac(6′)-II–blaCARB-8 and aac(6′)-II–blaCARB-8) located in the class 1 integron in 163 isolates (87% SXT-resistant vs 33.7% SXT-susceptible isolates, p = 0.000). A novel finding was the aar-3-dfrA27 (KC748137) gene cassette. The gene of sul2 linked to transposase in 50 SXT- resistant and 7 SXT- susceptible isolates was detected by TAIL-PCR. Conclusions The findings demonstrated a higher prevalence of sul, dfrA, intI1 and resistance gene cassettes in class 1 integron in SXT-resistant clinical S. maltophilia isolates in China. The sul1 and dfrA genes located in integrons and the sul2 linked to transposase may imply wide and rapid dissemination of resistance gene in bacteria.
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Moran RA, Holt KE, Hall RM. pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron. Plasmid 2016; 84-85:11-9. [PMID: 26855083 DOI: 10.1016/j.plasmid.2016.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 01/09/2023]
Abstract
The rare sulphonamide resistance gene sul3 was found in the commensal Escherichia coli ST95 strain 22.1-R1 that was isolated in 2010 from the faeces of a healthy Australian adult. The genome of 22.1-R1 was sequenced and a 144,344bp RepFII/FIB plasmid, pCERC3, carrying sul3 was assembled. The sul3 gene is part of a class 1 integron featuring a sul3-containing conserved segment (sul3-CS) that replaced the classic sul1-containing 3'-conserved segment (3'-CS) usually seen in class 1 integrons. The integron contained the cassette array dfrA12-orfF-aadA2-cmlA1-aadA1-qacH, conferring resistance to trimethoprim, streptomycin, spectinomycin, chloramphenicol and quaternary ammonium compound. Two additional antibiotic resistance genes, blaTEM (ampicillin resistance) and tetA(B) (tetracycline) were adjacent to the integron, forming a single resistance region. In pCERC3, the sul3-type class 1 integron was flanked by sequence derived from the tnp and mer modules of Tn21 and was in the same location as In2, the sul1-containing In5-type class 1 integron of Tn21. At one end the sequence extends into Tn2670-derived sequence and then into sequence derived from the plasmid NR1 (R100). Examination of the sequences of eleven more complete sul3-containing plasmids in GenBank confirmed the relationship between sul3-associated integrons and Tn21/Tn2670/NR1. This suggests that the events that formed sul3-associated class 1 integrons occurred within the Tn21/Tn2670 context, most likely in NR1 or a related plasmid. The backbone of pCERC3 is most closely related to the backbones of ColV virulence plasmids and contains a complete ColV operon as well as several virulence associated genes and gene clusters. Hence, pCERC3 is both an antibiotic resistance and virulence plasmid.
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Affiliation(s)
- Robert A Moran
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology and Centre for Systems Genomics, University of Melbourne, VIC, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia.
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Arais LR, Barbosa AV, Carvalho CA, Cerqueira AMF. Antimicrobial resistance, integron carriage, and gyrA and gyrB mutations in Pseudomonas aeruginosa isolated from dogs with otitis externa and pyoderma in Brazil. Vet Dermatol 2016; 27:113-7e31. [PMID: 26833540 DOI: 10.1111/vde.12290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is associated with otitis and pyoderma in dogs and is frequently resistant to several antimicrobial drugs. Resistance genes can be carried by integrons with quinolone resistance mainly due to mutations in DNA topoisomerases II and IV. OBJECTIVE To evaluate the antimicrobial susceptibility, integron carriage, and gyrA and gyrB mutations in P. aeruginosa isolates from canine otitis and pyoderma. ANIMALS One hundred and four P. aeruginosa strains isolated from dogs with otitis externa (n = 93) and pyoderma (n = 11). METHODS Antimicrobial susceptibility against 16 antibacterial agents was evaluated through agar diffusion tests. Integron carriage, class and gyrA and gyrB mutations were analysed by PCR, restriction fragment length polymorphism (RFLP)-PCR and genetic sequencing assays. RESULTS Isolates were mostly resistant to enrofloxacin (72.2%) and ticarcillin (59.7%). Lower resistance to ciprofloxacin (7.7%), tobramycin (3.8%) and polymixin B (0.0%) was detected. Ten (9.6%) multidrug-resistant (MDR) strains were detected. Eight (7.7%) strains carried class 1 integrons and this was associated with MDR (three isolates, P ≤ 0.05). Five of the integron-carrying strains exhibited aminoglycoside resistance genes. Mutations of gyrA and gyrB were observed in 10 isolates, seven of them resistant to all fluoroquinolones tested. CONCLUSIONS AND CLINICAL IMPORTANCE Enrofloxacin and ticarcilin resistance was widespread in P. aeruginosa isolated from dogs in Brazil. Pseudomonas aeruginosa carrying integrons may present a significant challenge for treatment.
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Affiliation(s)
- Lavicie R Arais
- Department of Microbiology and Parasitology, Federal Fluminense University (UFF), Rua Hernani Mello, 101, Niterói, 24210130, RJ, Brazil
| | - André V Barbosa
- Department of Microbiology and Parasitology, Federal Fluminense University (UFF), Rua Hernani Mello, 101, Niterói, 24210130, RJ, Brazil
| | - Cristiane A Carvalho
- Department of Microbiology and Parasitology, Federal Fluminense University (UFF), Rua Hernani Mello, 101, Niterói, 24210130, RJ, Brazil
| | - Aloysio M F Cerqueira
- Department of Microbiology and Parasitology, Federal Fluminense University (UFF), Rua Hernani Mello, 101, Niterói, 24210130, RJ, Brazil
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Prevalence and Characterization of Integrons in Multidrug Resistant Acinetobacter baumannii in Eastern China: A Multiple-Hospital Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:10093-105. [PMID: 26308028 PMCID: PMC4555331 DOI: 10.3390/ijerph120810093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/06/2015] [Accepted: 08/19/2015] [Indexed: 12/25/2022]
Abstract
Objective: The aim of this multiple-hospital study was to investigate the prevalence of integrons in multidrug-resistant Acinetobacter baumannii (MDRAB) in Eastern China, and characterize the integron-integrase genes, so as to provide evidence for the management and appropriate antibiotic use of MDRAB infections. Methods: A total of 425 clinical isolates of A. baumannii were collected from 16 tertiary hospitals in 11 cities of four provinces (Fujian, Jiangsu, Zhejiang and Shandong) from January 2009 to June 2012. The susceptibility of A. baumannii isolates to ampicillin/sulbactam, piperacillin/tazobactam, ceftazidime, ceftriaxone, cefepime, aztreonam, meropenem, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, sulfamethoxazole/trimenthoprim, minocycline and imipenem was tested, and integrons and their gene cassettes were characterized in these isolates using PCR assay. In addition, integron-positive A. baumannii isolates were genotyped using pulsed-field gel electrophoresis (PFGE) assay, and intI1 gene cassette was sequenced. Results: intI1 gene was carried in 69.6% of total A. baumannii isolates, while intI2 and intI3 genes were not detected. The prevalence of resistance to ampicillin/sulbactam, piperacillin/tazobactam, ceftazidime, ceftriaxone, cefepime, aztreonam, imipenem, meropenem, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin and sulfamethoxazole/trimenthoprim was significantly higher in integron-positive A. baumannii isolates than in negative isolates (all p values <0.05), while no significant difference was observed in the prevalence of minocycline resistance (p > 0.05). PFGE assay revealed 27 PFGE genotypes and 4 predominant genotypes, P1, P4, P7 and P19. The PFGE genotype P1 contained 13 extensive-drug resistant and 89 non-extensive-drug resistant A. baumannii isolates, while the genotype P4 contained 34 extensive-drug resistant and 67 non-extensive-drug resistant isolates, appearing a significant antimicrobial resistance pattern (both p values <0.05). Sequencing analysis revealed two gene cassette assays of aacA4-catB8-aadA1 and dfrXII-orfF-aadA2 in MDRAB isolates. Conclusions: The results of this study demonstrate a high prevalence of class 1 integrons in MDRAB in Eastern China, and a greater prevalence of antimicrobial resistance in intI1 gene-positive MDRAB isolates than in negative isolates. Four predominant PFGE genotypes are identified in intI1 gene-positive MDRAB isolates, in which P4 is an epidemic PFGE genotype in Fujian Province, and it has a high proportion of extensive drug resistant A. baumannii. The gene cassette dfrXII-orfF-aadA2 is reported, for the first time, in A. baumannii strains isolated from Fujian Province, Eastern China.
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Çıçek AÇ, Düzgün AÖ, Saral A, Kayman T, Çızmecı Z, Balcı PÖ, Dal T, Fırat M, Tosun İ, Alıtntop YA, Çalışkan A, Yazıcı Y, Sandallı C. Detection of class 1 integron in Acinetobacter baumannii isolates collected from nine hospitals in Turkey. Asian Pac J Trop Biomed 2014; 3:743-7. [PMID: 23998017 DOI: 10.1016/s2221-1691(13)60149-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/23/2013] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To investigate the antibiotic resistance genes inserted into class 1 and class 2 integrons in Acinetobacter baumannii (A. baumannii) isolates obtained from nine different cities in Turkey. METHODS A collection of 281 A. baumannii clinical isolates were collected from nine diferent state hospitals in Turkey and were confirmed as A. baumannii by conventional biochemical, API testing and bla-OXA-51 specific PCR. The isolates were examined by PCR for existence of class 1 and 2 integron gene cassettes. RESULTS They were characterized by antimicrobial susceptibility testing and the highest resistance rates were determined for piperacillin (90.03%), ciprofloxacin (87.54%), cefepime and trimethoprim/sulfamethoxazole (81.13%). The lowest resistance rates was for cefotaxime (3.55%). class I integrons were detected in 6.4% (18/281) of A. baumannii strains and no class 2 integron was detected. The gene cassettes of class 1 integrons AacC1-AAC(3)I-aadA1, AacC1-aadA1, AAC(3)-I, AAC(3)-I -AAC(3)-I -aadA1, TEM-1, AAC(3)-I-aadA1 - AAC(3)-I -AAC(3)-I, AAC(3)-I -AAC(3)-I -AAC(3)-I -aadA1, AAC(3)-I - aadA1, AAC(3)-I-AAC(3)-I, AAC(3)-I-aadA1- AAC(3)-I-aadA1, AAC(3)-I- AAC(3)-I- aadA1-AAC(3)-I-aadA1 were detected in eighteen strains. The aac genes family were most frequently found integrated into the class 1 integrons and it was followed by aadA genes and TEM-1 genes. CONCLUSIONS This is an extensive study on the distribution of class 1 integron among A. baumannii in Turkey. In addition to these, two new alleles were observed. Their percentage rates of similarity to other cassettes are 95% aadA1 ( TKA18) and 89% aadA1 (ANKA3).
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Affiliation(s)
- Ayşegül Çopur Çıçek
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
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Sun J, Zheng F, Wang F, Wu K, Wang Q, Chen Q, Yu S, Rui Y. Class 1 integrons in urinary isolates of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Southern China during the past five years. Microb Drug Resist 2013; 19:289-94. [PMID: 23573964 DOI: 10.1089/mdr.2012.0130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We analyzed extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (226) and Klebsiella pneumoniae (53) collected from urine specimens during 2005-2009 for the presence of ESBL genes, class 1 integrons, and characterization of gene cassettes. TEM and CTX-M β-lactamase genes were the most prevalent. One hundred and forty-four E. coli and 35 K. pneumoniae were positive for the class 1 integrase gene; among them, 99 E. coli and 14 K. pneumoniae detected gene cassettes. Gene cassette regions were identified by restriction fragment length polymorphism and DNA sequencing analysis. Eleven distinct gene cassette arrays were found in E. coli isolates, and seven distinct gene cassette arrays were found in K. pneumoniae isolates. The cassette array aacA4-catB8-aadA1 was first found in E. coli and dfrA1-orfC was first reported in K. pneumoniae. Most of the gene cassettes found in this class 1 integrons were for aminoglycoside resistance. Enterobacterial repetitive intergenic consensus-polymerase chain reaction fingerprint patterns revealed the isolates carrying gene cassettes were genetically unrelated. In conclusion, we studied the class 1 integrons among urinary isolates of ESBL-producing E. coli and K. pneumoniae in Southern China during the past 5 years and found that class 1 integrons were widely disseminated and played a major role in antibiotic resistance.
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Affiliation(s)
- Jingjing Sun
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Wu K, Wang F, Sun J, Wang Q, Chen Q, Yu S, Rui Y. Class 1 integron gene cassettes in multidrug-resistant Gram-negative bacteria in southern China. Int J Antimicrob Agents 2012; 40:264-7. [DOI: 10.1016/j.ijantimicag.2012.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/22/2012] [Accepted: 05/22/2012] [Indexed: 11/29/2022]
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