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Zhang Y, Su YA, Qiu X, Mao Q, Liu H, Liu H, Wen D, Su Z. Temperature affects variations of class 1 integron during sludge anaerobic digestion. BIORESOURCE TECHNOLOGY 2022; 364:128005. [PMID: 36155808 DOI: 10.1016/j.biortech.2022.128005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Revealing class 1 integron characteristics under different operating conditions is of great importance to control antibiotic resistance genes (ARGs) during sludge anaerobic digestion (AD). This study investigated the variations of class 1 integrons and the ARGs carried by class 1 integrons in anaerobic sludge digesters under 25 °C, 35 °C, and 55 °C. The results showed lower intI1 abundance and fewer class I integrons with long gene cassette arrays at 55 °C than at 25 °C and 35 °C. Multi-resistance gene cassette arrays were observed in the digesters at 25 °C and 35 °C. Abundant ARGs were detected on class 1 integrons in all digesters with aminoglycosides as the dominant class. The abundance of ARGs on class 1 integrons in digesters at 55 °C was lower than that at 25 °C and 35 °C. Thermophilic AD is better than mesophilic ones in the control of ARGs carried by class 1 integrons.
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Affiliation(s)
- Yan Zhang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - Yu-Ao Su
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xuyang Qiu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qiuyan Mao
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Hongbo Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - He Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism. Antimicrob Agents Chemother 2016; 60:6390-2. [PMID: 27458226 DOI: 10.1128/aac.01157-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Spectinomycin is an aminocyclitol antibiotic used clinically to treat a variety of infections in animals. Here, we characterized drug resistance prevalence in clinical Streptococcus suis isolates and discovered a novel resistance mechanism in which the s5 mutation (Gly26Asp) results in high spectinomycin resistance. Additionally, a novel integrative and conjugative element encompassing a multidrug resistance spw_like-aadE-lnu(B)-lsa(E) cluster and a cadmium resistance operon were identified, suggesting a possible cause for the wide dissemination of spectinomycin resistance in S. suis.
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Xia W, Xu T, Qin T, Li P, Liu Y, Kang H, Gu B, Ma P. Characterization of integrons and novel cassette arrays in bacteria from clinical isloates in China, 2000-2014. J Biomed Res 2016; 30:292-303. [PMID: 27533938 PMCID: PMC4946320 DOI: 10.7555/jbr.30.20150153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/20/2015] [Accepted: 03/08/2016] [Indexed: 12/19/2022] Open
Abstract
Rapid dissemination of antibiotic resistance genes among bacterial isolates is an increasing problem in China. Integron, a conserved DNA sequence, which is carried on episomal genetic structures, plays a very important role in development of antibiotic resistance. This systematic analysis was based on MEDLINE and EMBASE databases. We summarized the distribution and proportion of different types of gene cassette arrays of integrons (including class 1, 2, 3 and atypical class 1 integron) from clinical bacteria isolates in China. Fifty-six literatures were included in this study. Most of the strains were Gram-negative bacteria (94.1%, 7,364/7,822) while only 5.9% strains were Gram-positive bacteria. Class 1 integrons were detected in 54.2% (3956/7295) Gram-negative strains. aadA2 was the most popular gene cassette array detected from 60 Gram-positive bacteria while dfrA17-aadA5 were detected in 426 Gram-negative bacteria. This study identified 12 novel gene cassette arrays which have not been previously found in any species. All the novel gene cassette arrays were detected from Gram-negative bacteria. A regional characteristic of distribution of integrons was presented in this study. The results highlight a need for continuous surveillance of integrons and provide a guide for future research on integron-mediated bacteria resistance.
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Affiliation(s)
- Wenying Xia
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China.,National Key Clinical Department of Laboratory Medicine, Nanjing, Jiangsu 210029, China
| | - Ting Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China.,National Key Clinical Department of Laboratory Medicine, Nanjing, Jiangsu 210029, China
| | - Tingting Qin
- Medical Technology Institute of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China
| | - Pengpeng Li
- Medical Technology Institute of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China
| | - Yun Liu
- Medical Technology Institute of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China
| | - Bing Gu
- Medical Technology Institute of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China;
| | - Ping Ma
- Medical Technology Institute of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu 221002, China
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Bai J, Liu Q, Yang Y, Wang J, Yang Y, Li J, Li P, Li X, Xi Y, Ying J, Ren P, Yang L, Ni L, Wu J, Bao Q, Zhou T. Insights into the evolution of gene organization and multidrug resistance from Klebsiella pneumoniae plasmid pKF3-140. Gene 2013; 519:60-6. [PMID: 23402892 DOI: 10.1016/j.gene.2013.01.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 12/20/2012] [Accepted: 01/27/2013] [Indexed: 01/02/2023]
Abstract
Plasmid-mediated transfer of drug-resistance genes among various bacterial species is considered one of the most important mechanisms for the spread of multidrug resistance. To gain insights into the evolution of gene organization and antimicrobial resistance in clinical bacterial samples, a complete plasmid genome of Klebsiella pneumoniae pKF3-140 is determined, which has a circular chromosome of 147,416bp in length. Among the 203 predicted genes, 142 have function assignment and about 50 appear to be involved in plasmid replication, maintenance, conjugative transfer, iron acquisition and transport, and drug resistance. Extensive comparative genomic analyses revealed that pKF3-140 exhibits a rather low sequence similarity and structural conservation with other reported K. pneumoniae plasmids. In contrast, the overall organization of pKF3-140 is highly similar to Escherichia coli plasmids p1ESCUM and pUTI89, which indicates the possibility that K. pneumoniae pKF3-140 may have a potential origin in E. coli. Meanwhile, interestingly, several drug resistant genes show high similarity to the plasmid pU302L in Salmonella enterica serovar Typhimurium U302 strain G8430 and the plasmid pK245 in K. pneumoniae. This mosaic pattern of sequence similarities suggests that pKF3-140 might have arisen from E. coli and acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among enteric bacteria.
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Affiliation(s)
- Jie Bai
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, and The First Affiliated Hospital of Wenzhou Medical College, Wenzhou 325000, China
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Yaqoob M, Wang LP, Fang T, Lu CP. Occurrence and transmission of class 1 and 2 integrons among phenotypic highly ampicillin-resistant avian Escherichia coli isolates from Pakistan. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sequence of conjugative plasmid pIP1206 mediating resistance to aminoglycosides by 16S rRNA methylation and to hydrophilic fluoroquinolones by efflux. Antimicrob Agents Chemother 2008; 52:2581-92. [PMID: 18458128 DOI: 10.1128/aac.01540-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Self-transferable IncFI plasmid pIP1206, isolated from an Escherichia coli clinical isolate, carries two new resistance determinants: qepA, which confers resistance to hydrophylic fluoroquinolones by efflux, and rmtB, which specifies a 16S rRNA methylase conferring high-level aminoglycoside resistance. Analysis of the 168,113-bp sequence (51% G+C) revealed that pIP1206 was composed of several subregions separated by copies of insertion sequences. Of 151 open reading frames, 56 (37%) were also present in pRSB107, isolated from a bacterium in a sewage treatment plant. pIP1206 contained four replication regions (RepFIA, RepFIB, and two partial RepFII regions) and a transfer region 91% identical with that of pAPEC-O1-ColBM, a plasmid isolated from an avian pathogenic E. coli. A putative oriT region was found upstream from the transfer region. The antibiotic resistance genes tet(A), catA1, bla(TEM-1), rmtB, and qepA were clustered in a 33.5-kb fragment delineated by two IS26 elements that also carried a class 1 integron, including the sulI, qacEDelta1, aad4, and dfrA17 genes and Tn10, Tn21, and Tn3-like transposons. The plasmid also possessed a raffinose operon, an arginine deiminase pathway, a putative iron acquisition gene cluster, an S-methylmethionine metabolism operon, two virulence-associated genes, and a type I DNA restriction-modification (R-M) system. Three toxin/antitoxin systems and the R-M system ensured stabilization of the plasmid in the host bacteria. These data suggest that the mosaic structure of pIP1206 could have resulted from recombination between pRSB107 and a pAPEC-O1-ColBM-like plasmid, combined with structural rearrangements associated with acquisition of additional DNA by recombination and of mobile genetic elements by transposition.
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Chang LL, Chang TM, Chang CY. Variable Gene Cassette Patterns of Class 1 Integron-Associated Drug-Resistant Escherichia Coli in Taiwan. Kaohsiung J Med Sci 2007; 23:273-80. [PMID: 17525011 DOI: 10.1016/s1607-551x(09)70409-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
This study characterized class 1 integrons in Escherichia coli in Taiwan. The stability and changes in gene cassettes inserted into integrons were also evaluated. The study included 436 clinical strains of E. coli isolated in 2002. Class 1 integrons were characterized by polymerase chain reaction and direct sequencing. Genetic localization of class 1 integrons was determined by conjugal transfer and Southern hybridization. The results indicated that 64% of E. coli isolates carried class 1 integrons. Molecular analysis revealed that the class 1 integrons harbored 13 different antimicrobial resistance gene cassettes and two unknown gene cassettes; the predominant cassettes were aadA and dfrA. Novel gene cassettes first recovered from E. coli were aacA4 and linF. Cassette arrays orfD-aacA4-catB8 and aadA1-linF were also observed. Gene cassette dfrA12-orfF-aadA2 was stable. The class 1 integron and dfrA17-aadA5 gene cassette were located on the same transferable plasmids and were capable of transmission. Therefore, the increased drug resistance of clinical isolates may be explained by antibiotic selective pressure and widespread presence of integrons. Under antibiotic selective pressure, gene cassette-mediated resistance may not be easily lost. The potential role of integrons in the uptake and dissemination of resistance genes by plasmid between species of bacteria may decrease the therapeutic effectiveness of antibiotics.
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Affiliation(s)
- Lin-Li Chang
- Department of Microbiology, Faculty of Medicine, Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Cocchi S, Grasselli E, Gutacker M, Benagli C, Convert M, Piffaretti JC. Distribution and characterization of integrons in Escherichia coli strains of animal and human origin. ACTA ACUST UNITED AC 2007; 50:126-32. [PMID: 17456180 DOI: 10.1111/j.1574-695x.2007.00242.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One hundred and twenty clinical and commensal Escherichia coli strains isolated in Switzerland from humans and from companion and farm animals were analysed for the prevalence of integrons of classes 1, 2, and 3 and for the characterization of their gene cassettes. The relationships between integron carriage and host category, and between integron carriage and phylogenetic E. coli lineage were also analysed. Integrons were detected in 48 (40%) of the isolates and were thus widely disseminated in the human and animal E. coli strains considered. Moreover, the association between integron carriage and certain animal categories (farm animals) suggests that animals that are raised for economic purposes might be exposed to a major antibiotic pressure. Finally, our data confirm that E. coli commensal strains represent a significant source of antibiotic-resistant determinants.
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Affiliation(s)
- Stefano Cocchi
- Istituto Cantonale di Microbiologia, Bellinzona, Switzerland
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Solberg OD, Ajiboye RM, Riley LW. Origin of class 1 and 2 integrons and gene cassettes in a population-based sample of uropathogenic Escherichia coli. J Clin Microbiol 2006; 44:1347-51. [PMID: 16597861 PMCID: PMC1448660 DOI: 10.1128/jcm.44.4.1347-1351.2006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalence of urinary tract infections (UTI) caused by trimethoprim-sulfamethoxazole (TMP-SMX)-resistant Escherichia coli is increasing and varies geographically in the United States. Recent community-based UTI studies have demonstrated geographic clustering of an Escherichia coli clonal group, suggesting occurrence of a community outbreak of UTI. A large proportion of this clonal group (designated CgA) isolated from women in a California college community was found to be resistant to TMP-SMX. We wished to determine if the acquisition of TMP-SMX resistance by CgA occurred before or after the CgA strains were introduced into this community. Between October 1999 and January 2000 and between October 2000 and January 2001, 482 E. coli isolates were consecutively collected from the urine samples of women with UTI at a student health clinic and analyzed for determinants of TMP-SMX resistance. In particular, the distribution of integrons harboring resistance cassettes for TMP-SMX (dfr) was examined. Among 95 TMP-SMX-resistant isolates, 68 and 27 isolates carried class 1 and class 2 integrons, respectively. A class 1 integron was found in 25 (93%) of 27 TMP-SMX-resistant CgA isolates but in only 43 (63%) of 68 TMP-SMX-resistant non-CgA isolates (P < 0.001) and in none of 44 TMP-SMX-susceptible E. coli isolates (P < 0.0001). CgA strains carried only a single arrangement of class 1 gene cassettes (dfrA17-aadA5), while the non-clonal group strains carried nine different cassette arrangements. These results support the idea that CgA strains acquired their resistance at a common site prior to their spread to the college community.
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Affiliation(s)
- Owen D Solberg
- Divisions of Epidemiology and Infectious Diseases, School of Public Health, University of California-Berkeley, 140 Warren Hall, Berkeley CA 94720, USA.
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Abstract
Integrons are genetic elements composed of a gene encoding an integrase, gene cassettes and an integration site for the gene cassettes (att). The integrase excises and integrates the gene cassettes from and into the integron, but integrons themselves are not mobile. Two groups of integrons are known: resistance integrons and super-integrons. Nearly all known gene cassettes from resistance integrons encode resistance to antibiotics or disinfectants. These integrons are found on transposons, plasmids and the bacterial chromosome. Gene cassettes in super-integrons encode a variety of different functions. Super-integrons are located on the bacterial chromosome. More than 100 gene cassettes may be present, in contrast to resistance integrons where less than ten cassettes are present. Many species harbour super-integrons, which are species-specific, whereas particular resistance integrons can be found in a variety of species. The gene cassettes in resistance integrons probably originated from super-integrons. In the last few years, a variety of new gene cassettes have been described. Many of these encode resistance against newer antibiotics such as cephalosporins and carbapenems. Resistance integrons have been found in isolates from a wide variety of sources, including food.
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Affiliation(s)
- A C Fluit
- Eijkman-Winkler Center, P.O. Box 85500, 3508 GA Utrecht, The Netherlands.
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DeLappe N, O'Halloran F, Fanning S, Corbett-Feeney G, Cheasty T, Cormican M. Antimicrobial resistance and genetic diversity of Shigella sonnei isolates from western Ireland, an area of low incidence of infection. J Clin Microbiol 2003; 41:1919-24. [PMID: 12734227 PMCID: PMC154704 DOI: 10.1128/jcm.41.5.1919-1924.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella sonnei is a significant cause of gastroenteritis in both developing and industrialized countries. Definition of the diversity and antimicrobial susceptibility of S. sonnei isolates may be helpful in the management of individual cases and outbreaks. Antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) were performed with 67 isolates of S. sonnei predominantly (n = 59) from three counties in the west of Ireland. Phage typing (n = 17), plasmid profiling (n = 28), and integron analysis (n = 24) were performed with subsets of strains. PFGE typing permitted recognition of two major clusters: PFGE type A (n = 53) and PFGE type B (n = 14). PFGE type A was associated with resistance to ampicillin, streptomycin, and sulfonamides (51 of 53 isolates), and those that were phage typed (n = 6) were phage type 3. PFGE type B was associated with resistance to streptomycin, sulfonamides, tetracycline, and trimethoprim (11 of 14 isolates) and phage type 6 (9 of 11 isolates). Fifteen different plasmid profiles were identified among the 28 isolates analyzed. A class 2 integron was present in all 14 PFGE type B isolates. One of these isolates also contained a class 1 integron and showed a unique variant of the PFGE type B pattern. Sequence analysis of the gene cassette structures contained within these integrons identified distinct open reading frames that encoded determinants of resistance to trimethoprim, streptomycin, and streptothricin. Our data demonstrate two predominant PFGE types among S. sonnei isolates circulating in this region. The limited diversity of the S. sonnei isolates in this region means that detection of isolates indistinguishable by PFGE and according to their antibiograms in two or more patients is not persuasive evidence of a common-source food- or waterborne outbreak. Indistinguishable plasmid profiles in addition to indistinguishable PFGE and antibiogram types may be more suggestive of an epidemiologically relevant link between cases.
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Affiliation(s)
- Niall DeLappe
- National Salmonella Reference Laboratory, University College Hospital, Galway, Ireland
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