401
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Genome and Plasmid Analysis of blaIMP-4-Carrying Citrobacter freundii B38. Antimicrob Agents Chemother 2016; 60:6719-6725. [PMID: 27572407 DOI: 10.1128/aac.00588-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/23/2016] [Indexed: 01/21/2023] Open
Abstract
Sequencing of the blaIMP-4-carrying C. freundii B38 using the PacBio SMRT technique revealed that the genome contained a chromosome of 5,134,500 bp and three plasmids, pOZ172 (127,005 bp), pOZ181 (277,592 bp), and pOZ182 (18,467 bp). Plasmid pOZ172 was identified as IncFIIY, like pP10164-NDM and pNDM-EcGN174. It carries a class 1 integron with four cassettes (blaIMP-4-qacG2-aacA4-aphA15) and a complete hybrid tni module (tniR-tniQ-tniB-tniA). The recombination of tniR from Tn402 (identical) with tniQBA from Tn5053 (99%) occurred within the res site of Tn402/5053 The Tn402/5053-like integron, named Tn6017, was inserted into Tn1722 at the res II site. The replication, partitioning, and transfer systems of pOZ181 were similar to those of IncHI2 plasmids (e.g., R478) and contained a sul1-type class 1 integron with the cassette array orf-dfrA1-orf-gcu37-aadA5 linked to an upstream Tn1696 tnpA-tnpR and to a downstream 3' conserved sequence (3'-CS) and ISCR1 A Tn2 transposon encoding a blaTEM-1 β-lactamase was identified on pOZ182. Other interesting resistance determinants encoded on the B38 chromosome included multidrug resistance (MDR) efflux pumps, an AmpC β-lactamase, and resistances to Cu, Ag, As, and Zn. This is the first report of a complete tni module linked to a blaIMP-4-carrying class 1 integron, which, together with other recently reported non-sul1 integrons, represents the emergence of a distinct evolutionary lineage of class 1 integrons lacking a 3'-CS (qacEΔ1-sul1). The unique cassette array, complete tni module of Tn6017, and incompatibility group of pOZ172 suggest a blaIMP-4 evolutionary pathway in C. freundii B38 different from that for other blaIMP-4 genes found in Gram-negative bacteria in the Western Pacific region.
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402
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Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
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403
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Gillings MR. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 2016; 1389:20-36. [DOI: 10.1111/nyas.13213] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Michael R. Gillings
- Genes to Geoscience Research Centre, Department of Biological Sciences Macquarie University Sydney New South Wales Australia
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404
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IMP-27, a Unique Metallo-β-Lactamase Identified in Geographically Distinct Isolates of Proteus mirabilis. Antimicrob Agents Chemother 2016; 60:6418-21. [PMID: 27503648 PMCID: PMC5038328 DOI: 10.1128/aac.02945-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/21/2016] [Indexed: 12/23/2022] Open
Abstract
A novel metallo-β-lactamase gene, blaIMP-27, was identified in unrelated Proteus mirabilis isolates from two geographically distinct locations in the United States. Both isolates harbor blaIMP-27 as part of the first gene cassette in a class 2 integron. Antimicrobial susceptibility testing indicated susceptibility to aztreonam, piperacillin-tazobactam, and ceftazidime but resistance to ertapenem. However, hydrolysis assays indicated that ceftazidime was a substrate for IMP-27.
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405
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Dissemination of IMP-4-encoding pIMP-HZ1-related plasmids among Klebsiella pneumoniae and Pseudomonas aeruginosa in a Chinese teaching hospital. Sci Rep 2016; 6:33419. [PMID: 27641711 PMCID: PMC5027574 DOI: 10.1038/srep33419] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/26/2016] [Indexed: 01/03/2023] Open
Abstract
A total of 26 blaIMP-4-carrying strains of Pseudomonas aeruginosa and Klebsiella pneumoniae were isolated from 2009 to 2013 in a Chinese teaching hospital, and these strains can be assigned into multiple sequence types or allelic profiles as determined by multilocus sequence typing. Of these strains, P. aeruginosa P378 and K. pneumoniae 1220 harbor the IMP-4-encoding plasmids pP378-IMP and p1220-IMP, respectively, whose complete nucleotide sequences are determined to be genetically closely related to the IncN1-type plasmid pIMP-HZ1. pP378-IMP/p1220-IMP-like plasmids are hinted to be present in all the other blaIMP-4-carrying strains, indicating the dissemination of pIMP-HZ1-related plasmids among K. pneumoniae or P. aeruginosa of different genotypes in this hospital. pP378-IMP carries two distinct accessory resistance regions, a blaIMP-4-carrying class 1 integron In823b, and a truncated Tn3-family unit transposon ΔTn6292-3' harboring the quinolone resistance gene qnrS1. Massive fragmentation and rearrangement of these accessory genetic contents occur among p1220-IMP and IMP-HZ1 relative to pP378-IMP. blaIMP-4 is also present in the In823b remnants from p1220-IMP and IMP-HZ1, while qnrS1 is located in a Tn6292-derive fragment from pIMP-HZ1 but not found in p1220-IMP. pP378-IMP represents the first fully sequenced IncN-type plasmid from P. aeruginosa.
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406
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Goudarzi H, Azad M, Seyedjavadi SS, Azimi H, Salimi Chirani A, Fallah Omrani V, Goudarzi M. Characterization of integrons and associated gene cassettes in Acinetobacter baumannii strains isolated from intensive care unit in Tehran, Iran. JOURNAL OF ACUTE DISEASE 2016. [DOI: 10.1016/j.joad.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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407
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The Stringent Response Promotes Antibiotic Resistance Dissemination by Regulating Integron Integrase Expression in Biofilms. mBio 2016; 7:mBio.00868-16. [PMID: 27531906 PMCID: PMC4992968 DOI: 10.1128/mbio.00868-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class 1 integrons are genetic systems that enable bacteria to capture and express gene cassettes. These integrons, when isolated in clinical contexts, most often carry antibiotic resistance gene cassettes. They play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. The key element of integrons is the integrase, which allows gene cassettes to be acquired and shuffled. Planktonic culture experiments have shown that integrase expression is regulated by the bacterial SOS response. In natural settings, however, bacteria generally live in biofilms, which are characterized by strong antibiotic resilience and by increased expression of stress-related genes. Here, we report that under biofilm conditions, the stringent response, which is induced upon starvation, (i) increases basal integrase and SOS regulon gene expression via induction of the SOS response and (ii) exerts biofilm-specific regulation of the integrase via the Lon protease. This indicates that biofilm environments favor integron-mediated acquisition of antibiotic resistance and other adaptive functions encoded by gene cassettes. Multidrug-resistant bacteria are becoming a worldwide health problem. Integrons are bacterial genetic platforms that allow the bacteria to capture and express gene cassettes. In clinical settings, integrons play a major role in the dissemination of antibiotic resistance gene cassettes among Gram-negative bacteria. Cassette capture is catalyzed by the integron integrase, whose expression is induced by DNA damage and controlled by the bacterial SOS response in laboratory planktonic cultures. In natural settings, bacteria usually grow in heterogeneous environments known as biofilms, which have very different conditions than planktonic cultures. Integrase regulation has not been investigated in biofilms. Our results showed that in addition to the SOS response, the stringent response (induced upon starvation) is specifically involved in the regulation of class 1 integron integrases in biofilms. This study shows that biofilms are favorable environments for integron-mediated acquisition/exchange of antibiotic resistance genes by bacteria and for the emergence of multidrug-resistant bacteria.
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408
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Nõlvak H, Truu M, Kanger K, Tampere M, Espenberg M, Loit E, Raave H, Truu J. Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:678-689. [PMID: 27115621 DOI: 10.1016/j.scitotenv.2016.04.035] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH4NO3), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes (intI1 and intI2) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs (sul1, tetA, blaCTX-M, blaOXA2 and qnrS) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA, blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (p<0.001 in both cases), explaining 67.04% of the abundance and 42.95% of the proportion variations in the grassland soil. Both cattle slurry and cattle slurry digestate proved to be considerable sources of ARGs, especially sul1, as well as integron-integrases. Sul1, intI1 and intI2 levels in grassland soil were elevated in response to each organic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p<0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment.
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Affiliation(s)
- Hiie Nõlvak
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Marika Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Kärt Kanger
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Mailiis Tampere
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Evelin Loit
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Henn Raave
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Jaak Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
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409
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Distribution of spa Types, Integrons and Associated Gene Cassettes in Staphylococcus aureus Strains Isolated From Intensive Care Units of Hospitals in Tehran, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2016. [DOI: 10.5812/archcid.38813] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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410
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Power ML, Samuel A, Smith JJ, Stark JS, Gillings MR, Gordon DM. Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 215:58-65. [PMID: 27179324 DOI: 10.1016/j.envpol.2016.04.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/19/2016] [Accepted: 04/04/2016] [Indexed: 05/12/2023]
Abstract
Discharge of untreated sewage into Antarctic environments presents a risk of introducing non-native microorganisms, but until now, adverse consequences have not been conclusively identified. Here we show that sewage disposal introduces human derived Escherichia coli carrying mobile genetic elements and virulence traits with the potential to affect the diversity and evolution of native Antarctic microbial communities. We compared E. coli recovered from environmental and animal sources in Antarctica to a reference collection of E. coli from humans and non-Antarctic animals. The distribution of phylogenetic groups and frequency of 11 virulence factors amongst the Antarctic isolates were characteristic of E. coli strains more commonly associated with humans. The rapidly emerging E. coli ST131 and ST95 clones were found amongst the Antarctic isolates, and ST95 was the predominant E. coli recovered from Weddell seals. Class 1 integrons were found in 15% of the Antarctic E. coli with 4 of 5 identified gene cassette arrays containing antibiotic resistance genes matching those common in clinical contexts. Disposing untreated sewage into the Antarctic environment does disseminate non-native microorganisms, but the extent of this impact and implications for Antarctic ecosystem health are, as yet, poorly understood.
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Affiliation(s)
- Michelle L Power
- Biological Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Angelingifta Samuel
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT 2601, Australia.
| | - James J Smith
- Queensland University of Technology, Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences, GPO Box 2434, Brisbane, QLD 4001, Australia; JJSC Consulting Ltd., 16 Mullacor St., Ferny Grove, QLD 4055, Australia.
| | - Jonathon S Stark
- Antarctic Conservation and Management, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania 7050, Australia.
| | - Michael R Gillings
- Biological Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW 2109, Australia
| | - David M Gordon
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT 2601, Australia.
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411
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Pagano M, Martins AF, Barth AL. Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii. Braz J Microbiol 2016; 47:785-792. [PMID: 27522927 PMCID: PMC5052331 DOI: 10.1016/j.bjm.2016.06.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is widely recognized as an important pathogen associated with nosocomial infections. The treatment of these infections is often difficult due to the acquisition of resistance genes. A. baumannii presents a high genetic plasticity which allows the accumulation of these resistance determinants leading to multidrug resistance. It is highlighted the importance of the horizontal transfer of resistance genes, through mobile genetic elements and its relationship with increased incidence of multidrug resistant A. baumannii in hospitals. Considering that resistance to carbapenems is very important from the clinical and epidemiological point of view, the aim of this article is to present an overview of the current knowledge about genetic elements related to carbapenem resistance in A. baumannii such as integrons, transposons, resistance islands and insertion sequences.
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Affiliation(s)
- Mariana Pagano
- Universidade Federal do Rio Grande do Sul (UFRGS), Faculdade de Farmácia, Programa de Pós-Gradução em Ciências Farmacêuticas, Porto Alegre, Brazil; Hospital de Clínicas de Porto Alegre(HCPA), Porto Alegre, Brazil
| | - Andreza Francisco Martins
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Ciências Básicas da Saúde, Porto Alegre, Brazil; Hospital de Clínicas de Porto Alegre(HCPA), Porto Alegre, Brazil.
| | - Afonso Luis Barth
- Universidade Federal do Rio Grande do Sul (UFRGS), Faculdade de Farmácia, Programa de Pós-Gradução em Ciências Farmacêuticas, Porto Alegre, Brazil; Hospital de Clínicas de Porto Alegre(HCPA), Porto Alegre, Brazil
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412
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Marathe NP, Gaikwad SS, Vaishampayan AA, Rasane MH, Shouche YS, Gade WN. Mossambicus tilapia (Oreochromis mossambicus) collected from water bodies impacted by urban waste carries extended-spectrum beta-lactamases and integron-bearing gut bacteria. J Biosci 2016; 41:341-6. [DOI: 10.1007/s12038-016-9620-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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413
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Detection of Novel Integrons in the Metagenome of Human Saliva. PLoS One 2016; 11:e0157605. [PMID: 27304457 PMCID: PMC4909258 DOI: 10.1371/journal.pone.0157605] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
Integrons are genetic elements capable of capturing and expressing open reading frames (ORFs) embedded within gene cassettes. They are involved in the dissemination of antibiotic resistance genes (ARGs) in clinically important pathogens. Although the ARGs are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. In this work, a PCR-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral metagenomic DNA obtained from both the UK and Bangladesh. We identified a diverse array of gene cassettes containing ORFs predicted to confer antimicrobial resistance and other adaptive traits. The predicted proteins include a putative streptogramin A O-acetyltransferase, a bleomycin binding protein, cof-like hydrolase, competence and motility related proteins. This is the first study detecting integron gene cassettes directly from oral metagenomic DNA samples. The predicted proteins are likely to carry out a multitude of functions; however, the function of the majority is yet unknown.
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414
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Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
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Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
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415
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Species Diversity of Environmental GIM-1-Producing Bacteria Collected during a Long-Term Outbreak. Appl Environ Microbiol 2016; 82:3605-3610. [PMID: 27060121 DOI: 10.1128/aem.00424-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/06/2016] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Reports of outbreaks concerning carbapenemase-producing Gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. This study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase GIM-1 outbreak driven by plasmids and bacterial clones of Enterobacter cloacae and Pseudomonas aeruginosa in a tertiary care center. Environmental sampling targeting wet locations (especially sinks) was carried out on a surgical intensive care unit and on a medical ward on several occasions in 2012 and 2013. We were able to demonstrate 43 blaGIM-1-carrying bacteria (mainly nonfermenters but also Enterobacteriaceae) that were either related or unrelated to clinical strains in 30 sinks and one hair washbasin. GIM-1 was found in 12 different species, some of which are described here as carriers of GIM-1. Forty out of 43 bacteria displayed resistance to carbapenems and, in addition, to various non-beta-lactam antibiotics. Colistin resistance was observed in two E. cloacae isolates with MICs above 256 mg/liter. The blaGIM-1 gene was harbored in 12 different class 1 integrons, some without the typical 3' end. The blaGIM-1 gene was localized on plasmids in five isolates. In vitro plasmid transfer by conjugation was successful in one isolate. The environment, with putatively multispecies biofilms, seems to be an important biological niche for multidrug-resistant bacteria and resistance genes. Biofilms may serve as a "melting pot" for horizontal gene transfer, for dissemination into new species, and as a reservoir to propagate future hospital outbreaks. IMPORTANCE In Gram-negative bacteria, resistance to the clinically relevant broad-spectrum carbapenem antibiotics is a major public health concern. Major reservoirs for these resistant organisms are not only the gastrointestinal tracts of animals and humans but also the (hospital) environment. Due to the difficulty in eradicating biofilm formation in the latter, a sustained dissemination of multidrug-resistant bacteria from the environment can occur. In addition, horizontal transfer of resistance genes on mobile genetic elements within biofilms adds to the total "resistance gene pool" in the environment. To gain insight into the transmission pathways of a rare and locally restricted carbapenemases resistance gene (blaGIM-1), we analyzed the genetic background of the blaGIM-1 gene in environmental bacteria during a long-term polyspecies outbreak in a German hospital.
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416
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Cury J, Jové T, Touchon M, Néron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res 2016; 44:4539-50. [PMID: 27130947 PMCID: PMC4889954 DOI: 10.1093/nar/gkw319] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/13/2016] [Indexed: 12/13/2022] Open
Abstract
Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Thomas Jové
- Univ. Limoges, INSERM, CHU Limoges, UMR_S 1092, F-87000 Limoges, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Bertrand Néron
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France
| | - Eduardo Pc Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
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417
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Ertekin E, Hatt JK, Konstantinidis KT, Tezel U. Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4304-13. [PMID: 26992451 DOI: 10.1021/acs.est.5b05959] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Benzalkonium chlorides (BACs) are emerging pollutants. Identification of microorganisms and the genes involved in the biodegradation of BACs is crucial for better understanding the fate of BACs in the environment and developing treatment strategies. Four microbial communities degrading BACs were developed from sewage (SEW), activated sludge (AS), soil (SOIL) and sea sediment (SEA) samples. According to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundant species represented uncharacterized members of the Pseudomonas and Achromobacter genera. BAC biotransformation rates of the enriched microbial communities were 2.8, 3.2, 17.8, and 24.3 μM hr(-1) for SEA, AS, SOIL, and SEW, respectively, and were positively correlated with the relative abundance of a particular Pseudomonas sp. strain, BIOMIG1. The strain BIOMIG1 mineralizes BACs at a rate up to 2.40 μmol hr(-1) 10(-11) cells. Genomes of four BAC degrading and nondegrading BIOMIG1 phenotypes were sequenced and differentially compared with each other. As a result, a gene cluster encoding for transporters, an integrase and a dioxygenase were involved in BAC biotransformation. Our results suggest that BIOMIG1 plays a key role on the fate of BACs in the environment and genes, other than those reported to date, are involved in BAC biotransformation in various habitats.
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Affiliation(s)
- Emine Ertekin
- Institute of Environmental Sciences, Bogazici University, Bebek 34342 Istanbul, Turkey
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta Georgia 30332-0512, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta Georgia 30332-0512, United States
- School of Biology, Georgia Institute of Technology , Atlanta Georgia 30332-0512, United States
| | - Ulas Tezel
- Institute of Environmental Sciences, Bogazici University, Bebek 34342 Istanbul, Turkey
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418
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Abstract
Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.
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419
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Jechalke S, Radl V, Schloter M, Heuer H, Smalla K. Do drying and rewetting cycles modulate effects of sulfadiazine spiked manure in soil? FEMS Microbiol Ecol 2016; 92:fiw066. [DOI: 10.1093/femsec/fiw066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 12/19/2022] Open
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420
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Rahube TO, Marti R, Scott A, Tien YC, Murray R, Sabourin L, Duenk P, Lapen DR, Topp E. Persistence of antibiotic resistance and plasmid-associated genes in soil following application of sewage sludge and abundance on vegetables at harvest. Can J Microbiol 2016; 62:600-7. [PMID: 27277701 DOI: 10.1139/cjm-2016-0034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sewage sludge recovered from wastewater treatment plants contains antibiotic residues and is rich in antibiotic resistance genes, selected for and enriched in the digestive tracts of human using antibiotics. The use of sewage sludge as a crop fertilizer constitutes a potential route of human exposure to antibiotic resistance genes through consumption of contaminated crops. Several gene targets associated with antibiotic resistance (catA1, catB3, ereA, ereB, erm(B), str(A), str(B), qnrD, sul1, and mphA), mobile genetic elements (int1, mobA, IncW repA, IncP1 groups -α, -β, -δ, -γ, -ε), and bacterial 16S rRNA (rrnS) were quantified by qPCR from soil and vegetable samples obtained from unamended and sludge-amended plots at an experimental field in London, Ontario. The qPCR data reveals an increase in abundance of gene targets in the soil and vegetables samples, indicating that there is potential for additional crop exposure to antibiotic resistance genes carried within sewage sludge following field application. It is therefore advisable to allow an appropriate delay period before harvesting of vegetables for human consumption.
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Affiliation(s)
- Teddie O Rahube
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada.,b Department of Biology and Biotechnological Sciences, Botswana International University of Science and Technology, Palapye, Botswana
| | - Romain Marti
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Andrew Scott
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Yuan-Ching Tien
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Roger Murray
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Lyne Sabourin
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Peter Duenk
- c Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - David R Lapen
- d Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Edward Topp
- a Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada.,c Department of Biology, University of Western Ontario, London, Ontario, Canada
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421
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Oliveira-Pinto C, Costa PS, Reis MP, Chartone-Souza E, Nascimento AMA. Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals. Extremophiles 2016; 20:283-9. [PMID: 26961777 DOI: 10.1007/s00792-016-0820-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/23/2016] [Indexed: 11/25/2022]
Abstract
The integron-gene cassette system has typically been associated with antibiotic-resistant pathogens. However, the diversity of gene cassettes and the abundance of class 1 integrons outside of the clinical context are not fully explored. Primers targeting the conserved segments of attC recombination sites were used to amplify gene cassettes from the sediment of the Mina stream, which exhibited a higher degree of stress to metal pollution in the dry season than the rainy season. Of the 143 total analyzed sequences, 101 had no matches to proteins in the database, where cassette open reading frames could be identified by homology with database entries. There was a predominance of sequences encoding essential cellular functions. Each season that was sampled yielded a specific pool of gene cassettes. Real-time PCR revealed that 8.5 and 41.6 % of bacterial cells potentially harbored a class 1 integron in the rainy and dry seasons, respectively. In summary, our findings demonstrate that most of the gene cassettes have no ascribable function and, apparently, historically metal-contaminated sediment favors the maintenance of bacteria containing the intI1 gene. Thus, the diversity of gene cassettes is far from being fully explored deserving further attention.
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Affiliation(s)
- Clarisse Oliveira-Pinto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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422
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Graham DW, Knapp CW, Christensen BT, McCluskey S, Dolfing J. Appearance of β-lactam Resistance Genes in Agricultural Soils and Clinical Isolates over the 20th Century. Sci Rep 2016; 6:21550. [PMID: 26878889 PMCID: PMC4754643 DOI: 10.1038/srep21550] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/26/2016] [Indexed: 01/14/2023] Open
Abstract
Debate exists about whether agricultural versus medical antibiotic use drives increasing antibiotic resistance (AR) across nature. Both sectors have been inconsistent at antibiotic stewardship, but it is unclear which sector has most influenced acquired AR on broad scales. Using qPCR and soils archived since 1923 at Askov Experimental Station in Denmark, we quantified four broad-spectrum β-lactam AR genes (ARG; bla(TEM), bla(SHV), bla(OXA) and bla(CTX-M)) and class-1 integron genes (int1) in soils from manured (M) versus inorganic fertilised (IF) fields. "Total" β-lactam ARG levels were significantly higher in M versus IF in soils post-1940 (paired-t test; p < 0.001). However, dominant individual ARGs varied over time; bla(TEM) and bla(SHV) between 1963 and 1974, bla(OXA) slightly later, and bla(CTX-M) since 1988. These dates roughly parallel first reporting of these genes in clinical isolates, suggesting ARGs in animal manure and humans are historically interconnected. Archive data further show when non-therapeutic antibiotic use was banned in Denmark, bla(CTX-M) levels declined in M soils, suggesting accumulated soil ARGs can be reduced by prudent antibiotic stewardship. Conversely, int1 levels have continued to increase in M soils since 1990, implying direct manure application to soils should be scrutinized as part of future stewardship programs.
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Affiliation(s)
- David W Graham
- School of Civil Engineering &Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom, NE1 7RU
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom, G1 1XJ
| | - Bent T Christensen
- Department of Agroecology, Aarhus University, AU-Foulum, DK-8830 Tjele, Denmark
| | - Seánín McCluskey
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom, G1 1XJ
| | - Jan Dolfing
- School of Civil Engineering &Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom, NE1 7RU
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423
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Engelstädter J, Harms K, Johnsen PJ. The evolutionary dynamics of integrons in changing environments. ISME JOURNAL 2016; 10:1296-307. [PMID: 26849314 DOI: 10.1038/ismej.2015.222] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 11/09/2022]
Abstract
Integrons are genetic elements that are common in bacteria and are hotspots for genome evolution. They facilitate the acquisition and reassembly of gene cassettes encoding a variety of functions, including drug resistance. Despite their importance in clinical settings, the selective forces responsible for the evolution and maintenance of integrons are poorly understood. We present a mathematical model of integron evolution within bacterial populations subject to fluctuating antibiotic exposures. Bacteria carrying a functional integrase that mediates reshuffling of cassette genes and thereby modulates gene expression patterns compete with bacteria without a functional integrase. Our results indicate that for a wide range of parameters, the functional integrase can be stably maintained in the population despite substantial fitness costs. This selective advantage arises because gene-cassette shuffling generates genetic diversity, thus enabling the population to respond rapidly to changing selective pressures. We also show that horizontal gene transfer promotes stable maintenance of the integrase and can also lead to de novo assembly of integrons. Our model generates testable predictions for integron evolution, including loss of functional integrases in stable environments and selection for intermediate gene-shuffling rates in changing environments. Our results highlight the need for experimental studies of integron population biology.
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Affiliation(s)
- Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Klaus Harms
- Faculty of Health Sciences, Department of Pharmacy, UIT - The Arctic University of Norway, Tromsø, Norway.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Pål J Johnsen
- Faculty of Health Sciences, Department of Pharmacy, UIT - The Arctic University of Norway, Tromsø, Norway
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424
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Bi D, Xie Y, Tai C, Jiang X, Zhang J, Harrison EM, Jia S, Deng Z, Rajakumar K, Ou HY. A Site-Specific Integrative Plasmid Found in Pseudomonas aeruginosa Clinical Isolate HS87 along with A Plasmid Carrying an Aminoglycoside-Resistant Gene. PLoS One 2016; 11:e0148367. [PMID: 26841043 PMCID: PMC4739549 DOI: 10.1371/journal.pone.0148367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/19/2016] [Indexed: 12/30/2022] Open
Abstract
Plasmids play critical roles in bacterial fitness and evolution of Pseudomonas aeruginosa. Here two plasmids found in a drug-resistant P. aeruginosa clinical isolate HS87 were completely sequenced. The pHS87b plasmid (11.2 kb) carries phage-related genes and function-unknown genes. Notably, pHS87b encodes an integrase and has an adjacent tRNAThr-associated attachment site. A corresponding integrated form of pHS87b at the tRNAThr locus was identified on the chromosome of P. aeruginosa, showing that pHS87b is able to site-specifically integrate into the 3’-end of the tRNAThr gene. The pHS87a plasmid (26.8 kb) displays a plastic structure containing a putative replication module, stability factors and a variable region. The RepA of pHS87a shows significant similarity to the replication proteins of pPT23A-family plasmids. pHS87a carries a transposon Tn6049, a truncated insertion sequence ΔIS1071 and a Tn402-like class 1 integron which contains an aacA4 cassette that may confer aminoglycoside resistance. Thus, pHS87b is a site-specific integrative plasmid whereas pHS87a is a plastic antibiotic resistance plasmid. The two native plasmids may promote the fitness and evolution of P. aeruginosa.
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Affiliation(s)
- Dexi Bi
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Yingzhou Xie
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Ewan M. Harrison
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Shiru Jia
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Zixin Deng
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Kumar Rajakumar
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Hong-Yu Ou
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
- * E-mail:
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425
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Makowska N, Koczura R, Mokracka J. Class 1 integrase, sulfonamide and tetracycline resistance genes in wastewater treatment plant and surface water. CHEMOSPHERE 2016; 144:1665-73. [PMID: 26519797 DOI: 10.1016/j.chemosphere.2015.10.044] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 05/08/2023]
Abstract
Wastewater treatment plants are considered hot spots for multiplication and dissemination of antibiotic-resistant bacteria and resistance genes. In this study, we determined the presence of class 1 integron integrase and genes conferring resistance to tetracyclines and sulfonamides in the genomes of culturable bacteria isolated from a wastewater treatment plant and the river that receives the treated wastewater. Moreover, using PCR-based metagenomic approach, we quantified intI1, tet and sul genes. Wastewater treatment caused the decrease in the total number of culturable heterotrophs and bacteria resistant to tetracycline and sulfonamides, along with the decrease in the number of intI1, sul and tet gene copies per ml, with significant reduction of tet(B). On the other hand, the treatment process increased both the frequency of tetracycline- and sulfonamide-resistant bacteria and intI1-positive strains, and the relative abundance of all quantified antibiotic resistance genes (ARGs) and intI1 gene; in the case of tet(A) and sul2 significantly. The discharge of treated wastewater increased the number of intI1, tet and sul genes in the receiving river water both in terms of copy number per ml and relative abundance. Hence, despite the reduction of the number of ARGs and ARBs, wastewater treatment selects for bacteria with ARGs in effluent.
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Affiliation(s)
- Nicoletta Makowska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Ryszard Koczura
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland.
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426
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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427
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Brandt KK, Amézquita A, Backhaus T, Boxall A, Coors A, Heberer T, Lawrence JR, Lazorchak J, Schönfeld J, Snape JR, Zhu YG, Topp E. Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms. ENVIRONMENT INTERNATIONAL 2015; 85:189-205. [PMID: 26411644 DOI: 10.1016/j.envint.2015.09.013] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 09/03/2015] [Accepted: 09/10/2015] [Indexed: 05/06/2023]
Abstract
Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.
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Affiliation(s)
- Kristian K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark; Sino Danish Center for Education and Research, Beijing, China.
| | - Alejandro Amézquita
- Unilever-Safety & Environmental Assurance Centre, Sharnbrook, United Kingdom
| | - Thomas Backhaus
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Anja Coors
- ECT Oekotoxikologie GmbH, Flörsheim/Main, Germany
| | - Thomas Heberer
- Federal Office of Consumer Protection and Food Safety, Department 3: Veterinary Drugs, Berlin, Germany
| | | | - James Lazorchak
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Jens Schönfeld
- Umweltbundesamt, Federal Environment Agency, Dessau, Germany
| | - Jason R Snape
- AstraZeneca Global Environment, Alderley Park, United Kingdom
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Edward Topp
- Agriculture and Agri-Food Canada, London, Ontario, Canada.
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428
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Abella J, Fahy A, Duran R, Cagnon C. Integron diversity in bacterial communities of freshwater sediments at different contamination levels. FEMS Microbiol Ecol 2015; 91:fiv140. [DOI: 10.1093/femsec/fiv140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
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429
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Abella J, Bielen A, Huang L, Delmont TO, Vujaklija D, Duran R, Cagnon C. Integron diversity in marine environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015. [PMID: 26213132 DOI: 10.1007/s11356-015-5085-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.
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Affiliation(s)
- Justine Abella
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Ana Bielen
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Lionel Huang
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Euro Engineering, Technopole Hélioparc Bât Newton, 4 rue Jules Ferry, CS N 99207, 64053, Pau, Cedex 09, France
| | - Tom O Delmont
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA, USA
| | - Dušica Vujaklija
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France.
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Zhou G, Shi QS, Huang XM, Xie XB. The Three Bacterial Lines of Defense against Antimicrobial Agents. Int J Mol Sci 2015; 16:21711-33. [PMID: 26370986 PMCID: PMC4613276 DOI: 10.3390/ijms160921711] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial agents target a range of extra- and/or intracellular loci from cytoplasmic wall to membrane, intracellular enzymes and genetic materials. Meanwhile, many resistance mechanisms employed by bacteria to counter antimicrobial agents have been found and reported in the past decades. Based on their spatially distinct sites of action and distribution of location, antimicrobial resistance mechanisms of bacteria were categorized into three groups, coined the three lines of bacterial defense in this review. The first line of defense is biofilms, which can be formed by most bacteria to overcome the action of antimicrobial agents. In addition, some other bacteria employ the second line of defense, the cell wall, cell membrane, and encased efflux pumps. When antimicrobial agents permeate the first two lines of defense and finally reach the cytoplasm, many bacteria will make use of the third line of defense, including alterations of intracellular materials and gene regulation to protect themselves from harm by bactericides. The presented three lines of defense theory will help us to understand the bacterial resistance mechanisms against antimicrobial agents and design efficient strategies to overcome these resistances.
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Affiliation(s)
- Gang Zhou
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Qing-Shan Shi
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Mo Huang
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Bao Xie
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
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431
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Gillings MR, Paulsen IT, Tetu SG. Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics. Genes (Basel) 2015; 6:841-57. [PMID: 26371047 PMCID: PMC4584332 DOI: 10.3390/genes6030841] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Abstract
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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432
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Zhao JY, Mu XD, Zhu YQ, Xi L, Xiao Z. Identification of an integron containing the quinolone resistance geneqnrA1inShewanella xiamenensis. FEMS Microbiol Lett 2015; 362:fnv146. [DOI: 10.1093/femsle/fnv146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2015] [Indexed: 01/03/2023] Open
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433
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Malek MM, Amer FA, Allam AA, El-Sokkary RH, Gheith T, Arafa MA. Occurrence of classes I and II integrons in Enterobacteriaceae collected from Zagazig University Hospitals, Egypt. Front Microbiol 2015; 6:601. [PMID: 26157425 PMCID: PMC4477160 DOI: 10.3389/fmicb.2015.00601] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/01/2015] [Indexed: 12/30/2022] Open
Abstract
Integrons are genetic units characterized by the ability to capture and incorporate gene cassettes, thus can contribute to the emergence and transfer of antibiotic resistance. The objectives of this study were: (1) to investigate the presence and distribution of class I and class II integrons and the characteristics of the gene cassettes they carry in Enterobacteriaceae isolated from nosocomial infections at Zagzig University Hospital in Egypt, (2) to determine their impact on resistance, and (3) to identify risk factors for the existence of integrons. Relevant samples and full clinical history were collected from 118 inpatients. Samples were processed; isolated microbes were identified and tested for antibiotic susceptibilities. Integrons were detected by polymerase chain reaction (PCR) and were characterized into class I or II by restriction fragment length polymorphism (RFLP). Integron-positive isolates were subjected to another PCR to detect gene cassette, followed by gene cassette sequencing. Risk factors were analyzed by logistic regression analysis. Seventy-six Enterobacteriaceae isolates were recognized, 41 of them (53.9%) were integron-positive; 39 strains carried class I and 2 strains carried class II integrons. Integrons had gene cassettes encoding different combinations and types of resistance determinants. Interestingly, blaOXA129 gene was found and ereA gene was carried on class I integrons. The same determinants were carried within isolates of the same species as well as isolates of different species. The presence of integrons was significantly associated with multidrug resistance (MDR). No risk factors were associated for integron carriage. We conclude that integrons carrying gene cassettes encoding antibiotic resistance are significantly present among Enterobacteriaceae causing nosocomial infection in our hospital. Risk factors for acquisition remain to be identified.
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Affiliation(s)
- Mai M. Malek
- Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig UniversityCairo, Egypt
| | - Fatma A. Amer
- Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig UniversityCairo, Egypt
| | - Ayman A. Allam
- Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig UniversityCairo, Egypt
| | - Rehab H. El-Sokkary
- Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig UniversityCairo, Egypt
| | - Tarek Gheith
- Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig UniversityCairo, Egypt
| | - Mohamed A. Arafa
- Pediatrics Department, Faculty of Medicine, Zagazig UniversityZagazig, Egypt
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434
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Waldron LS, Gillings MR. Screening Foodstuffs for Class 1 Integrons and Gene Cassettes. J Vis Exp 2015:e52889. [PMID: 26132232 DOI: 10.3791/52889] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Antibiotic resistance is one of the greatest threats to health in the 21st century. Acquisition of resistance genes via lateral gene transfer is a major factor in the spread of diverse resistance mechanisms. Amongst the DNA elements facilitating lateral transfer, the class 1 integrons have largely been responsible for spreading antibiotic resistance determinants amongst Gram negative pathogens. In total, these integrons have acquired and disseminated over 130 different antibiotic resistance genes. With continued antibiotic use, class 1 integrons have become ubiquitous in commensals and pathogens of humans and their domesticated animals. As a consequence, they can now be found in all human waste streams, where they continue to acquire new genes, and have the potential to cycle back into humans via the food chain. This protocol details a streamlined approach for detecting class 1 integrons and their associated resistance gene cassettes in foodstuffs, using culturing and PCR. Using this protocol, researchers should be able to: collect and prepare samples to make enriched cultures and screen for class 1 integrons; isolate single bacterial colonies to identify integron-positive isolates; identify bacterial species that contain class 1 integrons; and characterize these integrons and their associated gene cassettes.
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435
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Anes J, McCusker MP, Fanning S, Martins M. The ins and outs of RND efflux pumps in Escherichia coli. Front Microbiol 2015; 6:587. [PMID: 26113845 PMCID: PMC4462101 DOI: 10.3389/fmicb.2015.00587] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/28/2015] [Indexed: 11/13/2022] Open
Abstract
Infectious diseases remain one of the principal causes of morbidity and mortality in the world. Relevant authorities including the WHO and CDC have expressed serious concern regarding the continued increase in the development of multidrug resistance among bacteria. They have also reaffirmed the urgent need for investment in the discovery and development of new antibiotics and therapeutic approaches to treat multidrug resistant (MDR) bacteria. The extensive use of antimicrobial compounds in diverse environments, including farming and healthcare, has been identified as one of the main causes for the emergence of MDR bacteria. Induced selective pressure has led bacteria to develop new strategies of defense against these chemicals. Bacteria can accomplish this by several mechanisms, including enzymatic inactivation of the target compound; decreased cell permeability; target protection and/or overproduction; altered target site/enzyme and increased efflux due to over-expression of efflux pumps. Efflux pumps can be specific for a single substrate or can confer resistance to multiple antimicrobials by facilitating the extrusion of a broad range of compounds including antibiotics, heavy metals, biocides and others, from the bacterial cell. To overcome antimicrobial resistance caused by active efflux, efforts are required to better understand the fundamentals of drug efflux mechanisms. There is also a need to elucidate how these mechanisms are regulated and how they respond upon exposure to antimicrobials. Understanding these will allow the development of combined therapies using efflux inhibitors together with antibiotics to act on Gram-negative bacteria, such as the emerging globally disseminated MDR pathogen Escherichia coli ST131 (O25:H4). This review will summarize the current knowledge on resistance-nodulation-cell division efflux mechanisms in E. coli, a bacteria responsible for community and hospital-acquired infections, as well as foodborne outbreaks worldwide.
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Affiliation(s)
- João Anes
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Matthew P McCusker
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Marta Martins
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
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436
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Quaternary ammonium disinfectants: microbial adaptation, degradation and ecology. Curr Opin Biotechnol 2015; 33:296-304. [DOI: 10.1016/j.copbio.2015.03.018] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 03/22/2015] [Accepted: 03/26/2015] [Indexed: 11/18/2022]
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437
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Yahiaoui M, Robin F, Bakour R, Hamidi M, Bonnet R, Messai Y. Antibiotic Resistance, Virulence, and Genetic Background of Community-Acquired Uropathogenic Escherichia coli from Algeria. Microb Drug Resist 2015; 21:516-26. [PMID: 26430940 DOI: 10.1089/mdr.2015.0045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to investigate antibiotic resistance mechanisms, virulence traits, and genetic background of 150 nonrepetitive community-acquired uropathogenic Escherichia coli (CA-UPEC) from Algeria. A rate of 46.7% of isolates was multidrug resistant. bla genes detected were blaTEM (96.8% of amoxicillin-resistant isolates), blaCTX-M-15 (4%), overexpressed blaAmpC (4%), blaSHV-2a, blaTEM-4, blaTEM-31, and blaTEM-35 (0.7%). All tetracycline-resistant isolates (51.3%) had tetA and/or tetB genes. Sulfonamides and trimethoprim resistance genes were sul2 (60.8%), sul1 (45.9%), sul3 (6.7%), dfrA14 (25.4%), dfrA1 (18.2%), dfrA12 (16.3%), and dfrA25 (5.4%). High-level fluoroquinolone resistance (22.7%) was mediated by mutations in gyrA (S83L-D87N) and parC (S80I-E84G/V or S80I) genes. qnrB5, qnrS1, and aac(6')-Ib-cr were rare (5.3%). Class 1 and/or class 2 integrons were detected (40.7%). Isolates belonged to phylogroups B2+D (50%), A+B1 (36%), and F+C+Clade I (13%). Most of D (72.2%) and 38.6% of B2 isolates were multidrug resistant; they belong to 14 different sequence types, including international successful ST131, ST73, and ST69, reported for the first time in the community in Algeria and new ST4494 and ST4529 described in this study. Besides multidrug resistance, B2 and D isolates possessed virulence factors of colonization, invasion, and long-term persistence. The study highlighted multidrug-resistant CA-UPEC with high virulence traits and an epidemic genetic background.
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Affiliation(s)
- Merzouk Yahiaoui
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | - Frédéric Robin
- 2 CHU Clermont-Ferrand, Laboratoire de Bactériologie , Clermont-Ferrand, France .,3 Clermont Université, Université d'Auvergne , Evolution des Bactéries Pathogènes et Susceptibilité de l'Hôte, Clermont-Ferrand, France
| | - Rabah Bakour
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | | | - Richard Bonnet
- 2 CHU Clermont-Ferrand, Laboratoire de Bactériologie , Clermont-Ferrand, France .,3 Clermont Université, Université d'Auvergne , Evolution des Bactéries Pathogènes et Susceptibilité de l'Hôte, Clermont-Ferrand, France
| | - Yamina Messai
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
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438
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Jechalke S, Broszat M, Lang F, Siebe C, Smalla K, Grohmann E. Effects of 100 years wastewater irrigation on resistance genes, class 1 integrons and IncP-1 plasmids in Mexican soil. Front Microbiol 2015; 6:163. [PMID: 25784901 PMCID: PMC4347510 DOI: 10.3389/fmicb.2015.00163] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/12/2015] [Indexed: 12/12/2022] Open
Abstract
Long-term irrigation with untreated wastewater can lead to an accumulation of antibiotic substances and antibiotic resistance genes in soil. However, little is known so far about effects of wastewater, applied for decades, on the abundance of IncP-1 plasmids and class 1 integrons which may contribute to the accumulation and spread of resistance genes in the environment, and their correlation with heavy metal concentrations. Therefore, a chronosequence of soils that were irrigated with wastewater from 0 to 100 years was sampled in the Mezquital Valley in Mexico in the dry season. The total community DNA was extracted and the absolute and relative abundance (relative to 16S rRNA genes) of antibiotic resistance genes (tet(W), tet(Q), aadA), class 1 integrons (intI1), quaternary ammonium compound resistance genes (qacE+qacEΔ1) and IncP-1 plasmids (korB) were quantified by real-time PCR. Except for intI1 and qacE+qacEΔ1 the abundances of selected genes were below the detection limit in non-irrigated soil. Confirming the results of a previous study, the absolute abundance of 16S rRNA genes in the samples increased significantly over time (linear regression model, p < 0.05) suggesting an increase in bacterial biomass due to repeated irrigation with wastewater. Correspondingly, all tested antibiotic resistance genes as well as intI1 and korB significantly increased in abundance over the period of 100 years of irrigation. In parallel, concentrations of the heavy metals Zn, Cu, Pb, Ni, and Cr significantly increased. However, no significant positive correlations were observed between the relative abundance of selected genes and years of irrigation, indicating no enrichment in the soil bacterial community due to repeated wastewater irrigation or due to a potential co-selection by increasing concentrations of heavy metals.
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Affiliation(s)
- Sven Jechalke
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI) Braunschweig, Germany
| | - Melanie Broszat
- Department of Infectious Diseases, University Hospital Freiburg Freiburg, Germany ; Microbiology, Faculty for Biology, Albert-Ludwigs-University Freiburg Freiburg, Germany
| | - Friederike Lang
- Chair of Soil Ecology, Albert-Ludwigs-University Freiburg Freiburg, Germany
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria Mexico City, Mexico
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI) Braunschweig, Germany
| | - Elisabeth Grohmann
- Department of Infectious Diseases, University Hospital Freiburg Freiburg, Germany ; Microbiology, Faculty for Biology, Albert-Ludwigs-University Freiburg Freiburg, Germany
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439
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Christgen B, Yang Y, Ahammad SZ, Li B, Rodriquez DC, Zhang T, Graham DW. Metagenomics shows that low-energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene levels from domestic wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2577-2584. [PMID: 25603149 DOI: 10.1021/es505521w] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Effective domestic wastewater treatment is among our primary defenses against the dissemination of infectious waterborne disease. However, reducing the amount of energy used in treatment processes has become essential for the future. One low-energy treatment option is anaerobic-aerobic sequence (AAS) bioreactors, which use an anaerobic pretreatment step (e.g., anaerobic hybrid reactors) to reduce carbon levels, followed by some form of aerobic treatment. Although AAS is common in warm climates, it is not known how its compares to other treatment options relative to disease transmission, including its influence on antibiotic resistance (AR) in treated effluents. Here, we used metagenomic approaches to contrast the fate of antibiotic-resistant genes (ARG) in anaerobic, aerobic, and AAS bioreactors treating domestic wastewater. Five reactor configurations were monitored for 6 months, and treatment performance, energy use, and ARG abundance and diversity were compared in influents and effluents. AAS and aerobic reactors were superior to anaerobic units in reducing ARG-like sequence abundances, with effluent ARG levels of 29, 34, and 74 ppm (198 ppm influent), respectively. AAS and aerobic systems especially reduced aminoglycoside, tetracycline, and β-lactam ARG levels relative to anaerobic units, although 63 persistent ARG subtypes were detected in effluents from all systems (of 234 assessed). Sulfonamide and chloramphenicol ARG levels were largely unaffected by treatment, whereas a broad shift from target-specific ARGs to ARGs associated with multi-drug resistance was seen across influents and effluents. AAS reactors show promise for future applications because they can reduce more ARGs for less energy (32% less energy here), but all three treatment options have limitations and need further study.
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Affiliation(s)
- Beate Christgen
- School of Civil Engineering and Geosciences, Newcastle University , Newcastle upon Tyne NE1 7RU, United Kingdom
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440
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Zeighami H, Haghi F, Masumian N, Hemmati F, Samei A, Naderi G. Distribution of Integrons and Gene Cassettes Among Uropathogenic and Diarrheagenic Escherichia coli Isolates in Iran. Microb Drug Resist 2015; 21:435-40. [PMID: 25658172 DOI: 10.1089/mdr.2014.0147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Integrons are considered to play a significant role in the evolution and spread of antimicrobial resistance genes. A total of 200 uropathogenic (UPEC) and diarrheagenic Escherichia coli (DEC) isolates from outpatients were investigated for antimicrobial susceptibility and the presence of class 1, 2, and 3 integron-associated integrase (intI) genes and gene cassettes. Conjugal transfer and Southern hybridization were performed to determine the genetic localization of class 1 integrons. One hundred ninety-two (96%) isolates were resistant to one or more antimicrobial agents. Antimicrobial resistance among DEC isolates was higher compared with the UPEC. Integrons were highly prevalent in both pathotypes (92.5%). Comparison of integrons among UPEC and DEC showed that DEC isolates harbored integrases (94% for intI1, 8% for intI2) with a slightly higher frequency than in UPEC isolates (87% for intI1, 7% for intI2) (p>0.05). Dihydrofolate reductase (dfrA) and aminoglycoside adenyl transferase (aad) gene cassettes were found most frequently in intI1-positive isolates. All isolates carried their class 1 integrons on conjugative plasmids. These results indicate that class 1 integrons are widespread among E. coli isolates. Therefore, appropriate surveillance and control measures are essential to prevent the further spread of integron-producing isolates.
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Affiliation(s)
- Habib Zeighami
- 1 Department of Microbiology, Zanjan University of Medical Sciences , Zanjan, Iran
| | - Fakhri Haghi
- 1 Department of Microbiology, Zanjan University of Medical Sciences , Zanjan, Iran
| | - Neda Masumian
- 2 Department of Microbiology, Zanjan Islamic Azad University , Zanjan, Iran
| | - Fatemeh Hemmati
- 1 Department of Microbiology, Zanjan University of Medical Sciences , Zanjan, Iran
| | - Ali Samei
- 1 Department of Microbiology, Zanjan University of Medical Sciences , Zanjan, Iran
| | - Ghazal Naderi
- 1 Department of Microbiology, Zanjan University of Medical Sciences , Zanjan, Iran
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441
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Wolters B, Kyselková M, Krögerrecklenfort E, Kreuzig R, Smalla K. Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup. Front Microbiol 2015; 5:765. [PMID: 25653641 PMCID: PMC4301011 DOI: 10.3389/fmicb.2014.00765] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/30/2022] Open
Abstract
Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.
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Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany ; Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry Braunschweig, Germany
| | - Martina Kyselková
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology České Budějovice, Czech Republic
| | - Ellen Krögerrecklenfort
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany
| | - Robert Kreuzig
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany
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442
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Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME JOURNAL 2014; 9:1269-79. [PMID: 25500508 PMCID: PMC4438328 DOI: 10.1038/ismej.2014.226] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital, Truro, UK
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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443
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Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front Microbiol 2014; 5:648. [PMID: 25520706 PMCID: PMC4251439 DOI: 10.3389/fmicb.2014.00648] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/07/2014] [Indexed: 11/27/2022] Open
Abstract
There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Fredrik Boulund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
| | - Jerker Fick
- Department of Chemistry, Umeå University Umeå, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
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444
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Graham DW, Collignon P, Davies J, Larsson DGJ, Snape J. Underappreciated role of regionally poor water quality on globally increasing antibiotic resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:11746-11747. [PMID: 25330712 DOI: 10.1021/es504206x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- David W Graham
- School of Civil Engineering & Geosciences, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K
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445
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Michael CA, Dominey-Howes D, Labbate M. The antimicrobial resistance crisis: causes, consequences, and management. Front Public Health 2014; 2:145. [PMID: 25279369 PMCID: PMC4165128 DOI: 10.3389/fpubh.2014.00145] [Citation(s) in RCA: 468] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 09/01/2014] [Indexed: 12/31/2022] Open
Abstract
The antimicrobial resistance (AMR) crisis is the increasing global incidence of infectious diseases affecting the human population, which are untreatable with any known antimicrobial agent. This crisis will have a devastating cost on human society as both debilitating and lethal diseases increase in frequency and scope. Three major factors determine this crisis: (1) the increasing frequency of AMR phenotypes among microbes is an evolutionary response to the widespread use of antimicrobials; (2) the large and globally connected human population allows pathogens in any environment access to all of humanity; and (3) the extensive and often unnecessary use of antimicrobials by humanity provides the strong selective pressure that is driving the evolutionary response in the microbial world. Of these factors, the size of the human population is least amenable to rapid change. In contrast, the remaining two factors may be affected, so offering a means of managing the crisis: the rate at which AMR, as well as virulence factors evolve in microbial world may be slowed by reducing the applied selective pressure. This may be accomplished by radically reducing the global use of current and prospective antimicrobials. Current management measures to legislate the use of antimicrobials and to educate the healthcare world in the issues, while useful, have not comprehensively addressed the problem of achieving an overall reduction in the human use of antimicrobials. We propose that in addition to current measures and increased research into new antimicrobials and diagnostics, a comprehensive education program will be required to change the public paradigm of antimicrobial usage from that of a first line treatment to that of a last resort when all other therapeutic options have failed.
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Affiliation(s)
- Carolyn Anne Michael
- School of Medical and Molecular Biosciences, University of Technology , Sydney, NSW , Australia
| | - Dale Dominey-Howes
- Asia - Pacific Natural Hazards Research Group, School of Geosciences, University of Sydney , Sydney, NSW , Australia
| | - Maurizio Labbate
- School of Medical and Molecular Biosciences, University of Technology , Sydney, NSW , Australia ; ithree Institute, University of Technology , Sydney, NSW , Australia
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