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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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2
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Koh XP, Shen Z, Woo CF, Yu Y, Lun HI, Cheung SW, Kwan JKC, Lau SCK. Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments. Front Microbiol 2022; 13:811755. [PMID: 35250929 PMCID: PMC8891540 DOI: 10.3389/fmicb.2022.811755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli not only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, cryptic Escherichia clades that were often misidentified as E. coli by conventional diagnostic methods were discovered. Failure to distinguish them from E. coli sensu stricto could lead to inaccurate conclusions about the population genetics of E. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity of E. coli and cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated with E. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades and E. coli showed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typical E. coli; some may even represent novel environmental Escherichia clades that were closely related to the original clade II strains of fecal origins. E. coli of diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonal E. coli. Notably, environmental E. coli were less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution of E. coli and clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and new E. coli genotypes reduces, while E. coli bearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity of E. coli and cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.
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Affiliation(s)
- Xiu Pei Koh
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Zhiyong Shen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Chun Fai Woo
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yanping Yu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Hau In Lun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Sze Wan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China
| | - Joseph Kai Cho Kwan
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Stanley Chun Kwan Lau
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Stanley Chun Kwan Lau,
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Fulham M, McDougall F, Power M, McIntosh RR, Gray R. Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups. PLoS One 2022; 17:e0258978. [PMID: 35089935 PMCID: PMC8797192 DOI: 10.1371/journal.pone.0258978] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants of AMR have become indicators of anthropogenic pollution due to their greater association with humans and rarer presence in environments less affected by humans. The objective of this study was to determine the distribution and frequency of the class 1 integron, a genetic determinant of AMR, in both the faecal microbiome and in Escherichia coli isolated from neonates of three pinniped species. Australian sea lion (Neophoca cinerea), Australian fur seal (Arctocephalus pusillus doriferus) and long-nosed fur seal (Arctocephalus forsteri) pups from eight breeding colonies along the Southern Australian coast were sampled between 2016-2019. DNA from faecal samples (n = 309) and from E. coli (n = 795) isolated from 884 faecal samples were analysed for class 1 integrons using PCRs targeting the conserved integrase gene (intI) and the gene cassette array. Class 1 integrons were detected in A. p. doriferus and N. cinerea pups sampled at seven of the eight breeding colonies investigated in 4.85% of faecal samples (n = 15) and 4.52% of E. coli isolates (n = 36). Integrons were not detected in any A. forsteri samples. DNA sequencing of the class 1 integron gene cassette array identified diverse genes conferring resistance to four antibiotic classes. The relationship between class 1 integron carriage and the concentration of five trace elements and heavy metals was also investigated, finding no significant association. The results of this study add to the growing evidence of the extent to which antimicrobial resistant bacteria are polluting the marine environment. As AMR determinants are frequently associated with bacterial pathogens, their occurrence suggests that these pinniped species are vulnerable to potential health risks. The implications for individual and population health as a consequence of AMR carriage is a critical component of ongoing health investigations.
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Affiliation(s)
- Mariel Fulham
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Fiona McDougall
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, New South Wales, Australia
| | - Michelle Power
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, New South Wales, Australia
| | | | - Rachael Gray
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
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Lüneberg K, Amábile-Cuevas CF, Mucito-Varela E, Martínez L, Salinas E, López-Vidal Y, Siebe C, Rosas I. Metallo-beta-lactamase-producing Escherichia coli in the sewage of Mexico City: where do they come from? Can J Microbiol 2021; 68:139-145. [PMID: 34662521 DOI: 10.1139/cjm-2021-0284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
While monitoring the presence of antibiotic resistance in municipal wastewater bacteria from Mexico City, five Escherichia coli isolates were found to be resistant to carbapenems, antibiotics of "last resort" used mostly in hospitals. Further analysis revealed that these carbapenem-resistant isolates carried the gene encoding a metallo-beta-lactamase, NDM-5. The gene was found to be beared by a large, ∼145 kb conjugative plasmid, which also carries putative genes encoding resistance to sulfonamides, trimethoprim, tetracycline, ciprofloxacin, and chloramphenicol (although no phenotypic chloramphenicol resistance was detected) and quaternary-ammonium compounds. The plasmid also carried gene mobility determinants, such as integron integrase and two transposases. In addition to the direct public health threat posed by the presence of such multi-resistant organisms in wastewater released into the environment and used for crop irrigation; it is particularly concerning that carbapenem-resistant E. coli is rather rare in Mexican hospitals (<1%), but was found in small, 100 mL samples of municipal wastewater. This suggests that these organisms are under-reported by clinical microbiology laboratories, underlining the usefulness of wastewater monitoring, or that there is an unknown source of such carbapenem-resistant organisms that are being dumped into the wastewater. The source of these bacteria must be assessed and controlled to prevent further spread of this multi-resistance plasmid among other environmental and clinical microorganisms.
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Affiliation(s)
- Kathia Lüneberg
- Laboratorio de Aerobiología, Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Eduardo Mucito-Varela
- Programa de Inmunología Molecular Microbiana, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leticia Martínez
- Laboratorio de Aerobiología, Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eva Salinas
- Laboratorio de Aerobiología, Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christina Siebe
- Departamento de Ciencias Ambientales y del Suelo, Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Irma Rosas
- Laboratorio de Aerobiología, Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Rao S, Linke L, Doster E, Hyatt D, Burgess BA, Magnuson R, Pabilonia KL, Morley PS. Genomic diversity of class I integrons from antimicrobial resistant strains of Salmonella Typhimurium isolated from livestock, poultry and humans. PLoS One 2020; 15:e0243477. [PMID: 33306723 PMCID: PMC7732114 DOI: 10.1371/journal.pone.0243477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022] Open
Abstract
Introduction Multidrug resistance (MDR) is a serious issue prevalent in various agriculture-related foodborne pathogens including Salmonella enterica (S. enterica) Typhimurium. Class I integrons have been detected in Salmonella spp. strains isolated from food producing animals and humans and likely play a critical role in transmitting antimicrobial resistance within and between livestock and human populations. Objective The main objective of our study was to characterize class I integron presence to identify possible integron diversity among and between antimicrobial resistant Salmonella Typhimurium isolates from various host species, including humans, cattle, swine, and poultry. Methods An association between integron presence with multidrug resistance was evaluated. One hundred and eighty-three S. Typhimurium isolates were tested for antimicrobial resistance (AMR). Class I integrons were detected and sequenced. Similarity of AMR patterns between host species was also studied within each integron type. Results One hundred seventy-four (95.1%) of 183 S.Typhimurium isolates were resistant to at least one antimicrobial and 82 (44.8%) were resistant to 5 or more antimicrobials. The majority of isolates resistant to at least one antimicrobial was from humans (45.9%), followed by swine (19.1%) and then bovine (16.9%) isolates; poultry showed the lowest number (13.1%) of resistant isolates. Our study has demonstrated high occurrence of class I integrons in S. Typhimurium across different host species. Only one integron size was detected in poultry isolates. There was a significant association between integron presence of any size and specific multidrug resistance pattern among the isolates from human, bovine and swine. Conclusions Our study has demonstrated a high occurrence of class I integrons of different sizes in Salmonella Typhimurium across various host species and their association with multidrug resistance. This demonstration indicates that multidrug resistant Salmonella Typhimurium is of significant public health occurrence and reflects on the importance of judicious use of antimicrobials among livestock and poultry.
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Affiliation(s)
- Sangeeta Rao
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, CO, United States of America
- * E-mail:
| | - Lyndsey Linke
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, CO, United States of America
| | - Enrique Doster
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, United States of America
- Veterinary Education, Research, and Outreach Program, Texas A&M University and West Texas A&M University, College Station, TX, United States of America
| | - Doreene Hyatt
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Brandy A. Burgess
- College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
| | - Roberta Magnuson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, CO, United States of America
| | - Kristy L. Pabilonia
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, CO, United States of America
| | - Paul S. Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University and West Texas A&M University, College Station, TX, United States of America
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Characterization of antibiotic resistance integrons harbored by Romanian Escherichia coli uropathogenic strains. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Because little is known about the integrons which constitute an important means of spreading resistance in bacteria circulating in Romania, this study aimed to detect antibiotic resistance gene cassettes embedded in integrons in a convenient collection of 60 ciprofloxacin-resistant Escherichia coli isolates of various phylogroups, associated with community-acquired urinary tract infections. Characterization of the integrons was accomplished by PCR, restriction fragment length polymorphism typing, and DNA sequencing of each identified type. More than half of the tested E. coli strains were positive for integrons of class 1 (31 strains) or 2 (1 strain). These strains derived more frequently from phylogenetic groups A (15 of 21 strains), B1 (10 of 14 strains), and F (3 of 4 strains), respectively. While 20 strains carried class 1 integrons which could be assigned to nine types, eleven strains carried integrons that lacked the 3’-end conserved segment. The attempts made to characterize the gene cassettes located within the variable region of the various integrons identified in this study revealed the presence of genes encoding resistance to trimethoprim, aminoglycosides, beta-lactams or chloramphenicol. The evidence of transferable resistance determinants already established in the autochthonous E. coli strains highlights the need for improved control of resistance-carrying bacteria.
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Sütterlin S, Bray JE, Maiden MCJ, Tano E. Distribution of class 1 integrons in historic and contemporary collections of human pathogenic Escherichia coli. PLoS One 2020; 15:e0233315. [PMID: 32484827 PMCID: PMC7266292 DOI: 10.1371/journal.pone.0233315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/01/2020] [Indexed: 02/07/2023] Open
Abstract
Integrons play a major role in the evolution and spread of antimicrobial resistance in human pathogens, including Escherichia coli. This study describes the occurrence of class 1 integrons in human pathogenic E. coli, in three isolate collections involving three periods from the last 100 years (i) the Murray collection (n = 58 bacteria isolated from the 1910s to 1940s); (ii) the E. coli reference (ECOR) collection (n = 37 isolates mainly from the 1980s); and (iii) a recently assembled collection (n = 88 isolates obtained in 2016). High-quality whole genome sequences (WGSs) were available for all isolates. Integrons were detected in the WGSs with the program IntegronFinder and the results compared with three established methods: (i) polymerase chain reaction detection of the integrase gene; (ii) BLAST searching using draft genomes; and (iii) mapping of short reads. No integrons were found in any of the Murray Collection isolates; however, integrons were present in 3% of the isolates from ECOR collection, assembled in the 1980s, and 26% of the isolates from the 2010s. Similarly, antimicrobial resistance determinants were not present in the Murray Collection isolates, whereas they were present in 19% of the ECOR Collection isolates and in 55% of the isolates obtained in during the 2010s.
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Affiliation(s)
- Susanne Sütterlin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Women’s and Child’s Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
- * E-mail:
| | - James E. Bray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Eva Tano
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Afema JA, Davis MA, Sischo WM. Antimicrobial use policy change in pre-weaned dairy calves and its impact on antimicrobial resistance in commensal Escherichia coli: a cross sectional and ecological study. BMC Microbiol 2019; 19:217. [PMID: 31514734 PMCID: PMC6739941 DOI: 10.1186/s12866-019-1576-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/25/2019] [Indexed: 12/02/2022] Open
Abstract
Background This study is based on data collected to investigate the relation of peri-parturient events (colostrum quality, passive transfer of immunity, calving difficulty) on calf health and antimicrobial use. A component of the study was to provide feedback to farm management to identify calves at risk for disease and promote antimicrobial stewardship. At the start of the study (May 2016), a combination of enrofloxacin, penicillin, and sulfamethoxazole was the first treatment given to clinically abnormal calves. Based on feedback and interaction between study investigators, farm management and consulting veterinarians, a new policy was implemented to reduce antimicrobial use in calves. In August, the first treatment was changed to a combination of ampicillin and sulfamethoxazole. In September, the first treatment was reduced to only sulfamethoxazole. We investigated the effects of these policy changes in antimicrobial use on resistance in commensal Escherichia coli. Results We enrolled 4301 calves at birth and documented antimicrobial use until weaning. Most calves (99.4%) received antimicrobials and 70.4% received a total of 2–4 treatments. Antimicrobial use was more intense in younger calves (≤ 28 days) relative to older calves. We isolated 544 E. coli from fecal samples obtained from 132 calves. We determined resistance to 12 antimicrobials and 85% of the isolates were resistant to at least 3 antimicrobial classes. We performed latent class analysis to identify underlying unique classes where isolates shared resistance patterns and selected a solution with 4 classes. The least resistant class had isolates that were mainly resistant to only tetracycline and sulfisoxazole. The other 3 classes comprised isolates with resistance to ampicillin, chloramphenicol, aminoglycosides, sulfonamides, tetracycline, in addition to either ceftiofur; or nalidixic acid; or ciprofloxacin plus nalidixic acid and ceftiofur. Overall, E coli from younger calves and calves that received multiple treatments were more likely to have extensive resistance including resistance to fluoroquinolones and ceftiofur. In general, there was a declining trend in resistance to most antimicrobials during and after policy changes were implemented, except for ampicillin, ciprofloxacin, ceftiofur and gentamicin. Conclusions Information feedback to farms can influence farm managers to reduce antimicrobial use and this can change endemic farm resistance patterns. Electronic supplementary material The online version of this article (10.1186/s12866-019-1576-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josephine A Afema
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA.,Department of Pathobiology, School of Veterinary Medicine, St. George's University, Saint George's, Grenada
| | - Margaret A Davis
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - William M Sischo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, P. O. Box 646610, Pullman, WA, 99164-7090, USA.
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Uyaguari-Díaz MI, Croxen MA, Luo Z, Cronin KI, Chan M, Baticados WN, Nesbitt MJ, Li S, Miller KM, Dooley D, Hsiao W, Isaac-Renton JL, Tang P, Prystajecky N. Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Front Microbiol 2018; 9:852. [PMID: 29765365 PMCID: PMC5938356 DOI: 10.3389/fmicb.2018.00852] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.
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Affiliation(s)
- Miguel I Uyaguari-Díaz
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Matthew A Croxen
- Provincial Laboratory for Public Health, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiyao Luo
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Kirby I Cronin
- Laboratory Services, Public Health Ontario, Toronto, ON, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael Chan
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Waren N Baticados
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Shaorong Li
- Pacific Biological Station, Nanaimo, BC, Canada
| | | | - Damion Dooley
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - William Hsiao
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Judith L Isaac-Renton
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Natalie Prystajecky
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
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Vázquez-Rosas-Landa M, Ponce-Soto GY, Eguiarte LE, Souza V. Comparative genomics of free-living Gammaproteobacteria: pathogenesis-related genes or interaction-related genes? Pathog Dis 2017; 75:3861975. [DOI: 10.1093/femspd/ftx059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022] Open
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11
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Oliveira-Pinto C, Diamantino C, Oliveira PL, Reis MP, Costa PS, Paiva MC, Nardi RMD, Magalhães PP, Chartone-Souza E, Nascimento AMA. Occurrence and characterization of class 1 integrons in Escherichia coli from healthy individuals and those with urinary infection. J Med Microbiol 2017; 66:577-583. [DOI: 10.1099/jmm.0.000468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Clarisse Oliveira-Pinto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Cristiane Diamantino
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia L Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Magna C Paiva
- Campus Dona Lindu, Universidade Federal de São João del Rei, Divinópolis, Minas Gerais, Brazil
| | - Regina M. D Nardi
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Paula P Magalhães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Andréa M. A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
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12
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Xu X, Li X, Luo M, Liu P, Su K, Qing Y, Chen S, Qiu J, Li Y. Molecular characterisations of integrons in clinical isolates of Klebsiella pneumoniae in a Chinese tertiary hospital. Microb Pathog 2017; 104:164-170. [DOI: 10.1016/j.micpath.2017.01.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/15/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
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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: 178] [Impact Index Per Article: 22.3] [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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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: 1.9] [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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Srivastava J, Chandra H, Nautiyal AR, Kalra SJS. Antimicrobial resistance (AMR) and plant-derived antimicrobials (PDA ms) as an alternative drug line to control infections. 3 Biotech 2014; 4:451-460. [PMID: 28324380 PMCID: PMC4162903 DOI: 10.1007/s13205-013-0180-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/07/2013] [Indexed: 12/26/2022] Open
Abstract
Infectious diseases caused by antimicrobial-resistant microbes (ARMs) and the treatment are the serious problems in the field of medical science today world over. The development of alternative drug line to treat such infectious diseases is urgently required. Researches on ARMs revealed the presence of membrane proteins responsible for effusing the antibiotics from the bacterial cells. Such proteins have successfully been treated by plant-derived antimicrobials (PDAms) synergistically along with the commercially available antibiotics. Such synergistic action usually inhibits the efflux pump. The enhanced activity of plant-derived antimicrobials is being researched and is considered as the future treatment strategy to cure the incurable infections. The present paper reviews the advancement made in the researches on antimicrobial resistance along with the discovery and the development of more active PDAms.
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Affiliation(s)
- Jatin Srivastava
- Department of Applied Sciences, Faculty of Environmental Science, Himalayan Institute of Technology and Management, BKT, NH 24, Lucknow, 227005, UP, India.
| | - Harish Chandra
- Department of Medicinal and Aromatic Plants, School of Agriculture and Allied Sciences, High Altitude Plant Physiology Research Center, H.N.B. Garhwal University, Srinagar, Uttrakhand, India
| | - Anant R Nautiyal
- Department of Medicinal and Aromatic Plants, School of Agriculture and Allied Sciences, High Altitude Plant Physiology Research Center, H.N.B. Garhwal University, Srinagar, Uttrakhand, India
| | - Swinder J S Kalra
- Department of Chemistry, Dayanand Anglo Vedic College, Civil Lines, Kanpur, UP, India
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Cristóbal-Azkarate J, Dunn JC, Day JMW, Amábile-Cuevas CF. Resistance to antibiotics of clinical relevance in the fecal microbiota of Mexican wildlife. PLoS One 2014; 9:e107719. [PMID: 25233089 PMCID: PMC4169449 DOI: 10.1371/journal.pone.0107719] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/21/2014] [Indexed: 11/30/2022] Open
Abstract
There are a growing number of reports of antibiotic resistance (ATBR) in bacteria living in wildlife. This is a cause for concern as ATBR in wildlife represents a potential public health threat. However, little is known about the factors that might determine the presence, abundance and dispersion of ATBR bacteria in wildlife. Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys (Alouatta palliata), spider monkeys (Ateles geoffroyi), tapirs (Tapirus bairdii) and felids (jaguars, Panthera onca; pumas, Puma concolor; jaguarundis, Puma yagouaroundi; and ocelots, Leopardus pardalis) living freely in two regions of the Mexican state of Veracruz under different degrees of human influence. Overall, our study shows that ATBR is commonplace in bacteria isolated from wildlife in southeast Mexico. Most of the resistances were towards old and naturally occurring antibiotics, but we also observed resistances of potential clinical significance. We found that proximity to humans positively affected the presence of ATBR and that ATBR was higher in terrestrial than arboreal species. We also found evidence suggesting different terrestrial and aerial routes for the transmission of ATBR between humans and wildlife. The prevalence and potential ATBR transfer mechanisms between humans and wildlife observed in this study highlight the need for further studies to identify the factors that might determine ATBR presence, abundance and distribution.
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Affiliation(s)
| | - Jacob C. Dunn
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer M. W. Day
- Center for Conservation Biology, Department of Biology, University of Washington, Seattle, Washington, United States of America
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Charnock C, Nordlie AL, Hjeltnes B. Toxin production and antibiotic resistances in Escherichia coli isolated from bathing areas along the coastline of the Oslo fjord. Curr Microbiol 2014; 69:317-28. [PMID: 24801333 DOI: 10.1007/s00284-014-0587-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/01/2014] [Indexed: 01/24/2023]
Abstract
The presence of enterovirulent and/or antibiotic resistant strains of Escherichia coli in recreational bathing waters would represent a clear health issue. In total, 144 E. coli isolated from 26 beaches along the inner Oslo fjord were examined for virulence determinants and resistance to clinically important antibiotics. No isolates possessed the genetic determinants associated with enterotoxigenic strains and none showed the prototypic sorbitol negative, O157:H7 phenotype. A small number (∼1 %) produced alpha-hemolysin. Occurrences and patterns of antibiotic resistances were similar to those of E. coli isolated previously from environmental samples. In total, 6 % of the strains showed one or more clinically relevant resistances and 1.4 % were multi-drug resistant. Microarray analyses suggested that the resistance determinants were generally associated with mobile genetic elements. Resistant strains were not clonally related, and were, furthermore not concentrated at one or a few beach sites. This suggests that these strains are entering the waters at a low rate but in a widespread manner. The study demonstrates that resistant E. coli are present in coastal bathing waters where they can come into contact with bathers, and that the resistance determinants are potentially transferable. Some of the resistances registered in the study are to important antibiotics used in human medicine such as fluoroquinolones. The spread of antibiotic resistant genes, from the clinical setting to the environment, has clear implications with respect to the current management of bacterial infections and the long term value of antimicrobial therapy. The present study is the first of its kind in Norway.
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Affiliation(s)
- Colin Charnock
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, St. Olavs Plass, Oslo, Norway,
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Zeighami H, Haghi F, Hajiahmadi F. Molecular characterization of integrons in clinical isolates of betalactamase-producing Escherichia coli and Klebsiella pneumoniae in Iran. J Chemother 2014; 27:145-51. [PMID: 24571248 DOI: 10.1179/1973947814y.0000000180] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Integrons are considered to play a significant role in the evolution and spread of antibiotic resistance genes. A total of 349 clinical isolates of Escherichia coli and Klebsiella pneumoniae were investigated for molecular characterization of integrons and betalactamases. Antimicrobial susceptibility testing was also performed as the Clinical and Laboratory Standards Institute (CLSI) guidelines. The frequency of extended spectrum betalactamases (ESBL) or metallo-betalactamases (MBL)-producing isolates, patient demographics, and the susceptibility to various antimicrobial agents were described. BlaCTX-M was the most frequently detected betalactamase in all isolates. Moreover, MBL producing K. pneumoniae carried blaIMP and blaVIM at 100 and 41·6%, respectively but no MBL-positive E. coli was detected. Class 1 integrons were more frequent among E. coli and K. pneumoniae isolates in comparison with class 2 integrons and the frequency of intI2 in K. pneumoniae was significantly higher than E. coli isolates. Five different resistance gene arrays were identified among class 1 integrons. Dihydrofolate reductase (dfrA) and aminoglycoside adenyltransferase (aad) gene cassettes were found to be predominant in the class 1 integrons. These results indicate that class 1 integrons are widespread among ESBL-producing isolates of K. pneumoniae and E. coli and appropriate surveillance and control measures are essential to prevent further dissemination of these elements among Enterobacteriaceae in our country.
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Mahmoudi-Aznaveh A, Bakhshi B, Najar-Peerayeh S, Kazemnejad A, Rafieepour Z, Rahbar M, Abbaspour S. Commensal E. coli as an Important Reservoir of Resistance Encoding Genetic Elements. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2013. [DOI: 10.17795/ijep13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Uyaguari MI, Scott GI, Norman RS. Abundance of class 1-3 integrons in South Carolina estuarine ecosystems under high and low levels of anthropogenic influence. MARINE POLLUTION BULLETIN 2013; 76:77-84. [PMID: 24095050 DOI: 10.1016/j.marpolbul.2013.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 06/02/2023]
Abstract
The impact of human activity on the spread of antibiotic resistant bacteria throughout coastal estuarine ecosystems is not well characterized. It has been suggested that laterally transferred genetic agents, such as integrons, play a role in the spread of resistant bacteria throughout ecosystems. This study compares the distribution of three integron classes throughout a coastal estuarine ecosystem. To determine integron distribution patterns, DNA was extracted from sediment and water collected at seven sites throughout two estuaries with different levels of anthropogenic input and integrons analyzed using quantitative PCR. The data show that while all three integron classes are present, the relative abundance is different, with class 2 integrons significantly elevated in areas of high anthropogenic input and class 1 integrons elevated in areas of low input. Our results provide a foundation for using integron gene distribution as a biomarker of urban impact on antibiotic resistance gene flow and ecosystem health.
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Affiliation(s)
- Miguel I Uyaguari
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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21
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Structural diversity of class 1 integrons and their associated gene cassettes in Klebsiella pneumoniae isolates from a hospital in China. PLoS One 2013; 8:e75805. [PMID: 24098729 PMCID: PMC3786929 DOI: 10.1371/journal.pone.0075805] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 08/20/2013] [Indexed: 12/02/2022] Open
Abstract
Background Klebsiella pneumoniae strains carrying class 1 integrons are becoming more common worldwide, and their role in the dissemination of drug resistance is significant. The aim of this study was to characterize the structural diversity of class 1 integrons and their associated gene cassettes in K. pneumoniae isolates from hospital settings. Methodology/Principal Findings We analyzed a total of 176 K. pneumoniae isolates in a tertiary-care hospital in Beijing, China for the period of November 1, 2010-October 31, 2011. The presence of class 1 integrons and gene cassettes was analyzed by PCR and sequencing. The prevalence of class 1 integrons was 51.1% (90/176). Fourteen different gene cassettes and 10 different gene cassette arrays were detected. dfrA and aadA cassettes were predominant and cassette combination dfrA1-orfC was most frequently found (13.6%, 24/176). Strong association between resistance to a variety of drugs (both phenotypes and the associated genes) and the presence of class 1 integrons was observed. In addition, we also identified an association between some previously identified prevalent sequence types (such as ST11, ST15, ST147, ST562, and ST716) and the presence of class 1 integrons. Conclusions/Significance Data from this study demonstrated that class 1 integrons are highly diverse and are associated with a variety of drug resistance phenotypes, drug resistance genes, as well as genotypes among K. pneumoniae isolates. Continuous monitoring of gene cassettes in class 1 integrons is warranted to improve the understanding and control of drug resistance among hospital settings.
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22
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Amábile-Cuevas CF. Antibiotic resistance: from Darwin to Lederberg to Keynes. Microb Drug Resist 2012; 19:73-87. [PMID: 23046150 DOI: 10.1089/mdr.2012.0115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The emergence and spread of antibiotic-resistant bacteria reflects both, a gradual, completely Darwinian evolution, which mostly yields slight decreases in antibiotic susceptibility, along with phenotypes that are not precisely characterized as "resistance"; and sudden changes, from full susceptibility to full resistance, which are driven by a vast array of horizontal gene transfer mechanisms. Antibiotics select for more than just antibiotic resistance (i.e., increased virulence and enhanced gene exchange abilities); and many non-antibiotic agents or conditions select for or maintain antibiotic resistance traits as a result of a complex network of underlying and often overlapping mechanisms. Thus, the development of new antibiotics and thoughtful, integrated anti-infective strategies is needed to address the immediate and long-term threat of antibiotic resistance. Since the biology of resistance is complex, these new drugs and strategies will not come from free-market forces, or from "incentives" for pharmaceutical companies.
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Nardelli M, Scalzo PM, Ramírez MS, Quiroga MP, Cassini MH, Centrón D. Class 1 integrons in environments with different degrees of urbanization. PLoS One 2012; 7:e39223. [PMID: 22761743 PMCID: PMC3382206 DOI: 10.1371/journal.pone.0039223] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 05/17/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Class 1 integrons are one of the most successful elements in the acquisition, expression and spread of antimicrobial resistance genes (ARG) among clinical isolates. Little is known about the gene flow of the components of the genetic platforms of class 1 integrons within and between bacterial communities. Thus it is important to better understand the interactions among "environmental" intI1, its genetic platforms and its distribution with human activities. METHODOLOGY/PRINCIPAL FINDINGS An evaluation of two types of genetic determinants, ARG (sul1 and qacE1/qacEΔ1 genes) and lateral genetic elements (LGE) (intI1, ISCR1 and tniC genes) in a model of a culture-based method without antibiotic selection was conducted in a gradient of anthropogenic disturbances in a Patagonian island recognized as being one of the last regions containing wild areas. The intI1, ISCR1 genes and intI1 pseudogenes that were found widespread throughout natural communities were not associated with urbanization (p>0.05). Each ARG that is embedded in the most common genetic platform of clinical class 1 integrons, showed different ecological and molecular behaviours in environmental samples. While the sul1 gene frequency was associated with urbanization, the qacE1/qacEΔ1 gene showed an adaptive role to several habitats. CONCLUSIONS/SIGNIFICANCE The high frequency of intI1 pseudogenes suggests that, although intI1 has a deleterious impact within several genomes, it can easily be disseminated among natural bacterial communities. The widespread occurrence of ISCR1 and intI1 throughout Patagonian sites with different degree of urbanization, and within different taxa, could be one of the causes of the increasing frequency of multidrug-resistant isolates that have characterized Argentina for decades. The flow of ARG and LGE between natural and clinical communities cannot be explained with a single general process but is a direct consequence of the interaction of multiple factors operating at molecular, ecological, phylogenetic and historical levels.
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Affiliation(s)
- Maximiliano Nardelli
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Marina Scalzo
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Soledad Ramírez
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Hernán Cassini
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
- Laboratorio de Biología del Comportamiento, IBYME, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
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Stalder T, Barraud O, Casellas M, Dagot C, Ploy MC. Integron involvement in environmental spread of antibiotic resistance. Front Microbiol 2012; 3:119. [PMID: 22509175 PMCID: PMC3321497 DOI: 10.3389/fmicb.2012.00119] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/13/2012] [Indexed: 11/13/2022] Open
Abstract
The spread of antibiotic-resistant bacteria is a growing problem and a public health issue. In recent decades, various genetic mechanisms involved in the spread of resistance genes among bacteria have been identified. Integrons - genetic elements that acquire, exchange, and express genes embedded within gene cassettes (GC) - are one of these mechanisms. Integrons are widely distributed, especially in Gram-negative bacteria; they are carried by mobile genetic elements, plasmids, and transposons, which promote their spread within bacterial communities. Initially studied mainly in the clinical setting for their involvement in antibiotic resistance, their role in the environment is now an increasing focus of attention. The aim of this review is to provide an in-depth analysis of recent studies of antibiotic-resistance integrons in the environment, highlighting their potential involvement in antibiotic-resistance outside the clinical context. We will focus particularly on the impact of human activities (agriculture, industries, wastewater treatment, etc.).
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Luo Y, Cui S, Li J, Yang J, Lin L, Hu C, Jin S, Ye L, Zhao Q, Ma Y. Characterization ofEscherichia coliIsolates from Healthy Food Handlers in Hospital. Microb Drug Resist 2011; 17:443-8. [PMID: 21612511 DOI: 10.1089/mdr.2011.0032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yanping Luo
- Department of Microbiology, Chinese PLA General Hospital, Beijing, China
| | - Shenghui Cui
- The National Institutes for Food and Drug Control, Beijing, China
| | - Jingyun Li
- The National Institutes for Food and Drug Control, Beijing, China
| | - Jiyong Yang
- Department of Microbiology, Chinese PLA General Hospital, Beijing, China
| | - Lan Lin
- The National Institutes for Food and Drug Control, Beijing, China
| | - Changqin Hu
- The National Institutes for Food and Drug Control, Beijing, China
| | - Shaohong Jin
- The National Institutes for Food and Drug Control, Beijing, China
| | - Liyan Ye
- Department of Microbiology, Chinese PLA General Hospital, Beijing, China
| | - Qiang Zhao
- Department of Microbiology, Chinese PLA General Hospital, Beijing, China
| | - Yue Ma
- The National Institutes for Food and Drug Control, Beijing, China
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Wu R, Alexander T, Li J, Munns K, Sharma R, McAllister T. Prevalence and diversity of class 1 integrons and resistance genes in antimicrobial-resistant Escherichia coli originating from beef cattle administered subtherapeutic antimicrobials. J Appl Microbiol 2011; 111:511-23. [DOI: 10.1111/j.1365-2672.2011.05066.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Stokes HW, Gillings MR. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 2011; 35:790-819. [PMID: 21517914 DOI: 10.1111/j.1574-6976.2011.00273.x] [Citation(s) in RCA: 372] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.
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Affiliation(s)
- Hatch W Stokes
- The i3 Institute, University of Technology, Broadway 2007, Sydney, NSW, Australia.
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Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob DNA 2011; 2:6. [PMID: 21529368 PMCID: PMC3108266 DOI: 10.1186/1759-8753-2-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 04/30/2011] [Indexed: 11/26/2022] Open
Abstract
Background Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain. Results Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes. Conclusions Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.
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Affiliation(s)
- Guillaume Cambray
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Neus Sanchez-Alberola
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Susana Campoy
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Émilie Guerin
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Sandra Da Re
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Bruno González-Zorn
- Departamento de Sanidad Animal, Facultad de Veterinaria, and VISAVET, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marie-Cécile Ploy
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Jordi Barbé
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
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Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 2010; 8:251-9. [DOI: 10.1038/nrmicro2312] [Citation(s) in RCA: 1411] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Bay DC, Turner RJ. Diversity and evolution of the small multidrug resistance protein family. BMC Evol Biol 2009; 9:140. [PMID: 19549332 PMCID: PMC2716321 DOI: 10.1186/1471-2148-9-140] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 06/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the small multidrug resistance (SMR) protein family are integral membrane proteins characterized by four alpha-helical transmembrane strands that confer resistance to a broad range of antiseptics and lipophilic quaternary ammonium compounds (QAC) in bacteria. Due to their short length and broad substrate profile, SMR proteins are suggested to be the progenitors for larger alpha-helical transporters such as the major facilitator superfamily (MFS) and drug/metabolite transporter (DMT) superfamily. To explore their evolutionary association with larger multidrug transporters, an extensive bioinformatics analysis of SMR sequences (> 300 Bacteria taxa) was performed to expand upon previous evolutionary studies of the SMR protein family and its origins. RESULTS A thorough annotation of unidentified/putative SMR sequences was performed placing sequences into each of the three SMR protein subclass designations, namely small multidrug proteins (SMP), suppressor of groEL mutations (SUG), and paired small multidrug resistance (PSMR) using protein alignments and phylogenetic analysis. Examination of SMR subclass distribution within Bacteria and Archaea taxa identified specific Bacterial classes that uniquely encode for particular SMR subclass members. The extent of selective pressure acting upon each SMR subclass was determined by calculating the rate of synonymous to non-synonymous nucleotide substitutions using Syn-SCAN analysis. SUG and SMP subclasses are maintained under moderate selection pressure in comparison to integron and plasmid encoded SMR homologues. Conversely, PSMR sequences are maintained under lower levels of selection pressure, where one of the two PSMR pairs diverges in sequence more rapidly than the other. SMR genomic loci surveys identified potential SMR efflux substrates based on its gene association to putative operons that encode for genes regulating amino acid biogenesis and QAC-like metabolites. SMR subclass protein transmembrane domain alignments to Bacterial/Archaeal transporters (BAT), DMT, and MFS sequences supports SMR participation in multidrug transport evolution by identifying common TM domains. CONCLUSION Based on this study, PSMR sequences originated recently within both SUG and SMP clades through gene duplication events and it appears that SMR members may be evolving towards specific metabolite transport.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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