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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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Wang Y, Dagan T. The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages. Nat Commun 2024; 15:4555. [PMID: 38811529 PMCID: PMC11137137 DOI: 10.1038/s41467-024-48352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
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Affiliation(s)
- Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany.
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3
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Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024:e0048223. [PMID: 38597634 DOI: 10.1128/iai.00482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.
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Affiliation(s)
- Andrew S Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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4
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Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:656-668. [PMID: 37794696 PMCID: PMC10667661 DOI: 10.1111/1758-2229.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid-encoded genes is similar to that of chromosome-encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
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Affiliation(s)
- Fabian Nies
- Institute of General MicrobiologyKiel UniversityKielGermany
| | - Tanita Wein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | | | - Benjamin L. Springstein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences FacultyPontifical Catholic University of ChileSantiagoChile
| | - Claudia Taubenheim
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Internal Medicine IIUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Tal Dagan
- Institute of General MicrobiologyKiel UniversityKielGermany
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5
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Das S, Mallick A, Barik M, Sarkar S, Saha P. The emergence of clonally diverse carbapenem-resistant Enterobacter cloacae complex in West Bengal, India: a dockyard of β-lactamases periling nosocomial infections. Int Microbiol 2023:10.1007/s10123-023-00451-0. [PMID: 37985632 DOI: 10.1007/s10123-023-00451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Carbapenem-resistant Enterobacter cloacae complex (CRECC) constitutes a global public health threat challenging clinical treatment and infection control, especially in low- and middle-income countries such as India. We analyzed the antimicrobial susceptibility, major β-lactamase genes, plasmid profiles, and genetic relatedness to understand the molecular epidemiology of CRECC clinical isolates (n = 44) in West Bengal, India, during 2021-2022. The majority (> 55%) of the isolates were resistant to fluoroquinolones, aminoglycosides, and co-trimoxazole, even > 20% for tigecycline and > 35% were extensively drug-resistant. Co-β-lactamase production was categorized into twenty-seven types, importantly NDM (84%), OXA-48 (40%), TEM (61%), CTX-M (46%), OXA-1 (55%), and MIR (27%). The NDM-1 and OXA-181 were major variants with the first observations of NDM-24 and -29 variants in India. Wide-range of plasmids (2 to > 212 kb) were harbored by the β-lactamase-producing isolates: small (91%), medium (27%), large (9%), and mega (71%). IncX3, ColE1, and HI2 were noted in about 30% of isolates, while IncF and R were carried by < 20% of isolates. The clonally diverse CRECC isolates were noted to cause cross-infections, especially at superficial site, bloodstream, and urinary-tract. This is the first molecular surveillance on CRECC in India. The study isolates serve as the dockyard of NDM, TEM, and CTX-M harboring a wide range of plasmids. The outcomes of the study may strengthen local and national policies for infection prevention and control practices, clarifying the genetic diversity among CRECC. Extensive genomic study may further intersect the relationships between these different plasmids, especially with their sizes, types, and antibiotic resistance markers.
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Affiliation(s)
- Surojit Das
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Abhi Mallick
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Mili Barik
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Soma Sarkar
- Department of Microbiology at Nil Ratan Sirkar Medical College Hospital, Kolkata, West Bengal, India
- Department of Microbiology at Infectious Diseases & Beleghata General Hospital, Kolkata, West Bengal, India
| | - Puranjoy Saha
- Department of Microbiology, Malda Medical College and Hospital, Malda, West Bengal, India
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6
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Traglia G, Ramirez MS, Tolmasky ME. Role of Xer site-specific recombination in the genesis of pJHCMW1: an evolutionary hypothesis. J Glob Antimicrob Resist 2023; 34:199-201. [PMID: 37517477 PMCID: PMC10984218 DOI: 10.1016/j.jgar.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- German Traglia
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de La República, Uruguay
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California.
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7
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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8
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Shaib H, Aoun P, Ghaddar A, Al Labadi H, Obeid Y. Multidrug Resistance and Plasmid Profiles of Escherichia coli Isolated from Lebanese Broiler Farms. Int J Microbiol 2023; 2023:8811675. [PMID: 37303775 PMCID: PMC10250091 DOI: 10.1155/2023/8811675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
The present study was undertaken to determine the antimicrobial resistance patterns and plasmid fingerprints of commensal Escherichia coli isolated from Lebanese broiler chickens. To that end, a total of 30 E. coli isolates were collected from 15 semi-open broiler farms from North Lebanon and Bekaa Valley. Results showed that all the isolates were resistant to at least nine out of 18 evaluated antimicrobial agents. The best-performing antibiotic families were Carbapenems (Imipenem) and Quinolones (Ciprofloxacin and Norfloxacin) to which only 0.0 and 8.3% of the isolates were resistant, respectively. Fifteen various plasmid profiles were depicted, and all the isolates were found to possess one or multiple plasmids. The plasmid sizes varied from 1.2 to 21.0 kbp, and the most commonly detected plasmid had a size of 5.7 kbp (23.3% of the isolates). There was no significant association between the number of plasmids per isolate and resistance to a particular drug. Nevertheless, the presence of specific plasmids, namely, the 2.2 or 7.7 kbp sized ones, was strongly correlated to Quinolones or Trimethoprim resistance, respectively. Both the 7.7 and 6.8 kbp plasmids showed mild correlation to Amikacin resistance, and the 5.7 kbp plasmid was mildly correlated to Piperacillin-Tazobactam resistance. Our findings highlight the need to revise the list of antimicrobials currently used in Lebanese poultry and associate the presence of specific plasmids to antimicrobial resistance patterns in E. coli isolates. The revealed plasmid profiles could also serve any future epidemiological investigation of poultry disease outbreaks in the country.
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Affiliation(s)
- Houssam Shaib
- Department of Agriculture, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Paul Aoun
- Department of Agriculture, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Ahmad Ghaddar
- Department of Agriculture, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Hamza Al Labadi
- Department of Agriculture, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Youssef Obeid
- Department of Agriculture, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon
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9
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Johnson J, Soehnlen M, Blankenship HM. Long read genome assemblers struggle with small plasmids. Microb Genom 2023; 9. [PMID: 37224062 DOI: 10.1099/mgen.0.001024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Whole-genome sequencing has become a preferred method for studying bacterial plasmids, as it is generally assumed to capture the entire genome. However, long-read genome assemblers have been shown to sometimes miss plasmid sequences - an issue that has been associated with plasmid size. The purpose of this study was to investigate the relationship between plasmid size and plasmid recovery by the long-read-only assemblers, Flye, Raven, Miniasm, and Canu. This was accomplished by determining the number of times each assembler successfully recovered 33 plasmids, ranging from 1919 to 194 062 bp in size and belonging to 14 bacterial isolates from six bacterial genera, using Oxford Nanopore long reads. These results were additionally compared to plasmid recovery rates by the short-read-first assembler, Unicycler, using both Oxford Nanopore long reads and Illumina short reads. Results from this study indicate that Canu, Flye, Miniasm, and Raven are prone to missing plasmid sequences, whereas Unicycler was successful at recovering 100 % of plasmid sequences. Excluding Canu, most plasmid loss by long-read-only assemblers was due to failure to recover plasmids smaller than 10 kb. As such, it is recommended that Unicycler be used to increase the likelihood of plasmid recovery during bacterial genome assembly.
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Affiliation(s)
- Jared Johnson
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48906, USA
| | - Marty Soehnlen
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48906, USA
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48906, USA
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10
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Identification and Characterization of Plasmids and Genes from Carbapenemase-Producing Klebsiella pneumoniae in Makkah Province, Saudi Arabia. Antibiotics (Basel) 2022; 11:antibiotics11111627. [PMID: 36421271 PMCID: PMC9686665 DOI: 10.3390/antibiotics11111627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is involved in several hospital and community-acquired infections. The prevalence of K. pneumoniae-producing-carbapenemase (KPC) resistance genes rapidly increases and threatens public health worldwide. This study aimed to assess the antibiotic resistance level of K. pneumoniae isolates from Makkah Province, Saudi Arabia, during the Islamic ‘Umrah’ ritual and to identify the plasmid types, presence of genes associated with carbapenem hydrolyzing enzymes, and virulence factors. The phenotypic and genotypic analyses based on the minimum inhibitory concentration (MIC), biofilm formation, PCR, and characterization of KPC-encoding plasmids based on the replicon typing technique (PBRT) were explored. The results showed that most isolates were resistant to carbapenem antibiotics and other antibiotics classes. This study identified sixteen different replicons of plasmids in the isolates and multiple genes encoding carbapenem factors, with blaVIM and blaOXA-48 being the most prevalent genes identified in the isolates. However, none of the isolates exhibited positivity for the KPC production activity. In addition, this study also identified six virulence-related genes, including kfu, wabG, uge, rmpA, fimH, and a capsular polysaccharide (CPS). Together, the data reported in this study indicate that the isolated K. pneumoniae during the pilgrimage in Makkah were all resistant to carbapenem antibiotics. Although the isolates lacked KPC production activity, they carried multiple carbapenem-resistant genes and virulence factors, which could drive their resistant phenotype. The need for specialized methods for KPC detection, monitoring the possibility of nosocomial transmission, and diverse therapeutic alternatives are necessary for controlling the spreading of KPC. This study can serve as a reference for clinicians and researchers on types of K. pneumoniae commonly found during religious gathering seasons in Saudi Arabia.
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11
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Sengeruan LP, van Zwetselaar M, Kumburu H, Aarestrup FM, Kreppel K, Sauli E, Sonda T. Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro, Tanzania. J Glob Antimicrob Resist 2022; 30:384-389. [DOI: 10.1016/j.jgar.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022] Open
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12
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Leyton-Carcaman B, Abanto M. Beyond to the Stable: Role of the Insertion Sequences as Epidemiological Descriptors in Corynebacterium striatum. Front Microbiol 2022; 13:806576. [PMID: 35126341 PMCID: PMC8811144 DOI: 10.3389/fmicb.2022.806576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022] Open
Abstract
In recent years, epidemiological studies of infectious agents have focused mainly on the pathogen and stable components of its genome. The use of these stable components makes it possible to know the evolutionary or epidemiological relationships of the isolates of a particular pathogen. Under this approach, focused on the pathogen, the identification of resistance genes is a complementary stage of a bacterial characterization process or an appendix of its epidemiological characterization, neglecting its genetic components’ acquisition or dispersal mechanisms. Today we know that a large part of antibiotic resistance is associated with mobile elements. Corynebacterium striatum, a bacterium from the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. Despite the different existing mobile genomic elements, there is evidence that acquired resistance genes are coupled to insertion sequences in C. striatum. This perspective article reviews the insertion sequences linked to resistance genes, their relationship to evolutionary lineages, epidemiological characteristics, and the niches the strains inhabit. Finally, we evaluate the potential of the insertion sequences for their application as a descriptor of epidemiological scenarios, allowing us to anticipate the emergence of multidrug-resistant lineages.
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13
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Ares-Arroyo M, Rocha EPC, Gonzalez-Zorn B. Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance. PLoS Genet 2021; 17:e1009919. [PMID: 34847155 PMCID: PMC8683028 DOI: 10.1371/journal.pgen.1009919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/17/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model (HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements. The extraordinary adaptability of bacteria and the massive prevalence of mobile genetic elements within populations has turned antimicrobial resistance into a growing threat to Public Health. Among all the mobile genetic elements, plasmids have been the focus of attention as these extrachromosomal molecules of DNA are able to mobilize several antimicrobial resistance genes at once through conjugation. However, although small mobilizable and non-conjugative replicons have been traditionally overlooked when analyzing plasmid-mediated antimicrobial resistance, they have recently been described as important carriers of AMR genes. In this work, we have analyzed the ColE1-like plasmid family, whose study has been neglected even if they are one of the main groups of small plasmids in natural populations of Proteobacteria. We observed that these plasmids have evolved for a long time within γ-Proteobacteria acquiring different genetic features in specific hosts, being major players in the spread of antimicrobial resistance determinants.
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Affiliation(s)
- Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
- * E-mail:
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14
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Wang Z, Ding Z, Li Z, Ding Y, Jiang F, Liu J. Antioxidant and antibacterial study of 10 flavonoids revealed rutin as a potential antibiofilm agent in Klebsiella pneumoniae strains isolated from hospitalized patients. Microb Pathog 2021; 159:105121. [PMID: 34343655 DOI: 10.1016/j.micpath.2021.105121] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The emergence of multidrug resistance (MDR) and extensive drug resistance (XDR) in Klebsiella pneumoniae strains has posed great threats to conventional antibiotics. Previous studies have shown that plant-derived flavonoids have inhibitory functions against pathogens. However, in K. pneumoniae, the antibacterial activity of different flavonoids against growth and biofilm formation remains a mystery. The aim of the present study was to evaluate the antioxidant abilities of different flavonoids, to screen active ingredients and to identify their inhibitory effects on K. pneumoniae growth and biofilm formation. In total, 10 flavonoids representing 4 major categories were screened and used in this study. The antioxidant capacity of each flavonoid was evaluated through a DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. Rutin showed the highest level of free radical scavenging capacity, followed by kaempferol, luteolin, quercetin, apigenin, hesperidin, sinensetin, naringenin, naringin and 3,5,6,7,8,3',4'-heptamethoxyflavone. The inhibitory effects of rutin and naringin on bacterial growth were also compared. The lowest MICs of rutin were found against K. pneumoniae ATCC700603 (1024 μg/mL) and E. coli ATCC25922 (512 μg/mL). However, the MBICs were not found. Rutin showed strong inhibitory ability against both the growth curve and biofilm production. The expression profiles of 15 biofilm-related genes were analyzed in biofilm cells both with and without rutin treatment. The luxS gene and wabG gene were downregulated significantly by rutin treatment. Correlation analysis showed that mrkA gene expression was positively correlated with biofilm biomass accumulation. Our study indicated that biofilm production is correlated with the expression of several genes rather than one. MrkA gene expression was positively correlated with biofilm biomass accumulation. Our study screened rutin as a potential agent to inhibit K. pneumoniae biofilm formation.
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Affiliation(s)
- Zhibin Wang
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Zixuan Ding
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Zhaoyinqian Li
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Yinhuan Ding
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Fan Jiang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Shandong University, Jinan, Shandong Province, 250012, China
| | - Jinbo Liu
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China.
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15
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Prevalence and Antimicrobial Resistance of Klebsiella Strains Isolated from a County Hospital in Romania. Antibiotics (Basel) 2021; 10:antibiotics10070868. [PMID: 34356789 PMCID: PMC8300768 DOI: 10.3390/antibiotics10070868] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/15/2021] [Indexed: 12/28/2022] Open
Abstract
The study evaluated the evolution of the incidence of infections with Klebsiella in the County Clinical Emergency Hospital of Craiova (SCJUC), Romania. Also, we monitored antibiotic resistance over more than two years and detected changes in resistance to various antimicrobial agents. Our study included 2062 patients (823 women and 1239 men) hospitalised in SCJUC during the period 1st of September 2017 to 30 June 2019. In 458 patients (22.21%) from the 2062 total patients, the collected samples (1116) were positive and from those, we isolated 251 strains of Klebsiella spp. We conducted a longitudinal analysis of the prevalence of Klebsiella spp. over calendar months, which showed a prevalence in surgical wards that ranged between 5.25% and 19.49% in June 2018, while in medical wards the variation was much wider, between 5.15% and 17.36% in April 2018. Klebsiella spp. strains showed significant resistance to Amoxicillin/Clavulanate, Aztreonam and Cephalosporins such as Ceftriaxone, Ceftazidime and Cefepime. We examined the possible link with the consumption of antibiotics in the same month by performing a multiple linear regression analysis. The evolution of antibiotic resistance in Klebsiella was correlated with the variation of resistance in other bacteria, which suggests common resistance mechanisms in the hospital environment. By performing the regression for dependency between antibiotic resistance and antibiotic consumption, we observed some correlations between antibiotic consumption and the development of antibiotic resistance after 1, 2 and even 3 months (e.g., resistance to meropenem was influenced by the consumption in the hospital ward of imipenem 1 month and two months before, but only 1 month before by the consumption of meropenem). The clustering of strains showed filiation between multiresistant Klebsiella spp. strains isolated from specific patients from the ICU. The evolution of prevalence and antibiotic resistance in Klebsiella correlated with the resistance in other bacteria, which suggest common resistance mechanisms in the hospital environment, and also with the consumption of antibiotics.
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16
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Butler DA, Rana AP, Krapp F, Patel SR, Huang Y, Ozer EA, Hauser AR, Bulman ZP. Optimizing aminoglycoside selection for KPC-producing Klebsiella pneumoniae with the aminoglycoside-modifying enzyme (AME) gene aac(6')-Ib. J Antimicrob Chemother 2021; 76:671-679. [PMID: 33326561 DOI: 10.1093/jac/dkaa480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/22/2020] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES KPC-producing Klebsiella pneumoniae (KPC-Kp) isolates commonly co-harbour the aminoglycoside-modifying enzyme (AME) gene aac(6')-Ib, which encodes an AME that can confer resistance to some of the commercially available aminoglycosides. We sought to determine the influence of AAC(6')-Ib in KPC-Kp on the pharmacodynamic activity of aminoglycosides. METHODS Six KPC-Kp clinical isolates, three with and three without aac(6')-Ib, were analysed. Using these isolates, the bacterial killing of amikacin, gentamicin and tobramycin was assessed in static time-kill experiments. The pharmacodynamic activity of the aminoglycosides was then assessed in a dynamic one-compartment infection model over 72 h using simulated human pharmacokinetics of once-daily dosing with amikacin (15 mg/kg), gentamicin (5 mg/kg) and tobramycin (5 mg/kg). RESULTS At clinically relevant aminoglycoside concentrations in time-kill experiments and the dynamic one-compartment model, gentamicin was more active than amikacin or tobramycin against the isolates harbouring aac(6')-Ib. Amikacin, gentamicin and tobramycin all showed progressively reduced bacterial killing with exposure to repeated doses against most isolates in the dynamic one-compartment model. MIC values were generally not a good predictor of gentamicin pharmacodynamic activity against KPC-Kp, but were more reliable for amikacin and tobramycin. CONCLUSIONS Gentamicin may be preferred over amikacin or tobramycin for treatment of KPC-Kp infections. However, gentamicin MICs are not a consistent predictor of its pharmacodynamic activity and unexpected treatment failures are possible.
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Affiliation(s)
- David A Butler
- University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Amisha P Rana
- University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Fiorella Krapp
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano, Lima, Peru
| | - Shitalben R Patel
- University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Yanqin Huang
- University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Egon A Ozer
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alan R Hauser
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zackery P Bulman
- University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
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17
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Toledano-Tableros JE, Gayosso-Vázquez C, Jarillo-Quijada MD, Fernández-Vázquez JL, Morfin-Otero R, Rodríguez-Noriega E, Giono-Cerezo S, Gutkind G, Di Conza J, Santos-Preciado JI, Alcántar-Curiel MD. Dissemination of bla NDM- 1 Gene Among Several Klebsiella pneumoniae Sequence Types in Mexico Associated With Horizontal Transfer Mediated by IncF-Like Plasmids. Front Microbiol 2021; 12:611274. [PMID: 33841344 PMCID: PMC8027308 DOI: 10.3389/fmicb.2021.611274] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/28/2021] [Indexed: 12/13/2022] Open
Abstract
Nosocomial infections caused by multidrug-resistant (MDR) Klebsiella pneumoniae are a major health problem worldwide. The aim of this study was to describe NDM-1-producing K. pneumoniae strains causing bacteremia in a tertiary referral hospital in Mexico. MDR K. pneumoniae isolates were screened by polymerase chain reaction for the presence of resistance genes. In resistant isolates, plasmids were identified and conjugation assays were performed. Clonal diversity and the sequence types were determined by pulsed-field gel electrophoresis and multilocus sequence typing. A total of 80 K. pneumoniae isolates were collected from patients with bacteremia over a 1-year period. These isolates showed a level of resistance of 59% (47/80) to aztreonam, 56-60% (45-48/80) to cephalosporins, 54% (43/80) to colistin and 12.5% (10/80) to carbapenems. The carbapenem resistant isolates were bla NDM- 1 carriers and negative for bla KPC, bla NDM, bla IMP, bla VIM and bla OXA- 48 -like carbapenemases genes. Conjugative plasmids IncFIIA and IncF group with sizes of 82-195 kbp were carriers of bla NDM- 1, bla CTX-M- 15, bla TEM- 1, aac(6')-Ib and/or aac(3')-IIa. Clonal variability and nine different multilocus sequence types were detected (ST661, ST683, ST1395, ST2706, ST252, ST1198, ST690, ST1535, and ST3368) for the first time in the isolates carrying bla NDM- 1 in Mexico. This study demonstrates that bla NDM- 1 has remained within this hospital in recent years and suggests that it is currently the most prevalent carbapenemase among K. pneumoniae MDR strains causing bacteremia in Mexico. The horizontal transfer of bla NDM- 1 gene through IncF-like plasmids among different clones demonstrates the dissemination pathway of antimicrobial resistance and underscore the need for strong and urgent joint measures to control the spread of NDM-1 carbapenemase in the hospital.
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Affiliation(s)
- José Eduardo Toledano-Tableros
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencia Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ma Dolores Jarillo-Quijada
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Silvia Giono-Cerezo
- Departamento de Microbiología, Escuela Nacional de Ciencia Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gabriel Gutkind
- Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José Di Conza
- Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José Ignacio Santos-Preciado
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Townsend EM, Moat J, Jameson E. CAUTI's next top model - Model dependent Klebsiella biofilm inhibition by bacteriophages and antimicrobials. Biofilm 2020; 2:100038. [PMID: 33381752 PMCID: PMC7762788 DOI: 10.1016/j.bioflm.2020.100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 01/21/2023] Open
Abstract
Klebsiella infections, including catheter associated urinary tract infections, are a considerable burden on health care systems. This is due to their difficulty to treat, caused by antimicrobial resistance and their ability to form biofilms. In this study, we investigated the use of a Klebsiella phage cocktail to reduce biofilm viability. We used two methodologies to investigate this, a standard 96-well plate assay and a more complicated Foley catheter-based model. The phage cocktail was used alone and in combination with clinically relevant antibiotic treatments. Viability was measured by both a resazurin based stain and colony forming unit counts, of cells sloughed off from the biofilm. We showed that phage infection dynamics and host survival vary significantly in different standard laboratory media, presumably due to the expression of different surface receptors and capsule composition by the bacteria effecting phage binding. This underscores the importance of a realistic model for developing phage therapy. We demonstrate that bacteriophage-based treatments are a viable option for preventing Klebsiella colonisation and biofilm formation on urinary catheters. Phage cocktails were able to significantly reduce the amount of biofilm that formed when they were present during early biofilm formation. The phages used in this study were unable to significantly reduce a pre-formed mature biofilm, despite encoding depolymerases. Phages applied together with antimicrobial treatments, showed synergistic interactions, in some cases the combined treatment was much more effective than antimicrobial treatments alone. We show that phage cocktails have the potential to prevent Klebsiella biofilms in catheters, if used early or as a preventative treatment and will work well alongside standard antibiotics in the treatment of catheter-associated urinary tract infections (CAUTI).
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Affiliation(s)
- Eleanor M. Townsend
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John Moat
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, United Kingdom
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Yang F, Han B, Gu Y, Zhang K. Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes. Sci Rep 2020; 10:15037. [PMID: 32929149 PMCID: PMC7490410 DOI: 10.1038/s41598-020-72149-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/25/2020] [Indexed: 11/25/2022] Open
Abstract
The overuse or abuse of antibiotics as veterinary medicine and growth promoters accelerates antibiotic resistance, creating a serious threat to public health in the world. Swine liquid manure as an important reservoir of antibiotic resistance genes (ARGs) has received much attention, but little information is known regarding the occurrence, persistence and fate of ARGs-associated mobile genetic elements (MGEs) in swine farms, especially their change patterns and removal in full-scale piggery wastewater treatment systems (PWWTSs). In this study, we searched the presence and distribution of MGEs and associated ARGs in swine farms, and addressed their fate and seasonal variation in full-scale PWWTSs by real-time quantitative PCR (qPCR). Our results revealed class 1 integrons, class 2 integrons and conjugative plasmids were prevalent in pig feces and piggery wastewater. A clear pattern of these MGE levels in swine liquid manure was also observed, i.e., intI1 > intI2 > traA (p < 0.01), and their absolute abundances in winter were all higher than that in summer with 0.07-2.23 logs. Notably, MGEs and ARGs prevailed through various treatment units of PWWTSs, and considerable levels of them were present in the treated effluent discharged from swine farms (up to 101-107 copies/mL for MGEs and 103-108 copies/mL for ARGs). There were significant correlations between most ARG abundance and MGE levels (p < 0.05), such as tetQ and traA (r = 0.775), sul1 and intI1 (r = 0.847), qnrS and inI2 (r = 0.859), suggesting the potential of ARGs-horizontal transfer. Thus the high prevalence and enrichment of MGEs and ARGs occurred in pig feces and piggery wastewater, also implicating that swine liquid manure could be a hotspot for horizontal transfer of ARGs.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yanru Gu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150036, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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20
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Ricker N, Trachsel J, Colgan P, Jones J, Choi J, Lee J, Coetzee JF, Howe A, Brockmeier SL, Loving CL, Allen HK. Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces. Front Vet Sci 2020; 7:255. [PMID: 32509805 PMCID: PMC7249142 DOI: 10.3389/fvets.2020.00255] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Oral antibiotics are a critical tool for fighting bacterial infections, yet their use can have negative consequences, such as the disturbance of healthy gut bacterial communities and the dissemination of antibiotic residues in feces. Altering antibiotic administration route may limit negative impacts on intestinal microbiota and reduce selective pressure for antimicrobial resistance genes (ARG) persistence and mobility. Thus, a study was performed in pigs to evaluate route of therapeutic oxytetracycline (oxytet) administration, an antibiotic commonly used in the U.S. swine industry, on intestinal microbial diversity and ARG abundance. Given that oral antibiotics would be in direct contact with intestinal bacteria, we hypothesized that oral administration would cause a major shift in intestinal bacterial community structure when compared to injected antibiotic. We further postulated that the impact would extend to the diversity and abundance of ARG in swine feces. At approximately 3 weeks-of-age, piglets were separated into three groups (n = 21–22 per group) with two groups receiving oxytet (one via injection and the second via feed) and a third non-medicated group. Oxytet levels in the plasma indicated injected antibiotic resulted in a spike 1 day after administration, which decreased over time, though oxytet was still detected in plasma 14 days after injection. Conversely, in-feed oxytet delivery resulted in lower but less variable oxytet levels in circulation and high concentrations in feces. Similar trends were observed in microbial community changes regardless of route of oxytet administration; however, the impact on the microbial community was more pronounced at all time points and in all samples with in-feed administration. Fecal ARG abundance was increased with in-feed administration over injected, with genes for tetracycline and aminoglycoside resistance enriched specifically in the feces of the in-feed group. Sequencing of plasmid-enriched samples revealed multiple genetic contexts for the resistance genes detected and highlighted the potential role of small plasmids in the movement of antibiotic resistance genes. The findings are informative for disease management in food animals, but also manure management and antibiotic therapy in human medicine for improved antibiotic stewardship.
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Affiliation(s)
- Nicole Ricker
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States.,Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Julian Trachsel
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Phillip Colgan
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Jennifer Jones
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Jinlyung Choi
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Jaejin Lee
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Johann F Coetzee
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Adina Howe
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Susan L Brockmeier
- Virus and Prion Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
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Abstract
Klebsiella pneumoniae is a common cause of antimicrobial-resistant opportunistic infections in hospitalized patients. The species is naturally resistant to penicillins, and members of the population often carry acquired resistance to multiple antimicrobials. However, knowledge of K. pneumoniae ecology, population structure or pathogenicity is relatively limited. Over the past decade, K. pneumoniae has emerged as a major clinical and public health threat owing to increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains producing extended-spectrum β-lactamases and/or carbapenemases. A parallel phenomenon of severe community-acquired infections caused by 'hypervirulent' K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. These distinct clinical concerns have stimulated renewed interest in K. pneumoniae research and particularly the application of genomics. In this Review, we discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance. A deeper understanding of K. pneumoniae population structure and diversity will be important for the proper design and interpretation of experimental studies, for interpreting clinical and public health surveillance data and for the design and implementation of novel control strategies against this important pathogen.
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