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García-Fernández S, Rodríguez-Grande J, Siller-Ruiz M, Fraile-Valcárcel N, Lara-Plaza I, Moure Z, Pablo-Marcos D, Rodríguez-Lozano J, Suberviola B, Cundín MPR, Fariñas MC, Ocampo-Sosa A, Calvo-Montes J. Within-host transition to GES-55 during a GES-6-producing Serratia marcescens outbreak: Emergence of ceftazidime-avibactam resistance and increased susceptibility to carbapenems. Int J Antimicrob Agents 2024; 64:107257. [PMID: 38914141 DOI: 10.1016/j.ijantimicag.2024.107257] [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: 01/16/2024] [Revised: 05/22/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
OBJECTIVES To describe the in vivo emergence of ceftazidime-avibactam resistance in GES-type carbapenemases and to characterize an unusual outbreak of GES-6-producing Serratia marcescens during the COVID-19 pandemic in Spain. METHODS Retrospective study to describe a GES-CPSM outbreak based on whole genome sequencing and antimicrobial susceptibility testing (AST). Transferability of blaGES-carrying plasmid was assessed by conjugation experiments. RESULTS In December 2020, we identified a cluster of S. marcescens harbouring blaGES-6 involving 9 patients. Whole-genome sequence analysis revealed a clonal relationship (≤3 SNPs) between the first isolates identified in each of the evolved patients and environmental samples with GES-CPSM detection. Plasmid analysis showed that the blaGES-6 gene was located in an IncQ3-type plasmid. Triparental mating experiments using a helper plasmid demonstrated mobilization of the blaGES-6-carrying plasmid. Our results also demonstrate within-host evolution in S. marcescens isolates, leading to a transition from blaGES-6 to the new blaGES-55, caused by the P162S mutation, in a subsequent infection in one of the affected patients. In blaGES-55 we identified emergence of ceftazidime-avibactam resistance along with an increase of carbapenems susceptibility. This patient had been treated with a 14-day course of ceftazidime-avibactam. AST of the transformants bearing blaGES-6 and blaGES-55 plasmids, confirmed susceptibility variation affecting ceftazidime-avibactam and carbapenems. CONCLUSIONS We report an unusual outbreak of GES-6 whose incidence is becoming increasing. Transition from GES-6 to GES-55 may readily occur in vivo leading to ceftazidime-avibactam resistance, which brings to the fore the critical need for developing more accurate diagnosis tools for detection of GES β-lactamases and optimise the use of antimicrobials.
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Affiliation(s)
- Sergio García-Fernández
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain; Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jorge Rodríguez-Grande
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain.
| | - María Siller-Ruiz
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Nuria Fraile-Valcárcel
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Isabel Lara-Plaza
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Zaira Moure
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Daniel Pablo-Marcos
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Jesús Rodríguez-Lozano
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Borja Suberviola
- Servicio de Medicina Preventiva, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - M Paz Rodríguez Cundín
- Servicio de Medicina Intensiva, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - María Carmen Fariñas
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Enfermedades Infecciosas, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Alain Ocampo-Sosa
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Calvo-Montes
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Ota Y, Prah I, Mahazu S, Gu Y, Nukui Y, Koike R, Saito R. Novel insights into genetic characteristics of blaGES-encoding plasmids from hospital sewage. Front Microbiol 2023; 14:1209195. [PMID: 37664110 PMCID: PMC10469963 DOI: 10.3389/fmicb.2023.1209195] [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: 04/20/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The prevalence of Guiana extended-spectrum (GES)-type carbapenemase producers is increasing worldwide, and hospital water environments are considered as potential reservoirs. However, the genetic features underlying this resistance are not yet fully understood. This study aimed to characterize blaGES-encoding plasmids from a single-hospital sewage sample in Japan. Methods Carbapenemase producers were screened using carbapenemase-selective agar and polymerase chain reaction. Whole-genome sequencing analyzes were performed on the carbapenemase-producing isolates. Results Eleven gram-negative bacteria (four Enterobacter spp., three Klebsiella spp., three Aeromonas spp., and one Serratia spp.) with blaGES-24 (n = 6), blaGES-6 (n = 4), and blaGES-5 (n = 1) were isolated from the sewage sample. Five blaGES-24 and a blaGES-5 were localized in IncP-6 plasmids, whereas three blaGES-6 plasmids were localized in IncC plasmids with IncF-like regions. The remaining blaGES-6 and blaGES-24 were, respectively, localized on IncFIB-containing plasmids with IncF-like regions and a plasmid with an IncW-like replication protein. The IncP-6 and IncW-like plasmids had a close genetic relationship with plasmids from Japan, whereas the IncC/IncF-like and IncFIB/IncF-like plasmids were closely related to those from the United States and Europe. All blaGES genes were located on the class 1 integron cassette of the Tn3 transposon-related region, and the IncC/IncF-like plasmid carried two copies of the integron cassette. Eight of the eleven blaGES-encoding plasmids contained toxin-antitoxin system genes. Discussion The findings on the plasmids and the novel genetic content from a single wastewater sample extend our understanding regarding the diversity of resistance and the associated spread of blaGES, suggesting their high adaptability to hospital effluents. These findings highlight the need for the continuous monitoring of environmental GES-type carbapenemase producers to control their dissemination.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiaki Gu
- Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuji Koike
- Clinical Research Center, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
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Characterization of a Novel Hybrid Plasmid Coharboring bla KPC-2 and qnrVC4 in a Clinical Citrobacter freundii Strain. Antimicrob Agents Chemother 2020; 64:AAC.01379-20. [PMID: 32900681 DOI: 10.1128/aac.01379-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Lerminiaux NA, Cameron ADS. Horizontal transfer of antibiotic resistance genes in clinical environments. Can J Microbiol 2018; 65:34-44. [PMID: 30248271 DOI: 10.1139/cjm-2018-0275] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable "superbugs" by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.
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Affiliation(s)
| | - Andrew D S Cameron
- a Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada.,b Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
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Kao CY, Chen JW, Liu TL, Yan JJ, Wu JJ. Comparative Genomics of Escherichia coli Sequence Type 219 Clones From the Same Patient: Evolution of the IncI1 blaCMY-Carrying Plasmid in Vivo. Front Microbiol 2018; 9:1518. [PMID: 30038606 PMCID: PMC6046403 DOI: 10.3389/fmicb.2018.01518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
This study investigates the evolution of an Escherichia coli sequence type 219 clone in a patient with recurrent urinary tract infection, comparing isolate EC974 obtained prior to antibiotic treatment and isolate EC1515 recovered after exposure to several β-lactam antibiotics (ceftriaxone, cefixime, and imipenem). EC974 had a smooth colony morphology, while EC1515 had a rough colony morphology on sheep blood agar. RAPD-PCR analysis suggested that both isolates belonged to the same clone. Antimicrobial susceptibility tests showed that EC1515 was more resistant to piperacillin/tazobactam, cefepime, cefpirome, and ertapenem than EC974. Comparative genomic analysis was used to investigate the genetic changes of EC974 and EC1515 within the host, and showed three plasmids with replicons IncI1, P0111, and IncFII in both isolates. P0111-type plasmids pEC974-2 and pEC1515-2, contained the antibiotic resistance genes aadA2, tetA, and drfA12. IncFII-type plasmids pEC974-3 and pEC1515-3 contained the antibiotic resistance genes blaTEM−1, aadA1, aadA22, sul3, and inuF. Interestingly, blaCMY−111 and blaCMY−4 were found in very similar IncI1 plasmids that also contained aadA22 and aac(3)-IId, from isolates EC974 (pEC974-1) and EC1515 (pEC1515-1), respectively. The results showed in vivo amino acid substitutions converting blaCMY−111 to blaCMY−4 (R221W and A238V substitutions). Conjugation experiments showed a high frequency of IncI1 and IncFII plasmid co-transference. Transconjugants and DH5α cells harboring blaCMY-4 or blaCMY-111 showed higher levels of resistance to ampicillin, amoxicillin, cefazolin, cefuroxime, cefotaxime, cefixime, and ceftazidime, but not piperacillin/tazobactam, cefpime, or ertapenem. All known genes (outer membrane proteins and extended-spectrum AmpC β-lactamases) involved in ETP resistance in E. coli were identical between EC974 and EC1515. This is the first study to identify the evolution of an IncI1 plasmid within the host, and to characterize blaCMY−111 in E. coli.
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Affiliation(s)
- Cheng-Yen Kao
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
| | - Jenn-Wei Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Lin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jing-Jou Yan
- Department of Pathology, Cheng Ching Hospital at Chung Kang, Taichung, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
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Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa. Antimicrob Agents Chemother 2018; 62:AAC.02178-17. [PMID: 29507063 DOI: 10.1128/aac.02178-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequence analyses revealed the presence of blaNDM-1 (n = 31), blaGES-5 (n = 8), blaOXA-232 (n = 1), or blaNDM-5 (n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], blaNDM-1 was part of a Tn1548-like structure (16.276 bp) delineated by IS26 The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the blaNDM-1-containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae (n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae (n = 4), Klebsiella michiganensis (n = 1), Serratia marcescens (n = 11), Enterobacter spp. (n = 7), and Citrobacter freundii (n = 1), revealing horizontal spread of this blaNDM-1-bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried blaGES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected blaOXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and blaNDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.
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Kukla R, Chudejova K, Papagiannitsis CC, Medvecky M, Habalova K, Hobzova L, Bolehovska R, Pliskova L, Hrabak J, Zemlickova H. Characterization of KPC-Encoding Plasmids from Enterobacteriaceae Isolated in a Czech Hospital. Antimicrob Agents Chemother 2018; 62:e02152-17. [PMID: 29263065 PMCID: PMC5826142 DOI: 10.1128/aac.02152-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/02/2017] [Indexed: 12/29/2022] Open
Abstract
Ten Enterobacteriaceae isolates collected in a Czech hospital carried blaKPC-positive plasmids of different sizes (∼30, ∼45, and ∼80 kb). Sequencing revealed three types of plasmids (A to C) with the Tn4401a transposon. Type A plasmids comprised an IncR backbone and a KPC-2-encoding multidrug resistance (MDR) region. Type B plasmids were derivatives of type A plasmids carrying an IncN3-like segment, while type C plasmids were IncP6 plasmids sharing the same KPC-2-encoding MDR region with type A and B plasmids.
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Affiliation(s)
- Rudolf Kukla
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Costas C Papagiannitsis
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Matej Medvecky
- Veterinary Research Institute, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Katerina Habalova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Lenka Hobzova
- Department of Hospital Hygiene, University Hospital, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, Czech Republic
| | - Lenka Pliskova
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, Czech Republic
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Helena Zemlickova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
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Results of the national surveillance of antimicrobial resistance of Enterobacteriaceae and Gram negative bacilli in health care-associated infections in Colombia, 2012-2014. BIOMEDICA 2017; 37:473-485. [DOI: 10.7705/biomedica.v37i4.3432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/12/2016] [Indexed: 01/16/2023]
Abstract
Introducción. En el tercer trimestre de 2012, comenzó a operar el Sistema Nacional de Vigilancia de Resistencia Antimicrobiana en las infecciones asociadas a la atención en salud, con el fin de recabar y analizar la información referente al problema en Colombia.Objetivo. Describir los perfiles de resistencia y los resultados de la vigilancia por el laboratorio con base en los datos recolectados en el Sistema.Materiales y métodos. Se hizo un estudio descriptivo y retrospectivo con base en la información del Sistema Nacional de Vigilancia en Salud Pública, Sivigila, 1 de septiembre de 2012 a 31 de diciembre de 2014, así como de las bases de datos Whonet con los datos notificados por las unidades primarias generadoras de datos y los resultados de la confirmación por el laboratorio de la caracterización fenotípica y genotípica de la resistencia a carbapenemasas en 1.642 aislamientos (927 de enterobacterias, 614 de Pseudomonas spp. y 101 de Acinetobacter spp.).Resultados. La resistencia de Escherichia coli a las cefalosporinas de tercera generación presentó un incremento significativo, alcanzando 26,3 % en unidades de cuidados intensivos y 22,5 % en otras áreas de hospitalización. La resistencia a ertapenem de Klebsiella pneumoniae registró un incremento y alcanzó 14,6 % en unidades de cuidados intensivos. La resistencia de Acinetobacter baumannii a los carbapenémicos superó el 50 % en dichas unidades, en tanto que en Pseudomonas aeruginosa se presentaron porcentajes más bajos (38,8 %). Las carbapenemasas más frecuentes en enterobacterias fueron la KPC (n=574), seguida de la NDM (n=57); en P. aeruginosa, la VIM (n=229) y la KPC (n=114), y en A. baumannii, la OXA-23 (n=87). Se detectaron varias combinaciones de carbapenemasas, siendo la de KPC y VIM la más frecuente en Pseudomonas spp., y en enterobacterias.Conclusión. La información obtenida a partir del Sistema Nacional de Vigilancia ha permitido conocer los perfiles y los mecanismos de resistencia a carbapenémicos de las cepas que están circulando en las instituciones de salud del país.
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Botts RT, Apffel BA, Walters CJ, Davidson KE, Echols RS, Geiger MR, Guzman VL, Haase VS, Montana MA, La Chat CA, Mielke JA, Mullen KL, Virtue CC, Brown CJ, Top EM, Cummings DE. Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland. Front Microbiol 2017; 8:1922. [PMID: 29067005 PMCID: PMC5641379 DOI: 10.3389/fmicb.2017.01922] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (blaWDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic blaCTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.
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Affiliation(s)
- Ryan T Botts
- Department of Mathematical, Information and Computer Sciences, Point Loma Nazarene University, San Diego, CA, United States
| | - Brooke A Apffel
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - C J Walters
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly E Davidson
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Ryan S Echols
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michael R Geiger
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria L Guzman
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria S Haase
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michal A Montana
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Chip A La Chat
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Jenna A Mielke
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly L Mullen
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Cierra C Virtue
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - David E Cummings
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
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Luk-In S, Pulsrikarn C, Bangtrakulnonth A, Chatsuwan T, Kulwichit W. Occurrence of a novel class 1 integron harboring qnrVC4 in Salmonella Rissen. Diagn Microbiol Infect Dis 2017; 88:282-286. [PMID: 28427794 DOI: 10.1016/j.diagmicrobio.2017.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 11/18/2022]
Abstract
We described qnrVC4 in S. Rissen 166ANSS50, a swine isolate, which was detected in the study on quinolone resistance mechanisms of nontyphoidal Salmonella in Thailand. The isolate was found to harbor a ̴17-kb non-conjugative plasmid carrying qnrVC4 within 8.91kb of a novel In4-like class 1 integron (In805). It contained the multi-drug resistance gene cassettes of qnrVC4-qacH4-aacA4-cmlA7-blaOXA-10-aadA1-dfrA14 and unusual 3'-CS of mobC-IS6100. This 1014-bp qnrVC4 cassette included with promoter (PqnrVC4: -35 TTGAGA and -10 TAGTCT) showed high homology with qnrVC4 in superintegron of V. cholerae O1 El Tor. The qnrVC4 recombinant plasmid resulted in 4-, 8-, and 16-fold increase in the MICs of nalidixic acid (2-8μg/mL), ciprofloxacin (0.015-0.125μg/mL), and norfloxacin (0.03-0.5μg/mL), respectively. In addition, the backbone plasmid revealed a novel replicon belonging to the MOBQ1 group from the broad-host-range mobilisable IncQ1 plasmid RFS1010 based on relaxase sequences. This is the first known report of qnrVC in Salmonella enterica. The qnrVC4 gene was co-transferred with other resistance genes via a novel plasmid-borne In805. This allowed the spread of this resistance gene to Enterobacteriaceae.
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Affiliation(s)
- Sirirat Luk-In
- Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Chaiwat Pulsrikarn
- World Health Organization National Salmonella and Shigella Centre, Nonthaburi, Thailand
| | - Aroon Bangtrakulnonth
- World Health Organization National Salmonella and Shigella Centre, Nonthaburi, Thailand
| | | | - Wanla Kulwichit
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Dang B, Xu Y, Mao D, Luo Y. Complete nucleotide sequence of plasmid pNA6 reveals the high plasticity of IncU family plasmids. Gene 2016; 591:74-79. [PMID: 27374151 DOI: 10.1016/j.gene.2016.06.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 12/27/2022]
Abstract
Antibiotic resistance is a serious problem in health care and is of widespread public concern. Conjugative plasmids are the most important vectors in the dissemination of antibiotic resistance genes. In this study, we determined the complete sequence of plasmid pNA6, a plasmid which was isolated from the sediments of Haihe River. This plasmid confers reduced susceptibility to ampicillin, erythromycin and sulfamethoxazole. The complete sequence of plasmid pNA6 was 52,210bp in length with an average G+C content of 52.70%. Plasmid pNA6 belongs to the IncU group by sequence queries against the GenBank database. This plasmid has a typical IncU backbone and shows the highest similarities with plasmid RA3 and plasmid pFBAOT6. Plasmid pNA6 carries a class 1 integron consisting of aacA4, ereA and dfrA1 genes. Moreover, plasmid pNA6 also harbors a blaTEM-1-containing complex structure which inserted into the replication region and maintenance region. This insertion site has never been found on other IncU plasmids. The sequencing of plasmid pNA6 will add new sequence information to IncU family plasmids and enhance our understanding of the plasticity of IncU family plasmids.
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Affiliation(s)
- Bingjun Dang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yan Xu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China.
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China.
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Dang B, Mao D, Luo Y. Complete Nucleotide Sequence of IncP-1β Plasmid pDTC28 Reveals a Non-Functional Variant of the blaGES-Type Gene. PLoS One 2016; 11:e0154975. [PMID: 27152950 PMCID: PMC4859535 DOI: 10.1371/journal.pone.0154975] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/21/2016] [Indexed: 01/02/2023] Open
Abstract
Plasmid pDTC28 was isolated from the sediments of Haihe River using E. coli CV601 (gfp-tagged) as recipient and indigenous bacteria from the sediment as donors. This plasmid confers reduced susceptibility to tetracycline and sulfamethoxazole. The complete sequence of plasmid pDTC28 was 61,503 bp in length with an average G+C content of 64.09%. Plasmid pDTC28 belongs to the IncP-1β group by phylogenetic analysis. The backbones of plasmid pDTC28 and other IncP-1β plasmids are very classical and conserved, whereas the accessory regions of these plasmids are diverse. A blaGES-5-like gene was found on the accessory region, and this blaGES-5-like gene contained 18 silent mutations and 7 missense mutations compared with the blaGES-5 gene. The mutations resulted in 7 amino acid substitutions in GES-5 carbapenemase, causing the loss of function of the blaGES-5-like gene on plasmid pDTC28 against carbapenems and even β-lactams. The enzyme produced by the blaGES-5-like gene cassette may be a new variant of GES-type enzymes. Thus, the plasmid sequenced in this study will expand our understanding of GES-type β-lactamases and provide insights into the genetic platforms used for the dissemination of GES-type genes.
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Affiliation(s)
- Bingjun Dang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- * E-mail: (YL); (DM)
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
- * E-mail: (YL); (DM)
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