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Miranda CD, Concha C, Godoy FA, Lee MR. Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance. Antibiotics (Basel) 2022; 11:1487. [PMID: 36358142 PMCID: PMC9687057 DOI: 10.3390/antibiotics11111487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 08/27/2023] Open
Abstract
The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.
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Affiliation(s)
- Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Félix A. Godoy
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile
| | - Matthew R. Lee
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile
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Fonseca ÉL, Vicente AC. Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation. Microorganisms 2022; 10:microorganisms10020224. [PMID: 35208680 PMCID: PMC8876359 DOI: 10.3390/microorganisms10020224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022] Open
Abstract
Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.
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Louge Uriarte EL, González Pasayo RA, Massó M, Carrera Paez L, Domínguez Moncla M, Donis N, Malena R, Méndez A, Morrell E, Giannitti F, Armendano JI, Faverin C, Centrón D, Parreño V, Odeón AC, Quiroga MP, Moreira AR. Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia. Microb Pathog 2022; 163:105378. [PMID: 34982979 DOI: 10.1016/j.micpath.2021.105378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022]
Abstract
Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::blaCTX-M-2) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.
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Affiliation(s)
- Enrique L Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina.
| | - Ramón A González Pasayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Mariana Massó
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Laura Carrera Paez
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Manuel Domínguez Moncla
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Nicolás Donis
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Rosana Malena
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Alejandra Méndez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Eleonora Morrell
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 50 km 11, Estación Experimental La Estanzuela, Semillero, 70006, Colonia, Uruguay
| | - Joaquín I Armendano
- Departamento de Fisiopatología, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil, 7000, Argentina
| | - Claudia Faverin
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Viviana Parreño
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT, INTA-CONICET), Castelar, 1712, Buenos Aires, Argentina
| | - Anselmo C Odeón
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - María Paula Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina.
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
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Ayobola EHWARIEMED, Oscar WHILIKIO, Ejovwokoghene EJUKONEMUF. Plasmid-mediated quinolone resistance genes transfer among enteric bacteria isolated from human and animal sources. AIMS Microbiol 2021; 7:200-215. [PMID: 34250375 PMCID: PMC8255902 DOI: 10.3934/microbiol.2021013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
This research investigates the transferability of plasmid-mediated quinolone resistance (PMQR) genes among enteric bacteria isolates in human and animal samples, as well as its implication on resistance of recipient cells. A total of 1,964 strains of five different enteric bacteria species (Escherichia coli, Salmonella sp., Shigella sp., Klebsiella sp. and Aeromonas sp.) were screened for plasmid-mediated quinolone resistance (PMQR) genes from a population of quinolone resistant (Q-r) isolates. Screening for PMQR isolates was achieved by plasmid curing using sub-lethal concentration of Sodium Dodecyl Sulphate and PMQR genes (qnrA, qnrB, qnrS, Aac(6')-Ib-crand Qep A) were detected by polymerase chain reaction (PCR). Conjugation and transformation experiments were attempted to ascertain transfer of genes from the Q-r isolates to a susceptible, standard recipient, E. coli J53-2. The minimum inhibitory concentration (MIC) was determined before and after gene transfer, using E-test strips. Results indicate that percentage resistance to the quinolones (Qs): Nalidixic acid, Ciprofloxacin, Pefloxacin and Ofloxacin determined by agar plate diffusion technique stood at 52.6, 47.3, 50.5, 70.6 and 46.0% for Escherichia coli, Salmonella sp., Shigellasp., Klebsiella sp. and Aeromonas sp. respectively. Analysis of variance indicated the occurrence of significant differences (F, 46.77-613.30; 0.00) in the resistance to each tested Qs. Generally, Human isolates showed greater resistance than Animal isolates (57.4 vs 47.2%). Investigation with specific primers indicated 11, 15, 7, 1 and 0 for qnrA, qnrB, qnrS, qepA and Aac(6')-Ib-cr genes respectively, out of 1018 Q-r and 29 PMQR isolates. Gene transfer experiments indicated the transfer of all genes except qepA either by conjugation or transformation. The MIC of tested Qs on recipient bacterium before gene transfer greatly increased from 0.0625 to 0.25 µg/mL, after transfer. This study demonstrates that PMQR genes amongst enteric bacteria in the Niger delta of Nigeria were transferable and transfer conferred a higher Q- resistance on recipient bacterium.
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Characterization of a Novel Variant of the Quinolone-Resistance Gene qnrB ( qnrB89) Carried by a Multi-Drug Resistant Citrobacter gillenii Strain Isolated from Farmed Salmon in Chile. Antibiotics (Basel) 2021; 10:antibiotics10030236. [PMID: 33652626 PMCID: PMC7996913 DOI: 10.3390/antibiotics10030236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 11/17/2022] Open
Abstract
The main objective of this study was to characterize using whole-genome sequencing analysis, a new variant of the qnrB gene (qnrB89) carried by a fluoroquinolone-susceptible bacterium isolated from mucus of farmed Salmo salar fingerling in Chile. Citrobacter gillenii FP75 was identified by using biochemical tests and 16S ribosomal gene analysis. Nucleotide and amino acid sequences of the qnrB89 gene exhibited an identity to qnrB of 81.24% and 91.59%, respectively. The genetic environment of qnrB89 was characterized by the upstream location of a sequence encoding for a protein containing a heavy metal-binding domain and a gene encoding for a N-acetylmuramoyl-L-alanine amidase protein, whereas downstream to qnrB89 gene were detected the csp and cspG genes, encoding cold-shock proteins. The qnrB89 gene was located on a large chromosomal contig of the FP75 genome and was not associated with the 10-kb plasmid and class 1 integron harbored by the FP75 strain. This study reports for the first time the carriage of a qnrB gene by the C. gillenii species, and its detection in a bacterial strain isolated from farmed salmon in Chile.
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Zhang S, Abbas M, Rehman MU, Huang Y, Zhou R, Gong S, Yang H, Chen S, Wang M, Cheng A. Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115260. [PMID: 32717638 DOI: 10.1016/j.envpol.2020.115260] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China; Livestock and Dairy Development Department Lahore, Punjab, 54000, Pakistan
| | - Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Yahui Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Rui Zhou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Siyue Gong
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Hong Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shuling Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China.
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Zhang G, Li J, Ai G, He J, Wang C, Feng J. A new intrinsic aminoglycoside 6'-N-acetyltransferase subclass, AAC(6')-III, in Burkholderia pseudomallei, Burkholderia mallei and Burkholderia oklahomensis. J Antimicrob Chemother 2020; 75:1352-1353. [PMID: 32016409 DOI: 10.1093/jac/dkaa011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jialiang He
- School of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Nwaiwu O, Aduba CC. An in silico analysis of acquired antimicrobial resistance genes in Aeromonas plasmids. AIMS Microbiol 2020; 6:75-91. [PMID: 32226916 PMCID: PMC7099201 DOI: 10.3934/microbiol.2020005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022] Open
Abstract
Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.
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Affiliation(s)
- Ogueri Nwaiwu
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, United Kingdom
| | - Chiugo Claret Aduba
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria
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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. Nat Commun 2020; 11:466. [PMID: 31980604 PMCID: PMC6981164 DOI: 10.1038/s41467-019-14139-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak. Antibiotic-resistant bacteria are an urgent threat to human health. Here, Roberts et al. characterise and monitor an ongoing hospital outbreak of carbapenemase-producing Enterobacter hormaechei by integrating several technologies for whole-genome sequencing and shotgun metagenomics.
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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Domínguez M, Miranda CD, Fuentes O, de la Fuente M, Godoy FA, Bello-Toledo H, González-Rocha G. Occurrence of Transferable Integrons and sul and dfr Genes Among Sulfonamide-and/or Trimethoprim-Resistant Bacteria Isolated From Chilean Salmonid Farms. Front Microbiol 2019; 10:748. [PMID: 31031727 PMCID: PMC6474311 DOI: 10.3389/fmicb.2019.00748] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/25/2019] [Indexed: 11/17/2022] Open
Abstract
Salmon farming industry in Chile currently uses a significant quantity of antimicrobials to control bacterial pathologies. The main aims of this study were to investigate the presence of transferable sulfonamide- and trimethoprim-resistance genes, sul and dfr, and their association with integrons among bacteria associated to Chilean salmon farming. For this purpose, 91 Gram-negative strains resistant to sulfisoxazole and/or trimethoprim recovered from various sources of seven Chilean salmonid farms and mainly identified as belonging to the Pseudomonas genus (81.0%) were studied. Patterns of antimicrobial resistance of strains showed a high incidence of resistance to florfenicol (98.9%), erythromycin (95.6%), furazolidone (90.1%) and amoxicillin (98.0%), whereas strains exhibited minimum inhibitory concentrations (MIC90) values of sulfisoxazole and trimethoprim of >4,096 and >2,048 μg mL−1, respectively. Strains were studied for their carriage of these genes by polymerase chain reaction, using specific primers, and 28 strains (30.8%) were found to carry at least one type of sul gene, mainly associated to a class 1 integron (17 strains), and identified by 16S rRNA gene sequencing as mainly belonging to the Pseudomonas genus (21 strains). Of these, 22 strains carried the sul1 gene, 3 strains carried the sul2 gene, and 3 strains carried both the sul1 and sul2 genes. Among these, 19 strains also carried the class 1 integron-integrase gene intI1, whereas the dfrA1, dfrA12 and dfrA14 genes were detected, mostly not inserted in the class 1 integron. Otherwise, the sul3 and intI2 genes were not found. In addition, the capability to transfer by conjugation these resistance determinants was evaluated in 22 selected strains, and sul and dfr genes were successfully transferred by 10 assayed strains, mainly mediated by a 10 kb plasmid, with a frequency of transfer of 1.4 × 10−5 to 8.4 × 10−3 transconjugant per recipient cell, and exhibiting a co-transference of resistance to florfenicol and oxytetracycline, currently the most used in Chilean salmon industry, suggesting an antibacterial co-selection phenomenon. This is the first report of the characterization and transferability of integrons as well as sul and dfr genes among bacteria associated to Chilean salmon farms, evidencing a relevant role of this environment as a reservoir of these genes.
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Affiliation(s)
- Mariana Domínguez
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | - Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile.,Centro AquaPacífico, Coquimbo, Chile
| | - Oliver Fuentes
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile.,Facultad de Medicina Veterinaria, Universidad San Sebastián, Concepción, Chile
| | - Mery de la Fuente
- Facultad de Medicina Veterinaria, Universidad San Sebastián, Concepción, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Talcahuano, Chile
| | - Félix A Godoy
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
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12
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Ribeiro TG, Novais Â, Rodrigues C, Nascimento R, Freitas F, Machado E, Peixe L. Dynamics of clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings over time. Int J Antimicrob Agents 2019; 53:650-656. [PMID: 30878669 DOI: 10.1016/j.ijantimicag.2019.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVES The objective of this work was to provide detailed molecular data on clinically acquired AmpC (qAmpC)-producing Enterobacteriaceae from two different periods (2002-2008 and 2010-2013) in order to clarify the contribution of clonal and plasmid genetic platforms for the current epidemiological scenario concerning extended-spectrum beta-lactams resistance. METHODS We analysed 1246 Enterobacteriaceae non-susceptible to third-generation cephalosporins from two hospitals and one community laboratory between 2010 and 2013. Bacterial identification, antibiotic susceptibility, identification of qAmpC and plasmid-mediated quinolone resistance genes, clonal (pulsed-field gel electrophoresis (PFGE), Multilocus sequence typing (MLST)) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed by standard methods. Whole-genome sequencing (WGS) was performed in two ST11-Klebsiella pneumoniae isolates harbouring DHA-1. RESULTS The occurrence of qAmpC was lower (2.6%) than that observed in a previous survey (7.4%), and varied slightly over time. Isolates produced DHA-1 (53%), CMY-2 (44%) or DHA-6 (3%), but significant epidemiological changes were observed in the two surveys. While DHA-1 persisted in different institutions by selection of a worldwide epidemic IncR plasmid in an ST11 harbouring KL105, CMY-2 rates increased over time linked to IncI1 plasmids (instead of IncK or IncA/C2) in multiple Escherichia coli clones. CONCLUSIONS The higher frequency of DHA-1 qAmpC in these species contrasts with the scenario in most European countries. Furthermore, the different genetic backgrounds associated with either extended-spectrum β-lactamases (ESBLs) or acquired AmpC β-lactamases (qAmpC) in our country might have contributed to their differential expansion.
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Affiliation(s)
- T G Ribeiro
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Â Novais
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - C Rodrigues
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - R Nascimento
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - F Freitas
- Centro Hospitalar Tondela-Viseu, Portugal
| | - E Machado
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; FP-ENAS/CEBIMED. Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, Porto, Portugal
| | - L Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.
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13
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Rui Y, Lu W, Li S, Cheng C, Sun J, Yang Q. Detection of common mobile genetic elements and genotyping of multidrug-resistant Gram-negative bacilli in blood specimens from septicemia patients in southern China. Infect Drug Resist 2018; 11:1741-1750. [PMID: 30349331 PMCID: PMC6190624 DOI: 10.2147/idr.s165513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background Integron, ISCR1 and complex class 1 integrons lead bacteria to become resistant to antibiotic regimens. The aim of this study was to detect common mobile genetic elements of multidrug-resistant Gram-negative bacilli and evaluate the genotyping of these bacilli in blood specimens from septicemia patients in southern China. Methods A total of 837 Gram-negative bacilli including 578 strains containing Enterobacteriaceae and 259 strains containing non-fermentative bacilli were investigated in blood samples collected from septicemia patients between 2011 and 2014 in southern China. Mobile genetic elements, such as class 1 integrons, the insertion sequence common region 1 (ISCR1), and complex class 1 integrons, were detected from the 837 strains. Results Twenty-seven types of gene cassette arrays were found among 837 strains in which 492 (58.8%) class 1 integron-positive isolates and 254 (51.6%) gene cassette-positive isolates were found, including the first description of two types, aacA4-blaIMP-1-blaOXA-30-catB3 and aac(6′)-II-aadA13-cmlA8-blaOXA-10, in the corresponding species and two gene cassettes, putative helicase and aadA-like, originally detected in integrons. Twelve types of ISCR1-linked resistance gene regions in 196 ISCR1-positive bacilli and seven different types of complex class 1 integron-positive strains were obtained including four distinct complex class 1 integrons that have never been described in any species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fngerprinting showed that isolates with identical gene profles were clonally unrelated. Conclusion Our results indicated that we should pay more attention to enhance the quality of infection control measures and prevent hospital infection, so as to avoid the outbreak of multidrug-resistant Gram-negative bacilli.
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Affiliation(s)
- Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Wengting Lu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Si Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Cancan Cheng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Jingjing Sun
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
| | - Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China,
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14
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Song M, Tang M, Ding Y, Wu Z, Xiang C, Yang K, Zhang Z, Li B, Deng Z, Liu J. Application of protein typing in molecular epidemiological investigation of nosocomial infection outbreak of aminoglycoside-resistant Pseudomonas aeruginosa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22437-22445. [PMID: 29249031 DOI: 10.1007/s11356-017-0960-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
Pseudomonas aeruginosan has emerged as an important pathogen elated to serious infections and nosocomial outbreaks worldwide. This study was conducted to understand the prevalence of aminoglycoside (AMG)-resistant P. aeruginosa in our hospital and to provide a scientific basis for control measures against nosocomial infections. Eighty-two strains of P. aeruginosa were isolated from clinical departments and divided into AMG-resistant strains and AMG-sensitive strains based on susceptibility test results. AMG-resistant strains were typed by drug resistance gene typing (DRGT) and protein typing. Five kinds of aminoglycoside-modifying enzyme (AME) genes were detected in the AMG-resistant group. AMG-resistant P. aeruginosa strains were classified into three types and six subtypes by DRGT. Four protein peaks, namely, 9900.02, 7600.04, 9101.25 and 10,372.87 Da, were significantly and differentially expressed between the two groups. AMG-resistant P. aeruginosa strains were also categorised into three types and six subtypes at the distance level of 10 by protein typing. AMG-resistant P. aeruginosa was cloned spread in our hospital; the timely implementation of nosocomial infection prevention and control strategies were needed in preventing outbreaks and epidemic of AMG-resistant P. aeruginosa. SELDI-TOF MS technology can be used for bacterial typing, which provides a new method of clinical epidemiological survey and nosocomial infection control.
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Affiliation(s)
- Min Song
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Min Tang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yinghuan Ding
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zecai Wu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chengyu Xiang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Kui Yang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhang Zhang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Baolin Li
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhenghua Deng
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China.
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15
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Alonso CA, Cortés-Cortés G, Maamar E, Massó M, Rocha-Gracia RDC, Torres C, Centrón D, Quiroga MP. Molecular diversity and conjugal transferability of class 2 integrons among Escherichia coli isolates from food, animal and human sources. Int J Antimicrob Agents 2018; 51:905-911. [DOI: 10.1016/j.ijantimicag.2018.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/21/2017] [Accepted: 02/03/2018] [Indexed: 01/03/2023]
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16
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Tomova A, Ivanova L, Buschmann AH, Godfrey HP, Cabello FC. Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area. MICROBIAL ECOLOGY 2018. [PMID: 28642992 DOI: 10.1007/s00248-017-1016-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Antimicrobial usage in aquaculture selects for antimicrobial-resistant microorganisms in the marine environment. The relevance of this selection to terrestrial animal and human health is unclear. Quinolone-resistance genes qnrA, qnrB, and qnrS were chromosomally located in four randomly chosen quinolone-resistant marine bacteria isolated from an aquacultural area with heavy quinolone usage. In quinolone-resistant uropathogenic clinical isolates of Escherichia coli from a coastal area bordering the same aquacultural region, qnrA was chromosomally located in two E. coli isolates, while qnrB and qnrS were located in small molecular weight plasmids in two other E. coli isolates. Three quinolone-resistant marine bacteria and three quinolone-resistant E. coli contained class 1 integrons but without physical association with PMQR genes. In both marine bacteria and uropathogenic E. coli, class 1 integrons had similar co-linear structures, identical gene cassettes, and similarities in their flanking regions. In a Marinobacter sp. marine isolate and in one E. coli clinical isolate, sequences immediately upstream of the qnrS gene were homologous to comparable sequences of numerous plasmid-located qnrS genes while downstream sequences were different. The observed commonality of quinolone resistance genes and integrons suggests that aquacultural use of antimicrobials might facilitate horizontal gene transfer between bacteria in diverse ecological locations.
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Affiliation(s)
- Alexandra Tomova
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Larisa Ivanova
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | | | - Henry P Godfrey
- Department of Pathology, New York Medical College, Valhalla, NY, USA
| | - Felipe C Cabello
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA.
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17
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Martini MC, Quiroga MP, Pistorio M, Lagares A, Centrón D, Del Papa MF. Novel environmental class 1 integrons and cassette arrays recovered from an on-farm bio-purification plant. FEMS Microbiol Ecol 2017; 94:4781311. [DOI: 10.1093/femsec/fix190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/27/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- María Carla Martini
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - María Paula Quiroga
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Daniela Centrón
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
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Ma L, Yin Z, Zhang D, Zhan Z, Wang Q, Duan X, Gao H, Liang Q, Zhao Y, Feng J, Zhao Y, Tong Y, Dai E, Zhou D. Comparative genomics of type 1 IncC plasmids from China. Future Microbiol 2017; 12:1511-1522. [PMID: 29140102 DOI: 10.2217/fmb-2017-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study dealt with genomic characterization of type 1 IncC resistance plasmids, capable of spreading across taxonomic borders, from China. Materials & methods: p112298-tetA was sequenced and compared with type 1 IncC reference plasmid pR148 and two available sequenced type 1 IncC plasmids pHS36-NDM and pVAS3-1 from China. Results: These plasmids contained one or more exogenous resistance islands, which included the ARI-A islands, the ARI-B islands, the ISEcp1-blaCMY units and the bla KPC-2 region and were inserted at various sites in the IncC backbone and thus represented three distinct lineages. Conclusion: Complex rearrangement and homologous recombination events have occurred during evolution of p112298-tetA, making it significantly differ modularly from the other three plasmids with respect to both plasmid backbone and exogenous resistance regions.
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Affiliation(s)
- Lizhi Ma
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Zhe Yin
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Zhe Zhan
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Qian Wang
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Xiongbo Duan
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Quanhui Liang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yuzong Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Jiao Feng
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yachao Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
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Du N, Liu S, Niu M, Duan Y, Zhang S, Yao J, Mao J, Chen R, Du Y. Transmission and characterization of bla NDM-1 in Enterobacter cloacae at a teaching hospital in Yunnan, China. Ann Clin Microbiol Antimicrob 2017; 16:58. [PMID: 28830556 PMCID: PMC5568220 DOI: 10.1186/s12941-017-0232-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/07/2017] [Indexed: 11/19/2022] Open
Abstract
Background In recent years, New Delhi metallo-beta-lactamases 1 (blaNDM-1) has been reported with increasing frequency and become prevalent. The present study was undertaken to investigate the epidemiological dissemination of the blaNDM-1 gene in Enterobacter cloacae isolates at a teaching hospital in Yunnan, China. Methods Antimicrobial susceptibility testing was performed using VITEK 2 system and E test gradient strips. The presence of integrons and insertion sequence common region 1 were examined by PCR and sequencing. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Conjugation experiments and Southern blot hybridization were performed to determine the transferability of plasmids. Results Ten E. cloacae isolates and their Escherichia coli transconjugants were exhibited similar resistant patterns to carbapenems, cephalosporins and penicillins. 8 (80%) of E. cloacae isolates carried class 1 integron and 1 (12.5%) carried class 2 integron. Integron variable regions harbored the genes which encoded resistance to aminoglycosides (aadA1, aadA2, aadA5, aadB, aac(6′)-Ib-cr), sulfamethoxazole/trimethoprim (dfrA17, dfrA12, dfrA15) and Streptozotocin (sat2). Six E. cloacae isolates belonged to ST74 and exhibited highly similar PFGE patterns. Each isolate shared an identical plasmid with ~33.3 kb size that carried the blaNDM-1 gene, except T3 strain, of which the blaNDM-1 gene was located on a ~50 kb plasmid. Conclusions Our findings suggested that plasmid was able to contribute to the dissemination of blaNDM-1. Hence, more attention should be devoted to monitor the dissemination of the blaNDM-1 gene due to its horizontal transfer via plasmid. In addition, nosocomial surveillance system should actively monitor the potential endemic clone of ST74 to prevent their further spread.
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Affiliation(s)
- Na Du
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Shumin Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Min Niu
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Yong Duan
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Shuangmeng Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Jing Yao
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Jian Mao
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Ran Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China
| | - Yan Du
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Laboratory Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, No. 295, Xichang Road, Wuhua, Kunming, Yunnan, China.
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Villa J, Arana DM, Viedma E, Perez-Montarelo D, Chaves F. Characterization of mobile genetic elements carrying VIM-1 and KPC-2 carbapenemases in Citrobacter freundii isolates in Madrid. Int J Med Microbiol 2017; 307:340-345. [PMID: 28711315 DOI: 10.1016/j.ijmm.2017.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 11/18/2022] Open
Abstract
Carbapenemase producing Citrobacter freundii (CPCF) infections are still uncommon in European countries. Here we report a molecular study conducted in a tertiary care facility in southern Madrid, Spain, from 2009 to 2014 to investigate the epidemiology of CPCF. The blaIMP-1,blaIMP-2,blaKPC,blaNDM,blaOXA-48,blaVIM-1 and blaVIM-2 genes were screened by PCR. Molecular typing was carried out by Pulsed-field gel electrophoresis analysis (PFGE) and multilocus sequence typing (MLST). Whole genome sequencing (WGS) was performed to characterize the resistome and the mobile genetic elements associated with the carbapenems resistance of CPCF. A total of 11/521 (2.1%) isolates had reduced susceptibility to carbapenems. PCR amplification revealed the presence of blaVIM-1 in 10 isolates and blaKPC-2 in 2 isolates. One C. freundii isolate co-harbored blaVIM-1 and blaKPC-2 genes. PFGE and MLST assigned 10 different clonal, 4 previously reported (ST11, ST18, ST22 and ST64) and 6 new STs (ST89, ST90, ST91, ST92, ST92 and ST94). The blaVIM-1 gene was part of In624 (intI1-blaVIM-1-aacA4-dfrB1-aadA1-catB2-qacEΔ1/sul1). In 3 of these isolates, plasmid-mediated quinolone resistance genes (qnrA1 and qnrB4) were present in its downstream region, taking part of a complex class 1 integron ([In624:ISCR1:qnrB4-blaDHA-1] and [In624:ISCR1:qnrA1]). On the other hand, the blaKPC-2 gene was associated with a Tn3-based transposon. The dissemination of the blaVIM-1 gene among various clones suggests a successful horizontal transfer of integron carrying elements that play a dominant role in the development of multidrug resistance in Enterobacteriaceae.
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Affiliation(s)
- Jennifer Villa
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - David M Arana
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Esther Viedma
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Fernando Chaves
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
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Expression of the aac(6')-Ib-cr Gene in Class 1 Integrons. Antimicrob Agents Chemother 2017; 61:AAC.02704-16. [PMID: 28223390 DOI: 10.1128/aac.02704-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/13/2017] [Indexed: 11/20/2022] Open
Abstract
aac(6')-Ib-cr is a plasmid-mediated quinolone resistance gene embedded within a gene cassette, most often within an integron. It confers resistance to quinolones and aminoglycosides. We investigated the role of a 101-bp fragment frequently present upstream of the aac(6')-Ib-cr gene cassette and found that it contributes to the expression of aac(6')-Ib-cr and provides an alternative start codon, confirming the length of the AAC(6')-Ib-cr protein to 199 amino acids.
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Complex Class 1 Integron Carrying qnrB62 and blaVIM-2 in a Citrobacter freundii Clinical Isolate. Antimicrob Agents Chemother 2016; 60:6937-6940. [PMID: 27572415 DOI: 10.1128/aac.00614-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/25/2016] [Indexed: 11/20/2022] Open
Abstract
The coexistence of qnrB62 and blaVIM-2 was detected in a Citrobacter clinical isolate. The reduced fluoroquinolone susceptibility is attributable to qnrB62, mutations of quinolone-resistance-determining regions, and an efflux pump or pumps. The genetic context surrounding chromosomal qnrB62 was a novel complex class 1 integron (In1184::ISCR1::qnrB62) containing a unique gene array (blaVIM-2-aacA4'-8-gucD). An 18-nucleotide deletion at the 3' end of the pspA gene [pspA(Δ18)], upstream of qnrB62, and an inverted repeat region (IRR2) were detected in In1184::ISCR1::qnrB62, indicating past transposition events.
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Sun F, Zhou D, Sun Q, Luo W, Tong Y, Zhang D, Wang Q, Feng W, Chen W, Fan Y, Xia P. Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata. Sci Rep 2016; 6:33982. [PMID: 27658354 PMCID: PMC5034289 DOI: 10.1038/srep33982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/06/2016] [Indexed: 02/04/2023] Open
Abstract
We previously reported the complete sequence of the resistance plasmid pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL (conferring bleomycin resistance), which is recovered from a clinical Leclercia adecarboxylata isolate P10164 from China. This follow-up work disclosed that there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3 coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and shown to carry a wealth of resistance genes, which encoded the resistance to at least 10 classes of antibiotics (β-lactams. macrolides, quinolones, aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds, sulphonamides, trimethoprim, and rifampicin) and 7 kinds of heavy mental (mercury, silver, copper, nickel, chromate, arsenic, and tellurium). All of these antibiotic resistance genes are associated with mobile elements such as transposons, integrons, and insertion sequence-based transposable units, constituting a total of three novel MDR regions, two in pP10164-2 and the other one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2 and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively drug-resistant.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.,College of Food Science and Project Engineering, Bohai University, Jinzhou 121013, China
| | - Qian Wang
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yahan Fan
- Transfusion Department, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
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Abstract
Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC code for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. The qnr genes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6')-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.
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Sun F, Zhou D, Wang Q, Feng J, Feng W, Luo W, Liu Y, Qiu X, Yin Z, Xia P. Genetic characterization of a novel blaDIM-2-carrying megaplasmid p12969-DIM from clinical Pseudomonas putida. J Antimicrob Chemother 2015; 71:909-12. [PMID: 26679251 DOI: 10.1093/jac/dkv426] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/10/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To characterize a blaDIM-2-carrying 409 kb megaplasmid p12969-DIM of Pseudomonas putida 12969 from a patient with pneumonia in China. METHODS The complete nucleotide sequence of p12969-DIM was determined with a paired-end library and a mate-pair library using next-generation sequencing technology. RESULTS blaDIM-2, a close blaDIM-1 variant, was identified in p12969-DIM. DIM-2 differs from DIM-1 by two amino acid substitutions Ser119Leu and Ser209Pro. The p12969-DIM backbone is highly similar to pOZ176, but the IncP-2-type stability/replication/conjugal transfer system in the pOZ176 backbone is absent from p12969-DIM. The p12969-DIM accessory regions, a 45.7 kb MDR and a novel insertion sequence, ISPpu23, are almost entirely distinct from pOZ176. The MDR region contains a novel Tn21-subgroup transposon Tn6286 inserted with two class 1 integrons, In1225 and In1226; a Tn5503-family transposon-like element inserted with a strAB locus; and a novel Tn21-subgroup transposon-like element inserted with a class 1 integron, In1224. The three integrons carry blaDIM-2 as well as a number of additional genes conferring resistance to quinolones, aminoglycosides, chloramphenicol, florfenicol, trimethoprim, streptomycin, quaternary ammonium compounds and sulphonamides. p12969-DIM has two distinct replication/stability systems, repA/parAB-parB2 of an unknown incompatibility group in the backbone and repABC/mazFE of the IncQ2 group in the MDR region. CONCLUSIONS The MDR region of p12969-DIM harbours many resistance genes as well as a second replication/stability system. This article is the first report of a fully sequenced blaDIM-carrying plasmid.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qian Wang
- Department of Pharmacy, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yao Liu
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Xuewen Qiu
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
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Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories of qnrB and Genetic Platforms within Particular Citrobacter Species. Antimicrob Agents Chemother 2015; 59:5951-8. [PMID: 26169406 DOI: 10.1128/aac.00027-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 07/06/2015] [Indexed: 11/20/2022] Open
Abstract
To gain insights into the diversification trajectories of qnrB genes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose, Citrobacter sp. isolates (n = 21) and genome or plasmid sequences (n = 56) available in public databases harboring complete or truncated qnrB genes were analyzed. Citrobacter species identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location of qnrB genes, and the genetic surroundings of qnrB genes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification of Citrobacter isolates was achieved using leuS and recN gene sequences, and isolates characterized in this study were diverse and harbored chromosomal qnrB genes. Phylogenetic analysis of all known qnrB genes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprising pspF and sapA and varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of these qnrB clusters, and the reliable identification of all Citrobacter isolates revealed that each platform evolved in different recognizable (Citrobacter freundii, C. braakii, C. werkmanii, and C. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome of Citrobacter spp. and in different plasmids of Enterobacteriaceae. Our data corroborate Citrobacter as the origin of qnrB and further suggest divergent evolution of closely related qnrB genes/platforms in particular Citrobacter spp., which were delineated using particular genotypic markers.
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Davin-Regli A, Pagès JM. Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment. Front Microbiol 2015; 6:392. [PMID: 26042091 PMCID: PMC4435039 DOI: 10.3389/fmicb.2015.00392] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/16/2015] [Indexed: 12/14/2022] Open
Abstract
Enterobacter aerogenes and E. cloacae have been reported as important opportunistic and multiresistant bacterial pathogens for humans during the last three decades in hospital wards. These Gram-negative bacteria have been largely described during several outbreaks of hospital-acquired infections in Europe and particularly in France. The dissemination of Enterobacter sp. is associated with the presence of redundant regulatory cascades that efficiently control the membrane permeability ensuring the bacterial protection and the expression of detoxifying enzymes involved in antibiotic degradation/inactivation. In addition, these bacterial species are able to acquire numerous genetic mobile elements that strongly contribute to antibiotic resistance. Moreover, this particular fitness help them to colonize several environments and hosts and rapidly and efficiently adapt their metabolism and physiology to external conditions and environmental stresses. Enterobacter is a versatile bacterium able to promptly respond to the antibiotic treatment in the colonized patient. The balance of the prevalence, E. aerogenes versus E. cloacae, in the reported hospital infections during the last period, questions about the horizontal transmission of mobile elements containing antibiotic resistance genes, e.g., the efficacy of the exchange of resistance genes Klebsiella pneumoniae to Enterobacter sp. It is also important to mention the possible role of antibiotic use in the treatment of bacterial infectious diseases in this E. aerogenes/E. cloacae evolution.
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Affiliation(s)
- Anne Davin-Regli
- Transporteurs Membranaires, Chimiorésistance et Drug Design, Facultés de Médecine et Pharmacie, UMR-MD1, IRBA - Aix-Marseille Université, Marseille France
| | - Jean-Marie Pagès
- Transporteurs Membranaires, Chimiorésistance et Drug Design, Facultés de Médecine et Pharmacie, UMR-MD1, IRBA - Aix-Marseille Université, Marseille France
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Characterization of Tn6238 with a new allele of aac(6')-Ib-cr. Antimicrob Agents Chemother 2015; 59:2893-7. [PMID: 25691640 DOI: 10.1128/aac.03213-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 02/08/2015] [Indexed: 11/20/2022] Open
Abstract
Here, we report that the genetic structure of Tn1331 remained conserved in Argentina from 1989 to 2013 (72 of 73 isolates), with the exception being the plasmid-borne Tn1331-like transposon Tn6238 containing a new aac(6')-Ib-cr allele recovered from a colistin-resistant Klebsiella pneumoniae clinical isolate. A bioinformatic analysis of aac(6')-Ib-like gene cassettes suggests that this new aac(6')-Ib-cr allele emerged through mutation or homologous recombination in the Tn1331 genetic platform. Tn6238 is a novel platform for the dissemination of aminoglycoside and fluoroquinolone resistance determinants.
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29
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Cruz GR, Radice M, Sennati S, Pallecchi L, Rossolini GM, Gutkind G, Conza JAD. Prevalence of plasmid-mediated quinolone resistance determinants among oxyiminocephalosporin-resistant Enterobacteriaceae in Argentina. Mem Inst Oswaldo Cruz 2015; 108:924-7. [PMID: 24037111 PMCID: PMC3970647 DOI: 10.1590/0074-0276130084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/13/2013] [Indexed: 12/27/2022] Open
Abstract
High quinolone resistance rates were observed among oxyiminocephalosporin-resistant enterobacteria. In the present study, we searched for the prevalence of plasmid-mediated quinolone resistance (PMQR) genes within the 55 oxyiminocephalosporin-resistant enterobacteria collected in a previous survey. The main PMQR determinants were aac(6')-Ib-cr and qnrB, which had prevalence rates of 42.4% and 33.3%, respectively. The aac(6')-Ib-cr gene was more frequently found in CTX-M-15-producing isolates, while qnrB was homogeneously distributed among all CTX-M producers.
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30
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Seija V, Medina Presentado JC, Bado I, Papa Ezdra R, Batista N, Gutierrez C, Guirado M, Vidal M, Nin M, Vignoli R. Sepsis caused by New Delhi metallo-β-lactamase (blaNDM-1) and qnrD-producing Morganella morganii, treated successfully with fosfomycin and meropenem: case report and literature review. Int J Infect Dis 2014; 30:20-6. [PMID: 25447717 DOI: 10.1016/j.ijid.2014.09.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES The objective of this study was to describe the microbiological characteristics of an extensively drug-resistant (XDR) isolate of Morganella morganii obtained from a patient with sepsis of urinary origin and to describe the patient's clinical characteristics. We further aimed to perform a literature review of the situation in Latin America regarding Gram-negative bacillus (GNB) carriers of New Delhi metallo-β-lactamase (NDM-1) and qnr genes and current reports on the treatment of infections caused by XDR enterobacteria, with particular attention to colistin-resistant isolates. METHODS The patient's clinical data were obtained from his medical history. Microbiological identification and susceptibility testing were done using the VITEK 2 Compact System. Resistance genes were detected by PCR and sequencing. RESULTS Blood and urine cultures grew an M. morganii isolate (Mm4232) harboring NDM-1 and qnrD1. The patient was treated successfully with fosfomycin and double doses of meropenem. There are no previous reports of the use of fosfomycin and meropenem to treat infections by XDR enterobacteria harboring NDM-1 carbapenemase. CONCLUSIONS This is the first report of qnrD1 in South America. We consider that this report could be helpful to physicians implementing treatments for infections caused by XDR GNB, including colistin-carbapenem-resistant GNB.
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Affiliation(s)
- Verónica Seija
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Julio César Medina Presentado
- Cátedra de Enfermedades Infecciosas, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Inés Bado
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Romina Papa Ezdra
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Noelia Batista
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Claudia Gutierrez
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mariana Guirado
- Cátedra de Enfermedades Infecciosas, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Macarena Vidal
- Cátedra de Enfermedades Infecciosas, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Marcelo Nin
- Centro de Nefrología Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay.
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Domingues S, da Silva GJ, Nielsen KM. Integrons: Vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elements 2014; 2:211-223. [PMID: 23550063 PMCID: PMC3575428 DOI: 10.4161/mge.22967] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies; Faculty of Pharmacy; University of Coimbra; Coimbra, Portugal ; Department of Pharmacy; Faculty of Health Sciences; University of Tromsø; Tromsø, Norway
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García-Fulgueiras V, Seija V, Aguerrebere P, Cordeiro NF, Vignoli R. First report of a clinical isolate of Leclercia adecarboxylata harbouring multiple resistance genes in Uruguay and review of the literature. J Glob Antimicrob Resist 2014; 2:77-81. [DOI: 10.1016/j.jgar.2014.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/27/2013] [Accepted: 01/02/2014] [Indexed: 11/16/2022] Open
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Bonelli RR, Moreira BM, Picão RC. Antimicrobial resistance among Enterobacteriaceae in South America: history, current dissemination status and associated socioeconomic factors. Drug Resist Updat 2014; 17:24-36. [PMID: 24618111 DOI: 10.1016/j.drup.2014.02.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
South America exhibits some of the higher rates of antimicrobial resistance in Enterobactericeae worldwide. This continent includes 12 independent countries with huge socioeconomic differences, where the ample access to antimicrobials, including counterfeit ones, coexists with ineffective health systems and sanitation problems, favoring the emergence and dissemination of resistant strains. This work presents a literature review concerning the evolution and current status of antimicrobial resistance threats found among Enterobacteriaceae in South America. Resistance to β-lactams, fluoroquinolones and aminoglycosides was emphasized along with description of key epidemiological studies that highlight the success of specific resistance determinants in different parts of the continent. In addition, a discussion regarding political and socioeconomic factors possibly related to the dissemination of antimicrobial resistant strains in clinical settings and at the community is presented. Finally, in order to assess the possible sources of resistant bacteria, we compile the current knowledge about the occurrence of antimicrobial resistance in isolates in South American' food, food-producing animals and off-hospitals environments. By addressing that intensive intercontinental commerce and tourism neutralizes the protective effect of geographic barriers, we provide arguments reinforcing that globally integrated efforts are needed to decelerate the emergence and dissemination of antimicrobial resistant strains.
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Affiliation(s)
- Raquel Regina Bonelli
- LIM Laboratório Integrado de Microbiologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beatriz Meurer Moreira
- LIM Laboratório Integrado de Microbiologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Cristina Picão
- LIM Laboratório Integrado de Microbiologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Colomer-Lluch M, Jofre J, Muniesa M. Quinolone resistance genes (qnrA and qnrS) in bacteriophage particles from wastewater samples and the effect of inducing agents on packaged antibiotic resistance genes. J Antimicrob Chemother 2014; 69:1265-74. [PMID: 24458509 DOI: 10.1093/jac/dkt528] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES This study quantifies quinolone antibiotic resistance genes (qnrA and qnrS) in DNA of phage particles isolated from faecally polluted waters and evaluates the influence of phage inducers on the abundance of antibiotic resistance genes in packaged DNA. METHODS qnrA and qnrS were quantified by qPCR in DNA of phage particles isolated from 18 raw urban wastewater samples, 18 river samples and 28 archived samples of animal wastewater. The bacterial fraction of the samples was treated with mitomycin C, ciprofloxacin, EDTA or sodium citrate under different conditions, and the number of resistance genes in DNA of phage particles was compared with the non-induced samples. RESULTS qnrA was more prevalent than qnrS, with 100% of positive samples in urban wastewater and river and 71.4% of positive samples in animal wastewater. Densities of qnrA ranged from 2.3 × 10(2) gene copies (GC)/mL in urban wastewater to 7.4 × 10(1) GC/mL in animal wastewater. qnrS was detected in 38.9% of urban wastewater samples, in 22.2% of river samples and only in one animal wastewater sample (3.6%). Despite the lower prevalence, qnrS densities reached values of 10(3) GC/mL. Both qnr genes and other resistance genes assayed (blaTEM and blaCTX-M) showed a significant increase in DNA of phage particles when treated with EDTA or sodium citrate, while mitomycin C and ciprofloxacin showed no effect under the different conditions assayed. CONCLUSIONS This study confirms the contribution of phages to the mobilization of resistance genes and the role of the environment and certain inducers in the spread of antibiotic resistance genes by means of phages.
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Affiliation(s)
- Marta Colomer-Lluch
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
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Martínez-Martínez L, Eliecer Cano M, Manuel Rodríguez-Martínez J, Calvo J, Pascual Á. Plasmid-mediated quinolone resistance. Expert Rev Anti Infect Ther 2014; 6:685-711. [DOI: 10.1586/14787210.6.5.685] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Quiroga MP, Arduino SM, Merkier AK, Quiroga C, Petroni A, Roy PH, Centrón D. “Distribution and functional identification of complex class 1 integrons”. INFECTION GENETICS AND EVOLUTION 2013; 19:88-96. [DOI: 10.1016/j.meegid.2013.06.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Structural diversity of class 1 integrons and their associated gene cassettes in Klebsiella pneumoniae isolates from a hospital in China. PLoS One 2013; 8:e75805. [PMID: 24098729 PMCID: PMC3786929 DOI: 10.1371/journal.pone.0075805] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 08/20/2013] [Indexed: 12/02/2022] Open
Abstract
Background Klebsiella pneumoniae strains carrying class 1 integrons are becoming more common worldwide, and their role in the dissemination of drug resistance is significant. The aim of this study was to characterize the structural diversity of class 1 integrons and their associated gene cassettes in K. pneumoniae isolates from hospital settings. Methodology/Principal Findings We analyzed a total of 176 K. pneumoniae isolates in a tertiary-care hospital in Beijing, China for the period of November 1, 2010-October 31, 2011. The presence of class 1 integrons and gene cassettes was analyzed by PCR and sequencing. The prevalence of class 1 integrons was 51.1% (90/176). Fourteen different gene cassettes and 10 different gene cassette arrays were detected. dfrA and aadA cassettes were predominant and cassette combination dfrA1-orfC was most frequently found (13.6%, 24/176). Strong association between resistance to a variety of drugs (both phenotypes and the associated genes) and the presence of class 1 integrons was observed. In addition, we also identified an association between some previously identified prevalent sequence types (such as ST11, ST15, ST147, ST562, and ST716) and the presence of class 1 integrons. Conclusions/Significance Data from this study demonstrated that class 1 integrons are highly diverse and are associated with a variety of drug resistance phenotypes, drug resistance genes, as well as genotypes among K. pneumoniae isolates. Continuous monitoring of gene cassettes in class 1 integrons is warranted to improve the understanding and control of drug resistance among hospital settings.
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Zhang S, Sun J, Liao XP, Hu QJ, Liu BT, Fang LX, Deng H, Ma J, Xiao X, Zhu HQ, Liu YH. Prevalence and Plasmid Characterization of theqnrDDeterminant inEnterobacteriaceaeIsolated from Animals, Retail Meat Products, and Humans. Microb Drug Resist 2013; 19:331-5. [DOI: 10.1089/mdr.2012.0146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sen Zhang
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Jian Sun
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiao-Ping Liao
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Qian-Jiang Hu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Bao-Tao Liu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Liang-Xing Fang
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Hui Deng
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Jun Ma
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Xia Xiao
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Heng-Qian Zhu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Ya-Hong Liu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
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Xia R, Ren Y, Xu H. Identification of plasmid-mediated quinolone resistance qnr genes in multidrug-resistant Gram-negative bacteria from hospital wastewaters and receiving waters in the Jinan area, China. Microb Drug Resist 2013; 19:446-56. [PMID: 23844849 DOI: 10.1089/mdr.2012.0210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) qnr genes by the polymerase chain reaction (PCR) in antibiotic-resistant bacteria isolates collected from aquatic environments in Jinan during 2 years (2008.3-2009.11). Genes were identified to variant level by PCR restriction fragment length polymorphism analysis or sequencing. qnrA1, qnrB2, qnrB4, qnrB6, qnrB9, qnrS1, and the new qnrB variant qnrB26 were detected in 31 strains from six genera (Klebsiella spp., Escherichia coli, Enterobacter spp., Proteus spp., Shigella spp., and Citrobacter spp.), four of which contained double qnr genes. Other PMQR genes, aac(6')-Ib-cr and qepA, were found in 12 (38.7%) and 5 (16.1%) of 31 isolates, respectively; while qepA was found in Shigella spp. for the first time. Eight types of β-lactamase genes and eight other types of resistance genes were also present in the 31 qnr-positive isolates. The detection rate for five β-lactamase genes (blaTEM, blaCTX, ampR, blaDHA, and blaSHV) was >45%. Class 1 integrons and complex class 1 integrons were prevalent in these strains, which contained 15 different gene cassette arrays and 5 different insertion sequence common region 1 (ISCR1)-mediated downstream structures. qnrA1, qnrB2, and qnrB6 were present in three ISCR1-mediated downstream structures: qnrA1-ampR, sapA-like-qnrB2, and sdr-qnrB6. We also analyzed the horizontal transferability of PMQR genes and other resistance determinants. The qnr genes and some integrons and resistance genes from 18 (58.1%) of the 31 qnr-positive strains could be transferred to E. coli J53 Azi(R) or E. coli DH5α recipient strains using conjugation or transformation methods. The results showed that a high number of qnr genes were associated with other resistance genes in aquatic environments in Jinan. This suggests that we should avoid over-using antibiotics and monitor aquatic environments to control the spread of antibiotic resistance genes.
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Affiliation(s)
- Ruirui Xia
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan, China
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Outbreak of a cluster with epidemic behavior due to Serratia marcescens after colistin administration in a hospital setting. J Clin Microbiol 2013; 51:2295-302. [PMID: 23698525 DOI: 10.1128/jcm.03280-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia marcescens causes health care-associated infections with important morbidity and mortality. Particularly, outbreaks produced by multidrug-resistant isolates of this species, which is already naturally resistant to several antibiotics, including colistin, are usually described with high rates of fatal outcomes throughout the world. Thus, it is important to survey factors associated with increasing frequency and/or emergence of multidrug-resistant S. marcescens nosocomial infections. We report the investigation and control of an outbreak with 40% mortality due to multidrug-resistant S. marcescens infections that happened from November 2007 to April 2008 after treatment with colistin for Acinetobacter baumannii meningitis was started at hospital H1 in 2005. Since that year, the epidemiological pattern of frequently recovered species has changed, with an increase of S. marcescens and Proteus mirabilis infections in 2006 in concordance with a significant decrease of the numbers of P. aeruginosa and A. baumannii isolates. A single pulsed-field gel electrophoresis (PFGE) cluster of S. marcescens isolates was identified during the outbreak. When this cluster was compared with S. marcescens strains (n = 21) from 10 other hospitals (1997 to 2010), it was also identified in both sporadic and outbreak isolates circulating in 4 hospitals in Argentina. In132::ISCR1::blaCTX-M-2 was associated with the multidrug-resistant cluster with epidemic behavior when isolated from outbreaks. Standard infection control interventions interrupted transmission of this cluster even when treatment with colistin continued in several wards of hospital H1 until now. Optimizing use of colistin should be achieved simultaneously with improved infection control to prevent the emergence of species naturally resistant to colistin, such as S. marcescens and P. mirabilis.
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Ramirez MS, Nikolaidis N, Tolmasky ME. Rise and dissemination of aminoglycoside resistance: the aac(6')-Ib paradigm. Front Microbiol 2013; 4:121. [PMID: 23730301 PMCID: PMC3656343 DOI: 10.3389/fmicb.2013.00121] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 04/29/2013] [Indexed: 11/21/2022] Open
Abstract
Enzymatic modification is a prevalent mechanism by which bacteria defeat the action of antibiotics. Aminoglycosides are often inactivated by aminoglycoside modifying enzymes encoded by genes present in the chromosome, plasmids, and other genetic elements. The AAC(6′)-Ib (aminoglycoside 6′-N-acetyltransferase type Ib) is an enzyme of clinical importance found in a wide variety of gram-negative pathogens. The AAC(6′)-Ib enzyme is of interest not only because of his ubiquity but also because of other characteristics, it presents significant microheterogeneity at the N-termini and the aac(6′)-Ib gene is often present in integrons, transposons, plasmids, genomic islands, and other genetic structures. Excluding the highly heterogeneous N-termini, there are 45 non-identical AAC(6′)-Ib related entries in the NCBI database, 32 of which have identical name in spite of not having identical amino acid sequence. While some variants conserved similar properties, others show dramatic differences in specificity, including the case of AAC(6′)-Ib-cr that mediates acetylation of ciprofloxacin representing a rare case where a resistance enzyme acquires the ability to utilize an antibiotic of a different class as substrate. Efforts to utilize antisense technologies to turn off expression of the gene or to identify enzymatic inhibitors to induce phenotypic conversion to susceptibility are under way.
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Affiliation(s)
- María S Ramirez
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton, CA, USA
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Lai J, Wang Y, Shen J, Li R, Han J, Foley SL, Wu C. Unique class 1 integron and multiple resistance genes co-located on IncHI2 plasmid is associated with the emerging multidrug resistance of Salmonella Indiana isolated from chicken in China. Foodborne Pathog Dis 2013; 10:581-8. [PMID: 23672474 DOI: 10.1089/fpd.2012.1455] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to clarify the molecular antimicrobial resistance mechanisms of Salmonella enterica serovar Indiana isolated from chickens in China. A total of 327 chicken intestinal content and feces were collected in Shandong, China in 2009. Isolates were serotyped and antimicrobial susceptibility testing was performed. Thirty-five (10.7%) Salmonella isolates were recovered, and 16 (45.7%) were Salmonella enterica serovar Indiana, which were resistant to at least 14 of 15 antimicrobial agents. The 16 Salmonella enterica serovar Indiana detected and other 13 Salmonella enterica serovar Indiana that were selected from 133 Salmonella enterica serovar Indiana isolated in 2008 were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Then class 1 integron and drug resistance genes were detected by polymerase chain reaction. Linkage between plasmids and resistance components was determined by conjugation, electrotransformation, S1 nuclease-PFGE, polymerase chain reaction-based replicon typing and Southern blot assays. Regions flanking integrons were sequenced by modified random primer walking strategy. PFGE and MLST suggested that all the 29 Salmonella enterica serovar Indiana isolates that shared >78% similarity in PFGE patterns were of the same MLST type, ST17. Two kinds of class 1 integrons had different integrase genes and the same variable region (dfrA7/aadA4/IS26/aac(6')-Ib/blaOXA-1/catB3/arr-3), and additional antimicrobial resistance genes such as blaCTX-M-24, floR, and so on were detected on IncHI2 plasmids in 29 Salmonella enterica serovar Indiana, and seven plasmids were conjugative. Analysis of the genetic environment of the integrons suggested that these integrons might have been formed by the help of IS26. To our knowledge, the variable region in class 1 integrons is the longest reported in Salmonella to date. The unique integrons and multiple resistance genes co-located on the IncHI2 plasmid contributed to the dissemination of multidrug resistance.
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Affiliation(s)
- Jing Lai
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China
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Differential distribution of plasmid-mediated quinolone resistance genes in clinical enterobacteria with unusual phenotypes of quinolone susceptibility from Argentina. Antimicrob Agents Chemother 2013; 57:2467-75. [PMID: 23478955 DOI: 10.1128/aac.01615-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We studied a collection of 105 clinical enterobacteria with unusual phenotypes of quinolone susceptibility to analyze the occurrence of plasmid-mediated quinolone resistance (PMQR) and oqx genes and their implications for quinolone susceptibility. The oqxA and oqxB genes were found in 31/34 (91%) Klebsiella pneumoniae and 1/3 Klebsiella oxytoca isolates. However, the oqxA- and oqxB-harboring isolates lacking other known quinolone resistance determinants showed wide ranges of susceptibility to nalidixic acid and ciprofloxacin. Sixty of the 105 isolates (57%) harbored at least one PMQR gene [qnrB19, qnrB10, qnrB2, qnrB1, qnrS1, or aac(6')-Ib-cr)], belong to 8 enterobacterial species, and were disseminated throughout the country, and most of them were categorized as susceptible by the current clinical quinolone susceptibility breakpoints. We developed a disk diffusion-based method to improve the phenotypic detection of aac(6')-Ib-cr. The most common PMQR genes in our collection [qnrB19, qnrB10, and aac(6')-Ib-cr] were differentially distributed among enterobacterial species, and two different epidemiological settings were evident. First, the species associated with community-acquired infections (Salmonella spp. and Escherichia coli) mainly harbored qnrB19 (a unique PMQR gene) located in small ColE1-type plasmids that might constitute its natural reservoirs. qnrB19 was not associated with an extended-spectrum β-lactamase phenotype. Second, the species associated with hospital-acquired infections (Enterobacter spp., Klebsiella spp., and Serratia marcescens) mainly harbored qnrB10 in ISCR1-containing class 1 integrons that may also have aac(6')-Ib-cr as a cassette within the variable region. These two PMQR genes were strongly associated with an extended-spectrum β-lactamase phenotype. Therefore, this differential distribution of PMQR genes is strongly influenced by their linkage or lack of linkage to integrons.
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Yim G, Kwong W, Davies J, Miao V. Complex integrons containing qnrB4-ampC (bla(DHA-1)) in plasmids of multidrug-resistant Citrobacter freundii from wastewater. Can J Microbiol 2012; 59:110-6. [PMID: 23461518 DOI: 10.1139/cjm-2012-0576] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial populations in wastewater treatment plants (WWTPs) are increasingly being recognized as environmental reservoirs of antibiotic resistance genes. PCR amplicons for plasmid-mediated quinolone resistance determinants qnrA, qnrB, and qnrS were recorded in samples from a WWTP in Vancouver, British Columbia. Six strains of ciprofloxacin-resistant Citrobacter freundii were isolated and found to carry mutations in gyrA and parC, as well as multiple plasmid-borne resistance genes, collectively including qnrB; aac(6')-Ib-cr; β-lactamase-encoding genes from molecular classes A (blaTEM-1), C (ampC), D (blaOXA-1, blaOXA-10); and genes for resistance to 5 other types of antibiotics. In 3 strains, large (>60 kb) plasmids carried qnrB4 and ampC as part of a complex integron in a 14 kb arrangement that has been reported worldwide but, until recently, only among pathogenic strains of Klebsiella. Analysis of single-nucleotide polymorphisms in the qnrB4-ampC regions infers 2 introductions into the WWTP environment. These results suggest recent passage of plasmid-borne fluoroquinolone and β-lactam resistance genes from pathogens to bacteria that may be indigenous inhabitants of WWTPs, thus contributing to an environmental pool of antibiotic resistance.
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Affiliation(s)
- Grace Yim
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Wang F, Wu K, Sun J, Wang Q, Chen Q, Yu S, Rui Y. Novel ISCR1-linked resistance genes found in multidrug-resistant Gram-negative bacteria in southern China. Int J Antimicrob Agents 2012; 40:404-8. [DOI: 10.1016/j.ijantimicag.2012.06.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/12/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
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Arduino SM, Quiroga MP, Ramírez MS, Merkier AK, Errecalde L, Di Martino A, Smayevsky J, Kaufman S, Centrón D. Transposons and integrons in colistin-resistant clones of Klebsiella pneumoniae and Acinetobacter baumannii with epidemic or sporadic behaviour. J Med Microbiol 2012; 61:1417-1420. [DOI: 10.1099/jmm.0.038968-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sonia M. Arduino
- Instituto de Educación Medica e Investigaciones Clínicas ‘Dr Norberto Quirno’ CEMIC, Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrea Karina Merkier
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Facultad de Medicina, Buenos Aires, Argentina
| | - Laura Errecalde
- Sección Microbiología, Hospital Fernández, Buenos Aires, Argentina
| | - Ana Di Martino
- Laboratorio de Bacteriología, Sanatorio de la Trinidad Mitre, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jorgelina Smayevsky
- Instituto de Educación Medica e Investigaciones Clínicas ‘Dr Norberto Quirno’ CEMIC, Buenos Aires, Argentina
| | - Sara Kaufman
- Sección Microbiología, Hospital Fernández, Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Facultad de Medicina, Buenos Aires, Argentina
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Mokracka J, Oszyńska A, Kaznowski A. Increased frequency of integrons and β-lactamase-coding genes among extraintestinal Escherichia coli isolated with a 7-year interval. Antonie Van Leeuwenhoek 2012; 103:163-74. [PMID: 22945863 PMCID: PMC3528966 DOI: 10.1007/s10482-012-9797-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/10/2012] [Indexed: 11/28/2022]
Abstract
We analyzed the level of antimicrobial resistance, and the presence of integrons and β-lactamase-coding genes in 69 clinically relevant Escherichia coli strains originating from extraintestinal infections isolated in 1999–2001 and 2008–2010. Comparison of the two groups showed significant differences in drug resistance frequency, and the presence of integron and β-lactamase-coding genes. The frequency of resistance to all antimicrobials beside imipenem, streptomycin, piperacillin/tazobactam, and sulfamethoxazole increased significantly, especially towards aminoglycosides, β-lactams and fluoroquinolones. Similarly, we noticed an increase in the number of strains with integrons from 31.6 to 80.7 %. The presence of integrase genes was associated with elevated frequency of resistance to each antimicrobial tested besides imipenem, piperacillin/tazobactam and ceftazidime. The presence of integrons was also associated with multidrug resistance phenotype. The genetic content of integrons comprised genes determining resistance toward aminoglycosides, sulfonamides and trimethoprim. Moreover, we noticed a significant increase in the frequency of blaCTX-M β-lactamases, with appearance of blaCTX-M-15 variant and newer plasmid-encoded β-lactamases like CMY-15 and DHA. The emergence of strains resistant to several classes of antimicrobials and carrying integrons, ESBL and AmpC β-lactamase-coding genes may predict the spread of isolates with limited treatment options.
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Affiliation(s)
- Joanna Mokracka
- Faculty of Biology, Department of Microbiology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland.
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Transferable mechanisms of quinolone resistance. Int J Antimicrob Agents 2012; 40:196-203. [DOI: 10.1016/j.ijantimicag.2012.02.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 11/20/2022]
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Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer. Curr Microbiol 2012; 65:673-8. [PMID: 22926720 PMCID: PMC3477587 DOI: 10.1007/s00284-012-0213-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 08/16/2012] [Indexed: 12/02/2022]
Abstract
In the last few years, numerous cases of multidrug-resistant Achromobacter xylosoxidans infections have been documented in immunocompromised and cystic fibrosis patients. To gain insights into the molecular mechanisms and mobile elements related to multidrug resistance in this bacterium, we studied 24 non-epidemiological A. xylosoxidans clinical isolates from Argentina. Specific primers for plasmids, transposons, insertion sequences, blaampC, intI1, and intI2 genes were used in PCR reactions. The obtained results showed the presence of wide host range IncP plasmids in ten isolates and a high dispersion of class 1 integrons (n = 10) and class 2 integrons (n = 3). Four arrays in the variable region (vr) of class 1 integrons were identified carrying different gene cassettes as the aminoglycoside resistance aac(6′)-Ib and aadA1, the trimethoprim resistance dfrA1 and dfrA16, and the β-lactamase blaOXA-2. In only one of the class 2 integrons, a vr was amplified that includes sat2-aadA1. The blaampC gene was found in all isolates, confirming its ubiquitous nature. Our results show that A. xylosoxidans clinical isolates contain a rich variety of genetic elements commonly associated with resistance genes and their dissemination. This supports the hypothesis that A. xylosoxidans is becoming a reservoir of horizontal genetic transfer elements commonly involved in spreading antibiotic resistance.
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Nardelli M, Scalzo PM, Ramírez MS, Quiroga MP, Cassini MH, Centrón D. Class 1 integrons in environments with different degrees of urbanization. PLoS One 2012; 7:e39223. [PMID: 22761743 PMCID: PMC3382206 DOI: 10.1371/journal.pone.0039223] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 05/17/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Class 1 integrons are one of the most successful elements in the acquisition, expression and spread of antimicrobial resistance genes (ARG) among clinical isolates. Little is known about the gene flow of the components of the genetic platforms of class 1 integrons within and between bacterial communities. Thus it is important to better understand the interactions among "environmental" intI1, its genetic platforms and its distribution with human activities. METHODOLOGY/PRINCIPAL FINDINGS An evaluation of two types of genetic determinants, ARG (sul1 and qacE1/qacEΔ1 genes) and lateral genetic elements (LGE) (intI1, ISCR1 and tniC genes) in a model of a culture-based method without antibiotic selection was conducted in a gradient of anthropogenic disturbances in a Patagonian island recognized as being one of the last regions containing wild areas. The intI1, ISCR1 genes and intI1 pseudogenes that were found widespread throughout natural communities were not associated with urbanization (p>0.05). Each ARG that is embedded in the most common genetic platform of clinical class 1 integrons, showed different ecological and molecular behaviours in environmental samples. While the sul1 gene frequency was associated with urbanization, the qacE1/qacEΔ1 gene showed an adaptive role to several habitats. CONCLUSIONS/SIGNIFICANCE The high frequency of intI1 pseudogenes suggests that, although intI1 has a deleterious impact within several genomes, it can easily be disseminated among natural bacterial communities. The widespread occurrence of ISCR1 and intI1 throughout Patagonian sites with different degree of urbanization, and within different taxa, could be one of the causes of the increasing frequency of multidrug-resistant isolates that have characterized Argentina for decades. The flow of ARG and LGE between natural and clinical communities cannot be explained with a single general process but is a direct consequence of the interaction of multiple factors operating at molecular, ecological, phylogenetic and historical levels.
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Affiliation(s)
- Maximiliano Nardelli
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Marina Scalzo
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Soledad Ramírez
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Hernán Cassini
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
- Laboratorio de Biología del Comportamiento, IBYME, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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