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Rodrigues SH, Nunes GD, Soares GG, Ferreira RL, Damas MSF, Laprega PM, Shilling RE, Campos LC, da Costa AS, Malavazi I, da Cunha AF, Pranchevicius MCDS. First report of coexistence of blaKPC-2 and blaNDM-1 in carbapenem-resistant clinical isolates of Klebsiella aerogenes in Brazil. Front Microbiol 2024; 15:1352851. [PMID: 38426065 PMCID: PMC10903355 DOI: 10.3389/fmicb.2024.1352851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Klebsiella aerogenes is an important opportunistic pathogen with the potential to develop resistance against last-line antibiotics, such as carbapenems, limiting the treatment options. Here, we investigated the antibiotic resistance profiles of 10 K. aerogenes strains isolated from patient samples in the intensive-care unit of a Brazilian tertiary hospital using conventional PCR and a comprehensive genomic characterization of a specific K. aerogenes strain (CRK317) carrying both the blaKPC-2 and blaNDM-1 genes simultaneously. All isolates were completely resistant to β-lactam antibiotics, including ertapenem, imipenem, and meropenem with differencing levels of resistance to aminoglycosides, quinolones, and tigecycline also observed. Half of the strains studied were classified as multidrug-resistant. The carbapenemase-producing isolates carried many genes of interest including: β-lactams (blaNDM-1, blaKPC-2, blaTEM-1, blaCTX-M-1 group, blaOXA-1 group and blaSHVvariants in 20-80% of the strains), aminoglycoside resistance genes [aac(6')-Ib and aph(3')-VI, 70 and 80%], a fluoroquinolone resistance gene (qnrS, 80%), a sulfonamide resistance gene (sul-2, 80%) and a multidrug efflux system transporter (mdtK, 70%) while all strains carried the efflux pumps Acr (subunit A) and tolC. Moreover, we performed a comprehensive genomic characterization of a specific K. aerogenes strain (CRK317) carrying both the blaKPC-2 and blaNDM-1 genes simultaneously. The draft genome assembly of the CRK317 had a total length of 5,462,831 bp and a GC content of 54.8%. The chromosome was found to contain many essential genes. In silico analysis identified many genes associated with resistance phenotypes, including β-lactamases (blaOXA-9, blaTEM-1, blaNDM-1, blaCTX-M-15, blaAmpC-1, blaAmpC-2), the bleomycin resistance gene (bleMBL), an erythromycin resistance methylase (ermC), aminoglycoside-modifying enzymes [aac(6')-Ib, aadA/ant(3")-Ia, aph(3')-VI], a sulfonamide resistance enzyme (sul-2), a chloramphenicol acetyltransferase (catA-like), a plasmid-mediated quinolone resistance protein (qnrS1), a glutathione transferase (fosA), PEtN transferases (eptA, eptB) and a glycosyltransferase (arnT). We also detected 22 genomic islands, eight families of insertion sequences, two putative integrative and conjugative elements with a type IV secretion system, and eight prophage regions. This suggests the significant involvement of these genetic structures in the dissemination of antibiotic resistance. The results of our study show that the emergence of carbapenemase-producing K. aerogenes, co-harboring blaKPC-2 and blaNDM-1, is a worrying phenomenon which highlights the importance of developing strategies to detect, prevent, and control the spread of these microorganisms.
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Affiliation(s)
- Saulo Henrique Rodrigues
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Gustavo Dantas Nunes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Gabriela Guerrera Soares
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Pedro Mendes Laprega
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Andrea Soares da Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Cheng Q, Ma Z, Gong Z, Liang Y, Guo J, Ye X, Han Z, Yao Z. Whole-genome sequencing analysis of Klebsiella aerogenes among men who have sex with men in Guangzhou, China. Front Microbiol 2023; 14:1102907. [PMID: 37333657 PMCID: PMC10272549 DOI: 10.3389/fmicb.2023.1102907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Klebsiella aerogenes is a common infectious bacterium that poses a threat to human health. Nevertheless, there are limited data on the population structure, genetic diversity, and pathogenicity of K. aerogenes, especially among men who have sex with men (MSM). The present study aimed to clarify the sequence types (STs), clonal complexes (CCs), resistance genes, and virulence factors of popular strains. Multilocus sequence typing was used to describe the population structure of K. aerogenes. The Virulence Factor Database and Comprehensive Antibiotic Resistance Database were used to assess the virulence and resistance profiles. In this study, next-generation sequencing was performed on nasal swabs specimens collected in an HIV Voluntary Counseling Testing outpatient department in Guangzhou, China, from April to August 2019. The identification results showed that a total of 258 K. aerogenes isolates were collected from 911 participants. We found that the isolates were most resistant to furantoin (89.53%, 231/258) and ampicillin (89.15%, 230/258), followed by imipenem (24.81%, 64/258) and cefotaxime (18.22%, 47/258). The most common STs in carbapenem-resistant K. aerogenes were ST4, ST93, and ST14. The population has at least 14 CCs, including several novel ones identified in this study (CC11-CC16). The main mechanism of drug resistance genes was antibiotic efflux. Based on the presence of the iron carrier production genes irp and ybt, we identified two clusters according to virulence profiles. In cluster A, CC3 and CC4 carry the clb operator encoding the toxin. Increased monitoring is needed for the three main ST type strains carried by MSM. The main clone group CC4 has a large number of toxin genes, and it spreads among MSM. Caution is needed to prevent further spread of this clone group in this population. In sum, our results may provide a foundation for the development of new therapeutic and surveillance strategies for treating MSM.
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Affiliation(s)
- Qi Cheng
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zheng Ma
- The Sixth People's Hospital of Dongguan, Dongguan, China
| | - Zijun Gong
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuelang Liang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiajia Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaohua Ye
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhigang Han
- Department of Acquired Immune Deficiency Syndrome/Sexually Transmitted Disease Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zhenjiang Yao
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
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Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antibiotics (Basel) 2022; 11:antibiotics11070906. [PMID: 35884160 PMCID: PMC9311965 DOI: 10.3390/antibiotics11070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
With the wide spread of multidrug-resistant bacteria, a variety of aminoglycosides have been used in clinical practice as one of the effective options for antimicrobial combinations. However, in recent years, the emergence of high-level resistance against pan-aminoglycosides has worsened the status of antimicrobial resistance, so the production of 16S rRNA methyltransferase (16S-RMTase) should not be ignored as one of the most important resistance mechanisms. What is more, on account of transferable plasmids, the horizontal transfer of resistance genes between pathogens becomes easier and more widespread, which brings challenges to the treatment of infectious diseases and infection control of drug-resistant bacteria. In this review, we will make a presentation on the prevalence and genetic environment of 16S-RMTase encoding genes that lead to high-level resistance to aminoglycosides.
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Sacco F, Raponi G, Oliva A, Bibbolino G, Mauro V, Lella FMD, Volpicelli L, Antonelli G, Venditti M, Carattoli A, Arcari G. An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and bla NDM: evaluation of the global dissemination of these resistance determinants. Int J Antimicrob Agents 2022; 60:106615. [PMID: 35691602 DOI: 10.1016/j.ijantimicag.2022.106615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/05/2022]
Abstract
The spread of extremely-drug resistant Klebsiella pneumoniae has become a major health threat worldwide. This is largely mediated by certain lineages, recognized as high-risk clones dispersed in all the world. The analysis of an outbreak of nine ST15, NDM-1 metallo-β-lactamase producing K. pneumoniae was performed. An IncC plasmid carrying the blaNDM-1 gene also carried the rare rmtC gene, encoding for a 16S rRNA methyltransferases (16RMTases), conferring resistance to all aminoglycosides. We studied the global spread of NDM variants and their association with the 16RMTases among K. pneumoniae complete genomes available in GenBank, producing a complete overview of the association of 16RMTases and NDM in K. pneumoniae genomics. NDM is more and more often associated with16RMTases and both are spreading in K. pneumoniae, conferring resistance to every beta-lactam and aminoglycoside. Our analysis suggest that aminoglycosides have limited future as second line treatment against NDM-producing K. pneumoniae.
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Affiliation(s)
- Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giammarco Raponi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome; Microbiology and Virology Unit, University Hospital Policlinico Umberto I, Rome, Italy
| | - Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | - Giulia Bibbolino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples
| | - Vera Mauro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | | | - Lorenzo Volpicelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | | | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Huang F, Li S, Lou L, Mo J, Xu H. Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes. Pol J Microbiol 2021; 70:409-412. [PMID: 34584536 PMCID: PMC8459003 DOI: 10.33073/pjm-2021-038] [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: 06/06/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 11/05/2022] Open
Abstract
Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.
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Affiliation(s)
- Fang Huang
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lan Lou
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junjun Mo
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Pan F, Xu Q, Zhang H. Emergence of NDM-5 Producing Carbapenem-Resistant Klebsiella aerogenes in a Pediatric Hospital in Shanghai, China. Front Public Health 2021; 9:621527. [PMID: 33718321 PMCID: PMC7947282 DOI: 10.3389/fpubh.2021.621527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Carbapenem-resistant Klebsiella aerogenes (CRKA) has posed a serious threat for clinical anti-infective therapy. However, the molecular characteristics of CRKA in Shanghai are rarely reported. Objective: This study aimed to investigate the resistance profiles, dissemination mechanism, and molecular characteristics of CRKA strains isolated from children in a pediatric hospital, Shanghai. Method: Fifty CRKA isolates were collected in 2019. Antimicrobial susceptibility of the strains was determined by broth microdilution method. The β-lactamases and outer membrane porin genes were characterized by polymerase chain reaction (PCR). Conjugation experiments were performed to determine the transferability of the plasmids. The plasmids were typed based on their incompatibility group using the PCR-based replicon typing method. Multilocus sequence typing (MLST) and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) were performed for the genetic relationship. Results: All CRKA strains showed high level of resistance to cephalosporins and carbapenems, but still susceptible to aminoglycosides, colistin, and tigecycline. Forty five of fifty isolates carried blaNDM−5 genes (45/50, 90%), alongside with other β-Lactamase genes including blaCTX−M−1, blaTEM−1, and blaSHV−11 being detected. Loss of ompK35 and ompK36 genes were observed in 14% (7/50) and 28% (14/50), respectively, with 5 isolates lacking both ompK35 and ompK36. MLST analysis demonstrated that the majority of isolates belonged to ST4 (47/50, 94%) and ERIC-PCR fingerprinting was performed to identify NDM-5-producing isolates with approximately or more than 80% similarity levels. Plasmids carrying blaNDM−5 were successfully transferred to the E. coli recipient and plasmid typing showed that IncX3 were the prevalent among CRKA isolates. Conclusions: Our finding revealed the emergence of NDM-5 producing CRKA belonging to ST4 among children in Shanghai. Further attention should be paid to control the horizontal spread of the Class B carbapenemases like NDM in children.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qi Xu
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
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Hobson C, Chan AN, Wright GD. The Antibiotic Resistome: A Guide for the Discovery of Natural Products as Antimicrobial Agents. Chem Rev 2021; 121:3464-3494. [PMID: 33606500 DOI: 10.1021/acs.chemrev.0c01214] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of life-saving antibiotics has long been plagued by the ability of pathogenic bacteria to acquire and develop an array of antibiotic resistance mechanisms. The sum of these resistance mechanisms, the antibiotic resistome, is a formidable threat to antibiotic discovery, development, and use. The study and understanding of the molecular mechanisms in the resistome provide the basis for traditional approaches to combat resistance, including semisynthetic modification of naturally occurring antibiotic scaffolds, the development of adjuvant therapies that overcome resistance mechanisms, and the total synthesis of new antibiotics and their analogues. Using two major classes of antibiotics, the aminoglycosides and tetracyclines as case studies, we review the success and limitations of these strategies when used to combat the many forms of resistance that have emerged toward natural product-based antibiotics specifically. Furthermore, we discuss the use of the resistome as a guide for the genomics-driven discovery of novel antimicrobials, which are essential to combat the growing number of emerging pathogens that are resistant to even the newest approved therapies.
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Affiliation(s)
- Christian Hobson
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Andrew N Chan
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports. mSystems 2020; 5:5/6/e00783-20. [PMID: 33323413 PMCID: PMC7771540 DOI: 10.1128/msystems.00783-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.
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Vasconcelos NG, Silva KE, Croda J, Simionatto S. Antibacterial activity of Cinnamomum cassia L. essential oil in a carbapenem- and polymyxin-resistant Klebsiella aerogenes strain. Rev Soc Bras Med Trop 2020; 53:e20200032. [PMID: 33027413 PMCID: PMC7534965 DOI: 10.1590/0037-8682-0032-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Essential oils can serve as novel sources of antibiotics for multidrug-resistant bacteria. METHODS The multidrug-resistance profile of a Klebsiella aerogenes strain was assessed by PCR and sequencing. The antibacterial activity of Cinnamomum cassia essential oil (CCeo) against K. aerogenes was assessed by broth microdilution and time-kill methods. RESULTS K. aerogenes showed high antibiotic resistance. The genes bla KPC-2, ampC, bla CTX-M-15, bla OXA-1, and bla TEM were present. CCeo exhibited an inhibitory effect with a minimum inhibitory concentration of 17.57 μg/mL. CONCLUSIONS The antibacterial activity of CCeo makes it a potential candidate for treating carbapenem- and polymyxin-resistant K. aerogenes strains.
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Affiliation(s)
- Nathalie Gaebler Vasconcelos
- Universidade Federal da Grande Dourados, Laboratório de Pesquisa em Ciências da Saúde, Dourados, MS, Brasil.,Universidade Federal da Grande Dourados, Hospital Universitário de Dourados, Dourados, MS, Brasil
| | - Késia Esther Silva
- Universidade Federal da Grande Dourados, Laboratório de Pesquisa em Ciências da Saúde, Dourados, MS, Brasil
| | - Júlio Croda
- Fundação Oswaldo Cruz, Campo Grande, MS, Brasil.,Universidade Federal do Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Simone Simionatto
- Universidade Federal da Grande Dourados, Laboratório de Pesquisa em Ciências da Saúde, Dourados, MS, Brasil
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