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Gontijo M, Pereira Teles M, Martins Correia H, Pérez Jorge G, Rodrigues Santos Goes IC, Fasabi Flores AJ, Braz M, de Moraes Ceseti L, Zonzini Ramos P, Rosa e Silva I, Pereira Vidigal PM, Kobarg J, Miguez Couñago R, Alvarez-Martinez CE, Pereira C, Freire CSR, Almeida A, Brocchi M. Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001462. [PMID: 38739436 PMCID: PMC11170124 DOI: 10.1099/mic.0.001462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 μg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 μg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 μg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 μg ml-1) and P. aeruginosa P2307 (65.00 μg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.
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Affiliation(s)
- Marco Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mateus Pereira Teles
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Hugo Martins Correia
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Genesy Pérez Jorge
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Research Group Statistics and Mathematical Modeling Applied to Educational Quality (GEMMA), University of Sucre, Sincelejo, Sucre, Colombia
| | - Isabella Carolina Rodrigues Santos Goes
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Anthony Jhoao Fasabi Flores
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Márcia Braz
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Lucas de Moraes Ceseti
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Ivan Rosa e Silva
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Viçosa, MG 36570-900, Brazil
| | - Jörg Kobarg
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Rafael Miguez Couñago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Cristina Elisa Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Carla Pereira
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Carmen S. R. Freire
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
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Rahmat Ullah S, Irum S, Mahnoor I, Ismatullah H, Mumtaz M, Andleeb S, Rahman A, Jamal M. Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance. BMC Genomics 2024; 25:408. [PMID: 38664636 PMCID: PMC11044325 DOI: 10.1186/s12864-024-10139-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 02/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected Klebsiella pneumoniae isolates from a local tertiary care hospital from February 2019-February 2021. To gain molecular insight into the resistome, virulome, and genetic environment of significant genes of multidrug-resistant K. pneumoniae isolates, we performed the short-read whole-genome sequencing of 10 K. pneumoniae isolates recovered from adult patients, neonates, and hospital tap water samples. RESULTS The draft genomes of the isolates varied in size, ranging from 5.48 to 5.96 Mbp suggesting the genome plasticity of this pathogen. Various genes conferring resistance to different classes of antibiotics e.g., aminoglycosides, quinolones, sulfonamides, tetracycline, and trimethoprim were identified in all sequenced isolates. The highest resistance was observed towards carbapenems, which has been putatively linked to the presence of both class B and class D carbapenemases, blaNDM, and blaOXA, respectively. Moreover, the biocide resistance gene qacEdelta1 was found in 6/10 of the sequenced strains. The sequenced isolates exhibited a broad range of sequence types and capsular types. The significant antibiotic resistance genes (ARGs) were bracketed by a variety of mobile genetic elements (MGEs). Various spontaneous mutations in genes other than the acquired antibiotic-resistance genes were observed, which play an indirect role in making these bugs resistant to antibiotics. Loss or deficiency of outer membrane porins, combined with ESBL production, played a significant role in carbapenem resistance in our sequenced isolates. Phylogenetic analysis revealed that the study isolates exhibited evolutionary relationships with strains from China, India, and the USA suggesting a shared evolutionary history and potential dissemination of similar genes amongst the isolates of different origins. CONCLUSIONS This study provides valuable insight into the presence of multiple mechanisms of carbapenem resistance in K. pneumoniae strains including the acquisition of multiple antibiotic-resistance genes through mobile genetic elements. Identification of rich mobilome yielded insightful information regarding the crucial role of insertion sequences, transposons, and integrons in shaping the genome of bacteria for the transmission of various resistance-associated genes. Multi-drug resistant isolates that had the fewest resistance genes exhibited a significant number of mutations. K. pneumoniae isolate from water source displayed comparable antibiotic resistance determinants to clinical isolates and the highest number of virulence-associated genes suggesting the possible interplay of ARGs amongst bacteria from different sources.
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Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Sidra Irum
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Iqra Mahnoor
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Humaira Ismatullah
- Research Centre for Modelling & Simulation (RCMS), National University of Sciences and Technology, Islamabad, Pakistan
| | - Mariam Mumtaz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan.
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
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Pustam A, Jayaraman J, Ramsubhag A. Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. J Glob Antimicrob Resist 2024; 37:141-149. [PMID: 38608934 DOI: 10.1016/j.jgar.2024.03.019] [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: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVES Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. METHODS Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. RESULTS The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. CONCLUSION This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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Harmer CJ, Hall RM. IS 26 and the IS 26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024:e0011922. [PMID: 38436262 DOI: 10.1128/mmbr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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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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Di Pilato V, Pollini S, Miriagou V, Rossolini GM, D'Andrea MM. Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge. Expert Rev Anti Infect Ther 2024; 22:25-43. [PMID: 38236906 DOI: 10.1080/14787210.2024.2305854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. AREAS COVERED Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae. EXPERT OPINION CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vivi Miriagou
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Sun L, Chen Y, Qu T, Shi K, Han X, Wu W, Jiang Y, Yu Y. Characterisation of a Novel Hybrid IncFII pHN7A8:IncR:IncN Plasmid Co-Harboring blaNDM-5 and blaKPC-2 from a Clinical ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain. Infect Drug Resist 2023; 16:7621-7628. [PMID: 38107435 PMCID: PMC10725640 DOI: 10.2147/idr.s435195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Purpose We aimed to characterize a novel blaNDM-5 and blaKPC-2 co-carrying hybrid plasmid from a clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) strain. Methods Antimicrobial susceptibility was determined by the broth microdilution method. Plasmid size and localization were estimated using S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting. Plasmid transfer ability was evaluated by conjugation experiments. Whole genome sequencing (WGS) was performed using Illumina NovaSeq6000 and Oxford Nanopore MinION platforms. Genomic characteristics were analyzed using bioinformatics methods. Results Strain ZY27320 was a multidrug-resistant (MDR) clinical ST11 K. pneumoniae strain that confers high-level resistance to carbapenems (meropenem, MIC 128 mg/L; imipenem, MIC 64 mg/L) and ceftazidime/avibactam (MIC >128/4 mg/L). Both S1-PFGE-Southern blotting and whole genome sequencing revealed that the carbapenemase genes blaKPC-2 and blaNDM-5 were carried by the same IncFIIpHN7A8:IncR:IncN hybrid plasmid (pKPC2_NDM5). Conjugation experiments indicated that pKPC2_NDM5 was a non-conjugative plasmid. Conclusion This is the first report of a hybrid plasmid carrying both carbapenemase genes blaNDM-5 and blaKPC-2 in a clinical K. pneumoniae ST11 isolate that confers resistance to both ceftazidime/avibactam and carbapenems, thereby presenting a serious threat to treatment in clinical practice.
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Affiliation(s)
- Lingyan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, People’s Republic of China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xinhong Han
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Wenhao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Idris N, Leong KH, Wong EH, Abdul Rahim N. Unveiling synergism of polymyxin B with chloramphenicol derivatives against multidrug-resistant (MDR) Klebsiella pneumoniae. J Antibiot (Tokyo) 2023; 76:711-719. [PMID: 37821539 DOI: 10.1038/s41429-023-00659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Polymyxins are last-line antibiotics against multidrug-resistant Klebsiella pneumoniae but using polymyxins alone may not be effective due to emerging resistance. A previous study found that combining polymyxin B with chloramphenicol effectively kills MDR K. pneumoniae, although the bone marrow toxicity of chloramphenicol is concerning. The aim of this study is to assess the antibacterial efficacy and cytotoxicity of polymyxin B when combined with chloramphenicol and its derivatives, namely thiamphenicol and florfenicol (reported to have lesser toxicity compared to chloramphenicol). The antibacterial activity was evaluated with antimicrobial susceptibility testing using broth microdilution and time-kill assays, while the cytotoxic effect on normal bone marrow cell line, HS-5 was evaluated using the MTT assay. All bacterial isolates tested were found to be susceptible to polymyxin B, but resistant to chloramphenicol, thiamphenicol, and florfenicol when used alone. The use of polymyxin B alone showed bacterial regrowth for all isolates at 24 h. The combination of polymyxin B and florfenicol demonstrated additive and synergistic effects against all isolates (≥ 2 log10 cfu ml-1 reduction) at 4 and 24 h, respectively, while the combination of polymyxin B and thiamphenicol resulted in synergistic killing at 24 h against ATCC BAA-2146. Furthermore, the combination of polymyxin B with florfenicol had the lowest cytotoxic effect on the HS-5 cells compared to polymyxin B combination with chloramphenicol and thiamphenicol. Overall, the combination of polymyxin B with florfenicol enhanced bacterial killing against MDR K. pneumoniae and exerted minimal cytotoxic effect on HS-5 cell line.
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Affiliation(s)
- Nurulain Idris
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Universiti Malaya, 50603, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Kok Hoong Leong
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, 50603, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Eng Hwa Wong
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University, 47500, Subang Jaya, Malaysia
- Medical Advancement for Better Quality of Life Impact Lab, Taylor's University, 47500, Subang Jaya, Malaysia
| | - Nusaibah Abdul Rahim
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Universiti Malaya, 50603, Wilayah Persekutuan Kuala Lumpur, Malaysia.
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9
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Chandler M, Ross K, Varani AM. The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes. Mol Microbiol 2023; 120:658-669. [PMID: 37574851 DOI: 10.1111/mmi.15140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.
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Affiliation(s)
- Mick Chandler
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Karen Ross
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Alessandro M Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Sao Paulo, Brazil
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10
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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11
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Elgriw N, Métayer V, Drapeau A, François P, Azaiez S, Mastouri M, Rhim H, Elzagheid A, Soufiyah N, Madec JY, Chaouch C, Mansour W, Haenni M. Clonal, Plasmidic and Genetic Diversity of Multi-Drug-Resistant Enterobacterales from Hospitalized Patients in Tripoli, Libya. Antibiotics (Basel) 2023; 12:1430. [PMID: 37760726 PMCID: PMC10525897 DOI: 10.3390/antibiotics12091430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESC) and carbapenems in Enterobacterales is a major issue in public health. Carbapenem resistance in particular is associated with increased morbidity and mortality. Moreover, such resistance is often co-harbored with resistance to non-beta-lactam antibiotics, and pathogens quickly become multi-drug-resistant (MDR). Only a few studies have been published on AMR in Libyan hospitals, but all reported worrisome results. Here, we studied 54 MDR isolates that were collected from 49 patients at the Tripoli University Hospital between 2019 and 2021. They were characterized using phenotypic methods, PCR and PFGE, and a sub-set of isolates were short- and long-read whole-genome sequenced. The results showed the frequent occurrence of Klebsiella pneumoniae (49/54), among which several high-risk clones were responsible for the spread of resistance, namely, ST11, ST17, ST101 and ST147. ESC and carbapenem resistance was due to a wide variety of enzymes (CTX-M, OXA-48, NDM, KPC), with their corresponding genes carried by different plasmids, including IncF-IncHI2 and IncF-IncR hybrids. This study highlights that implementation of infection prevention, control and surveillance measures are needed in Libya to fight against AMR.
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Affiliation(s)
- Nada Elgriw
- Department of Microbiology, Libyan Biotechnology Reseaerch Center, Tripoli P.O. Box 30313, Libya;
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Véronique Métayer
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Pauline François
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Sana Azaiez
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, LR12ES02, Sousse 4002, Tunisia; (S.A.); (W.M.)
| | - Maha Mastouri
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Hajer Rhim
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Reseaerch Center, Tripoli P.O. Box 30313, Libya;
| | - Najeeb Soufiyah
- Medical Microbiology and Immunology Department, Faculty of Pharmacy, University of Tripoli, Tripoli P.O. Box 13275, Libya;
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Cherifa Chaouch
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Wejdene Mansour
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, LR12ES02, Sousse 4002, Tunisia; (S.A.); (W.M.)
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
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12
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Li H, Sun L, Qiao H, Sun Z, Wang P, Xie C, Hu X, Nie T, Yang X, Li G, Zhang Y, Wang X, Li Z, Jiang J, Li C, You X. Polymyxin resistance caused by large-scale genomic inversion due to IS 26 intramolecular translocation in Klebsiella pneumoniae. Acta Pharm Sin B 2023; 13:3678-3693. [PMID: 37719365 PMCID: PMC10501869 DOI: 10.1016/j.apsb.2023.06.003] [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: 04/13/2023] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 09/19/2023] Open
Abstract
Polymyxin B and polymyxin E (colistin) are presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae. Yet resistance to this last-line drugs is a major public health threat and is rapidly increasing. Polymyxin S2 (S2) is a polymyxin B analogue previously synthesized in our institute with obviously high antibacterial activity and lower toxicity than polymyxin B and colistin. To predict the possible resistant mechanism of S2 for wide clinical application, we experimentally induced bacterial resistant mutants and studied the preliminary resistance mechanisms. Mut-S, a resistant mutant of K. pneumoniae ATCC BAA-2146 (Kpn2146) induced by S2, was analyzed by whole genome sequencing, transcriptomics, mass spectrometry and complementation experiment. Surprisingly, large-scale genomic inversion (LSGI) of approximately 1.1 Mbp in the chromosome caused by IS26 mediated intramolecular transposition was found in Mut-S, which led to mgrB truncation, lipid A modification and hence S2 resistance. The resistance can be complemented by plasmid carrying intact mgrB. The same mechanism was also found in polymyxin B and colistin induced drug-resistant mutants of Kpn2146 (Mut-B and Mut-E, respectively). This is the first report of polymyxin resistance caused by IS26 intramolecular transposition mediated mgrB truncation in chromosome in K. pneumoniae. The findings broaden our scope of knowledge for polymyxin resistance and enriched our understanding of how bacteria can manage to survive in the presence of antibiotics.
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Affiliation(s)
- Haibin Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lang Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Han Qiao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zongti Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Penghe Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Chunyang Xie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinxin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tongying Nie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guoqing Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Youwen Zhang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiukun Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Jiandong Jiang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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13
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Almasian Tehrani N, Azimi L, Armin S, Soleimani N, Fallah F, Karimi A, Shamsian BS, Nazari S, Alebouyeh M. Endogenous Bacteremia Caused by Intestinal Colonization of Carbapenem-Resistant Enterobacteriaceae (CR E) in Immunocompromised Children. Trop Med Infect Dis 2023; 8:402. [PMID: 37624340 PMCID: PMC10458169 DOI: 10.3390/tropicalmed8080402] [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: 06/19/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Carbapenem-resistant Enterobacteriaceae (CRE) infection is life-threatening, especially for immunocompromised children. The source tracking of CRE could prevent bacteremia during hospitalization. In this study, the intestinal colonization of CRE and their translocation to blood were investigated. METHODS Stool samples from immunocompromised pediatric patients were collected after admission, and secondary stool and blood samples were collected in case of fever. After CRE phonotypic detection, the OXA-48, NDM-1, VIM, IMP, and KPC genes were detected by PCR. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was used to determine the phylogenic relatedness of the blood and fecal isolates. RESULTS Bacteremia was recorded in 71.4% of the patients. Enterobacteriaceae spp. were recorded in 100% of the stool samples and 31% of the blood samples. The correlation between the length of stay (LOS), days of fever, chemotherapy regimens, and death rate was significant (p-value ≤ 0.05). OXA-48 was present in all CRE isolates in both the primary and the secondary stool samples and the blood samples. According to the phylogenetic data, 58.33% of the patients with bacteremia had identical blood and stool isolates. The death rate was 24.4% in children with CRE bacteremia. CONCLUSIONS The primary intestinal colonization with CRE in immunocompromised pediatrics and their translocation to blood was established in this study. The implementation of infection control programs and the application of infection prevention strategies for immunocompromised children is necessary.
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Affiliation(s)
- Nasim Almasian Tehrani
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
- Department of Microbiology and Microbial Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Shahnaz Armin
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Neda Soleimani
- Department of Microbiology and Microbial Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Fatemeh Fallah
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Bibi Shahin Shamsian
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Shiva Nazari
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
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14
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Siguier P, Rousseau P, Cornet F, Chandler M. A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites. Plasmid 2023; 127:102696. [PMID: 37302728 DOI: 10.1016/j.plasmid.2023.102696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
We describe here a new family of IS which are related to IS1202, originally isolated from Streptococcus pneumoniae in the mid-1990s and previously tagged as an emerging IS family in the ISfinder database. Members of this family have impacted some important properties of their hosts. We describe here another potentially important property of certain family members: specific targeting of xrs recombination sites. The family could be divided into three subgroups based on their transposase sequences and the length on the target repeats (DR) they generate on insertion: subgroup IS1202 (24-29 bp); ISTde1 (15-18 bp); and ISAba32 (5-6 bp). Members of the ISAba32 subgroup were repeatedly found abutting Xer recombinase recombination sites (xrs), separated by an intervening copy of a DR. These xrs sites, present in multiple copies in a number of Acinetobacter plasmids flanking antibiotic resistance genes, were proposed to form a new type of mobile genetic element using the chromosomally-encoded XerCD recombinase for mobility. Transposase alignments identified subgroup-specific indels which may be responsible for the differences in the transposition properties of the three subgroups (i.e. DR length and target specificity). We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of three subgroups, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France.
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - Michael Chandler
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.
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15
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Gilcrease EB, Casjens SR, Bhattacharjee A, Goel R. A Klebsiella pneumoniae NDM-1+ bacteriophage: Adaptive polyvalence and disruption of heterogenous biofilms. Front Microbiol 2023; 14:1100607. [PMID: 36876079 PMCID: PMC9983693 DOI: 10.3389/fmicb.2023.1100607] [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: 11/17/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Bacteriophage KL-2146 is a lytic virus isolated to infect Klebsiella pneumoniae BAA2146, a pathogen carrying the broad range antibiotic resistance gene New Delhi metallo-betalactamase-1 (NDM-1). Upon complete characterization, the virus is shown to belong to the Drexlerviridae family and is a member of the Webervirus genus located within the (formerly) T1-like cluster of phages. Its double-stranded (dsDNA) genome is 47,844 bp long and is predicted to have 74 protein-coding sequences (CDS). After challenging a variety of K. pneumoniae strains with phage KL-2146, grown on the NDM-1 positive strain BAA-2146, polyvalence was shown for a single antibiotic-sensitive strain, K. pneumoniae 13,883, with a very low initial infection efficiency in liquid culture. However, after one or more cycles of infection in K. pneumoniae 13,883, nearly 100% infection efficiency was achieved, while infection efficiency toward its original host, K. pneumoniae BAA-2146, was decreased. This change in host specificity is reversible upon re-infection of the NDM-1 positive strain (BAA-2146) using phages grown on the NDM-1 negative strain (13883). In biofilm infectivity experiments, the polyvalent nature of KL-2146 was demonstrated with the killing of both the multidrug-resistant K. pneumoniae BAA-2146 and drug-sensitive 13,883 in a multi-strain biofilm. The ability to infect an alternate, antibiotic-sensitive strain makes KL-2146 a useful model for studying phages infecting the NDM-1+ strain, K. pneumoniae BAA-2146. GRAPHICAL ABSTRACT.
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Affiliation(s)
- Eddie B Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, United States
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States.,Division of Microbiology and Immunology, Pathology Department, University of Utah, Salt Lake City, UT, United States
| | - Ananda Bhattacharjee
- Department of Environmental Sciences, University of California, Riverside, CA, United States
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, United States
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16
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Sharma RK, Dey G, Banerjee P, Maity JP, Lu CM, Siddique JA, Wang SC, Chatterjee N, Das K, Chen CY. New aspects of lipopeptide-incorporated nanoparticle synthesis and recent advancements in biomedical and environmental sciences: a review. J Mater Chem B 2022; 11:10-32. [PMID: 36484467 DOI: 10.1039/d2tb01564a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The toxicity of metal nanoparticles has introduced promising research in the current scenario since an enormous number of people have been potentially facing this problem in the world. The extensive attention on green nanoparticle synthesis has been focussed on as a vital step in bio-nanotechnology to improve biocompatibility, biodegradability, eco-friendliness, and huge potential utilization in various environmental and clinical assessments. Inherent influence on the study of green nanoparticles plays a key role to synthesize the controlled and surface-influenced molecule by altering the physical, chemical, and biological assets with the provision of various precursors, templating/co-templating agents, and supporting solvents. However, in this article, the dominant characteristics of several kinds of lipopeptide biosurfactants are discussed to execute a critical study of factors affecting synthesis procedure and applications. The recent approaches of metal, metal oxide, and composite nanomaterial synthesis have been deliberated as well as the elucidation of the reaction mechanism. Furthermore, this approach shows remarkable boosts in the production of nanoparticles with the very less employed harsh and hazardous processes as compared to chemical or physical method-based nanoparticle synthesis. This study also shows that the advances in strain selection for green nanoparticle production could be a worthwhile and strong economical approach in futuristic medical science research.
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Affiliation(s)
- Raju Kumar Sharma
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan.,Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan.
| | - Gobinda Dey
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan. .,Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pritam Banerjee
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan. .,Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan. .,Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Chung-Ming Lu
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan. .,Department of Chemical Engineering, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | | | - Shau-Chun Wang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Nalonda Chatterjee
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan.
| | - Koyeli Das
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan. .,Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan.
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17
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Chakraborty J, Roy RP, Chatterjee R, Chaudhuri P. Performance assessment of genomic island prediction tools with an improved version of Design-Island. Comput Biol Chem 2022; 98:107698. [PMID: 35597186 DOI: 10.1016/j.compbiolchem.2022.107698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/03/2022]
Abstract
Genomic Islands (GIs) play an important role in the evolution and adaptation of prokaryotes. The origin and extent of ecological diversity of prokaryotes can be analyzed by comparing GIs across closely or distantly related prokaryotes. Understanding the importance of GI and to study the bacterial evolution, several GI prediction tools have been generated. An unsupervised method, Design-Island, was developed to identify GIs using Monte-Carlo statistical test on randomly selected segments of a chromosome. Here, in the present study Design-Island was modified with the incorporation of majority voting, multiple hypothesis testing correction. The performance of the modified version, Design-Island-II was tested and compared with the existing GI prediction tools. The performance assessment and benchmarking of the GI prediction tools require experimentally validated dataset, which is lacking. So, different datasets, generated or taken from literature were utilized to compare the sensitivity (SN), specificity (SP), precision (PPV) and accuracy (AC) of Design-Island-II. It showed substantial enhancement in term of SN, SP, PPV and AC, and significantly reduced the computation time of the algorithm. The performance of Design-Island-II has also been compared with several GI prediction tools using curated dataset of putative horizontally transferred genes. Design-Island-II showed the highest sensitivity and F1 score, comparable specificity, precision and accuracy in comparison to the other available methods. IslandViewer4 and Islander outperformed all the available methods in terms of AC and PPV respectively. Our study suggested Design-Island-II, IslandViewer4 and GIHunter among the top performing GI prediction tools considering both sensitivity and specificity of the methods.
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Affiliation(s)
- Joyeeta Chakraborty
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700 108, India.
| | - Rudra Prasad Roy
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700 108, India.
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700 108, India.
| | - Probal Chaudhuri
- Theoretical Statistics and Mathematics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700 108, India.
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18
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Kaushik S, Yadav J, Das S, Karthikeyan D, Chug R, Jyoti A, Srivastava VK, Jain A, Kumar S, Sharma V. Identification of Protein Drug Targets of Biofilm Formation and Quorum
Sensing in Multidrug Resistant Enterococcus faecalis. Curr Protein Pept Sci 2022; 23:248-263. [DOI: 10.2174/1389203723666220526155644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Enterococcus faecalis (E. faecalis) is an opportunistic multidrug-resistant (MDR) pathogen
found in the guts of humans and farmed animals. Due to the occurrence of (MDR) strain there is an
urgent need to look for an alternative treatment approach. E. faecalis is a Gram-positive bacterium,
which is among the most prevalent multidrug resistant hospital pathogens. Its ability to develop quorum
sensing (QS) mediated biofilm formation further exacerbates the pathogenicity and triggers lifethreatening
infections. Therefore, developing a suitable remedy for curing E. faecalis mediated enterococcal
infections is an arduous task. Several putative virulence factors and proteins are involved in the
development of biofilms in E. faecalis. Such proteins often play important roles in virulence, disease,
and colonization by pathogens. The elucidation of the structure-function relationship of such protein
drug targets and the interacting compounds could provide an attractive paradigm towards developing
structure-based drugs against E. faecalis. This review provides a comprehensive overview of the current
status, enigmas that warrant further studies, and the prospects toward alleviating the antibiotic resistance
in E. faecalis. Specifically, the role of biofilm and quorum sensing (QS) in the emergence of
MDR strains had been elaborated along with the importance of the protein drug targets involved in both
the processes.
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Affiliation(s)
- Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Structural Biology Lab, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Ravneet Chug
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology,
Chandigarh University, Chandigarh, India
| | | | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT
University, Vellore-632014, Tamil Nadu, India
| | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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19
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Comparative Genomic Analysis of Statistically Significant Genomic Islands of Helicobacter pylori strains for better understanding the disease prognosis. Biosci Rep 2022; 42:230988. [PMID: 35258077 PMCID: PMC8935386 DOI: 10.1042/bsr20212084] [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: 08/31/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial virulence factors are often located in their genomic islands (GIs). Helicobacter pylori, a highly diverse organism is reported to be associated with several gastrointestinal diseases like, gastritis, gastric cancer, peptic ulcer, duodenal ulcer etc. A novel similarity score-based comparative analysis with GIs of fifty H. pylori strains revealed clear idea of the various factors which promote disease progression. Two putative pathogenic GIs in some of the H. pylori strains were identified. One GI, having a putative labile enterotoxin and other dynamin-like proteins (DLPs), is predicted to increase the release of toxin by membrane vesicular formation. Another island contains a virulence-associated protein D (vapD) which is a component of a type-II toxin-antitoxin system (TAs), leads to enhance the severity of the H. pylori infection. Besides the well-known virulence factors like CagA, and VacA, several GIs have been identified which showed to have direct or indirect impact on H. pylori clinical outcomes. One such GI, containing lipopolysaccharide (LPS) biosynthesis genes was revealed to be directly connected with disease development by inhibiting the immune response. Another collagenase-containing GI worsens ulcers by slowing down the healing process. GI consisted of fliD operon was found to be connected to flagellar assembly and biofilm production. By residing in biofilms, bacteria can avoid antibiotic therapy, resulting in chronic infection. Along with well-studied CagA and VacA virulent genes, it is equally important to study these identified virulence factors for better understanding H. pylori induced disease prognosis.
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20
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Bharathi KS, Pruthi G, Lathashree S, Simha P. The Bacteriological and Clinical Outcomes of Ventilator-associated Pneumonia Post-cardiac Surgery in the Pediatric Surgical Intensive Care Unit: A Prospective, Observational Study. BALI JOURNAL OF ANESTHESIOLOGY 2022. [DOI: 10.4103/bjoa.bjoa_174_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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21
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Maebed AZM, Gaber Y, Bakeer W, Dishisha T. Microbial etiologies of ventilator-associated pneumonia (VAP) in intensive care unit of Beni-Suef University's Hospital. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:41. [PMID: 34341765 PMCID: PMC8319904 DOI: 10.1186/s43088-021-00130-x] [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: 06/19/2021] [Accepted: 07/17/2021] [Indexed: 11/22/2022] Open
Abstract
Background Ventilator-associated pneumonia (VAP) is a major health problem for people intubated in intensive care units (ICUs), leading to increased mortality rates, hospital stay, and treatment costs. In the present study, the core pathogens causing VAP in Beni-Suef University's Hospital, Egypt, was investigated over a study period of 2 years (2017–2019). Results Of a total of 213 patients subjected to mechanical ventilation, 60 have developed VAP during their stay in the ICU. The mortality rate reached 41.7% among VAP patients. Sixty bacteria were isolated from an endotracheal aspirate of hospitalized patients. The different isolates were cultured followed by running biochemical tests, sensitivity assays, and automated VITEK®2 System analysis. Unexpectedly, all the isolates were Gram-negative bacteria. Klebsiella pneumoniae were the main pathogen encountered (27/60 isolates) followed by Acientobacter baumannnii (7/60) and other microorganisms belonging to the genera Moraxella, Escherichia, and Pseudomonas (11/60). Antibiotic sensitivity testing was performed via the VITEK®2 System using up to 16 different antibiotics representing 8 different antibiotic classes and subclasses (aminoglycosides, carbapenems, fluoroquinolones, penicillin/β-lactamase inhibitor, extended-spectrum cephalosporins, aminopenicillins, aminopenicillins/β-lactamase inhibitor, folic acid synthesis inhibitor). Majority of the isolates (28/60) showed a remarkable extensive drug resistance (XDR) pattern, while 15 isolates were multi-drug resistant (MDR) and only 6 were pan-drug resistant (PDR) with regard to antibiotics under evaluation. Conclusion The association of VAP with multi-drug-resistant bacteria is alarming, and rapid management is crucial. Identification of core pathogens is essential for identifying the most appropriate technique for infection control.
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Affiliation(s)
- Al Zahraa M Maebed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Nahda University, Beni Suef, Egypt
| | - Yasser Gaber
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, Egypt.,Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Mutah University, Kerak, 61710 Jordan
| | - Walid Bakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, Egypt
| | - Tarek Dishisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, Egypt
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22
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Öztürk B, Werner J, Meier-Kolthoff JP, Bunk B, Spröer C, Springael D. Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax. Genome Biol Evol 2021; 12:827-841. [PMID: 32359160 PMCID: PMC7313664 DOI: 10.1093/gbe/evaa085] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 01/07/2023] Open
Abstract
Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20–839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.
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Affiliation(s)
- Başak Öztürk
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Division of Soil and Water Management, KU Leuven, Belgium
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Jan P Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Belgium
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23
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Caméléna F, Morel F, Merimèche M, Decousser JW, Jacquier H, Clermont O, Darty M, Mainardis M, Cambau E, Tenaillon O, Denamur E, Berçot B. Genomic characterization of 16S rRNA methyltransferase-producing Escherichia coli isolates from the Parisian area, France. J Antimicrob Chemother 2021; 75:1726-1735. [PMID: 32300786 DOI: 10.1093/jac/dkaa105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/15/2020] [Accepted: 02/27/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The resistance to all aminoglycosides (AGs) conferred by 16S rRNA methyltransferase enzymes (16S-RMTases) is a major public health concern. OBJECTIVES To characterize the resistance genotype, its genetic environment and plasmid support, and the phylogenetic relatedness of 16S-RMTase-producing Escherichia coli from France. METHODS We screened 137 E. coli isolates resistant to all clinically relevant AGs from nine Parisian hospitals for 16S-RMTases. WGS was performed on clinical isolates with high-level AG resistance (MIC ≥256 mg/L) and their transformants. RESULTS Thirty of the 137 AG-resistant E. coli produced 16S-RMTases: 11 ArmA, 18 RmtB and 1 RmtC. The 16S-RMTase producers were also resistant to third-generation cephalosporins (90% due to a blaCTX-M gene), co-trimoxazole, fluoroquinolones and carbapenems (blaNDM and blaVIM genes) in 97%, 83%, 70% and 10% of cases, respectively. Phylogenomic diversity was high in ArmA producers, with 10 different STs, but a similar genetic environment, with the Tn1548 transposon carried by a plasmid closely related to pCTX-M-3 in 6/11 isolates. Conversely, RmtB producers belonged to 12 STs, the most frequent being ST405 and ST complex (STc) 10 (four and four isolates, respectively). The rmtB gene was carried by IncF plasmids in 10 isolates and was found in different genetic environments. The rmtC gene was carried by the pNDM-US plasmid. CONCLUSIONS ArmA and RmtB are the predominant 16S-RMTases in France, but their spread follows two different patterns: (i) dissemination of a conserved genetic support carrying armA in E. coli with high levels of genomic diversity; and (ii) various genetic environments surrounding rmtB in clonally related E. coli.
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Affiliation(s)
- François Caméléna
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
| | - Florence Morel
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | - Manel Merimèche
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
| | - Jean-Winoc Decousser
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie et d'Hygiène Hospitalière, Hôpital Henri Mondor, Créteil, France
| | - Hervé Jacquier
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | | | - Mélanie Darty
- AP-HP, Service de Bactériologie et d'Hygiène Hospitalière, Hôpital Henri Mondor, Créteil, France
| | - Mary Mainardis
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France
| | - Emmanuelle Cambau
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | | | - Erick Denamur
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Béatrice Berçot
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
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24
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Panlilio H, Lam AK, Heydarian N, Haight T, Wouters CL, Moen EL, Rice CV. Dual-Function Potentiation by PEG-BPEI Restores Activity of Carbapenems and Penicillins against Carbapenem-Resistant Enterobacteriaceae. ACS Infect Dis 2021; 7:1657-1665. [PMID: 33945257 PMCID: PMC8689638 DOI: 10.1021/acsinfecdis.0c00863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rise of life-threatening carbapenem-resistant Enterobacteriaceae (CRE) infections has become a critical medical threat. Some of the most dangerous CRE bacteria can produce enzymes that degrade a wide range of antibiotics, including carbapenems and β-lactams. Infections by CRE have a high mortality rate, and survivors can have severe morbidity from treatment with toxic last-resort antibiotics. CRE have mobile genetic elements that transfer resistance genes to other species. These bacteria also circulate throughout the healthcare system. The mobility and spread of CRE need to be curtailed, but these goals are impeded by having few agents that target a limited range of pathogenic CRE species. Against CRE possessing the metallo-β-lactamase NDM-1, Klebsiella pneumoniae ATCC BAA-2146 and Escherichia coli ATCC BAA-2452, the potentiation of meropenem and imipenem is possible with low-molecular weight branched polyethylenimine (600 Da BPEI) and its poly(ethylene glycol) (PEG)ylated derivative (PEG-BPEI) that has a low in vivo toxicity. The mechanism of action is elucidated with fluorescence assays of drug influx and isothermal calorimetry data showing the chelation of essential Zn2+ ions. These results suggested that 600 Da BPEI and PEG-BPEI may also improve the uptake of antibiotics and β-lactamase inhibitors. Indeed, the CRE E. coli strain is rendered susceptible to the combination of piperacillin and tazobactam. These results expand the possible utility of 600 Da BPEI potentiators, where previously we have demonstrated the ability to improve antibiotic efficacy against antibiotic resistant clinical isolates of Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis.
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Affiliation(s)
- Hannah Panlilio
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Anh K Lam
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Neda Heydarian
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Tristan Haight
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Cassandra L Wouters
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Erika L Moen
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Charles V Rice
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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25
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Detection of a New Resistance-Mediating Plasmid Chimera in a blaOXA-48-Positive Klebsiella pneumoniae Strain at a German University Hospital. Microorganisms 2021; 9:microorganisms9040720. [PMID: 33807212 PMCID: PMC8066831 DOI: 10.3390/microorganisms9040720] [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: 03/17/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven blaOXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All blaOXA-48 genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in K. pneumoniae in Germany.
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26
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Tolentino FM, De Almeida IAZC, Dos Santos CCM, Teixeira ISDC, Silva SIDLE, Nogueira MCL, Arroyo MG, Faim WR, De Almeida MTG, Peresi JTM. Phenotypic and genotypic profile of the antimicrobial resistance of bacterial isolates and evaluation of physical and chemical potability indicators in groundwater in Brazil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2021; 31:186-201. [PMID: 31293171 DOI: 10.1080/09603123.2019.1640354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/02/2019] [Indexed: 06/09/2023]
Abstract
The aquatic environment has received increasing attention regarding the evolution of bacterial resistance, either as a source of resistance genes or as a matrix for the dissemination of these genes. We evaluated the physicochemical, microbiological and antimicrobial resistance characteristics of 160 samples from alternative water well solutions. According to Ordinance 2914/2011 - MS, 44 (27.5%) samples were considered unsafe if at least one physicochemical parameter exceeded permissible limits. Escherichia coli were found in 30.6% of the unregistered housing estates (UHE) and 1.9% of the local sanitary surveillance system (RW). The total of 158 bacterial strains were isolated from 13 (25%) RW and 68 (63%) UHE, 132 of which (83.5%) were obtained from UHE samples. In the investigation of resistance genes, tetA, qnrS and qnrB genes were detected in three, one and eight isolates, respectively. Our results emphasize the importance of constant surveillance and control of the quality of water supplies.
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Affiliation(s)
- Fernanda Modesto Tolentino
- Instituto Adolfo Lutz - Centro de Laboratório Regional de São José do Rio Preto - Rua Alberto Sufredine Bertone , São José do Rio Preto-SP, Brasil
| | | | - Cecilia Cristina Marques Dos Santos
- Instituto Adolfo Lutz - Centro de Laboratório Regional de São José do Rio Preto - Rua Alberto Sufredine Bertone , São José do Rio Preto-SP, Brasil
| | - Inara Siqueira De Carvalho Teixeira
- Instituto Adolfo Lutz - Centro de Laboratório Regional de São José do Rio Preto - Rua Alberto Sufredine Bertone , São José do Rio Preto-SP, Brasil
| | - Sonia Izaura De Lima E Silva
- Instituto Adolfo Lutz - Centro de Laboratório Regional de São José do Rio Preto - Rua Alberto Sufredine Bertone , São José do Rio Preto-SP, Brasil
| | - Mara Correa Lelles Nogueira
- Centro de Pesquisas de Micro-organismos da Faculdade de Medicina de São José do Rio Preto , São José do Rio Preto-SP, Brasil
| | - Máira Gazzola Arroyo
- Centro de Pesquisas de Micro-organismos da Faculdade de Medicina de São José do Rio Preto , São José do Rio Preto-SP, Brasil
| | - Wilson Roberto Faim
- Secretaria Municipal de Saúde e Higiene - Vigilância Sanitária de São José do Rio Preto , São José do Rio Preto-SP, Brasil
| | | | - Jacqueline Tanury Macruz Peresi
- Instituto Adolfo Lutz - Centro de Laboratório Regional de São José do Rio Preto - Rua Alberto Sufredine Bertone , São José do Rio Preto-SP, Brasil
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27
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Assafiri O, Song AAL, Tan GH, Hanish I, Hashim AM, Yusoff K. Klebsiella virus UPM2146 lyses multiple drug-resistant Klebsiella pneumoniae in vitro and in vivo. PLoS One 2021; 16:e0245354. [PMID: 33418559 PMCID: PMC7794032 DOI: 10.1371/journal.pone.0245354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae are opportunistic bacteria found in the gut. In recent years they have been associated with nosocomial infections. The increased incidence of multiple drug-resistant K. pneumoniae makes it necessary to find new alternatives to treat the disease. In this study, phage UPM2146 was isolated from a polluted lake which can lyse its host K. pneumoniae ATCC BAA-2146. Observation from TEM shows that UPM2146 belongs to Caudoviriales (Order) based on morphological appearance. Whole genome analysis of UPM2146 showed that its genome comprises 160,795 bp encoding for 214 putative open reading frames (ORFs). Phylogenetic analysis revealed that the phage belongs to Ackermannviridae (Family) under the Caudoviriales. UPM2146 produces clear plaques with high titers of 1010 PFU/ml. The phage has an adsorption period of 4 min, latent period of 20 min, rise period of 5 min, and releases approximately 20 PFU/ bacteria at Multiplicity of Infection (MOI) of 0.001. UPM2146 has a narrow host-range and can lyse 5 out of 22 K. pneumoniae isolates (22.72%) based on spot test and efficiency of plating (EOP). The zebrafish larvae model was used to test the efficacy of UPM2146 in lysing its host. Based on colony forming unit counts, UPM2146 was able to completely lyse its host at 10 hours onwards. Moreover, we show that the phage is safe to be used in the treatment against K. pneumoniae infections in the zebrafish model.
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Affiliation(s)
- Omar Assafiri
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Geok Hun Tan
- Faculty of Agriculture, Department of Agriculture Technology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Biosciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Irwan Hanish
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Khatijah Yusoff
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Biosciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Hu Y, Anes J, Devineau S, Fanning S. Klebsiella pneumoniae: Prevalence, Reservoirs, Antimicrobial Resistance, Pathogenicity, and Infection: A Hitherto Unrecognized Zoonotic Bacterium. Foodborne Pathog Dis 2020; 18:63-84. [PMID: 33124929 DOI: 10.1089/fpd.2020.2847] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen, constituting an ongoing health concern for immunocompromised patients, the elderly, and neonates. Reports on the isolation of K. pneumoniae from other sources are increasing, many of which express multidrug-resistant (MDR) phenotypes. Three phylogroups were identified based on nucleotide differences. Niche environments, including plants, animals, and humans appear to be colonized by different phylogroups, among which KpI (K. pneumoniae) is commonly associated with human infection. Infections with K. pneumoniae can be transmitted through contaminated food or water and can be associated with community-acquired infections or between persons and animals involved in hospital-acquired infections. Increasing reports are describing detections along the food chain, suggesting the possibility exists that this could be a hitherto unexplored reservoir for this opportunistic bacterial pathogen. Expression of MDR phenotypes elaborated by these bacteria is due to the nature of various plasmids carrying antimicrobial resistance (AMR)-encoding genes, and is a challenge to animal, environmental, and human health alike. Raman spectroscopy has the potential to provide for the rapid identification and screening of antimicrobial susceptibility of Klebsiella isolates. Moreover, hypervirulent isolates linked with extraintestinal infections express phenotypes that may support their niche adaptation. In this review, the prevalence, reservoirs, AMR, Raman spectroscopy detection, and pathogenicity of K. pneumoniae are summarized and various extraintestinal infection pathways are further narrated to extend our understanding of its adaptation and survival ability in reservoirs, and associated disease risks.
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Affiliation(s)
- Yujie Hu
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China
| | - João Anes
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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29
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Frenk S, Rakovitsky N, Temkin E, Schechner V, Cohen R, Kloyzner BS, Schwaber MJ, Solter E, Cohen S, Stepansky S, Carmeli Y. Investigation of Outbreaks of Extended-Spectrum Beta-Lactamase-Producing Klebsiella Pneumoniae in Three Neonatal Intensive Care Units Using Whole Genome Sequencing. Antibiotics (Basel) 2020; 9:antibiotics9100705. [PMID: 33081087 PMCID: PMC7650633 DOI: 10.3390/antibiotics9100705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023] Open
Abstract
Infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are on a constant rise and are a noted cause of outbreaks in neonatal intensive care units (NICUs). We used whole genome sequencing (WGS) to investigate the epidemiology of consecutive and overlapping outbreaks caused by ESBL-KP in NICUs in three hospitals in close proximity. Clonality of 43 ESBL-KP isolates from 40 patients was determined by BOX-PCR. Short-read sequencing was performed on representative isolates from each clone. The dominant clones from each NICU were sequenced using long-read sequencing. Bioinformatics methods were used to define multilocus sequence type (MLST), analyze plasmid content, resistomes, and virulence factors. In each NICU, we found a unique dominant clone (ST985, ST37, and ST35), each belonging to a distinct sequence type (ST), as well as satellite clones. A satellite strain in NICU-2 (ST35) was the dominant strain in NICU-3, where it was isolated four weeks later, suggesting transmission. NICU-1- and NICU-2-dominant strains had blaCTX-M-15 carried on a similar transposable element (Tn3-ISEcp1) but at different locations: on a plasmid and on the chromosome, respectively. We concluded that the overlapping ESBL-KP outbreaks were a combination of clonal transmission within NICUs, possible transposable element transmission between NICUs, and repeated importation of ESBL-KP from the community.
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Affiliation(s)
- Sammy Frenk
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
- Correspondence: ; Tel.: +972-3-6974892
| | - Nadya Rakovitsky
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
| | - Elizabeth Temkin
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
| | - Vered Schechner
- Division of Epidemiology and Preventive Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel; (V.S.); (S.S.)
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Regev Cohen
- Infectious Diseases Unit, Laniado Hospital, Netanya 42150, Israel; (R.C.); (S.C.)
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Bat Sheva Kloyzner
- Department of Epidemiology, Mayanei Hayeshua Medical Center, Bnei Brak 51544, Israel;
| | - Mitchell J. Schwaber
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ester Solter
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
| | - Shoshana Cohen
- Infectious Diseases Unit, Laniado Hospital, Netanya 42150, Israel; (R.C.); (S.C.)
| | - Sarit Stepansky
- Division of Epidemiology and Preventive Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel; (V.S.); (S.S.)
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv 64239, Israel; (N.R.); (E.T.); (M.J.S.); (E.S.); (Y.C.)
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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El-Gohary FA, Abdel-Hafez LJM, Zakaria AI, Shata RR, Tahoun A, El-Mleeh A, Abo Elfadl EA, Elmahallawy EK. Enhanced Antibacterial Activity of Silver Nanoparticles Combined with Hydrogen Peroxide Against Multidrug-Resistant Pathogens Isolated from Dairy Farms and Beef Slaughterhouses in Egypt. Infect Drug Resist 2020; 13:3485-3499. [PMID: 33116668 PMCID: PMC7550212 DOI: 10.2147/idr.s271261] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/11/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose The last few decades have witnessed a rapid and global increase in multidrug-resistant bacteria (MDR) emergence. Methods The aim of the current study is to isolate the most common MDR bacteria from dairy farms and beef slaughterhouses followed by evaluation of their antimicrobial resistance pattern and assessment of the antibacterial activity of AgNPs-H2O2 as an alternative to conventional antibiotics. In this regard, 200 samples were collected from two dairy farms and one beef slaughterhouse located in Dakhliya Governorate, Egypt. Results Interestingly, out of 120 collected samples from dairy farms, the prevalence of the isolated strains was 26.7, 23.3, 21.7, 16.7, and 11.7% for S. typhimurium, E. coli O157:H7, L. monocytogenes, K. pneumoniae and P. aeruginosa, respectively. Meanwhile, the overall prevalence was 30, 25, 22.5, 17.5, and 5% for E. coli O157:H7, L. monocytogenes, S. typhimurium, P. aeruginosa, and K. pneumoniae, respectively, for the 80 samples collected from a beef slaughterhouse. The antimicrobial susceptibility pattern elucidated that all isolated strains exhibited resistance to at least four of the tested antimicrobials, with multiple-antibiotic resistance index values (MAR) ranging between 0.44 and 0.88. Furthermore, the commercial AgNPs-H2O2 product was characterized by transmission electron microscopy (TEM) and zeta potential that showed spherical particles with a surface charge of -0.192 mV. The antimicrobial activity of synergized nano-silver (AgNP) with H2O2 product toward MDR strains was assessed via measuring minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and time-kill curve. Conclusion The present data report high prevalence rates of MDR pathogens in dairy farms and abattoirs. More importantly, AgNPs-H2O2 exerted broad-spectrum bactericidal activity toward MDR bacterial strains, suggesting their promising usage as safe, ecofriendly, cost-effective antibacterial agents. To our knowledge, this study is a pioneer in investigating the potential alternative antimicrobial role of silver nanoparticles for control of multiple drug-resistant pathogens in Egypt.
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Affiliation(s)
- Fatma A El-Gohary
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Lina Jamil M Abdel-Hafez
- Department of Microbiology and Immunology, Faculty of Pharmacy, October 6 University, October 6 City, Giza, Egypt
| | - Amira I Zakaria
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Radwa Reda Shata
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Amin Tahoun
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelshkh University, Kafrelsheikh 33511, Egypt
| | - Amany El-Mleeh
- Department of Pharmacology, Faculty of Veterinary Medicine, Menoufia University, Sheibin Elkom 32511, Egypt
| | - Eman A Abo Elfadl
- Department of Animal Husbandry and Development of Animal Wealth (Biostatistics), Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Ehab Kotb Elmahallawy
- Department of Biomedical Sciences, University of León (ULE), León 24071, Spain.,Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
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31
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Chaudhry TH, Aslam B, Arshad MI, Alvi RF, Muzammil S, Yasmeen N, Aslam MA, Khurshid M, Rasool MH, Baloch Z. Emergence of bla NDM-1 Harboring Klebsiella pneumoniae ST29 and ST11 in Veterinary Settings and Waste of Pakistan. Infect Drug Resist 2020; 13:3033-3043. [PMID: 32904734 PMCID: PMC7457595 DOI: 10.2147/idr.s248091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/17/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction Intense livestock farming practices enforcing the farmers to use antibiotics as food supplements on a routine basis. Aberrant use of antibiotics is associated with the emergence of antibiotics resistance and resistant superbugs. Keeping in view the current scenario, the present study was designed for the first time from Pakistan with a specific aim to estimate the prevalence of the carbapenem-resistant Klebsiella pneumoniae in veterinary settings and the waste in Pakistan. Methods A total of 138 samples from various veterinary sources were collected by employing a nonprobability sampling technique. Isolation and phenotypic identification of carbapenem-resistant K. pneumoniae were performed according to the CLSI standard. Molecular detection of various antibiotic resistance genes (ARGs) was done through PCR by using specific primers against each ARG. According to the pasture scheme, the multilocus sequence typing (MLST) was performed to characterize the K. pneumoniae sequence types (STs). Results According to the results of the study, overall 9.4% (13/138) isolates were confirmed carbapenem-resistant K. pneumoniae. Among various carbapenem ARGs particularly, the bla NDM-1 was found in 92.3% (12/13) isolates followed by bla OXA-48 84.6% (11/13). MLST results revealed that overall 3 STs were found in the study which includes ST29, ST11, and ST258. Taking together, this is the first study to our best knowledge which demonstrated the prevalence of carbapenem-resistant K. pneumoniae and its various STs prevalent in veterinary settings and the waste of Pakistan. Conclusion Based on the above-mentioned facts, we suggested that veterinary settings and waste are the potential source and reservoir of carbapenem-resistant K. pneumoniae, which may be disseminated to the environment and ultimately can affect the public and companion livestock health.
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Affiliation(s)
- Tamoor Hamid Chaudhry
- Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, People's Republic of China.,Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Bilal Aslam
- Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, People's Republic of China.,Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Imran Arshad
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Roman Farooq Alvi
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Muhammad Aamir Aslam
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Zulqarnain Baloch
- Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, People's Republic of China
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Iwu CD, du Plessis EM, Korsten L, Nontongana N, Okoh AI. Antibiogram Signatures of Some Enterobacteria Recovered from Irrigation Water and Agricultural Soil in two District Municipalities of South Africa. Microorganisms 2020; 8:microorganisms8081206. [PMID: 32784678 PMCID: PMC7463487 DOI: 10.3390/microorganisms8081206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/15/2022] Open
Abstract
This study was undertaken to evaluate the antibiogram fingerprints of some Enterobacteria recovered from irrigation water and agricultural soil in two District Municipalities of the Eastern Cape Province, South Africa using standard culture-based and molecular methods. The prevalent resistance patterns in the isolates follow the order: Salmonella enterica serovar Typhimurium [tetracycline (92.3%), ampicillin (69.2%)]; Enterobacter cloacae [amoxicillin/clavulanic acid (77.6%), ampicillin (84.5%), cefuroxime (81.0%), nitrofurantoin (81%), and tetracycline (80.3%)]; Klebsiella pneumoniae [amoxicillin/clavulanic acid (80.6%), ampicillin (88.9%), and cefuroxime (61.1%)]; and Klebsiella oxytoca [chloramphenicol (52.4%), amoxicillin/clavulanic acid (61.9%), ampicillin (61.9%), and nitrofurantoin (61.9%)]. Antibiotic resistance genes detected include tetC (86%), sulII (86%), and blaAmpC (29%) in Salmonella enterica serovar Typhimurium., tetA (23%), tetB (23%), tetC (12%), sulI (54%), sulII (54%), catII (71%), blaAmpC (86%), blaTEM (43%), and blaPER (17%) in Enterobacter cloacae., tetA (20%), tetC (20%), tetD (10%), sulI (9%), sulII (18%), FOX (11%) and CIT (11%)-type plasmid-mediated AmpC, blaTEM (11%), and blaSHV (5%) in Klebsiella pneumoniae and blaAmpC (18%) in Klebsiella oxytoca. Our findings document the occurrence of some antibiotic-resistant Enterobacteria in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities, Eastern Cape Province of South Africa, thus serving as a potential threat to food safety.
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Affiliation(s)
- Chidozie Declan Iwu
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
- Correspondence:
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (E.M.d.P.); (L.K.)
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (E.M.d.P.); (L.K.)
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Raro OHF, da Silva RMC, Filho EMR, Sukiennik TCT, Stadnik C, Dias CAG, Oteo Iglesias J, Pérez-Vázquez M. Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring bla KPC- 2 or bla NDM- 1. Front Microbiol 2020; 11:1563. [PMID: 32760368 PMCID: PMC7374196 DOI: 10.3389/fmicb.2020.01563] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/16/2020] [Indexed: 11/17/2022] Open
Abstract
Objectives Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) is a major cause of infections in transplanted patients and has been associated with high mortality rates in this group. There is a lack of information about the Brazilian structure population of CP-Kp isolated from transplanted patients. By whole-genome sequencing (WGS), we analyzed phylogeny, resistome, virulome of CP-Kp isolates, and the structure of plasmids encoding blaKPC–2 and blaNDM–1 genes. Methods One K. pneumoniae isolated from each selected transplanted patient colonized or infected by CP-Kp over a 16-month period in a hospital complex in Porto Alegre (Brazil) was submitted for WGS. The total number of strains sequenced was 80. The hospital complex in Porto Alegre comprised seven different hospitals. High-resolution SNP typing, core genome multilocus sequence typing (cgMLST), resistance and virulence genes inference, and plasmid reconstruction were performed in 80 CP-Kp. Results The mortality rate of CP-Kp colonized or infected transplanted inpatients was 21.3% (17/80). Four CP-Kp epidemic clones were described: ST11/KPC-2, ST16/KPC-2, and ST15/NDM-1, all responsible for interhospital outbreaks; and ST437/KPC-2 affecting a single hospital. The average number of acquired resistance and virulence genes was 9 (range = 2–14) and 27 (range = 6–36), respectively. Two plasmids carrying the blaKPC–2 were constructed and belonged to IncN and IncM types. Additionally, an IncFIB plasmid carrying the blaNDM–1 was described. Conclusion We detected intrahospital and interhospital spread of mobile structures and international K. pneumoniae clones as ST11, ST16, and ST15 among transplanted patients, which carry a significant range of acquired resistance and virulence genes and keep spreading across the world.
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Affiliation(s)
- Otávio Hallal Ferreira Raro
- Departamento de Ciências da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil.,Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III - CNM-ISCIII, Madrid, Spain
| | - Ravena Maya Cardoso da Silva
- Departamento de Ciências da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | | | | | - Claudio Stadnik
- Serviço de Controle de Infecção, Santa Casa de Misericórdia de Porto Alegre - SCMPA, Porto Alegre, Brazil
| | - Cícero Armídio Gomes Dias
- Departamento de Ciências da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Jesús Oteo Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III - CNM-ISCIII, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III - CNM-ISCIII, Madrid, Spain
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Genome Sequences of Burkholderia thailandensis Strains E421, E426, and DW503. Microbiol Resour Announc 2020; 9:9/21/e00312-20. [PMID: 32439666 PMCID: PMC7242668 DOI: 10.1128/mra.00312-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the draft genome sequences of three Burkholderia thailandensis strains, E421, E426, and DW503. E421 consists of 90 contigs of 6,639,935 bp and 67.73% GC content. E426 consists of 106 contigs of 6,587,853 bp and 67.73% GC content. DW503 consists of 102 contigs of 6,458,767 bp and 67.64% GC content. We present the draft genome sequences of three Burkholderia thailandensis strains, E421, E426, and DW503. E421 consists of 90 contigs of 6,639,935 bp and 67.73% GC content. E426 consists of 106 contigs of 6,587,853 bp and 67.73% GC content. DW503 consists of 102 contigs of 6,458,767 bp and 67.64% GC content.
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Ramirez MS, Bonomo RA, Tolmasky ME. Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace. Biomolecules 2020; 10:biom10050720. [PMID: 32384624 PMCID: PMC7277208 DOI: 10.3390/biom10050720] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.
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Affiliation(s)
- Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
| | - Robert A. Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA;
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics; Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- WRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
- Correspondence: ; Tel.: +657-278-5263
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Kothari A, Kumar S, Omar BJ, Kiran K. Detection of extended-spectrum beta-lactamase (ESBL) production by disc diffusion method among Pseudomonas species from various clinical samples. J Family Med Prim Care 2020; 9:683-693. [PMID: 32318403 PMCID: PMC7114052 DOI: 10.4103/jfmpc.jfmpc_570_19] [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: 07/22/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 11/04/2022] Open
Abstract
Aim/Objectives This study was aimed to detect extended-spectrum beta-lactamase (ESBL) producing Pseudomonas species isolated from various clinical samples by phenotypic methods with their susceptibility testing. Materials and Methods Hundred Pseudomonas isolates were taken from various clinical samples of patients attending outpatient department (OPD) and inpatient department (IPD). Antimicrobial susceptibility test and ESBL detection were assessed using CLSI guidelines on Mueller Hinton agar. Results Out of 100 Pseudomonas isolates, 46 isolates were from female and 54 were from male patients. More cases of pseudomonal infection were in the age group between 46 and 60 years (34%), and 59% of Pseudomonas species were isolated from patients belongs to urban areas and the rest 41% were from rural. The isolates collected from OPD were 61% and rest 39% from IPD. Pseudomonas species showed maximum resistance to cephalosporin group of antibiotics and showed least resistance to imipenem, and showed 100% susceptibility to colistin. ESBL production was detected in 42% of total isolates. Conclusion The present study highlights that the Pseudomonas species remains an important cause of nosocomial infections. ESBL producing Pseudomonas species continue to be an important organism causing life-threatening infections. Multidrug resistance was seen in most of the strains. Resistance is developing even to combination of ceftazidime clavulanic acid. Resistance is developing to last resort of antibiotic, i.e. imipenem also. This gives the alarming signal for the future, making the therapeutic options more difficult. Strict infection control measures are to be taken to contain this so-called water and soil organisms as Pseudomonas.
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Affiliation(s)
- Ashish Kothari
- Department of Microbiology, All India Institute of Medical Science, Rishikesh, Uttarakhand, India
| | - Shailesh Kumar
- Department of Dentistry, All India Institute of Medical Science, Rishikesh, Uttarakhand, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Science, Rishikesh, Uttarakhand, India
| | - Kamini Kiran
- Department of Pathology, All India Institute of Medical Science, Rishikesh, Uttarakhand, India
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Genome Sequence of a Klebsiella pneumoniae NDM-1 Producer Isolated in Quebec City. Microbiol Resour Announc 2020; 9:9/3/e00829-19. [PMID: 31948953 PMCID: PMC6965571 DOI: 10.1128/mra.00829-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the complete genome sequence of Klebsiella pneumoniae CCRI-22199, isolated from a patient from India treated in Quebec City, Canada. Genes encoding beta-lactamases NDM-1 and CTX-M-15 were identified on two distinct plasmids. While the chromosome is similar to that of strain BAA-2146, CCRI-22199 provides a further example of rearrangements in plasmids.
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Shen X, Liu L, Yu J, Cao X, Zhan Q, Guo Y, Wang L, Yu F. Coexistence of bla NDM-1 and rmtC on a Transferrable Plasmid of a Novel ST192 Klebsiella aerogenes Clinical Isolate. Infect Drug Resist 2019; 12:3883-3891. [PMID: 31853191 PMCID: PMC6916698 DOI: 10.2147/idr.s228130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/02/2019] [Indexed: 01/14/2023] Open
Abstract
Introduction The occurrence and development of antibiotic resistance are mainly caused by the spread of large plasmids carrying multiple antibiotic resistance genes. Recently, the association between 16S rRNA methyltransferase genes and β-lactamase genes carried by the same plasmid is of concern. Methods The Klebsiella aerogenes 1564 was isolated from the catheter tip of a patient in a tertiary hospital, Shanghai, China. The presence of the bla NDM-1 and rmtC genes were assessed by PCR. Complete sequence of plasmid p1564 was determined. The K. aerogenes 1564 was characterized by antimicrobial susceptibility testing, Carbapenemase phenotype confirmation testing, conjugation experiment, S1-PFGE and multilocus sequence typing (MLST). Results Herein, we found that a New Delhi Metallo-β-lactamase-1 gene (bla NDM-1) and a 16S rRNA methyltransferase gene (rmtC) coexisted on a transferrable plasmid of a carbapenem-resistant K. aerogenes clinical isolate. The K. aerogenes clinical isolate was found to belong to a novel sequence type 192 (ST192) determined by MLST. The sequencing results of the plasmid p1564 carrying bla NDM-1 gene and rmtC gene showed that the size and guanine-cytosine content of the plasmid were 136, 902 bp and 51.8%, with 164 putative ORFs and two multidrug resistance gene islands. In addition to bla NDM-1and rmtC, the plasmid contained bleomycin resistance gene (ble MBL), CMY-6β-lactamase gene (bla CMY-6), quaternary ammonium compound resistance gene (sugE), truncated quaternary ammonium compound resistance gene (qacEΔ1), aminoglycoside resistance gene (aacA4) and sulfonamide resistance gene (sul1). By comparison, p1564 has high homology with pHS36-NDM from Salmonella enterica subsp. enterica serovar Stanley reported in China, with similar size and both belonging to plasmid incompatibility group A/C. Conclusion The present study demonstrated for the first time the co-existence of rmtC and bla NDM-1 in a novel ST192 K. aerogenes. The spread of plasmids harboring both bla NDM-1 and rmtC may occur among Enterobacteriaceae in China.
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Affiliation(s)
- Xiaofei Shen
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Li Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Jingyi Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Xingwei Cao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China
| | - Qing Zhan
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang 330006, People's Republic of China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
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Iwu CD, Okoh AI. Preharvest Transmission Routes of Fresh Produce Associated Bacterial Pathogens with Outbreak Potentials: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E4407. [PMID: 31717976 PMCID: PMC6888529 DOI: 10.3390/ijerph16224407] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023]
Abstract
Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause disease outbreaks. Most of these pathogens acquire antimicrobial resistance (AR) determinants due to AR selective pressure within the agroecosystem and become resistant against most available treatment options, further aggravating risks to human and environmental health, and food safety. This review critically outlines the following issues with regards to fresh produce; the global burden of fresh produce-related foodborne diseases, contamination between the continuum of farm to table, preharvest transmission routes, AR profiles, and possible interventions to minimize the preharvest contamination of fresh produce. This review reveals that the primary production niches of the agro-ecosystem play a significant role in the transmission of fresh produce associated pathogens as well as their resistant variants, thus detrimental to food safety and public health.
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Affiliation(s)
- Chidozie Declan Iwu
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa;
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa;
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Ramirez MS, Iriarte A, Reyes-Lamothe R, Sherratt DJ, Tolmasky ME. Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance. Front Microbiol 2019; 10:2182. [PMID: 31616398 PMCID: PMC6764390 DOI: 10.3389/fmicb.2019.02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is the causative agent of community- and, more commonly, hospital-acquired infections. Infections caused by this bacterium have recently become more dangerous due to the acquisition of multiresistance to antibiotics and the rise of hypervirulent variants. Plasmids usually carry genes coding for resistance to antibiotics or virulence factors, and the recent sequence of complete K. pneumoniae genomes showed that most strains harbor many of them. Unlike large plasmids, small, usually high copy number plasmids, did not attract much attention. However, these plasmids may include genes coding for specialized functions, such as antibiotic resistance, that can be expressed at high levels due to gene dosage effect. These genes may be part of mobile elements that not only facilitate their dissemination but also participate in plasmid evolution. Furthermore, high copy number plasmids may also play a role in evolution by allowing coexistence of mutated and non-mutated versions of a gene, which helps to circumvent the constraints imposed by trade-offs after certain genes mutate. Most K. pneumoniae plasmids 25-kb or smaller replicate by the ColE1-type mechanism and many of them are mobilizable. The transposon Tn1331 and derivatives were found in a high percentage of these plasmids. Another transposon that was found in representatives of this group is the bla KPC-containing Tn4401. Common resistance determinants found in these plasmids were aac(6')-Ib and genes coding for β-lactamases including carbapenemases.
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Affiliation(s)
- Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República de Uruguay, Montevideo, Uruguay
| | | | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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41
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Martino F, Tijet N, Melano R, Petroni A, Heinz E, De Belder D, Faccone D, Rapoport M, Biondi E, Rodrigo V, Vazquez M, Pasteran F, Thomson NR, Corso A, Gomez SA. Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient. PLoS One 2019; 14:e0221960. [PMID: 31498841 PMCID: PMC6733481 DOI: 10.1371/journal.pone.0221960] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 11/18/2022] Open
Abstract
In Argentina, NDM metallo-β-lactamase was first reported in 2013. By now, it has disseminated throughout the country in diverse Gram negative bacteria. Here, we report the case of a paediatric patient that underwent a 1-year hospitalisation due to erythrodermic psoriasis in 2014 and received multiple antimicrobial treatments. During his stay, five isolates were obtained from rectal swabs (rs) or blood culture (bc) suspicious of carbapenemase production: a K. quasipneumoniae subsp. quasipneumoniae (rs), Citrobacter freundii (rs), Escherichia coli (bc), Enterobacter cloacae (rs), and a Serratia marcescens (bc). The isolates were studied with broth microdilution, biparental conjugation and plasmid and whole genome sequencing (Illumina). All isolates harboured an 138,998-bp type 1 IncC plasmid that carried blaNDM-1, bleMBL, blaCMY-6, rmtC, aac(6’)-Ib, and sul1 resistance genes. Additionally, the blaNDM-plasmids contained ISKpn8 an insertion sequence previously described as associated only to blaKPC. One isolate, a colistin-resistant E. coli, also carried a mcr-1-containing an IncI2 plasmid, which did not harbour additional resistance. The whole genome of K. quasipneumoniae subsp. quasipneumoniae isolate was fully sequenced. This isolate harboured, additionally to blaNDM, three plasmid-mediated quinolone resistance genes: qnrB4, qnrB52 and aac(6’)-Ib-cr1. The E. cloacae isolate also harboured qnrA1. These findings alert to the underestimated horizontal dissemination of multidrug-resistant plasmids limiting treatment options with last resort antimicrobials.
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Affiliation(s)
- F. Martino
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - N. Tijet
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - R. Melano
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - A. Petroni
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - E. Heinz
- The Welcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - D. De Belder
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - D. Faccone
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - M. Rapoport
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - E. Biondi
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - V. Rodrigo
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - M. Vazquez
- Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
| | - F. Pasteran
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - N. R. Thomson
- The Welcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A. Corso
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - S. A. Gomez
- Servicio Antimicrobianos (National Reference Laboratory on Antimicrobial Resistance), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
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Zhang Y, Lei CW, Wang HN. Identification of a novel conjugative plasmid carrying the multiresistance gene cfr in Proteus vulgaris isolated from swine origin in China. Plasmid 2019; 105:102440. [DOI: 10.1016/j.plasmid.2019.102440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022]
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Cui M, Zhang P, Li J, Sun C, Song L, Zhang C, Zhao Q, Wu C. Prevalence and Characterization of Fluoroquinolone Resistant Salmonella Isolated From an Integrated Broiler Chicken Supply Chain. Front Microbiol 2019; 10:1865. [PMID: 31456779 PMCID: PMC6700324 DOI: 10.3389/fmicb.2019.01865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
The objectives of this study were to investigate the prevalence and fluoroquinolone resistant Salmonella isolated from an integrated broiler chicken supply chain and their molecular characterization. In total, 73 Salmonella isolates were recovered from a broiler chicken supply chain in Shanghai. Salmonella isolates were tested for susceptibility to 11 antimicrobial agents using the broth dilution method and were characterized using pulsed-field gel electrophoresis (PFGE). Then, the Salmonella isolates were examined for mutations in quinolone resistance-determining region (QRDR) of gyrA, gyrB, parC, and parE, and were screened for plasmid-mediated quinolone resistance (PMQR) genes. Lastly, we sequenced the plasmids carrying qnrS1 in six Salmonella isolates from three sources (two isolated per source). Among 73 Salmonella isolates, 45 isolates were identified as S. Indiana, 24 were S. Schwarzengrund, 2 were S. Enteritidis, and 2 were S. Stanleyville. In addition, high rates of resistance were detected for nalidixic acid (41.1%) and ciprofloxacin (37.0%), while resistance to other test agents was diverse (2.0–100%). S. Indiana and S. Schwarzengrund isolates from different sources exhibited the same PFGE pattern, suggesting that the Salmonella isolates possessed high potential to spread along the broiler chicken supply chain. gyrA and parC exhibited frequent missense mutations. Moreover, qnrS1 was the most prevalent PMQR gene in the 73 Salmonella isolates, and it was found about a new hybrid plasmid. This study concludes a high prevalence of fluoroquinolone resistant Salmonella in chicken supply chain, threatening the treatment of Salmonella foodborne diseases. In particular, the emergence of a new hybrid plasmid carrying qnrS1 indicates that the recombination of plasmid carrying resistance gene might be a potential risk factor for the prevention and control strategies of drug resistance.
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Affiliation(s)
- Mingquan Cui
- China Institute of Veterinary Drug Control, Beijing, China
| | - Peng Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Detection for Veterinary Drug Residue and Illegal Additive, MOA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiyun Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Detection for Veterinary Drug Residue and Illegal Additive, MOA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chengtao Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Detection for Veterinary Drug Residue and Illegal Additive, MOA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Li Song
- China Institute of Veterinary Drug Control, Beijing, China
| | - Chunping Zhang
- China Institute of Veterinary Drug Control, Beijing, China
| | - Qi Zhao
- China Institute of Veterinary Drug Control, Beijing, China
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Detection for Veterinary Drug Residue and Illegal Additive, MOA, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Peirano G, Matsumura Y, Adams MD, Bradford P, Motyl M, Chen L, Kreiswirth BN, Pitout JDD. Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014. Emerg Infect Dis 2019; 24:1010-1019. [PMID: 29774858 PMCID: PMC6004858 DOI: 10.3201/eid2406.171648] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.
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Duran-Bedolla J, Bocanegra-Ibarias P, Silva-Sanchez J, Garza-González E, Morfín-Otero R, Hernández-Castro R, Lozano L, Garza-Ramos U, Barrios-Camacho H. Genetic characterization of multiple NDM-1-producing clinical isolates in Mexico. Diagn Microbiol Infect Dis 2019; 94:195-198. [PMID: 30642720 DOI: 10.1016/j.diagmicrobio.2018.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/21/2018] [Accepted: 12/02/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), CISEI, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico
| | - Paola Bocanegra-Ibarias
- Servicio de Gastroenterología, Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Jesús Silva-Sanchez
- Instituto Nacional de Salud Pública (INSP), CISEI, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico
| | - Elvira Garza-González
- Servicio de Gastroenterología, Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Rayo Morfín-Otero
- Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Hospital Civil de Guadalajara Fray Antonio Alcalde, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | - L Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico.
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), CISEI, Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, Mexico.
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Koulenti D, Song A, Ellingboe A, Abdul-Aziz MH, Harris P, Gavey E, Lipman J. Infections by multidrug-resistant Gram-negative Bacteria: What's new in our arsenal and what's in the pipeline? Int J Antimicrob Agents 2018; 53:211-224. [PMID: 30394301 DOI: 10.1016/j.ijantimicag.2018.10.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023]
Abstract
The spread of multidrug-resistant bacteria is an ever-growing concern, particularly among Gram-negative bacteria because of their intrinsic resistance and how quickly they acquire and spread new resistance mechanisms. Treating infections caused by Gram-negative bacteria is a challenge for medical practitioners and increases patient mortality and cost of care globally. This vulnerability, along with strategies to tackle antimicrobial resistance development, prompts the development of new antibiotic agents and exploration of alternative treatment options. This article summarises the new antibiotics that have recently been approved for Gram-negative bacterial infections, looks down the pipeline at promising agents currently in phase I, II, or III clinical trials, and introduces new alternative avenues that show potential in combating multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Despoina Koulenti
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Royal Brisbane Clinical Unit, Faculty of Medicine, The University of Queensland, Brisbane, Australia; 2nd Critical Care Department, Attikon University Hospital, Athens, Greece.
| | - Andrew Song
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Aaron Ellingboe
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Mohd Hafiz Abdul-Aziz
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia; School of Pharmacy, International Islamic University, Malaysia, Kuantan, Malaysia
| | - Patrick Harris
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Pathology Queensland, Central Laboratory, Herston, Queensland, Australia; Infection Management Services, Princess Alexandra Hospital, Queensland, Australia
| | - Emile Gavey
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Royal Brisbane Clinical Unit, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Department of Intensive Care Medicine, Royal Brisbane and Women's Hospital, Brisbane
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47
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Zhao H, Chen W, Xu X, Zhou X, Shi C. Transmissible ST3-IncHI2 Plasmids Are Predominant Carriers of Diverse Complex IS 26-Class 1 Integron Arrangements in Multidrug-Resistant Salmonella. Front Microbiol 2018; 9:2492. [PMID: 30405560 PMCID: PMC6206278 DOI: 10.3389/fmicb.2018.02492] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Diverse mobile genetic elements (MGEs) including plasmids, insertion sequences, and integrons play an important role in the occurrence and spread of multidrug resistance (MDR) in bacteria. It was found in previous studies that IS26 and class 1 integrons integrated on plasmids to speed the dissemination of antibiotic-resistance genes in Salmonella. It is aimed to figure out the patterns of specific genetic arrangements between IS26 and class 1 integrons located in plasmids in MDR Salmonella in this study. A total of 74 plasmid-harboring Salmonella isolates were screened for the presence of IS26 by PCR amplification, and 39 were IS26-positive. Among them, 37 isolates were resistant to at least one antibiotic. The thirty-seven antibiotic-resistant isolates were further involved in PCR detection of class 1 integrons and variable regions, and all were positive for class 1 integrons. Six IS26-class 1 integron arrangements with IS26 inserted into the upstream or downstream of class 1 integrons were characterized. Eight combinations of these IS26-class 1 integron arrangements were identified among 31 antibiotic-resistant isolates. Multidrug-resistance plasmids of the IncHI2 incompatibility group were dominant, which all belonged to ST3 by plasmid double locus sequence typing. These 21 IncHI2-positive isolates harbored six complex IS26-class 1 integron arrangement patterns. Conjugation assays and Southern blot hybridizations confirmed that conjugative multidrug-resistance IncHI2 plasmids harbored the different complex IS26-class 1 integron arrangements. The conjugation frequency of IncHI2 plasmids transferring alone was 10−5-10−6, reflecting that different complex IS26-class 1 integron arrangement patterns didn't significantly affect conjugation frequency (P > 0.05). These data suggested that class 1 integrons represent the hot spot for IS26 insertion, forming diverse MDR loci. And ST3-IncHI2 was the major plasmid lineage contributing to the horizontal transfer of composite IS26-class 1 integron MDR elements in Salmonella.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyao Chen
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Xiujuan Zhou
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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48
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Risk Factors for Carbapenem Resistant Klebsiella pneumoniae Hospital Infection in the Intensive Care Unit. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2018. [DOI: 10.2478/sjecr-2018-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) has become a major threat to patients in hospitals, increasing mortality, length of stay and costs.
The aim of this study was to discover risk factors for the development of hospital infections (HIs) caused by CR-Kp.
A prospective cohort study was conducted in the Medical-Surgical Intensive Care Unit of the Clinical Centre in Kragujevac, Kragujevac, Serbia, from January 1, 2011, to December 31, 2015. The “cases” were patients with HIs caused by CR-Kp, while the “controls” were patients infected with carbapenem-sensitive Klebsiella pneumoniae (CS-Kp). The significance of multiple putative risk factors for HIs caused by CR-Kp was tested using multivariate logistic regression.
Although univariate analyses pointed to many risk factors, with a significant influence on the occurrence of hospital CR-Kp infections, the multivariate logistic regression identified five independent risk factors: use of mechanical ventilation (OR=6.090; 95% CI=1.030-36.020; p=0.046); length of antibiotic therapy before HIs (days) (OR=1.080; 95% CI=1.003-1.387; p=0.045); previous use of carbapenems (OR=7.005; 95% CI=1.054-46.572; p=0.044); previous use of ciprofloxacin (OR=20.628; 95% CI=2.292-185.687; p=0.007) and previous use of metronidazole (OR=40.320; 95% CI=2.347-692.795; p=0.011)
HIs caused by CR-Kp are strongly associated with the use of mechanical ventilation and the duration of the previous use of certain antibiotics (carbapenems, ciprofloxacin and metronidazole).
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49
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Dong N, Yang X, Zhang R, Chan EWC, Chen S. Tracking microevolution events among ST11 carbapenemase-producing hypervirulent Klebsiella pneumoniae outbreak strains. Emerg Microbes Infect 2018; 7:146. [PMID: 30100608 PMCID: PMC6087712 DOI: 10.1038/s41426-018-0146-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 12/15/2022]
Abstract
The recent convergence of genetic elements encoding phenotypic carbapenem-resistance and hypervirulence within a single Klebsiella pneumoniae host strain represents a major public concern. To obtain a better understanding of the genetic characteristic of this emerging ‘superbug’, the complete genomes of 3 isolates of ST11 carbapenemase-producing hypervirulent K. pneumoniae were generated using the Oxford nanopore MinION platform. Comparative whole-genome analysis identified 13 SNPs and 3 major regions of indels in the chromosomes of the clonally disseminated isolates. ISKpn18-mediated disruption in the mgrB gene, which was associated with colistin resistance, was identified in two later strains, leading to the emergence of hypervirulent K. pneumoniae that was simultaneously colistin- and carbapenem-resistant. Five plasmids were recovered from each isolate, including a 178 Kb IncHI1B/FIB-type rmpA2-bearing virulence plasmid, a 177.5 Kb IncFII/R self-transferable blaKPC-2-bearing MDR plasmid, a 99.7 Kb Incl1 plasmid and two ColRNAI-type plasmids of sizes of 11.9 and 5.6 Kb, respectively. The presence of homologous regions between the non-conjugative virulence plasmid and conjugative blaKPC-2-bearing MDR plasmid suggests that transmission of the virulence plasmid from ST23 K. pneumoniae to ST11 CRKP may be mediated by the co-integrated transfer of these two plasmids. Emergence of colistin-resistant and carbapenemase-producing hypervirulent K. pneumoniae strains further emphasizes the urgency for the establishment of a coordinated global program to eradicate hypervirulent and/or pan-drug-resistant strains of K. pneumoniae from clinical settings and the community.
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Affiliation(s)
- Ning Dong
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Xuemei Yang
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Rong Zhang
- Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China. .,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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50
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Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40-55. [PMID: 30081066 DOI: 10.1016/j.plasmid.2018.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023]
Abstract
The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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