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Timková I, Maliničová L, Nosáľová L, Kolesárová M, Lorková Z, Petrová N, Pristaš P, Kisková J. Genomic insights into the adaptation of Acinetobacter johnsonii RB2-047 to the heavy metal-contaminated subsurface mine environment. Biometals 2024; 37:371-387. [PMID: 37973678 PMCID: PMC11006771 DOI: 10.1007/s10534-023-00555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023]
Abstract
The subsurface mine environments characterized by high levels of toxic metals and low nutrient availability represent an extreme threat to bacterial persistence. In recent study, the genomic analysis of the Acinetobacter johnsonii strain RB2-047 isolated from the Rozália Gold Mine in Slovakia was performed. As expected, the studied isolate showed a high level of heavy metal tolerance (minimum inhibitory concentrations were 500 mg/L for copper and nickel, 1,500 mg/L for lead, and 250 mg/L for zinc). The RB2-047 strain also showed noticeable resistance to several antibiotics (ampicillin, kanamycin, chloramphenicol, tetracycline and ciprofloxacin). The genomic composition analysis demonstrated a low number of antibiotic and metal resistance coding genes, but a high occurrence of efflux transporter genes located on the bacterial chromosome. The experimental inhibition of efflux pumps resulted in decreased tolerance to Zn and Ni (but not to Cu and Pb) and to all antibiotics tested. In addition, the H33342 dye-accumulation assay confirmed the high efflux activity in the RB2-047 isolate. These findings showed the important role of efflux pumps in the adaptation of Acinetobacter johsonii strain RB2-047 to metal polluted mine environment as well as in development of multi-antibiotic resistance.
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Affiliation(s)
- Ivana Timková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lenka Maliničová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lea Nosáľová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Mariana Kolesárová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Zuzana Lorková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Nikola Petrová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Peter Pristaš
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| | - Jana Kisková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia.
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Molina-Menor E, Carlotto N, Vidal-Verdú À, Pérez-Ferriols A, Pérez-Pastor G, Porcar M. Ecology and resistance to UV light and antibiotics of microbial communities on UV cabins in the dermatology service of a Spanish hospital. Sci Rep 2023; 13:14547. [PMID: 37666842 PMCID: PMC10477284 DOI: 10.1038/s41598-023-40996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/20/2023] [Indexed: 09/06/2023] Open
Abstract
Microorganisms colonize all possible ecological habitats, including those subjected to harsh stressors such as UV radiation. Hospitals, in particular the UV cabins used in phototherapy units, constitute an environment in which microbes are intermittently subjected to UV irradiation. This selective pressure, in addition to the frequent use of antibiotics by patients, may represent a threat in the context of the increasing problem of antimicrobial resistance. In this work, a collection of microorganisms has been established in order to study the microbiota associated to the inner and outer surfaces of UV cabins and to assess their resistance to UV light and the antibiotics frequently used in the Dermatology Service of a Spanish hospital. Our results show that UV cabins harbor a relatively diverse biocenosis dominated by typically UV-resistant microorganisms commonly found in sun-irradiated environments, such as Kocuria, Micrococcus or Deinococcus spp., but also clinically relevant taxa, such as Staphylococcus or Pseudomonas spp. The UV-radiation assays revealed that, although some isolates displayed some resistance, UV is not a major factor shaping the biocenosis living on the cabins, since a similar pool of resistant microorganisms was identified on the external surface of the cabins. Interestingly, some Staphylococcus spp. displayed resistance to one or more antibiotics, although the hospital reported no cases of antibiotic-resistance infections of the patients using the cabins. Finally, no association between UV and antibiotic resistances was found.
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Affiliation(s)
- Esther Molina-Menor
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), Valencia, Spain
| | - Nicolás Carlotto
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), Valencia, Spain
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), Valencia, Spain
| | | | - Gemma Pérez-Pastor
- Servicio de Dermatología, Consorcio Hospital General de Valencia, Valencia, Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), Valencia, Spain.
- Darwin Bioprospecting Excellence SL (Parc Científic Universitat de València, C/ Catedràtic Agustín Escardino Benlloch 9, Paterna, Spain.
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Mączyńska B, Jama-Kmiecik A, Sarowska J, Woronowicz K, Choroszy-Król I, Piątek D, Frej-Mądrzak M. Changes in Antibiotic Resistance of Acinetobacter baumannii and Pseudomonas aeruginosa Clinical Isolates in a Multi-Profile Hospital in Years 2017-2022 in Wroclaw, Poland. J Clin Med 2023; 12:5020. [PMID: 37568422 PMCID: PMC10420100 DOI: 10.3390/jcm12155020] [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: 06/22/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
In recent years, we have witnessed increasing drug resistance among bacteria, which is associated with the use and availability of an increasing number of broad-spectrum antimicrobials, as well as with their irrational and excessive use. The present study aims to analyze changes in the drug resistance of Gram-negative Pseudomonas aeruginosa and Acinetobacter baumannii, isolated from infections in a multi-profile hospital over a five-year period (from 2017 to 2022). Among the practical results of the evaluation of these data will be the possibility to determine changes in susceptibility to the antibiotics used in the hospital. This, in turn, will help propose new therapeutic options, especially for empirical therapy, which is essential in severe infections. Analysis of the use of different antibiotic groups has made it possible to identify the causes of increasing resistance in the analyzed Gram-negative bacilli. The highest antibiotic use was observed in the hospital between 2020 and 2022, most probably due to the COVID-19 pandemic and the higher number of patients in severe condition requiring hospitalization. Unfortunately, during the period analyzed, the number of multi-resistant strains of A. baumannii was successively increasing; this seems to be related to the increased use, especially during the pandemic period, of broad-spectrum antibiotics, mainly penicillins with inhibitors, third-generation cephalosporins and carbapenems.
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Affiliation(s)
- Beata Mączyńska
- Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Medical University, 50-367 Wroclaw, Poland
| | - Agnieszka Jama-Kmiecik
- Department of Basic Sciences, Faculty of Health Sciences, Medical University, 50-367 Wroclaw, Poland
| | - Jolanta Sarowska
- Department of Basic Sciences, Faculty of Health Sciences, Medical University, 50-367 Wroclaw, Poland
| | | | - Irena Choroszy-Król
- Department of Basic Sciences, Faculty of Health Sciences, Medical University, 50-367 Wroclaw, Poland
| | - Daniel Piątek
- Lower Silesian T. Marciniak Specialist Hospital-Center for Emergency Medicine, 54-049 Wroclaw, Poland
| | - Magdalena Frej-Mądrzak
- Department of Basic Sciences, Faculty of Health Sciences, Medical University, 50-367 Wroclaw, Poland
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Chiș AA, Rus LL, Morgovan C, Arseniu AM, Frum A, Vonica-Țincu AL, Gligor FG, Mureșan ML, Dobrea CM. Microbial Resistance to Antibiotics and Effective Antibiotherapy. Biomedicines 2022; 10:biomedicines10051121. [PMID: 35625857 PMCID: PMC9138529 DOI: 10.3390/biomedicines10051121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.
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Ragheb SM, Govinden U, Osei Sekyere J. Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa. Ann N Y Acad Sci 2021; 1509:50-73. [PMID: 34753206 DOI: 10.1111/nyas.14703] [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: 05/21/2020] [Revised: 09/06/2021] [Accepted: 09/26/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.
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Affiliation(s)
- Suzan Mohammed Ragheb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - John Osei Sekyere
- Department of Microbiology & Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana.,Department of Dermatology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Sharma S, Das A, Banerjee T, Barman H, Yadav G, Kumar A. Adaptations of carbapenem resistant Acinetobacter baumannii (CRAB) in the hospital environment causing sustained outbreak. J Med Microbiol 2021; 70. [PMID: 33739918 DOI: 10.1099/jmm.0.001345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction. Carbapenem resistance in Acinetobacter baumannii (A. baumannii) is an emerging global threat.Gap statement. The adaptation strategies of A. baumannii for this emergence as a nosocomial pathogen has been less studied.Aim. This prospective study analysed a sustained outbreak of carbapenem resistant Acinetobacter baumannii (CRAB) in the intensive care unit (ICU) with reference to antimicrobial resistance and virulence in the colonizing and pathogenic isolates under carbapenem stress.Results. The CRAB isolates from initial and sustained outbreak were found harbouring multiple carbapenemase genes. These genes included bla OXA-23 ,bla IMP, bla VIM and bla NDM. From NICU environment three phenotypically carbapenem susceptible isolates were found carrying bla OXA-23, bla IMP, bla VIM genes. Prior imipenem therapy was one of the risk factors (P=0.0016). The outbreak was polyclonal. Under imipenem stress, outbreak isolates showed no loss of carbapenemase genes against stress free conditions (23.7±1.33 days). Biofilm formation increased with imipenem concentration, with outbreak isolates producing highest biomass. While the pathogens showed a slow growth rate on imipenem exposure, the colonisers grew rapidly (P <0.0001).Methods. Sustained outbreak of CRAB was identified in the ICU (July 2015 to December 2017). Risk factors for acquisition of CRAB was studied. A. baumannii isolates were also collected from the environments of ICU and neonatal ICU (NICU) and blood cultures of septic neonates. Isolates were characterized based on antimicrobial susceptibility, genetic profile, integrons carriage and clonality. Biofilm formation and growth kinetics were studied under varying carbapenem stress.Conclusion. Intense carbapenem exposure in the ICU facilitates persistence of CRAB by several adaptations causing sustained outbreaks.
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Affiliation(s)
- Swati Sharma
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Arghya Das
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Tuhina Banerjee
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Hiranmay Barman
- Department of Anaesthesiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ghanshyam Yadav
- Department of Anaesthesiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ashok Kumar
- Department of Paediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Alzuhairi MA, Abdulmohsen AM, Falih MN, Hanafiah MM. Genomic sequencing analysis of Acinetobacter baumannii strain ABIQM1, isolated from a meningitis patient. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Detection of Antimicrobial Resistance Genes Associated with Carbapenem Resistance from the Whole-Genome Sequence of Acinetobacter baumannii Isolates from Malaysia. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:5021064. [PMID: 32318127 PMCID: PMC7154965 DOI: 10.1155/2020/5021064] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022]
Abstract
Background The spread of carbapenem-resistant A. baumannii (CrAb) is gaining worldwide attention. The spread of this pathogen is largely due to its ability to acquire various resistance genes of intrinsic and extrinsic origins that confer unpredictable susceptibility to β-lactams. The aim of this study was to analyze β-lactamase genetic compositions of CrAb in Malaysia. Methods Whole-genome sequencing (WGS) was carried out on 13 CrAb isolates from clinical samples in Malaysia from 2011 to 2016. Results Endotracheal aspirate was the dominant clinical sample source (n = 6), and only one isolate was obtained from wound swab. A total of 6 sequence types (STs) of the Oxford scheme were identified, including 4 reported STs and 2 novel STs. Eleven isolates were classified into clonal complex 92 (CC92/ICII), among which ST195 and ST208 were the most prevalent STs. All 13 CrAb isolates harbored multiple β-lactamase genes. blaOXA-23 (n = 13) and blaOXA-66 (n = 11) were the dominant carbapenemase gene families found in these isolates. All isolates harbor blaADC, blaOXA-51-like, and blaOXA-23-like genes. blaTEM (n = 7), blaNDM-1 (n = 3), blaCARB-8 (n = 1), and blaPER-3 (n = 1) are amongst other β-lactamase genes found in this study. ISAba1 was found upstream to blaOXA-23 (n = 13), blaOXA-66 (n = 1), and blaADC (n = 11). All blaNDM-1 isolates had ISAba125 (mobile genetic element) upstream to the genes. All isolates were positive for Tn2006/2008 and Tn2009 but were negative for Tn2007. Conclusion Most of the isolates were grouped under the CC92 clonal complex which belongs to international clonal lineage 2. These findings predict that carriage of carbapenem-resistant genes possibly constitutes the underlying basis of high level of international clone II prevalence. Therefore, molecular surveillance and antimicrobial stewardship are essential in implementing policies to prevent and control the spread of CrAb in hospital settings.
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Fariba Akrami, Amirmorteza Ebrahimzadeh Namvar. Acinetobacter baumannii as Nosocomial Pathogenic Bacteria. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Freitas DY, Araújo S, Folador ARC, Ramos RTJ, Azevedo JSN, Tacão M, Silva A, Henriques I, Baraúna RA. Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil. Front Microbiol 2019; 10:364. [PMID: 30873145 PMCID: PMC6403167 DOI: 10.3389/fmicb.2019.00364] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/12/2019] [Indexed: 12/14/2022] Open
Abstract
Aquatic systems have been described as antibiotic resistance reservoirs, where water may act as a vehicle for the spread of resistant bacteria and resistance genes. We evaluated the occurrence and diversity of third generation cephalosporin-resistant gram-negative bacteria in a lake in the Amazonia region. This water is used for human activities, including consumption after appropriate treatment. Eighteen samples were obtained from six sites in October 2014. Water quality parameters were generally within the legislation limits. Thirty-three bacterial isolates were identified as Escherichia (n = 7 isolates), Acinetobacter, Enterobacter, and Klebsiella (n = 5 each), Pseudomonas (n = 4), Shigella (n = 3), and Chromobacterium, Citrobacter, Leclercia, Phytobacter (1 isolate each). Twenty nine out of 33 isolates (88%) were resistant to most beta-lactams, except carbapenems, and 88% (n = 29) were resistant to antibiotics included in at least three different classes. Among the beta-lactamase genes inspected, the blaCTX–M was the most prevalent (n = 12 positive isolates), followed by blaTEM (n = 5) and blaSHV (n = 4). blaCTX–M–15 (n = 5), blaCTX–M–14 (n = 1) and blaCTX–M–2 (n = 1) variants were detected in conserved genomic contexts: blaCTX–M–15 flanked by ISEcp1 and Orf477; blaCTX–M–14 flanked by ISEcp1 and IS903; and blaCTX–M–2 associated to an ISCR element. For 4 strains the transfer of blaCTX–M was confirmed by conjugation assays. Compared with the recipient, the transconjugants showed more than 500-fold increases in the MICs of cefotaxime and 16 to 32-fold increases in the MICs of ceftazidime. Two isolates (Escherichia coli APC43A and Acinetobacter baumannii APC25) were selected for whole genome analysis. APC43A was predicted as a E. coli pathogen of the high-risk clone ST471 and serotype O154:H18. blaCTX–M–15 as well as determinants related to efflux of antibiotics, were noted in APC43A genome. A. baumannii APC25 was susceptible to carbapenems and antibiotic resistance genes detected in its genome were intrinsic determinants (e.g., blaOXA–208 and blaADC–like). The strain was not predicted as a human pathogen and belongs to a new sequence type. Operons related to metal resistance were predicted in both genomes as well as pathogenicity and resistance islands. Results suggest a high dissemination of ESBL-producing bacteria in Lake Água Preta which, although not presenting characteristics of a strongly impacted environment, contains multi-drug resistant pathogenic strains.
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Affiliation(s)
- Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Susana Araújo
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Rommel T J Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Marta Tacão
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Isabel Henriques
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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Chang KC, Chung CY, Yeh CH, Hsu KH, Chin YC, Huang SS, Liu BR, Chen HA, Hu A, Soo PC, Peng WP. Direct detection of carbapenemase-associated proteins of Acinetobacter baumannii using nanodiamonds coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2018; 147:36-42. [PMID: 29499232 DOI: 10.1016/j.mimet.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 12/25/2022]
Abstract
The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR assays need only a few hours but due to its specificity, can only detect known genetic targets encoding carbapenem-resistance genes. Therefore, new approaches to detect carbapenemase-producing A. baumannii are of great importance. Here, we have developed a rapid and novel method using detonation nanodiamonds (DNDs) as a platform for concentration and extraction of A. baumannii carbapenemase-associated proteins prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS) analysis. To concentrate and extract the A. baumannii carbapenemase-associated proteins, we tested several protein precipitation conditions and found a 0.5% trifluoroacetic acid (TFA) solution within the bacterial suspension could result in strong ion signals with DNDs. A total of 66 A. baumannii clinical-isolates including 51 carbapenem-resistant strains and 15 carbapenem-susceptible strains were tested. Our result showed that among the 51 carbapenem-resistant strains 49 strains had a signal at m/z ~40,279 (±87); among the 15 carbapenem-susceptible strains, 4 strains showed a signal at m/z ~40,279. With on-diamond digestion, we confirmed that the captured protein at m/z ~40,279 was related to ADC family extended-spectrum class C beta-lactamase, from A. baumannii. Using this ADC family protein as a biomarker (m/z ~ 40,279) for carbapenem susceptibility testing of A. baumannii, the sensitivity and the specificity could reach 96% and 73% as compared to traditional imipenem susceptibility testing (MIC results). However, the sensitivity and specificity of this method reached 100% as compared to polymerase chain reaction (PCR) result. Our approach could directly detect the carbapenemase-associated proteins of A. baumannii within 90 min and does not require addition of carbapenemase substrate which is required in the MHT or other mass spectrometric methods. For future applications, our method could be efficiently used in the detection of other carbapenemase-producing bacteria.
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Affiliation(s)
- Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan; Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Chin-Yi Chung
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Hsing Yeh
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Kuo-Hsiu Hsu
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Ya-Ching Chin
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Sin-Siang Huang
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Bo-Rong Liu
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Hsi-An Chen
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Anren Hu
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Hualien, Taiwan.
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Kittinger C, Kirschner A, Lipp M, Baumert R, Mascher F, Farnleitner AH, Zarfel GE. Antibiotic Resistance of Acinetobacter spp. Isolates from the River Danube: Susceptibility Stays High. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 15:ijerph15010052. [PMID: 29301193 PMCID: PMC5800151 DOI: 10.3390/ijerph15010052] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 12/13/2022]
Abstract
Acinetobacter spp. occur naturally in many different habitats, including food, soil, and surface waters. In clinical settings, Acinetobacter poses an increasing health problem, causing infections with limited to no antibiotic therapeutic options left. The presence of human generated multidrug resistant strains is well documented but the extent to how widely they are distributed within the Acinetobacter population is unknown. In this study, Acinetobacter spp. were isolated from water samples at 14 sites of the whole course of the river Danube. Susceptibility testing was carried out for 14 clinically relevant antibiotics from six different antibiotic classes. Isolates showing a carbapenem resistance phenotype were screened with PCR and sequencing for the underlying resistance mechanism of carbapenem resistance. From the Danube river water, 262 Acinetobacter were isolated, the most common species was Acinetobacter baumannii with 135 isolates. Carbapenem and multiresistant isolates were rare but one isolate could be found which was only susceptible to colistin. The genetic background of carbapenem resistance was mostly based on typical Acinetobacter OXA enzymes but also on VIM-2. The population of Acinetobacter (baumannii and non-baumannii) revealed a significant proportion of human-generated antibiotic resistance and multiresistance, but the majority of the isolates stayed susceptible to most of the tested antibiotics.
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Affiliation(s)
- Clemens Kittinger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria.
| | - Alexander Kirschner
- Institute for Hygiene and Applied Immunology, Water Hygiene, Medical University of Vienna, 1090 Vienna, Austria.
- Interuniversity Cooperation Centre for Water and Health, Vienna University of Technology, 1060 Vienna, Austria.
| | - Michaela Lipp
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria.
| | - Rita Baumert
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria.
| | - Franz Mascher
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria.
| | - Andreas H Farnleitner
- Interuniversity Cooperation Centre for Water and Health, Vienna University of Technology, 1060 Vienna, Austria.
- Institute of Chemical Engineering, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, 1060 Vienna, Austria.
- Karl Landsteiner University for Health Sciences, 3500 Krems, Austria.
| | - Gernot E Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria.
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13
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Mohd Rani F, A Rahman NI, Ismail S, Alattraqchi AG, Cleary DW, Clarke SC, Yeo CC. Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology. Front Microbiol 2017; 8:2479. [PMID: 29312188 PMCID: PMC5733036 DOI: 10.3389/fmicb.2017.02479] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022] Open
Abstract
Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987–2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008–2009 and thereafter, rates have remained fairly constant (e.g., 50–60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that blaOXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.
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Affiliation(s)
- Farahiyah Mohd Rani
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Salwani Ismail
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | | | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University of Southampton, Southampton, United Kingdom.,Global Health Research Institute, University of Southampton, Southampton, United Kingdom.,International Medical University, Kuala Lumpur, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
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14
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Oh MH, Choi CH, Lee JC. The effect of ISAba1-mediated adeN gene disruption on Acinetobacter baumannii pathogenesis. Virulence 2017; 8:1088-1090. [PMID: 28598246 DOI: 10.1080/21505594.2017.1339859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Man Hwan Oh
- a Department of Nanobiomedical Science , Dankook University , Cheonan , South Korea
| | - Chul Hee Choi
- b Department of Microbiology and Medical Sciences , Chungnam National University, School of Medicine , Daejeon , South Korea
| | - Je Chul Lee
- c Department of Microbiology , Kyungpook National University School of Medicine , Daegu , South Korea
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15
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Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii. Microorganisms 2016; 4:microorganisms4030029. [PMID: 27681923 PMCID: PMC5039589 DOI: 10.3390/microorganisms4030029] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.
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16
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Brandt C, Zander E, Pfeifer Y, Braun SD, Ehricht R, Makarewicz O, Pletz MW. Development of a rapid diagnostic assay based on magnetic bead purification of OXA-β-lactamase mRNA. Future Microbiol 2016; 11:617-29. [PMID: 27164315 DOI: 10.2217/fmb.16.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIM To countermeasure the global spread of β-lactamases, we developed a rapid molecular test for the highly variable OXA-β-lactamases that allows minimizing the time to effective treatment. METHODS OXA-mRNA was specifically enriched from total RNA using group-specific biotinylated DNA probes and streptavidin-coated magnetic beads. Phylogenetic OXA groups were distinguished by PCR product size. RESULTS This mRNA fishing method is highly sensitive, yielding specific results from as little as 1 ng total RNA. It enables discrimination of OXA-extended substrate spectrum β-lactamases and carbapenemases and the semi-quantitative detection of highly expressed ISAba1-controlled variants. CONCLUSION Targeting mRNA with specific probes on magnetic beads will allow for adaptation to automated systems, such as point-of-care diagnostics.
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Affiliation(s)
- Christian Brandt
- Center for Infectious Diseases & Infection Control, Jena University Hospital, Jena, Germany.,Infectognostics Research Campus, Jena, Germany
| | - Esther Zander
- Institute for Medical Microbiology, Immunology & Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens & Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Sascha D Braun
- Infectognostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Ralf Ehricht
- Infectognostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Oliwia Makarewicz
- Center for Infectious Diseases & Infection Control, Jena University Hospital, Jena, Germany.,Infectognostics Research Campus, Jena, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases & Infection Control, Jena University Hospital, Jena, Germany.,Infectognostics Research Campus, Jena, Germany
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17
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Sun X, Liu B, Chen Y, Huang H, Wang G, Li F, Ni Z. Molecular characterization of Ambler class A to D β-lactamases, ISAba1, and integrons reveals multidrug-resistant Acinetobacter spp. isolates in northeastern China. J Chemother 2016; 28:469-475. [PMID: 27077928 DOI: 10.1080/1120009x.2015.1133014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The prevalence of various Ambler class A to D β-lactamases, ISAba1, and class 1 and 2 integrons as well as the clonal relatedness in 105 Acinetobacter spp. isolates found in northeastern China was investigated. All 105 Acinetobacter spp. isolates were determined to be multidrug resistant (MDR), and the resistance rates to carbapenem agents were approximately 50%. PER, IMP, AmpC, and OXA-23 were found to be dominant β-lactamases belonging to different classes, respectively. This is the first report of the coexistence of blaPER, blaIMP, blaAmpC, and blaOXA-23-like genes in Acinetobacter spp. isolates from northeastern China. ISAba1 was found upstream of the blaOXA-23-like gene in 87.8% (36/41) strains and upstream of the blaOXA-51-like gene in 26.5% (13/49) strains. ISAba3-like element was found upstream of the blaOXA-58-like gene in one blaOXA-58-like-positive strain. The presence of IntI1 was detected in 63.8% (67/105) of the isolates and the most prevalent gene cassettes were aacA4, aadA1, and catB8. The highly prevalent isolates belong to international clonal lineage (ICL)-II. These results indicate that the wide horizontal and clonal spread of MDR Acinetobacter spp. isolates harbouring multiple β-lactamase genes has become a serious problem in northeastern China.
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Affiliation(s)
- Xiaoyu Sun
- a Key Laboratory of Zoonosis, Ministry of Education, Department of Pathogenobiology , College of Basic Medical Science, Jilin University , Changchun , P.R. China
| | - Bin Liu
- b Cardiovascular Disease Center, The First Hospital of Jilin University , Changchun , P.R. China
| | - Yan Chen
- c Department of Neurosurgery , The Second Hospital of Jilin University , Changchun , P.R. China
| | - Honglan Huang
- a Key Laboratory of Zoonosis, Ministry of Education, Department of Pathogenobiology , College of Basic Medical Science, Jilin University , Changchun , P.R. China
| | - Guoqing Wang
- a Key Laboratory of Zoonosis, Ministry of Education, Department of Pathogenobiology , College of Basic Medical Science, Jilin University , Changchun , P.R. China
| | - Fan Li
- a Key Laboratory of Zoonosis, Ministry of Education, Department of Pathogenobiology , College of Basic Medical Science, Jilin University , Changchun , P.R. China
| | - Zhaohui Ni
- a Key Laboratory of Zoonosis, Ministry of Education, Department of Pathogenobiology , College of Basic Medical Science, Jilin University , Changchun , P.R. China
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18
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Maravić A, Skočibušić M, Fredotović Ž, Šamanić I, Cvjetan S, Knezović M, Puizina J. Urban riverine environment is a source of multidrug-resistant and ESBL-producing clinically important Acinetobacter spp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:3525-3535. [PMID: 26490931 DOI: 10.1007/s11356-015-5586-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
Some Acinetobacter species have emerged as very important opportunistic pathogens in humans. We investigated Acinetobacter spp. from the polluted urban riverine environment in Croatia in regard to species affiliation, antibiotic resistance pattern, and resistance mechanisms. Considerable number of isolates produced acquired extended-spectrum β-lactamase(s) (ESBLs), CTX-M-15 solely or with TEM-116. By Southern blot hybridization, bla TEM-116 was identified on plasmids ca. 10, 3, and 1.2 kb in Acinetobacter junii, A. gandensis, and A. johnsonii. The bla TEM-116-carrying plasmid in A. gandensis was successfully transferred by conjugation to azide-resistant Escherichia coli J53. A. radioresistens isolate also carried an intrinsic carbapenemase gene bla OXA-133 with ISAba1 insertion sequence present upstream to promote its expression. Majority of ESBL-producing isolates harbored integrases intI1 and/or intI2 and the sulfamethoxazole resistance gene sul1. Almost all isolates had overexpressed resistance-nodulation-cell division (RND) efflux system, indicating that this mechanism may have contributed to multidrug resistance phenotypes. This is the first report of environmental CTX-M-15-producing Acinetobacter spp. and the first identification of CTX-M-15 in A. johnsonii, A. junii, A. calcoaceticus, A. gandensis, A. haemolyticus, and A. radioresistens worldwide. We identified, also for the first time, the environmental Acinetobacter-producing TEM ESBLs, highlighting the potential risk for human health, and the role of these bacteria in maintenance and dissemination of clinically important antibiotic resistance genes in community through riverine environments.
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Affiliation(s)
- Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia.
| | - Mirjana Skočibušić
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia
| | - Svjetlana Cvjetan
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Mediterranean Institute for Life Sciences, Meštrovićevo šetalište 45, 21000, Split, Croatia
| | - Mia Knezović
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia
| | - Jasna Puizina
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000, Split, Croatia
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19
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Smith CA, Antunes NT, Stewart NK, Frase H, Toth M, Kantardjieff KA, Vakulenko S. Structural Basis for Enhancement of Carbapenemase Activity in the OXA-51 Family of Class D β-Lactamases. ACS Chem Biol 2015; 10:1791-6. [PMID: 26042471 DOI: 10.1021/acschembio.5b00090] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Class D β-lactamases of Acinetobacter baumannii are enzymes of the utmost clinical importance, producing resistance to last resort carbapenem antibiotics. Although the OXA-51-like enzymes constitute the largest family of class D β-lactamases, they are poorly studied and their importance in conferring carbapenem resistance is controversial. We present the detailed microbiological, kinetic, and structural characterization of the eponymous OXA-51 β-lactamase. Kinetic studies show that OXA-51 has low catalytic efficiency for carbapenems, primarily due to the low affinity of the enzyme for these substrates. Structural studies demonstrate that this low affinity results from the obstruction of the enzyme active site by the side chain of Trp222, which presents a transient steric barrier to an incoming carbapenem substrate. The Trp222Met substitution relieves this steric hindrance and elevates the affinity of the mutant enzyme for carbapenems by 10-fold, significantly increasing the levels of resistance to these antibiotics. The ability of OXA-51 to evolve into a robust carbapenemase as the result of a single amino acid substitution may, in the near future, elevate the ubiquitous enzymes of the OXA-51 family to the status of the most deleterious A. baumannii carbapenemases, with dire clinical consequences.
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Affiliation(s)
- Clyde A. Smith
- Stanford
Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025, United States
| | - Nuno Tiago Antunes
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nichole K. Stewart
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Hilary Frase
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Marta Toth
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Katherine A. Kantardjieff
- College
of Science and Mathematics, California State University, San Marcos, California 92078, United States
| | - Sergei Vakulenko
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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20
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A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. Genome Biol 2015. [PMID: 26195261 PMCID: PMC4507327 DOI: 10.1186/s13059-015-0701-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference genome, limiting our understanding of gene order and content. A consensus representation of multiple genomes will provide a better framework for comparison. A large-scale comparative study will identify genomic determinants associated with their diversity and adaptation as a successful pathogen. Results We determine draft-level genomic sequence of 50 diverse military isolates and conduct the largest bacterial pan-genome analysis of 249 genomes. The pan-genome of A. baumannii is open when the input genomes are normalized for diversity with 1867 core proteins and a paralog-collapsed pan-genome size of 11,694 proteins. We developed a novel graph-based algorithm and use it to assemble the first consensus pan-chromosome, identifying both the order and orientation of core genes and flexible genomic regions. Comparative genome analyses demonstrate the existence of novel resistance islands and isolates with increased numbers of resistance island insertions over time, from single insertions in the 1950s to triple insertions in 2011. Gene clusters responsible for carbon utilization, siderophore production, and pilus assembly demonstrate frequent gain or loss among isolates. Conclusions The highly variable and dynamic nature of the A. baumannii genome may be the result of its success in rapidly adapting to both abiotic and biotic environments through the gain and loss of gene clusters controlling fitness. Importantly, some archaic adaptation mechanisms appear to have reemerged among recent isolates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0701-6) contains supplementary material, which is available to authorized users.
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21
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Zhao WH, Hu ZQ. Acquired metallo-β-lactamases and their genetic association with class 1 integrons and ISCR elements in Gram-negative bacteria. Future Microbiol 2015; 10:873-87. [DOI: 10.2217/fmb.15.18] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT Metallo-β-lactamases (MBLs) can hydrolyze almost all β-lactam antibiotics and are resistant to clinically available β-lactamase inhibitors. Numerous types of acquired MBLs have been identified, including IMP, VIM, NDM, SPM, GIM, SIM, DIM, KHM, TMB, FIM and AIM. IMPs and VIMs are the most frequent MBLs and disseminate in members of the family Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp. Acquired MBL genes are often embedded in integrons, and some are associated with insertion sequence (IS) elements. The class 1 integrons and IS common region (ISCR) elements are usually harbored in transposons and/or plasmids, forming so-called mobile vesicles for horizontal transfer of captured genes between bacteria. Here, we review the MBL superfamily identified in Gram-negative bacteria, with an emphasis on the phylogeny of acquired MBLs and their genetic association with class 1 integrons and IS common region elements.
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Affiliation(s)
- Wei-Hua Zhao
- Department of Microbiology & Immunology, Showa University School of Medicine, 1–5–8 Hatanodai, Shinagawa-ku, Tokyo 142–8555, Japan
| | - Zhi-Qing Hu
- Department of Microbiology & Immunology, Showa University School of Medicine, 1–5–8 Hatanodai, Shinagawa-ku, Tokyo 142–8555, Japan
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22
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Sahuquillo-Arce JM, Hernández-Cabezas A, Yarad-Auad F, Ibáñez-Martínez E, Falomir-Salcedo P, Ruiz-Gaitán A. Carbapenemases: A worldwide threat to antimicrobial therapy. World J Pharmacol 2015; 4:75-95. [DOI: 10.5497/wjp.v4.i1.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/07/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
Carbapenems are potent β-lactams with activity against extended-spectrum cephalosporinases and β-lactamases. These antibiotics, derived from thienamycn, a carbapenem produced by the environmental bacterium Streptomyces cattleya, were initially used as last-resort treatments for severe Gram-negative bacterial infections presenting resistance to most β-lactams but have become an empirical option in countries with high prevalence of Extended Spectrum β-lactamase-producing bacterial infections. Imipenem, the first commercially available carbapenem, was approved for clinical use in 1985. Since then, a wide variety of carbapenem-resistant bacteria has appeared, primarily Enterobacteriaceae such as Escherichia coli or Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa and Acinetobacter baumannii, presenting different resistance mechanisms. The most relevant mechanism is the production of carbapenem-hydrolyzing β-lactamases, also known as carbapenemases. These enzymes also inactivate all known β-lactams, and some of these enzymes can be acquired through horizontal gene transfer. Moreover, plasmids, transposons and integrons harboring these genes typically carry other resistance determinants, rendering the recipient bacteria resistant to almost all currently used antimicrobials, as is the case for K. pneumoniae carbapenemase - or New Delhi metallo-β-lactamases-type enzymes. The recent advent of these enzymes in the health landscape presents a serious challenge. First, the emergence of carbapenemases limits the currently available treatment options; second, these enzymes pose a risk to patients, as some studies have demonstrated high mortality associated with carbapenemase-producing bacterial infections; and third, these circumstances require an extra cost to sanitary systems, which are particularly cumbersome in developing countries. Therefore, emphasis should be placed on the early detection of these enzymes, the prevention of the spread of carbapenemase-producing bacteria and the development of new drugs resistant to carbapenemase hydrolysis.
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23
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Antunes NT, Fisher JF. Acquired Class D β-Lactamases. Antibiotics (Basel) 2014; 3:398-434. [PMID: 27025753 PMCID: PMC4790369 DOI: 10.3390/antibiotics3030398] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/31/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022] Open
Abstract
The Class D β-lactamases have emerged as a prominent resistance mechanism against β-lactam antibiotics that previously had efficacy against infections caused by pathogenic bacteria, especially by Acinetobacter baumannii and the Enterobacteriaceae. The phenotypic and structural characteristics of these enzymes correlate to activities that are classified either as a narrow spectrum, an extended spectrum, or a carbapenemase spectrum. We focus on Class D β-lactamases that are carried on plasmids and, thus, present particular clinical concern. Following a historical perspective, the susceptibility and kinetics patterns of the important plasmid-encoded Class D β-lactamases and the mechanisms for mobilization of the chromosomal Class D β-lactamases are discussed.
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Affiliation(s)
- Nuno T Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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24
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Carbapenem resistance in a human clinical isolate identified to be closely related to Acinetobacter indicus. Int J Antimicrob Agents 2014; 44:345-50. [PMID: 25245212 DOI: 10.1016/j.ijantimicag.2014.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 11/22/2022]
Abstract
Here we report a case of carbapenem resistance in a human clinical isolate that was found to be closely related to the newly described environmental species Acinetobacter indicus. This strain harboured the blaOXA-23 carbapenemase gene located on a conjugative plasmid. Partial sequencing of 16S rDNA and rpoB genes, together with matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) analysis, showed that this strain was distantly related to the Acinetobacter baumannii-calcoaceticus complex and was closely related to A. indicus.
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25
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Transmission electron microscopic morphological study and flow cytometric viability assessment of Acinetobacter baumannii susceptible to Musca domestica cecropin. ScientificWorldJournal 2014; 2014:657536. [PMID: 24883421 PMCID: PMC4032720 DOI: 10.1155/2014/657536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/29/2014] [Accepted: 04/16/2014] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii infections are difficult to treat owing to the extremely limited armamentarium. Expectations about antimicrobial peptides' use as new powerful antibacterial agents have been raised on the basis of their unique mechanism of action. Musca domestica cecropin (Mdc), a novel antimicrobial peptide from the larvae of Housefly (Musca domestica), has potently active against Gram-positive and Gram-negative bacteria standard strain. Here we evaluated the antibacterial activity of Mdc against clinical isolates of MDR-A. baumannii and elucidate the related antibacterial mechanisms. The minimal inhibitory concentration (MIC) of Mdc was 4 μg/mL. Bactericidal kinetics of Mdc revealed rapid killing of A. baumannii (30 min). Flow cytometry using viability stain demonstrated that Mdc causes A. baumannii membrane permeabilization in a concentration- and time-dependent process, which correlates with the bactericidal action. Moreover, transmission electron microscopic (TEM) examination showed that Mdc is capable of disrupting the membrane of bacterial cells, resulting in efflux of essential cytoplasmic components. Overall, Mdc could be a promising antibacterial agent for MDR-A. baumannii infections.
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26
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Bhattacharya M, Toth M, Antunes NT, Smith CA, Vakulenko SB. Structure of the extended-spectrum class C β-lactamase ADC-1 from Acinetobacter baumannii. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:760-71. [PMID: 24598745 PMCID: PMC3949520 DOI: 10.1107/s1399004713033014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/05/2013] [Indexed: 11/10/2022]
Abstract
ADC-type class C β-lactamases comprise a large group of enzymes that are encoded by genes located on the chromosome of Acinetobacter baumannii, a causative agent of serious bacterial infections. Overexpression of these enzymes renders A. baumannii resistant to various β-lactam antibiotics and thus severely compromises the ability to treat infections caused by this deadly pathogen. Here, the high-resolution crystal structure of ADC-1, the first member of this clinically important family of antibiotic-resistant enzymes, is reported. Unlike the narrow-spectrum class C β-lactamases, ADC-1 is capable of producing resistance to the expanded-spectrum cephalosporins, rendering them inactive against A. baumannii. The extension of the substrate profile of the enzyme is likely to be the result of structural differences in the R2-loop, primarily the deletion of three residues and subsequent rearrangement of the A10a and A10b helices. These structural rearrangements result in the enlargement of the R2 pocket of ADC-1, allowing it to accommodate the bulky R2 substituents of the third-generation cephalosporins, thus enhancing the catalytic efficiency of the enzyme against these clinically important antibiotics.
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Affiliation(s)
- Monolekha Bhattacharya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nuno Tiago Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are enzymes of the utmost clinical importance due to their ability to produce resistance to carbapenems, the antibiotics of last resort for the treatment of various life-threatening infections. The vast majority of these enzymes have been identified in Acinetobacter spp., notably in Acinetobacter baumannii. The OXA-2 and OXA-10 enzymes predominantly occur in Pseudomonas aeruginosa and are currently classified as narrow-spectrum class D β-lactamases. Here we demonstrate that when OXA-2 and OXA-10 are expressed in Escherichia coli strain JM83, they produce a narrow-spectrum antibiotic resistance pattern. When the enzymes are expressed in A. baumannii ATCC 17978, however, they behave as extended-spectrum β-lactamases and confer resistance to carbapenem antibiotics. Kinetic studies of OXA-2 and OXA-10 with four carbapenems have demonstrated that their catalytic efficiencies with these antibiotics are in the same range as those of some recognized class D carbapenemases. These results are in disagreement with the classification of the OXA-2 and OXA-10 enzymes as narrow-spectrum β-lactamases, and they suggest that other class D enzymes that are currently regarded as noncarbapenemases may in fact be CHDLs.
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Bonnin RA, Nordmann P, Poirel L. Screening and deciphering antibiotic resistance inAcinetobacter baumannii: a state of the art. Expert Rev Anti Infect Ther 2014; 11:571-83. [DOI: 10.1586/eri.13.38] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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Identification of 50 class D β-lactamases and 65 Acinetobacter-derived cephalosporinases in Acinetobacter spp. Antimicrob Agents Chemother 2013; 58:936-49. [PMID: 24277043 DOI: 10.1128/aac.01261-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing of a collection of 103 Acinetobacter strains belonging to 22 validly named species and another 16 putative species allowed detection of genes for 50 new class D β-lactamases and 65 new Acinetobacter-derived cephalosporinases (ADC). All oxacillinases (OXA) contained the three typical motifs of class D β-lactamases, STFK, (F/Y)GN, and K(S/T)G. The phylogenetic tree drawn from the OXA sequences led to an increase in the number of OXA groups from 7 to 18. The topologies of the OXA and RpoB phylogenetic trees were similar, supporting the ancient acquisition of blaOXA genes by Acinetobacter species. The class D β-lactamase genes appeared to be intrinsic to several species, such as Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter calcoaceticus, and Acinetobacter lwoffii. Neither blaOXA-40/143- nor blaOXA-58-like genes were detected, and their origin remains therefore unknown. The phylogenetic tree analysis based on the alignment of the sequences deduced from blaADC revealed five main clusters, one containing ADC belonging to species closely related to A. baumannii and the others composed of cephalosporinases from the remaining species. No indication of blaOXA or blaADC transfer was observed between distantly related species, except for blaOXA-279, possibly transferred from Acinetobacter genomic species 6 to Acinetobacter parvus. Analysis of β-lactam susceptibility of seven strains harboring new oxacillinases and cloning of the corresponding genes in Escherichia coli and in a susceptible A. baumannii strain indicated very weak hydrolysis of carbapenems. Overall, this study reveals a large pool of β-lactamases in different Acinetobacter spp., potentially transferable to pathogenic strains of the genus.
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Globally expanding carbapenemase finally appears in Spain: nosocomial outbreak of acinetobacter baumannii producing plasmid-encoded OXA-23 in Barcelona, Spain. Antimicrob Agents Chemother 2013; 57:5155-7. [PMID: 23877694 DOI: 10.1128/aac.01486-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Resistance of Acinetobacter baumannii clinical isolates to carbapenems is on the rise worldwide mainly in association with the production of OXA-23. Until recently, however, OXA-23 was absent in Spain. In this work, we report the molecular characterization of a hospital outbreak of OXA-23-producing A. baumannii in Barcelona caused by a multidrug-resistant (MDR) clone belonging to international clone IC-II/sequence type ST85 between October 2010 and May 2011. blaOXA-23 was carried in a plasmid of 90 kb and located within the composite transposon Tn2006.
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Cantón R, Ruiz-Garbajosa P. Acinetobacter baumannii: ¿debemos seguir prestando atención? Enferm Infecc Microbiol Clin 2013; 31:1-3. [DOI: 10.1016/j.eimc.2012.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 08/28/2012] [Indexed: 12/01/2022]
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32
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Zhao WH, Hu ZQ. Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria. Crit Rev Microbiol 2012; 39:79-101. [PMID: 22697133 PMCID: PMC4086240 DOI: 10.3109/1040841x.2012.691460] [Citation(s) in RCA: 203] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CTX-M enzymes, the plasmid-mediated cefotaximases, constitute a rapidly growing family of extended-spectrum β-lactamases (ESBLs) with significant clinical impact. CTX-Ms are found in at least 26 bacterial species, particularly in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. At least 109 members in CTX-M family are identified and can be divided into seven clusters based on their phylogeny. CTX-M-15 and CTX-M-14 are the most dominant variants. Chromosome-encoded intrinsic cefotaximases in Kluyvera spp. are proposed to be the progenitors of CTX-Ms, while ISEcp1, ISCR1 and plasmid are closely associated with their mobilization and dissemination.
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Affiliation(s)
- Wei-Hua Zhao
- Department of Microbiology and Immunology, Showa University School of Medicine, Tokyo, Japan.
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Roca I, Espinal P, Vila-Farrés X, Vila J. The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace. Front Microbiol 2012; 3:148. [PMID: 22536199 PMCID: PMC3333477 DOI: 10.3389/fmicb.2012.00148] [Citation(s) in RCA: 243] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/28/2012] [Indexed: 12/28/2022] Open
Abstract
During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth.
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Affiliation(s)
- Ignasi Roca
- Department of Clinical Microbiology, School of Medicine, IDIBAPS and Barcelona Centre for International Health Research, Hospital Clínic-Universitat de Barcelona Barcelona, Spain
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