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Chung CR, Wang HY, Chou PH, Wu LC, Lu JJ, Horng JT, Lee TY. Towards Accurate Identification of Antibiotic-Resistant Pathogens through the Ensemble of Multiple Preprocessing Methods Based on MALDI-TOF Spectra. Int J Mol Sci 2023; 24:ijms24020998. [PMID: 36674514 PMCID: PMC9865071 DOI: 10.3390/ijms24020998] [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: 11/15/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been used to identify microorganisms and predict antibiotic resistance. The preprocessing method for the MS spectrum is key to extracting critical information from complicated MS spectral data. Different preprocessing methods yield different data, and the optimal approach is unclear. In this study, we adopted an ensemble of multiple preprocessing methods--FlexAnalysis, MALDIquant, and continuous wavelet transform-based methods--to detect peaks and build machine learning classifiers, including logistic regressions, naïve Bayes classifiers, random forests, and a support vector machine. The aim was to identify antibiotic resistance in Acinetobacter baumannii, Acinetobacter nosocomialis, Enterococcus faecium, and Group B Streptococci (GBS) based on MALDI-TOF MS spectra collected from two branches of a referral tertiary medical center. The ensemble method was compared with the individual methods. Random forest models built with the data preprocessed by the ensemble method outperformed individual preprocessing methods and achieved the highest accuracy, with values of 84.37% (A. baumannii), 90.96% (A. nosocomialis), 78.54% (E. faecium), and 70.12% (GBS) on independent testing datasets. Through feature selection, important peaks related to antibiotic resistance could be detected from integrated information. The prediction model can provide an opinion for clinicians. The discriminative peaks enabling better prediction performance can provide a reference for further investigation of the resistance mechanism.
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Affiliation(s)
- Chia-Ru Chung
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
- Ph.D. Program in Biomedical Engineering, Chang Gung University, Taoyuan 333323, Taiwan
| | - Po-Han Chou
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 320317, Taiwan
| | - Li-Ching Wu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 320317, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan 333323, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 333323, Taiwan
| | - Jorng-Tzong Horng
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
- Correspondence: (J.-T.H.); (T.-Y.L.)
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Correspondence: (J.-T.H.); (T.-Y.L.)
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Casarotta E, Bottari E, Vannicola S, Giorgetti R, Domizi R, Carsetti A, Damiani E, Scorcella C, Gabbanelli V, Pantanetti S, Marini B, Donati A, Adrario E. Antibiotic Treatment of Acinetobacter baumannii Superinfection in Patients With SARS-CoV-2 Infection Admitted to Intensive Care Unit: An Observational Retrospective Study. Front Med (Lausanne) 2022; 9:910031. [PMID: 35721097 PMCID: PMC9203965 DOI: 10.3389/fmed.2022.910031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/18/2022] [Indexed: 12/17/2022] Open
Abstract
Introduction In COVID-19 patients on mechanical ventilation, VAP from Acinetobacter baumannii remains a crucial risk factor for death. Antibiotic resistance represents an important problem in treating this infection. This study aims to describe the evolution of the superinfection from PDR Acinetobacter baumannii in patients with acute respiratory failure from SARS-CoV-2 infection admitted to ICU and compare the impact of two different antibiotic strategies on microbiological negativization. Methods Single-center observational retrospective study, including patients admitted to our ICU from March 2020 to May 2021 for acute respiratory failure from SARS-CoV-2 infection who developed PDR Acinetobacter baumannii superinfection. Clinical data at ICU admission were collected, as well as the timing of isolation of Acinetobacter baumannii, its resistance profile, the site of infection, and the antibiotic therapy. Results Of the 32 patients enrolled, 10 patients (31.2%) were treated with the combination of high-dose ampicillin/sulbactam, high-dose tigecycline, intravenous and inhaled colistin (Protocol), the other 22 (68.8%) were treated with the combination of two antibiotics (Control). Of the 10 patients in the Protocol group, 8 patients (80%) received also fosfomycin. All patients (100%) in the Protocol group had microbiological negativization, while in the Control group microbiological negativization was observed in 8 (36.4%) patients, p < 0.01. Conclusion Our report shows microbiological negativization in all patients treated with the combination therapy of nebulized and intravenous colistin, high-dose tigecycline, and high-dose ampicillin/sulbactam. This combination of antibiotics seems to be a useful alternative when other treatments are not available or fail.
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Affiliation(s)
- Erika Casarotta
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Elisa Bottari
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Sara Vannicola
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Rachele Giorgetti
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Roberta Domizi
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Andrea Carsetti
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Elisa Damiani
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Claudia Scorcella
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Vincenzo Gabbanelli
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Simona Pantanetti
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Benedetto Marini
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Abele Donati
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
| | - Erica Adrario
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria “Ospedali Riuniti”, Ancona, Italy
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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Choudhury SD. Nano-Medicines a Hope for Chagas Disease! Front Mol Biosci 2021; 8:655435. [PMID: 34141721 PMCID: PMC8204082 DOI: 10.3389/fmolb.2021.655435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chagas disease, is a vector-mediated tropical disease whose causative agent is a parasitic protozoan named Trypanosoma cruzi. It is a very severe health issue in South America and Mexico infecting millions of people every year. Protozoan T. cruzi gets transmitted to human through Triatominae, a subfamily of the Reduviidae, and do not have any effective treatment or preventative available. The lack of economic gains from this tropical parasitic infection, has always been the reason behind its negligence by researchers and drug manufacturers for many decades. Hence there is an enormous requirement for more efficient and novel strategies to reduce the fatality associated with these diseases. Even, available diagnosis protocols are outdated and inefficient and there is an urgent need for rapid high throughput diagnostics as well as management protocol. The current advancement of nanotechnology in the field of healthcare has generated hope for better management of many tropical diseases including Chagas disease. Nanoparticulate systems for drug delivery like poloxamer coated nanosuspension of benzimidazole have shown promising results in reducing toxicity, elevating efficacy and bioavailability of the active compound against the pathogen, by prolonging release, thereby increasing the therapeutic index. Moreover, nanoparticle-based drug delivery has shown promising results in inducing the host’s immune response against the pathogen with very few side effects. Besides, advances in diagnostic assays, such as nanosensors, aided in the accurate detection of the parasite. In this review, we provide an insight into the life cycle stages of the pathogen in both vertebrate host and the insect vector, along with an overview of the current therapy for Chagas disease and its limitations; nano carrier-based delivery systems for antichagasic agents, we also address the advancement of nano vaccines and nano-diagnostic techniques, for treatment of Chagas disease, majorly focusing on the novel perspectives in combating the disease.
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Bagudo AI, Obande GA, Harun A, Singh KKB. Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex. ASIAN BIOMED 2020; 14:177-186. [PMID: 37551265 PMCID: PMC10373397 DOI: 10.1515/abm-2020-0026] [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] [Indexed: 08/09/2023]
Abstract
Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.
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Affiliation(s)
- Ahmad Ibrahim Bagudo
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Godwin Attah Obande
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
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Lima WG, Brito JCM, da Cruz Nizer WS. Ventilator-associated pneumonia (VAP) caused by carbapenem-resistant Acinetobacter baumannii in patients with COVID-19: Two problems, one solution? Med Hypotheses 2020; 144:110139. [PMID: 32758905 PMCID: PMC7833701 DOI: 10.1016/j.mehy.2020.110139] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 01/22/2023]
Affiliation(s)
- William Gustavo Lima
- Researcher of the Group (CNPq) for Epidemiological, Economic and Pharmacological Studies of Arboviruses (EEPIFARBO), Brazil; Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
| | - Júlio César Moreira Brito
- Researcher of the Group (CNPq) for Epidemiological, Economic and Pharmacological Studies of Arboviruses (EEPIFARBO), Brazil; Ezequiel Dias Foundation (FUNED), Belo Horizonte, MG, Brazil
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Lima WG, Brito JCM, Cardoso BG, Cardoso VN, de Paiva MC, de Lima ME, Fernandes SOA. Rate of polymyxin resistance among Acinetobacter baumannii recovered from hospitalized patients: a systematic review and meta-analysis. Eur J Clin Microbiol Infect Dis 2020; 39:1427-1438. [PMID: 32533271 DOI: 10.1007/s10096-020-03876-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/23/2020] [Indexed: 01/08/2023]
Abstract
We conducted a systematic review and meta-analysis to determine the rate of polymyxin resistance among Acinetobacter baumannii isolates causing infection in hospitalized patients around the world during the period of 2010-2019. The systematic review was performed on September 1, 2019, using PubMed/MEDLINE, Scopus, and Web of Science; studies published after January 1, 2010, were selected. The data were summarized in tables, critically analyzed, and treated statistically using the RStudio® Software with Meta package and Metaprop Command. After applying exclusion factors, 41 relevant studies were selected from 969 articles identified on literature search. The overall rate of polymyxin-resistant A. baumannii (PRAB) related to hospitalized patients was estimated to be 13% (95% CI, 0.06-0.27), where a higher rate was observed in America (29%; 95% CI, 0.12-0.55), followed by Europe (13%; 95% CI, 0.02-0.52), and Asia (10%; 95% CI, 0.02-0.32). The extensive use of polymyxins on veterinary to control bacterial infection and growth promotion, as well as the resurgence in prescription and use of polymyxins in the clinics against carbapenem-resistant gram-negative bacteria, may have contributed to the increased incidence of PRAB. The findings of this meta-analysis revealed that the rate of PRAB recovered from hospitalized patients is distinctively high. Thus, action needs to be taken to develop strategies to combat the clinical incidence of PRAB-induced hospital infections.
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Affiliation(s)
- William Gustavo Lima
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil. .,Laboratório de Diagnóstico Laboratorial e Microbiologia Clínica, Campus Centro-Oeste/Dona Lindu, Universidade Federal de São João del-Rei, Rua Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-293, Brazil.
| | - Júlio César Moreira Brito
- Fundação Ezequiel Dias (FUNED), Belo Horizonte, MG, Brazil.,Programa de Pós-Graduação em Inovação Tecnológica e Biofarmacêutica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bárbara Gatti Cardoso
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Valbert Nascimento Cardoso
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Magna Cristina de Paiva
- Laboratório de Diagnóstico Laboratorial e Microbiologia Clínica, Campus Centro-Oeste/Dona Lindu, Universidade Federal de São João del-Rei, Rua Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-293, Brazil
| | - Maria Elena de Lima
- Programa de Pós-Graduação em Inovação Tecnológica e Biofarmacêutica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Ensino e Pesquisa, Santa Casa-Belo Horizonte, Belo Horizonte, Brazil
| | - Simone Odília Antunes Fernandes
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Lima WG, Silva Alves GC, Sanches C, Antunes Fernandes SO, de Paiva MC. Carbapenem-resistant Acinetobacter baumannii in patients with burn injury: A systematic review and meta-analysis. Burns 2019; 45:1495-1508. [DOI: 10.1016/j.burns.2019.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/09/2019] [Accepted: 07/03/2019] [Indexed: 12/25/2022]
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Abstract
Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of blaOXA-51-like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex. Acinetobacter species are considered to be one of the most important pathogens and associated with increased mortality. The species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex have emerged as high priority pathogens, especially in intensive care units, thereby posing a challenge to infection management practices. However, identification of Acinetobacter to the species level is difficult. Clear differentiation among various Acinetobacter species with available standard biochemical methods and automated systems is challenging. Although various molecular methods are available, they are not regularly used in diagnostic laboratories. The advantages and disadvantages of different methods useful in the accurate identification of Acinetobacter species are discussed in this review.
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Hrenovic J, Seruga Music M, Durn G, Dekic S, Hunjak B, Kisic I. Carbapenem-Resistant Acinetobacter baumannii Recovered from Swine Manure. Microb Drug Resist 2019; 25:725-730. [DOI: 10.1089/mdr.2018.0087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Jasna Hrenovic
- Division of Biology, Department of Microbiology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Martina Seruga Music
- Division of Biology, Department of Microbiology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Goran Durn
- Department of Mineralogy, Petrology and Mineral Resources, Faculty of Mining, Geology and Petroleum Engineering, University of Zagreb, Zagreb, Croatia
| | - Svjetlana Dekic
- Division of Biology, Department of Microbiology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Blazenka Hunjak
- Department of Bacteriology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Ivica Kisic
- Department of General Agronomy, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Hrenovic J, Ivankovic T, Durn G, Dekic S, Kazazic S, Kisic I. Presence of carbapenem-resistant bacteria in soils affected by illegal waste dumps. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2019; 29:154-163. [PMID: 30230363 DOI: 10.1080/09603123.2018.1522423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
The carbapenem-resistant bacteria (CRB) are currently at the top of the WHO priority list of bacteria that pose the greatest threat to human health. Considering that soil is one of the important environments for the emergence of antibiotic-resistant bacteria, we isolated and quantified cultivable CRB in soils across Croatia, including ones affected by illegal dumps.We cultivated CRB at two temperatures, distinguishing between the intrinsically resistant CRB (37°C, mostly Stenotrophomonas spp.) and the ones that are presumably human-associated and clinically relevant (42°C, Acinetobacter sp., Enterobacteriaceae, Burkholderia spp.). Our study demonstrated that distinguishing between the two offers a better insight into the diversity of CRB in the environment. The ones cultivated at 37°C were found in almost all soil samples, while the presumably clinically relevant ones were absent from uncontaminated pasture and grassland, indicating that human-associated CRB are unlikely to be found in soils spared from anthropogenic influence.
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Affiliation(s)
- Jasna Hrenovic
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Goran Durn
- Faculty of Mining, Geology and Petroleum Engineering, University of Zagreb, Zagreb, Croatia
| | | | - Snjezana Kazazic
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivica Kisic
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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A Prospective Study of Acinetobacter baumannii Complex Isolates and Colistin Susceptibility Monitoring by Mass Spectrometry of Microbial Membrane Glycolipids. J Clin Microbiol 2019; 57:JCM.01100-18. [PMID: 30567747 DOI: 10.1128/jcm.01100-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/13/2018] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is a prevalent nosocomial pathogen with a high incidence of multidrug resistance. Treatment of infections due to this organism with colistin, a last-resort antibiotic of the polymyxin class, can result in the emergence of colistin-resistant strains. Colistin resistance primarily occurs via modifications of the terminal phosphate moieties of lipopolysaccharide-derived lipid A, which reduces overall membrane electronegativity. These modifications are readily identified by mass spectrometry (MS). In this study, we prospectively collected Acinetobacter baumannii complex clinical isolates from a hospital system in Pennsylvania over a 3-year period. All isolates were evaluated for colistin resistance using standard MIC testing by both agar dilution and broth microdilution, as well as genospecies identification and lipid A profiling using MS analyses. Overall, an excellent correlation between colistin susceptibility and resistance, determined by MIC testing, and the presence of a lipid A modification, determined by MS, was observed with a sensitivity of 92.9% and a specificity of 94.0%. Additionally, glycolipid profiling was able to differentiate A. baumannii complex organisms based on their membrane lipids. With the growth of MS use in clinical laboratories, a reliable MS-based glycolipid phenotyping method that identifies colistin resistance in A. baumannii complex clinical isolates, as well as other Gram-negative organisms, represents an alternative or complementary approach to existing diagnostics.
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Teixeira AM, Nemec A, Sousa C. Differentiation of Taxonomically Closely Related Species of the Genus Acinetobacter Using Raman Spectroscopy and Chemometrics. Molecules 2019; 24:molecules24010168. [PMID: 30621147 PMCID: PMC6337300 DOI: 10.3390/molecules24010168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022] Open
Abstract
In recent years, several efforts have been made to develop quick and low cost bacterial identification methods. Genotypic methods, despite their accuracy, are laborious and time consuming, leaving spectroscopic methods as a potential alternative. Mass and infrared spectroscopy are among the most reconnoitered techniques for this purpose, with Raman having been practically unexplored. Some species of the bacterial genus Acinetobacter are recognized as etiological agents of nosocomial infections associated with high rates of mortality and morbidity, which makes their accurate identification important. The goal of this study was to assess the ability of Raman spectroscopy to discriminate between 16 Acinetobacter species belonging to two phylogroups containing taxonomically closely related species, that is, the Acinetobacter baumannii-Acinetobacter calcoaceticus complex (six species) and haemolytic clade (10 species). Bacterial spectra were acquired without the need for any sample pre-treatment and were further analyzed with multivariate data analysis, namely partial least squares discriminant analysis (PLSDA). Species discrimination was achieved through a series of sequential PLSDA models, with the percentage of correct species assignments ranging from 72.1% to 98.7%. The obtained results suggest that Raman spectroscopy is a promising alternative for identification of Acinetobacter species.
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Affiliation(s)
- A Margarida Teixeira
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic.
- Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Šrobárova 50, 100 34 Prague 10, Czech Republic.
| | - Clara Sousa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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Šedo O, Radolfová-Křížová L, Nemec A, Zdráhal Z. Limitations of routine MALDI-TOF mass spectrometric identification of Acinetobacter species and remedial actions. J Microbiol Methods 2018; 154:79-85. [PMID: 30332615 DOI: 10.1016/j.mimet.2018.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/09/2018] [Accepted: 10/13/2018] [Indexed: 11/15/2022]
Abstract
A set of 204 taxonomically well-defined strains belonging to 17 Acinetobacter spp., including 11 recently described species (A. albensis, A. bohemicus, A. colistiniresistens, A. courvalinii. A. dispersus, A. gandensis, A. modestus, A. proteolyticus, A. seifertii, A. variabilis, and A. vivianii) and six species of the so-called haemolytic clade (A. beijerinckii, A. gyllenbergii, A. haemolyticus, A. junii, A. parvus, and A. venetianus), were subjected to MALDI-TOF mass spectrometric profiling. The identification outputs were evaluated using the current version (8.0.0.0) of the commercially available Bruker Daltonics, Biotyper database, which does not contain reference entries for six of the species tested. Up to 29% of the strains were falsely identified as different Acinetobacter spp. present in the Biotyper database, resulting mostly from the close phylogenetic relationship of species of the haemolytic clade. To obtain more reliable identification, extending the commercial database showed only partial improvement, while the use of an alternative MALDI matrix solution (strongly acidified ferulic acid) allowed correct identification of nearly all problematic strains.
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Affiliation(s)
- Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Lenka Radolfová-Křížová
- Laboratory of Bacterial Genetics, National Institute of Public Health, Šrobárova 48, 10042 Prague, Czech Republic
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Šrobárova 48, 10042 Prague, Czech Republic; Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Higgins PG, Hrenovic J, Seifert H, Dekic S. Characterization of Acinetobacter baumannii from water and sludge line of secondary wastewater treatment plant. WATER RESEARCH 2018; 140:261-267. [PMID: 29723815 DOI: 10.1016/j.watres.2018.04.057] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/13/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
The elimination of potentially pathogenic bacteria in wastewater treatment plants (WWTPs) attracts much attention in public health. Reports on the occurrence of the emerging hospital pathogen Acinetobacter baumannii in wastewaters do not include a continuous monitoring at all WWTP stages. The objective of this study was to characterize A. baumannii recovered from the water and sludge line of the secondary WWTP in Zagreb, Croatia over the period of one year. Recovery of A. baumannii was performed using CHROMagar Acinetobacter plates. Antimicrobial susceptibility testing was performed with broth microdilution and results interpreted using EUCAST breakpoints for clinical isolates of A. baumannii. Molecular characterization was performed by WGS and cgMLST. The secondary WWTP treating the urban wastewater is constantly receiving viable A. baumannii along with genes encoding carbapenem resistance, and emitting them via effluent into the environment. Furthermore, A. baumannii from influent are incorporated into activated sludge flocs in aeration basin. A. baumannii can survive the technological process of anaerobic mesophilic sludge digestion, and is finally destroyed in alkaline lime-treated stabilized sludge. The majority (102/119) of A. baumannii isolates were carbapenem-resistant, while antibiotic-susceptible isolates (17/119) were rarely recovered from all WWTP stages. Carbapenem-resistant isolates belonged to international clonal lineage IC2 carrying OXA-23 and IC1 carrying OXA-72, while the susceptible isolates belonged to IC5 or were unclustered. Increased resistance to antibiotics, together with the appearance of carbapenem- and even pandrug-resistant isolates in effluent as compared to influent wastewater, suggests the need of additional disinfection of effluent prior to its discharge into the natural recipient.
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Affiliation(s)
- Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jasna Hrenovic
- Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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Silva L, Mourão J, Grosso F, Peixe L. Uncommon carbapenemase-encoding plasmids in the clinically emergent Acinetobacter pittii. J Antimicrob Chemother 2018; 73:52-56. [PMID: 29069366 DOI: 10.1093/jac/dkx364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/07/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives Two carbapenemase-carrying plasmids, pLS488 (blaOXA-23) and pLS535 (blaOXA-58) from Acinetobacter pittii clinical isolates, were characterized in this study, including their ability to be transferred to Acinetobacter baumannii. Methods The clinical isolates were obtained from drainage fluid of a patient with biliary tract cancer and from an exudate of a patient with a hip infection (Portuguese University Hospital, 2012). Isolate characterization included antimicrobial susceptibility tests, carbapenemase production by Blue-Carba, carbapenem-hydrolysing class D β-lactamase (CHDL) gene search by PCR sequencing, ApaI-PFGE, CHDL genetic location and plasmid size by hybridization and WGS. Plasmid transfer was performed by conjugation or electroporation. Results pLS488 constitutes the first conjugative plasmid reported to carry a carbapenem resistance gene in A. pittii and is part of a potential new incompatibility group that might also account for the dissemination of OXA-23 in A. baumannii. pLS535 belongs to the Acinetobacter GR7 incompatibility group and presents a new scaffold for OXA-58. This plasmid lacked the machinery for conjugation, but was transferable by electroporation to A. baumannii. Both isolates, which displayed the same PFGE pattern, represent the first report of CHDL-carrying A. pittii in Portuguese hospitals. Conclusions Altogether, these results emphasize the importance of A. pittii, or particular A. pittii clones, as a source of resistance genes, facilitating their dissemination among different bacterial species.
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Affiliation(s)
- Liliana Silva
- UCIBIO/REQUIMTE Departamento de Ciências Biológicas Laboratório de Microbiologia Faculdade de Farmácia Universidade do Porto, Porto, Portugal.,ESALD, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal.,FEUP Faculdade de Engenharia da Universidade do Porto, Porto, Portugal
| | - Joana Mourão
- UCIBIO/REQUIMTE Departamento de Ciências Biológicas Laboratório de Microbiologia Faculdade de Farmácia Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE Departamento de Ciências Biológicas Laboratório de Microbiologia Faculdade de Farmácia Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE Departamento de Ciências Biológicas Laboratório de Microbiologia Faculdade de Farmácia Universidade do Porto, Porto, Portugal
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Hrenovic J, Durn G, Music MS, Dekic S, Troskot-Corbic T, Skoric D. Extensively and multi drug-resistant Acinetobacter baumannii recovered from technosol at a dump site in Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:1049-1055. [PMID: 28724243 DOI: 10.1016/j.scitotenv.2017.07.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/09/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
In a karst pit above City of Rijeka in Croatia the hazardous industrial waste was continuously disposed from 1955 to 1990, and later it was periodically used as an illegal dump site. The surface part of a technosol at the edge of dump was analysed mineralogically, geochemically and bacteriologically. From the technosol rich in petroleum hydrocarbons and heavy metals three isolates of Acinetobacter baumannii were recovered. Isolates from technosol shared many features that are previously described for clinically isolates: the affiliation to IC1 and 2, multi-drug resistant (MDR) or extensively drug-resistant (XDR) antibiotic resistance profile, carbapenem resistance mediated by blaOXA72 and blaOXA23 genes, and the expression of virulence factors. In in vitro conditions, isolates were able to survive in contact with technosol during 58days of monitoring. The most probable source of A. baumannii in technosol was the illegally disposed hospital waste. Proper management and disposal of human solid waste is mandatory to prevent the spread of clinically important A. baumannii in nature.
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Affiliation(s)
- Jasna Hrenovic
- University of Zagreb, Faculty of Science, Zagreb, Croatia
| | - Goran Durn
- University of Zagreb, Faculty of Mining, Geology and Petroleum Engineering, Croatia.
| | | | | | | | - Dijana Skoric
- University of Zagreb, Faculty of Science, Zagreb, Croatia
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18
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Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
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Seruga Music M, Hrenovic J, Goic-Barisic I, Hunjak B, Skoric D, Ivankovic T. Emission of extensively-drug-resistant Acinetobacter baumannii from hospital settings to the natural environment. J Hosp Infect 2017; 96:323-327. [DOI: 10.1016/j.jhin.2017.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
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Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study. J Clin Microbiol 2017; 55:2480-2490. [PMID: 28592553 PMCID: PMC5527427 DOI: 10.1128/jcm.01744-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/28/2017] [Indexed: 01/11/2023] Open
Abstract
In recent years, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has become the standard for routine bacterial species identification due to its rapidity and low costs for consumables compared to those of traditional DNA-based methods. However, it has been observed that strains of some bacterial species, such as Acinetobacter baumannii strains, cannot be reliably identified using mass spectrometry (MS). Raman spectroscopy is a rapid technique, as fast as MALDI-TOF, and has been shown to accurately identify bacterial strains and species. In this study, we compared hierarchical clustering results for MS, genomic, and antimicrobial susceptibility test data to hierarchical clustering results from Raman spectroscopic data for 31 A. baumannii clinical isolates labeled according to their pulsed-field gel electrophoresis data for strain differentiation. In addition to performing hierarchical cluster analysis (HCA), multiple chemometric methods of analysis, including principal-component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), were performed on the MS and Raman spectral data, along with a variety of spectral preprocessing techniques for best discriminative results. Finally, simple HCA algorithms were performed on all of the data sets to explore the relationships between, and natural groupings of, the strains and to compare results for the four data sets. To obtain numerical comparison values of the clustering results, the external cluster evaluation criteria of the Rand index of the HCA dendrograms were calculated. With a Rand index value of 0.88, Raman spectroscopy outperformed the other techniques, including MS (with a Rand index value of 0.58).
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Goic-Barisic I, Seruga Music M, Kovacic A, Tonkic M, Hrenovic J. Pan Drug-Resistant Environmental Isolate of Acinetobacter baumannii from Croatia. Microb Drug Resist 2017; 23:494-496. [DOI: 10.1089/mdr.2016.0229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ivana Goic-Barisic
- Department of Clinical Microbiology, University of Split School of Medicine, Split, Croatia
- University Hospital Centre Split, Split, Croatia
| | - Martina Seruga Music
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ana Kovacic
- Institute of Public Health of Split and Dalmatia County, Split, Croatia
| | - Marija Tonkic
- Department of Clinical Microbiology, University of Split School of Medicine, Split, Croatia
- University Hospital Centre Split, Split, Croatia
| | - Jasna Hrenovic
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Rapid detection of high-risk Enterococcus faecium clones by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Diagn Microbiol Infect Dis 2017; 87:299-307. [DOI: 10.1016/j.diagmicrobio.2016.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/07/2016] [Accepted: 12/11/2016] [Indexed: 12/18/2022]
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23
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Silva AS, Quintelas C, Ferreira EC, Lopes JA, Sousa C. Exploiting intrinsic fluorescence spectroscopy to discriminate between Acinetobacter calcoaceticus–Acinetobacter baumannii complex species. RSC Adv 2017. [DOI: 10.1039/c6ra27531a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spectroscopy for bacterial typing purposes. Instrisinc fluorescence versus FTIR-ATR and MALDI-TOF MS.
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Affiliation(s)
- Ana Sofia Silva
- CEB-Centre of Biological Engineering
- University of Minho
- Braga
- Portugal
| | | | | | - João A. Lopes
- Research Institute for Medicines (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Clara Sousa
- LAQV/REQUIMTE
- Departamento de Ciências Químicas
- Faculdade de Farmácia
- Universidade do Porto
- 4050-313 Porto
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Bianco A, Quirino A, Giordano M, Marano V, Rizzo C, Liberto MC, Focà A, Pavia M. Control of carbapenem-resistant Acinetobacter baumannii outbreak in an intensive care unit of a teaching hospital in Southern Italy. BMC Infect Dis 2016; 16:747. [PMID: 27955639 PMCID: PMC5154034 DOI: 10.1186/s12879-016-2036-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/15/2016] [Indexed: 12/27/2022] Open
Abstract
Background Acinetobacter baumannii is an opportunistic pathogen that has become a major cause of concern, since it is a frequent cause of healthcare-associated infections (HAIs). The aim of the study was to describe the occurrence, the management and the control of an outbreak that occurred in an intensive care unit (ICU) of a teaching hospital in Southern Italy caused by multiple strains of extensively drug-resistant A. baumannii (XDRAB). Methods Case-patient was defined as a patient with an healthcare-associated infection caused by an XDRAB isolate identified in a clinically significant culture. Environmental samples were collected from different surfaces. The isolates were identified by typical Gram stain morphology, using the Vitek 2 system (bioMérieux, France) and by MALDI-TOF MS mass spectrometry (bioMèrieux, France). Genotyping was performed through rep-PCR analysis. Results A patient presented an XDRAB ventilator-associated pneumonia at admission and was managed with strict isolation precautions until discharge. Five patients had a ventilator-associated pneumonia and two had a central line-associated bloodstream infection. Of the environmental samples, 1 sample obtained from the side of the bed of an infected patient yielded growth of XDRAB. Infection control measures were adopted. Rep-PCR analysis identified four patterns. Conclusions The integration of epidemiological and microbiological data and the application of infection control measures were crucial to bring such an outbreak to a rapid halt. The distinctive characteristic of this study was the complex molecular pattern of the outbreak, which subsided in a short period of time due to adherence to infection-control measures, confirming the fundamental role of molecular typing in the comprehension of outbreaks dynamics and of integrated control interventions for the interruption of epidemic events. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2036-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aida Bianco
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Angela Quirino
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Mariavalentina Giordano
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Vito Marano
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Claudia Rizzo
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Maria Carla Liberto
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Alfredo Focà
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy
| | - Maria Pavia
- Department of Health Sciences, University of Catanzaro "Magna Græcia", 88100, Catanzaro, Italy.
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MALDI-TOF/MS identification of species from the Acinetobacter baumannii (Ab) group revisited: inclusion of the novel A. seifertii and A. dijkshoorniae species. Clin Microbiol Infect 2016; 23:210.e1-210.e9. [PMID: 27919649 DOI: 10.1016/j.cmi.2016.11.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Rapid identification of Acinetobacter species is critical as members of the A. baumannii (Ab) group differ in antibiotic susceptibility and clinical outcomes. A. baumannii, A. pittii, and A. nosocomialis can be identified by MALDI-TOF/MS, while the novel species A. seifertii and A. dijkshoorniae cannot. Low identification rates for A. nosocomialis also have been reported. We evaluated the use of MALDI-TOF/MS to identify isolates of A. seifertii and A. dijkshoorniae and revisited the identification of A. nosocomialis to update the Bruker taxonomy database. METHODS Species characterization was performed by rpoB-clustering and MLSA. MALDI-TOF/MS spectra were recovered from formic acid/acetonitrile bacterial extracts overlaid with α-cyano-4-hydroxy-cinnamic acid matrix on a MicroflexLT in linear positive mode and 2000-20 000 m/z range mass. Spectra were examined with the ClinProTools v2.2 software. Mean spectra (MSP) were created with the BioTyper software. RESULTS Seventy-eight Acinetobacter isolates representative of the Ab group were used to calculate the average spectra/species and generate pattern recognition models. Species-specific peaks were identified for all species, and MSPs derived from three A. seifertii, two A. dijkshoorniae, and two A. nosocomialis strains were added to the Bruker taxonomy database, allowing successful identification of all isolates using spectra from either bacterial extracts or direct colonies, resulting in a positive predictive value (PPV) of 99.6% (777/780) and 96.8% (302/312), respectively. CONCLUSIONS The use of post-processing data software identified statistically significant species-specific peaks to generate reference signatures for rapid accurate identification of species within the Ab group, providing relevant information for the clinical management of Acinetobacter infections.
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Goic-Barisic I, Hrenovic J, Kovacic A, Musić MŠ. Emergence of Oxacillinases in Environmental Carbapenem-Resistant Acinetobacter baumannii Associated with Clinical Isolates. Microb Drug Resist 2016; 22:559-563. [DOI: 10.1089/mdr.2015.0275] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ivana Goic-Barisic
- Department of Clinical Microbiology, University Hospital Centre Split, Split, Croatia
- University of Split School of Medicine, Split, Croatia
| | - Jasna Hrenovic
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ana Kovacic
- Institute of Public Health of Split and Dalmatia County, Split, Croatia
| | - Martina Šeruga Musić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Sanguinetti M, Posteraro B. Mass spectrometry applications in microbiology beyond microbe identification: progress and potential. Expert Rev Proteomics 2016; 13:965-977. [DOI: 10.1080/14789450.2016.1231578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy
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28
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Montaña S, Schramm STJ, Traglia GM, Chiem K, Parmeciano Di Noto G, Almuzara M, Barberis C, Vay C, Quiroga C, Tolmasky ME, Iriarte A, Ramírez MS. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer. PLoS One 2016; 11:e0161528. [PMID: 27548264 PMCID: PMC4993456 DOI: 10.1371/journal.pone.0161528] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/08/2016] [Indexed: 02/08/2023] Open
Abstract
Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.
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Affiliation(s)
- Sabrina Montaña
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Sareda T. J. Schramm
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - German Matías Traglia
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Kevin Chiem
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Gisela Parmeciano Di Noto
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Claudia Barberis
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marcelo E. Tolmasky
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - María Soledad Ramírez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
- * E-mail:
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Cosgaya C, Marí-Almirall M, Van Assche A, Fernández-Orth D, Mosqueda N, Telli M, Huys G, Higgins PG, Seifert H, Lievens B, Roca I, Vila J. Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex mainly recovered from clinical samples in different countries. Int J Syst Evol Microbiol 2016; 66:4105-4111. [PMID: 27432448 DOI: 10.1099/ijsem.0.001318] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent advances in bacterial species identification methods have led to the rapid taxonomic diversification of the genus Acinetobacter. In the present study, phenotypic and molecular methods have been used to determine the taxonomic position of a group of 12 genotypically distinct strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, initially described by Gerner-Smidt and Tjernberg in 1993, that are closely related to Acinetobacter pittii. Strains characterized in this study originated mostly from human samples obtained in different countries over a period of 15 years. rpoB gene sequences and multilocus sequence typing were used for comparisons against 94 strains representing all species included in the ACB complex. Cluster analysis based on such sequences showed that all 12 strains grouped together in a distinct clade closest to Acinetobacter pittiithat was supported by bootstrap values of 99 %. Values of average nucleotide identity based on blast between the genome sequence of strain JVAP01T (NCBI accession no. LJPG00000000) and those of other species from the ACB complex were always <91.2 %, supporting the species status of the group. In addition, the metabolic characteristics of the group matched those of the ACB complex and the analysis of their protein signatures by matrix-assisted laser desorption ionization time-of-flight MS identified some specific peaks. Our results support the designation of these strains as representing a novel species, for which the name Acinetobacter dijkshoorniae sp. nov. is proposed. The type strain is JVAP01T (=CECT 9134T=LMG 29605T).
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Affiliation(s)
- Clara Cosgaya
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Marta Marí-Almirall
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Sint-Katelijne-Waver, Belgium
| | - Dietmar Fernández-Orth
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Noraida Mosqueda
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Murat Telli
- Department of Clinical Microbiology, School of Medicine, Adnan Menderes University, Aydin, Turkey
| | - Geert Huys
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, Germany
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Sint-Katelijne-Waver, Belgium
| | - Ignasi Roca
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Department of Clinical Microbiology and ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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30
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Hrenovic J, Goic-Barisic I, Kazazic S, Kovacic A, Ganjto M, Tonkic M. Carbapenem-resistant isolates of Acinetobacter baumannii in a municipal wastewater treatment plant, Croatia, 2014. Euro Surveill 2016; 21:30195. [DOI: 10.2807/1560-7917.es.2016.21.15.30195] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/14/2016] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is an emerging hospital pathogen. Whereas A. baumannii isolated from patients or hospitals has been reported, there are few data regarding propagation of viable A. baumannii in the natural environment. This study investigates the occurrence and antimicrobial susceptibility of viable A. baumannii in municipal wastewater and its persistence through the wastewater treatment process. A total of 21 A. baumannii isolates were recovered at a secondary type of municipal wastewater treatment plant in Zagreb, Croatia: 15 from raw influent wastewater and six from final effluent. All isolates were carbapenem- and multidrug-resistant. Among 14 isolates tested for bla
OXA genes, all harboured the constitutive bla
OXA-51-like gene, while the acquired bla
OXA-23-like and bla
OXA-40-like genes were found in 10 and three isolates respectively. Six A. baumannii isolates recovered from effluent wastewater multiplied and survived in sterilised effluent wastewater up to 50 days. These findings support the idea that multidrug-resistant A. baumannii can occur and have the ability to survive in the environment.
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Affiliation(s)
- Jasna Hrenovic
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia
| | - Ivana Goic-Barisic
- University Hospital Centre Split, Department of Clinical Microbiology and University of Split School of Medicine, Split, Croatia
| | - Snjezana Kazazic
- Ruđer Boskovic Institute, Division of Physical Chemistry, Zagreb, Croatia
| | - Ana Kovacic
- Institute of Public Health of Split and Dalmatia County, Split, Croatia
| | - Marin Ganjto
- Zagreb Wastewater - Management and Operation Ltd., Zagreb, Croatia
| | - Marija Tonkic
- University Hospital Centre Split, Department of Clinical Microbiology and University of Split School of Medicine, Split, Croatia
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31
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van Belkum A, Chatellier S, Girard V, Pincus D, Deol P, Dunne WM. Progress in proteomics for clinical microbiology: MALDI-TOF MS for microbial species identification and more. Expert Rev Proteomics 2015; 12:595-605. [DOI: 10.1586/14789450.2015.1091731] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Pailhoriès H, Daure S, Eveillard M, Joly-Guillou ML, Kempf M. Using Vitek MALDI-TOF mass spectrometry to identify species belonging to the Acinetobacter calcoaceticus–Acinetobacter baumannii complex: a relevant alternative to molecular biology? Diagn Microbiol Infect Dis 2015. [DOI: 10.1016/j.diagmicrobio.2015.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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33
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Insufficient Discriminatory Power of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Dendrograms to Determine the Clonality of Multi-Drug-Resistant Acinetobacter baumannii Isolates from an Intensive Care Unit. BIOMED RESEARCH INTERNATIONAL 2015; 2015:535027. [PMID: 26101775 PMCID: PMC4458526 DOI: 10.1155/2015/535027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/27/2015] [Indexed: 12/16/2022]
Abstract
While pulsed-field gel electrophoresis (PFGE) is recognized as the gold standard method for clonality analysis, MALDI-TOF MS has recently been spotlighted as an alternative tool for species identification. Herein, we compared the dendrograms of multi-drug-resistant (MDR) Acinetobacter baumannii isolates by using MALDI-TOF MS with those by using PFGE. We used direct colony and protein extraction methods for MALDI-TOF MS dendrograms. The isolates with identical PFGE patterns were grouped into different branches in MALDI-TOF MS dendrograms. Among the isolates that were classified as very close isolates in MALDI-TOF MS dendrogram, PFGE band patterns visually showed complete differences. We numeralized similarity among isolates by measuring distance levels. The Spearman rank correlation coefficient values were 0.449 and 0.297 between MALDI-TOF MS dendrogram using direct colony and protein extraction method versus PFGE, respectively. This study is the first paper focusing solely on the dendrogram function of MALDI-TOF MS compared with PFGE. Although MALDI-TOF MS is a promising tool to identify species in a rapid manner, our results showed that MALDI-TOF MS dendrograms could not substitute PFGE for MDR Acinetobacter baumannii clonality analysis.
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34
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Sousa C, Botelho J, Grosso F, Silva L, Lopes J, Peixe L. Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions. Front Microbiol 2015; 6:481. [PMID: 26042113 PMCID: PMC4436932 DOI: 10.3389/fmicb.2015.00481] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/01/2015] [Indexed: 11/13/2022] Open
Abstract
MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) is now in the forefront for routine bacterial species identification methodologies, being its value for clonality assessment controversial. In this work we evaluated the potential of MALDI-TOF MS for assisting infection control by depicting Acinetobacter baumannii clones. Mass spectra of 58 A. baumannii clinical isolates belonging to the worldwide spread lineages (ST98, ST103, ST208, and ST218) isolated in our country, were obtained and analyzed with several chemometric tools (pseudo gel views, peakfind function, and partial least squares discriminant analysis). The clonal lineages were obtained using the “Oxford” scheme, belonging ST98, ST208, and ST218 to the international clone II and ST103 to an epidemic clonal lineage (SG5). Additionally, mass spectra of a highly diverse international collection of 38 isolates belonging to 22 sequence types (STs) were obtained for further comparisons. Pseudo gel views and direct peak pattern analysis did not allow the discrimination of A. baumannii isolates belonging to ST98, ST103, ST208, or ST218. Moreover, a partial least square discriminant analysis of the mass spectra considering two spectral ranges (2–20 kDa and 4–10 kDa) revealed a poor degree of discrimination with only 64.6 and 65.8% of correct ST assignments, respectively. Also, mass spectra of the international isolates (n = 38, 22STs) revealed a very congruent peak pattern among them as well as among the four lineages included in this work. Despite the increasing interest of MALDI-TOF MS for bacterial typing at different taxonomical levels, we demonstrated, using routine experimental conditions, the unsuitability of this methodology for A. baumannii clonal discrimination.
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Affiliation(s)
- Clara Sousa
- Centro de Engenharia Biológica, Universidade do Minho Braga, Portugal
| | - João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - Liliana Silva
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - João Lopes
- Departamento de Farmácia Galénica e Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
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35
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Awad F, Ramprasath C, Mathivanan N, Aruna PR, Ganesan S. Optical Fiber-Based Steady State and Fluorescence Lifetime Spectroscopy for Rapid Identification and Classification of Bacterial Pathogens Directly from Colonies on Agar Plates. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:430412. [PMID: 27379265 PMCID: PMC4897486 DOI: 10.1155/2014/430412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/09/2014] [Indexed: 11/17/2022]
Abstract
Fluorescence spectroscopy was examined as a potential technique for identification and classification of bacterial pathogens. Colonies of Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella typhi, and Klebsiella pneumoniae on agar plates were measured directly using a laboratory spectrofluorimeter coupled with optical fiber. Steady state fluorescence spectra were collected following excitation at 280 nm (tryptophan) and 380 nm (NADH). Results showed that fluorescence lifetime decays of tryptophan at 280 nm excitation from the four organisms were best described with triexponential fit and it reveals the existence of different protein conformation. The emission spectroscopy of the four bacteria at 380 nm excitation (NADH) provided better classification (100% of original grouped cases correctly classified and 98.1% of cross-validated grouped cases correctly classified) than that of 280 nm excitation (tryptophan). Our results demonstrated that optical fiber-based fluorescence identification and classification of bacteria is rapid, easy to perform, and of low cost compared to standard methods.
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Affiliation(s)
- Fathi Awad
- Department of Medical Physics, Anna University, Chennai 600025, India; Department of Medical Physics, Red Sea University, P.O. Box 24, Port Sudan, Sudan
| | | | | | - Prakasa Rao Aruna
- Department of Medical Physics, Anna University, Chennai 600025, India
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