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Lellouche J, Keren-Paz A, Rov R, Efrati Epchtien R, Frenk S, Hameir A, Temkin E, Schwartz D, Carmeli Y. Carbapenem-resistant Acinetobacter baumannii carrier detection: a simple and efficient protocol. Microbiol Spectr 2024; 12:e0406223. [PMID: 38426764 PMCID: PMC10986532 DOI: 10.1128/spectrum.04062-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Timely detection of carbapenem-resistant Acinetobacter baumannii (CRAB) carriers is essential to direct infection control measures. In this work, we aimed to develop a practical protocol to detect CRAB from screening samples. To choose a selective medium that detects CRAB with high sensitivity and specificity, 111 A. baumannii clinical isolates were inoculated on three types of agar: mSuperCARBA (SC), CHROMagar Acinetobacter (CaA), and modified CHROMagar Acinetobacter (mCaA) containing 4.5 mg/mL meropenem. SC was non-selective, CaA was the most sensitive (100%), but only moderately specific (72%), and mCaA was highly specific (97%) and sensitive (98%). Confirmation of the carbapenem-resistant phenotype using PCR-based detection of blaOXA-23, blaOXA-24, and blaOXA-58 genes was specific but not sensitive, detecting only 58% of CRAB isolates. Identification of A. baumannii using either gyrB or blaOXA-51 PCR was excellent. Next, we used the same methodology in routine screening for CRAB carriage. mCaA had the best yield, with high sensitivity but moderate specificity to differentiate between CRAB and other carbapenem-resistant organisms. Skin sampling using sponges and 6 hour enrichment was highly sensitive (98%), while other body sites had poor sensitivity (27%- 41%). Shorter incubation had slightly lower yield, and longer incubation did not improve the detection. Performing PCR for blaOXA-51 and gyrB on colonies growing on modified mCaA differentiated between CRAB and other species with high accuracy (98% and 99%, respectively). Based on our results, we present a procedure for easy and reliable detection of CRAB carriage using skin sampling, short enrichment, selection on mCaA, and PCR-based identification. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAB) is a substantial cause of nosocomial infections, classified among the most significant multidrug-resistant pathogens by the World Health Organization and by the US Centers for Disease Control. Limiting the spread of CRAB is an important goal of infection control, but laboratory methods for identification of CRAB carriers are not standardized. In this work, we compared different selective agar plates, tested the efficiency of A. baumannii identification by PCR for species-specific genes, and used PCR-based detection of common resistance genes to confirm the carbapenem-resistant phenotype. During a prospective study, we also determined the optimal sample enrichment time. Based on our results, we propose a simple and efficient protocol for the detection of CRAB carriage using skin sampling, short enrichment, selection on appropriate agar plates, and PCR-based identification, resulting in a turn-around time of 24 hours.
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Affiliation(s)
- Jonathan Lellouche
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Alona Keren-Paz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Reut Rov
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Reut Efrati Epchtien
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Sammy Frenk
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Amichay Hameir
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Elizabeth Temkin
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - David Schwartz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
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Wang L, Liu R, Yan F, Chen W, Zhang M, Lu Q, Huang B, Liu R. A newly isolated intestinal bacterium involved in the C-ring cleavage of flavan-3-ol monomers and the antioxidant activity of the metabolites. Food Funct 2024; 15:580-590. [PMID: 37927225 DOI: 10.1039/d3fo03601d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Flavan-3-ols are an important class of secondary metabolites in many plants. Their bioavailability and bioactivity are largely determined by the metabolism of intestinal microbiota. However, little is known about the intestinal bacteria involved in the metabolism of flavan-3-ols and the activities of the metabolites. C-ring cleavage is the initial and key step in the metabolism of flavan-3-ol monomers. Here, we isolated a strain from porcine cecum content, which is capable of cleaving the heterocyclic C-ring to form 1-(3',4'-dihydroxyphenyl)-3-(2'',4'',6''-trihydroxyphenyl)propan-2-ol from (+)-catechin and (-)-epicatechin, and 1-(3',4',5'-trihydroxyphenyl)-3-(2'',4'',6''-trihydroxyphenyl) propan-2-ol from (-)-epigallocatechin. The strain was identified as Streptococcus pasteurianus (Streptococcus gallolyticus subsp. Pasteurianus, designated as F32-1) based on 16S rDNA similarity and MALDI-TOF-MS identification. The formation of the C-ring cleavage structural unit by the F32-1 strain enhanced the chemical antioxidant ability and altered the cellular antioxidant activity of (+)-catechin, (-)-epicatechin and (-)-epigallocatechin. Overall, in this study we isolated a new intestinal bacterium involved in the C-ring cleavage of flavan-3-ol monomers and elucidated the bioactivity of their metabolites.
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Affiliation(s)
- Li Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
| | - Ruonan Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
| | - Fangfang Yan
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
| | - Wanbing Chen
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guang Dong 430073, China
| | - Mo Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
| | - Qun Lu
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, China
| | - Bijun Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
| | - Rui Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wu Han 430000, China.
- Wuhan Engineering Research Center of Bee Products on Quality and Safety Control, Wu Han 430000, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, P. R. China
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Krishnaraj A, Gupta P, Bhatia M, Omar BJ. Role of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry for Species Identification of Acinetobacter Strains. J Lab Physicians 2023; 15:336-343. [PMID: 37564221 PMCID: PMC10411205 DOI: 10.1055/s-0042-1760401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Introduction Acinetobacter species has become a leading cause of nosocomial infections in recent years. Objectives The aim of the study was to establish the usefulness of matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of Acinetobacter species with respect to conventional biochemical methods and MicroScan WalkAway 96 Plus system and to compare the antibiotic susceptibility test results Kirby-Bauer disk diffusion method with MicroScan WalkAway 96 Plus automated identification and antimicrobial susceptibility testing system. Materials and Methods The study sample comprised 100 clinical isolates of Acinetobacter species. They were all identified using MALDI-TOF MS and compared with other two identification systems. Statistical Analysis Comparison of categorical variables by Fisher's exact test or Pearson's chi-square test was done. All statistical tools were two tailed, and a significant level p < 0.05 was used. All statistical tests were performed using SPSS v22.0 (Armonk IBM Corp., New York, United States). Cohen's kappa coefficients were also calculated and used as applicable. Results MALDI-TOF MS revealed 92 A. baumannii , 2 Acinetobacter nosocomialis , 3 Acinetobacter lwoffii , and 1 each was identified as Acinetobacter junii , Acinetobacter johnsonii , and Acinetobacter tandoii . There was moderate agreement between identification by MicroScan WalkAway and MALDI-TOF, and substantial agreement between conventional biochemical tests and MALDI-TOF. We found that there was a 100% categorical agreement with respect to susceptibility of aminoglycosides (amikacin, gentamicin, tobramycin) and cephalosporins (ceftazidime, cefepime, cefotaxime) between disk diffusion method and MicroScan WalkAway 96 Plus system. Total of 16 errors were observed. Conclusion Although MALDI-TOF MS could be useful to identify A. baumannii but not other species in the genus, it is a rapid, reliable method and can be routinely used in clinical laboratories.
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Affiliation(s)
- Anusha Krishnaraj
- Department of Microbiology, St John's Medical College, Bengaluru, Karnataka, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences, Deoghar, Jharkhand, India
| | - Mohit Bhatia
- Department of Microbiology, All India Institute of Medical Sciences, Deoghar, Jharkhand, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Deoghar, Jharkhand, India
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Manfredi E, Rocca MF, Zintgraff J, Irazu L, Miliwebsky E, Carbonari C, Deza N, Prieto M, Chinen I. Rapid and accurate detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 by mass spectrometry directly from the isolate, using 10 potential biomarker peaks and machine learning predictive models. J Med Microbiol 2023; 72. [PMID: 37130048 DOI: 10.1099/jmm.0.001675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Introduction. The different pathotypes of Escherichia coli can produce a large number of human diseases. Surveillance is complex since their differentiation is not easy. In particular, the detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 consists of stool culture of a diarrhoeal sample on enriched and/or selective media and identification of presumptive colonies and confirmation, which require a certain level of training and are time-consuming and expensive.Hypothesis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a quick and easy way to obtain the protein spectrum of a microorganism, identify the genus and species, and detect potential biomarker peaks of certain characteristics.Aim. To verify the usefulness of MALDI-TOF MS to rapidly identify and differentiate STEC O157 : H7 from other E. coli pathotypes.Methodology. The direct method was employed, and the information obtained using Microflex LT platform-based analysis from 60 clinical isolates (training set) was used to detect differences between the peptide fingerprints of STEC O157 : H7 and other E. coli strains. The protein profiles detected laid the foundations for the development and evaluation of machine learning predictive models in this study.Results. The detection of potential biomarkers in combination with machine learning predictive models in a new set of 142 samples, called 'test set', achieved 99.3 % (141/142) correct classification, allowing us to distinguish between the isolates of STEC O157 : H7 and the other E. coli group. Great similarity was also observed with respect to this last group and the Shigella species when applying the potential biomarkers algorithm, allowing differentiation from STEC O157 : H7Conclusion. Given that STEC O157 : H7 is the main causal agent of haemolytic uremic syndrome, and based on the performance values obtained in the present study (sensitivity=98.5 % and specificity=100.0 %), the implementation of this technique provides a proof of principle for MALDI-TOF MS and machine learning to identify biomarkers to rapidly screen or confirm STEC O157 : H7 versus other diarrhoeagenic E. coli in the future.
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Affiliation(s)
- Eduardo Manfredi
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - María Florencia Rocca
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Jonathan Zintgraff
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Lucía Irazu
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Elizabeth Miliwebsky
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Carolina Carbonari
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Natalia Deza
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Monica Prieto
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Isabel Chinen
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
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Chukamnerd A, Singkhamanan K, Chongsuvivatwong V, Palittapongarnpim P, Doi Y, Pomwised R, Sakunrang C, Jeenkeawpiam K, Yingkajorn M, Chusri S, Surachat K. Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand. Comput Struct Biotechnol J 2022; 20:545-558. [PMID: 36284706 PMCID: PMC9582705 DOI: 10.1016/j.csbj.2021.12.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/25/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the blaOXA-23 gene, while certain isolates harbored the blaNDM-1 or blaIMP-14 genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., armA, aph(6)-Id, and aph(3″)-Ib), fosfomycin resistance gene (abaF), and tetracycline resistance genes (tet(B) and tet(39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the ompA, adeF, pgaA, lpxA, and bfmR genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology, Fujita Health University, Aichi, Japan
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Mingkwan Yingkajorn
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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Vargas JM, Moreno Mochi MP, López CG, Alarcón JA, Acosta N, Soria K, Nuñez JM, Villafañe S, Ramacciotti J, Del Campo R, Jure MA. [Impact of an active surveillance program and infection control measures on the incidence of carbapenem-resistant Gram-negative bacilli in an intensive care unit]. Rev Argent Microbiol 2021; 54:134-142. [PMID: 34088536 DOI: 10.1016/j.ram.2021.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 03/11/2021] [Accepted: 03/28/2021] [Indexed: 11/30/2022] Open
Abstract
Hospital-acquired infections caused by carbapenem-resistant Gram-negative bacteria (CRGNB) have been increasingly reported worldwide and are associated with high rates of mortality especially in intensive care units(ICUs). Early identification through rectal surveillance cultures and implementation of infection control measures(ICM) including contact precautions, staff education on cleaning and hand hygiene may reduce the spread of these microorganisms. The aim of this work was to assess the impact of enhanced ICM on CRGNB colonization and to describe the molecular epidemiology of these bacteria in a polyvalent ICU in a tertiary level hospital. A prospective study including audits and active surveillance culture program, with molecular characterization, was conducted before and after the implementation of prevention programs and infection control measures. Microbiological screening was performed in chromogenic media; PCR targeting β-lactamases genes (blaKPC, blaNDM, blaVIM and blaOXA-48, blaSHV and blaCTX-M), molecular typing by PFGE; and MLST in K. pneumoniae were performed. CRGNB colonization was reduced from 16.92% to 9.67% upon implementing the infection control measures. In K. pneumoniae the most frequent carbapenemase type was KPC-2 associated with SHV-2 and CTX-M-15, and was disseminated in various STs (ST17, ST13, ST2256, ST353); there was no persistence of particular clones and virulence factors showed no association with hypervirulence. IMP-1 carbapenemase predominated in A. baumannii and the PFGE analysis individualized 3 clusters, assuming that the dissemination in the ICU was clonal. The early detection of patients colonized with CRBGN by using epidemiological surveillance cultures and the implementation of prophylactic measures are key to reducing the incidence of these microorganisms.
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Affiliation(s)
- Juan Martín Vargas
- Laboratorio de Bacteriología Certificado, Cátedra de Bacteriología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina.
| | - María Paula Moreno Mochi
- Laboratorio de Bacteriología Certificado, Cátedra de Bacteriología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
| | - Carolina Graciela López
- Laboratorio de Bacteriología Certificado, Cátedra de Bacteriología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
| | - Janet Alejandra Alarcón
- Laboratorio de Bacteriología Certificado, Cátedra de Bacteriología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
| | - Nancy Acosta
- Unidad de cuidados intensivos 1 (UCI1), Hospital Ángel Cruz Padilla, San Miguel de Tucumán, Tucumán, Argentina
| | - Karina Soria
- Departamento de Infectología, Hospital Ángel Cruz Padilla, San Miguel de Tucumán, Tucumán, Argentina
| | - Juan Manuel Nuñez
- Departamento de Infectología, Hospital Ángel Cruz Padilla, San Miguel de Tucumán, Tucumán, Argentina
| | - Sandra Villafañe
- Departamento de Infectología, Hospital Ángel Cruz Padilla, San Miguel de Tucumán, Tucumán, Argentina
| | - Jorge Ramacciotti
- Unidad de cuidados intensivos 1 (UCI1), Hospital Ángel Cruz Padilla, San Miguel de Tucumán, Tucumán, Argentina
| | - Rosa Del Campo
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, España
| | - María Angela Jure
- Laboratorio de Bacteriología Certificado, Cátedra de Bacteriología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
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7
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Wang J, Wang H, Cai K, Yu P, Liu Y, Zhao G, Chen R, Xu R, Yu M. Evaluation of three sample preparation methods for the identification of clinical strains by using two MALDI-TOF MS systems. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4696. [PMID: 33421261 PMCID: PMC7900945 DOI: 10.1002/jms.4696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 05/07/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the microbial identification, especially in the clinical microbiology laboratories. However, although numerous studies on the identification of microorganisms by MALDI-TOF MS have been reported previously, few studies focused on the effect of pretreatment on identification. Due to the sensitivity of MALDI-TOF MS, different preparation methods will lead to changes in microbial protein fingerprints. In this study, for evaluating a more appropriate preparation method for the clinical microbiology identification, we analyzed the performance of three sample preparation methods on two different MALDI-TOF MS systems. A total of 321 clinical isolates, 127 species, were employed in the comparative study of three different sample preparation methods including the direct colony transfer method (DCTM), the on-target extraction method (OTEM), and the in-tube extraction method (ITEM) compatible with MALDI-TOF MS. All isolates were tested on the Microflex LT and Autof ms1000 devices. The spectra were analyzed using the Bruker biotyper and the Autof ms1000 systems. The results were confirmed by 16/18S rRNA sequencing. Results reveal that the accuracies of isolates identification by Bruker biotyper successfully identified 83.8%, 96.0%, and 95.3% after performing the DCTM, OTEM, and ITEM, respectively, while the Autof ms1000 identified 97.5%, 100%, and 99.7%. These data suggested that the identification rates are comparable among the three preparation methods using the Autof ms1000 and Bruker microflex LT systems but the OTEM is more suitable and necessary for clinical application, owing to its key advantages of simplicity and accuracy.
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Affiliation(s)
- Jinghua Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Hualiang Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Keya Cai
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Peijuan Yu
- Department of Clinical LaboratorySecond Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yajuan Liu
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Gaoling Zhao
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Rong Chen
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Rong Xu
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Maowen Yu
- Department of Clinical LaboratoryJintang First People's HospitalChengduChina
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8
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Acinetobacter baumannii as a community foodborne pathogen: Peptide mass fingerprinting analysis, genotypic of biofilm formation and phenotypic pattern of antimicrobial resistance. Saudi J Biol Sci 2020; 28:1158-1166. [PMID: 33424412 PMCID: PMC7783781 DOI: 10.1016/j.sjbs.2020.11.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 01/02/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common Gram-negative pathogens that represent a major threat to human life. Because the prevalence of Multidrug-resistant biofilm-forming A. baumannii is increasing all over the world, this may lead to outbreaks of hospital infections. Nonetheless, the role of raw meat as a reservoir for A. baumannii remains unclear. Here our research was aimed to exhibit the frequency, precise identification, and genotyping of biofilm-related genes as well as antimicrobial resistance of A. baumannii isolates of raw meat specimens. Fifty-five A. baumannii strains were recovered from 220 specimens of different animal meat and then identified by Peptide Mass Fingerprinting Technique (PMFT). All identified isolates were genotyped by the qPCR method for the existence of biofilm-related genes (ompA, bap, blaPER-1, csuE, csgA, and fimH). In addition, the antimicrobial resistance against A. baumannii was detected by the Kirby-Bauer method. Based on our findings, the frequency rate of 55 A. baumannii isolates was 46.55%, 32.50%, 15.00%, and 9.68% of sheep, chicken, cow, and camel raw meat samples, respectively. The PMFT was able to identify all strains by 100%. the percentages of csuE, ompA, blaPER-1, bap, and csgA genes in biofilm and non-biofilm producer A. baumannii were 72.73%, 60%, 58.2%, 52.74%, and 25.45%, respectively. In contrast, the fimH was not detected in all non-biofilm and biofilm producer strains. The ompA, bap, blaPER-1, csgA were detected only in biofilm-producing A. baumannii isolates. The maximum degree of resistance was observed against amoxicillin/clavulanic acid (89.10%), gentamicin (74.55%), tetracycline (72.73%), ampicillin (65.45%), and tobramycin (52.73%). In conclusion, our investigation demonstrated the high incidence of multi-drug resistant A. baumannii in raw meat samples, with a high existence of biofilm-related virulence genes of ompA, bap, blaPER-1, csgA. Therefore, it has become necessary to take the control measures to limit the development of A. baumannii.
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Ruiz de Alegría-Puig C, De-Malet-Pintos-Fonseca A, Angulo-López I, Agüero-Balbín J, Marco F, Cayô R, Roca I, Vila J, Martínez-Martínez L. Evaluation of Vitek-MS™ and Microflex LT™ commercial systems for identification of Acinetobacter calcoaceticus-baumannii complex. Enferm Infecc Microbiol Clin 2020; 39:9-13. [PMID: 32307128 DOI: 10.1016/j.eimc.2020.02.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Acinetobacter is a genus that comprises a group of opportunistic pathogens responsible for a variety of nosocomial infections. The Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex includes some species of clinical importance, mainly A. baumannii, A. pittii and A. nosocomialis, which share phenotypic similarities that make it very difficult to distinguish between them using a phenotypic approach. The aim of this study was to evaluate two commercial matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems for the identification of different Acinetobacter species, with a special focus among those belonging to the Acb complex. METHODS One hundred and fifty-six Acinetobacter spp. clinical strains, identified by amplified ribosomal DNA restriction analysis (ARDRA) and rpoB gene sequencing, were analysed by two different MALDI-TOF systems. RESULTS Considering only the 144 strains of the Acb complex evaluated in this study, the Vitek-MS™ and Microflex LT™ systems correctly identified 129 (89.6%) and 143 (99.3%) strains, respectively. CONCLUSION After analysing 156 strains belonging to Acinetobacter spp., both Vitek-MS™ and Microflex LT™ proved to be rapid and accurate systems for the identification of Acb complex species showing a good correlation. However, both manufacturers should improve their databases to include new species in them.
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Affiliation(s)
| | | | - Itziar Angulo-López
- Microbiology Service, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Jesús Agüero-Balbín
- Microbiology Service, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain; Department of Molecular Biology, School of Medicine, University of Cantabria, Santander, Spain
| | - Francesc Marco
- ISGlobal, Hospital Clinic - Universitat de Barcelona, Barcelona, Spain; Department of Clinical Microbiology. Hospital Clinic-Universitat de Barcelona, Spain
| | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Inmunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Inmunologia - Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, SP, Brazil; Universidade Federal de São Paulo - UNIFESP, Laboratório Alerta, Disciplina de Infectología, Departamento de Medicina, Escola Paulista de Medicina - EPM, São Paulo, SP, Brazil
| | - Ignasi Roca
- ISGlobal, Hospital Clinic - Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- ISGlobal, Hospital Clinic - Universitat de Barcelona, Barcelona, Spain; Department of Clinical Microbiology. Hospital Clinic-Universitat de Barcelona, Spain
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofia, Cordoba, Spain; Department of Microbiology, University of Cordoba, Cordoba, Spain; Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Spain
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Kumar S, Singhal L, Ray P, Gautam V. In vitro and in vivo fitness of clinical isolates of carbapenem-resistant and -susceptible Acinetobacter baumannii. Indian J Med Microbiol 2020; 38:52-57. [PMID: 32719209 DOI: 10.4103/ijmm.ijmm_19_468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Context Acinetobacter baumannii is one among the leading nosocomial pathogens in the healthcare settings worldwide. Limited data on relative fitness and virulence of carbapenem-resistant A. baumannii (CRAB) are known. New methods are required to curb the rapidly rising antimicrobial resistance of this bug. Aims We aimed to study the comparative in vitro and in vivo fitness of clinical isolates of CRAB and carbapenem-susceptible A. baumannii (CSAB). Settings and Design A total of nine A. baumannii isolates were included in this study. CSAB ATCC-19606 was taken as a reference control strain. Subjects and Methods Matrix-assisted laser desorption ionisation-time of flight mass spectrometry and gyrB and blaOXA-51PCR were used for species identification. Antimicrobial susceptibility was performed using Kirby-Bauer disk-diffusion method. Minimum inhibitory concentration for carbapenems (imipenem, meropenem and doripenem) was determined using agar dilution method. End point analysis, competitive index (CI), growth kinetics and generation time were determined for CRAB and CSAB isolates. In vivo fitness of CRAB and CSAB was determined using Caenorhabditis elegans host model. Multilocus sequence typing was performed to see the genetic relatedness of the isolates under study. Results End point analysis, in vitro CI and growth kinetics experiments showed better fitness of clinical isolates of CRAB over CSAB ones. In vivo'nematode fertility assay' using C. elegans also supported the in vitro results. Conclusions To the best of our knowledge, this is the first study of its kind from India showing difference in fitness of clinical isolates of CRAB and CSAB.
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Affiliation(s)
- Sunil Kumar
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh; Department of Biotechnology, Maharishi Markandeshwar Deemed to be University, Mullana (Ambala), Haryana, India
| | - Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Sector -12, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikas Gautam
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Askari N, Momtaz H, Tajbakhsh E. Prevalence and phenotypic pattern of antibiotic resistance of Acinetobacter baumannii isolated from different types of raw meat samples in Isfahan, Iran. Vet Med Sci 2019; 6:147-153. [PMID: 31576672 PMCID: PMC7036315 DOI: 10.1002/vms3.199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 02/02/2023] Open
Abstract
Resistant Acinetobacter baumannii isolates are not only known as opportunistic nosocomial bacteria but may also be regarded as emerging bacterial contaminants in foods of animal origins. The present investigation was done to assess the prevalence and antibiotic resistance pattern of A. baumannii isolated from different types of raw meat samples. One hundred and ninety-four raw meat samples were collected and cultured for A. baumannii isolates. Culture-positive bacteria were also approved using the loop-mediated isothermal amplification (LAMP) technique. The disc diffusion method was used for antibiotic susceptibility testing. Out of 194 raw meat samples, 39 (20.10%) were positive for A. baumannii isolates. Ovine raw meat was the most commonly contaminated samples (32.14%). All of the culture-positive A. baumannii isolates were also approved using the LAMP assay. A. baumannii isolates harboured the highest prevalence of resistance against gentamicin (87.17%), tetracycline (79.48%), erythromycin (74.35%), azithromycin (66.66%), ciprofloxacin (58.97%), trimethoprim/sulphamethoxazole (56.41%) and rifampin (51.28%). The lowest prevalence of resistance was found against imipenem (17.94%) and chloramphenicol (28.20%). Raw bovine, ovine, caprine, camel and poultry meat samples were considered as the important sources of isolates resistant to some of the categories of antimicrobials used to treat infections caused by A. baumannii. Further studies are required to find the exact role of resistant A. baumannii isolates in the dissemination of antibiotic resistance to human population.
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Affiliation(s)
- Neda Askari
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Elahe Tajbakhsh
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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12
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Askari N, Momtaz H, Tajbakhsh E. Acinetobacter baumannii in sheep, goat, and camel raw meat: virulence and antibiotic resistance pattern. AIMS Microbiol 2019; 5:272-284. [PMID: 31663061 PMCID: PMC6787353 DOI: 10.3934/microbiol.2019.3.272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter genus belongs to a group of Gram-negative coccobacillus. These bacteria are isolated from human and animal origins. Antimicrobial agents play a vital role in treating infectious diseases in both humans and animals, and Acinetobacter in this regard is defined as an organism of low virulence. The current study aimed to evaluate antibiotic resistance properties and virulence factor genes in Acinetobacterbaumannii strains isolated from raw animal meat samples. Fresh meat samples from 124 sheep, 162 goat, and 95 camels were randomly collected from Isfahan and Shahrekord cities in Iran. Most A. baumannii strains isolated from sheep meat samples represented fimH (82.35%), aac(3)-IV (78.43%), sul1 (78.43%) and Integron Class I (96.07%) genes. Moreover, more than 50% of A. baumannii strains isolated from sheep samples were resistant to streptomycin (54.90%), gentamycin (74.50%), co-trimoxazole (70.58%), tetracycline (82.35%), and trimethoprim (62.74%). Current findings revealed significant association between the presence of fimH, cnfI, afa/draBC, dfrA1, sulI, aac(3)-IV genes in sheep samples. Furthermore, significant association was observed between fimH, cnfI, sfa/focDE and dfrA1genes in goat meat samples. In sheep meat samples, significant differences were identified in resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics. Finally, there were statistically significant differences between the incidences of resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics in all strains. In conclusion, the presence of virulence factors and antibiotic resistance in A. baumannii strains isolated from animal meat samples showed that animals should be considered as a potential reservoir of multidrug-resistant A. baumannii.
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Affiliation(s)
- Neda Askari
- Ph.D Student of Microbiology, Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Elahe Tajbakhsh
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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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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Marí-Almirall M, Cosgaya C, Pons MJ, Nemec A, Ochoa TJ, Ruiz J, Roca I, Vila J. Pathogenic Acinetobacter species including the novel Acinetobacter dijkshoorniae recovered from market meat in Peru. Int J Food Microbiol 2019; 305:108248. [PMID: 31226568 DOI: 10.1016/j.ijfoodmicro.2019.108248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/17/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022]
Abstract
Species of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex are important human pathogens which can be recovered from animals and food, potential sources for their dissemination. The aim of the present study was to characterise the Acinetobacter isolates recovered from market meat samples in Peru. From July through August 2012, 138 meat samples from six traditional markets in Lima were cultured in Lysogeny and Selenite broths followed by screening of Gram-negative bacteria in selective media. Bacterial isolates were identified by MALDI-TOF MS and DNA-based methods and assessed for their clonal relatedness and antimicrobial susceptibility. Twelve Acinetobacter isolates were recovered from calf samples. All but one strain were identified as members of the clinically-relevant Acinetobacter calcoaceticus-Acinetobacter baumannii complex: 9 strains as Acinetobacter pittii, 1 strain as A. baumannii, and 1 strain as the recently described novel species A. dijkshoorniae. The remaining strain could not be identified at the species level unambiguously but all studies suggested close relatedness to A. bereziniae. All isolates were well susceptible to antibiotics. Based on macrorestriction analysis, six isolates were further selected and some of them were associated with novel MLST profiles. The presence of pathogenic Acinetobacter species in human consumption meat might pose a risk to public health as potential reservoirs for their further spread into the human population. Nevertheless, the Acinetobacter isolates from meat found in this study were not multidrug resistant and their prevalence was low. To our knowledge, this is also the first time that the A. dijkshoorniae species is reported in Peru.
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Affiliation(s)
- Marta Marí-Almirall
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Cosgaya
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Maria J Pons
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Universidad Científica del Sur, Lima, Peru
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague, Czech Republic; Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Theresa J Ochoa
- Tropical Medicine Institute "Alexander von Humboldt", Universidad Peruana Cayetano Hereida, Lima, Peru
| | - Joaquim Ruiz
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Roca
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
| | - Jordi Vila
- Department of Clinical Microbiology, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Subhadra B, Surendran S, Lim BR, Yim JS, Kim DH, Woo K, Han K, Oh MH, Choi CH. Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102. Genes Genomics 2019; 41:1063-1075. [PMID: 31177378 DOI: 10.1007/s13258-019-00834-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Acinetobacter has emerged recently as one of the most challenging nosocomial pathogens because of its increased rate of antimicrobial resistance. The genetic complexity and genome diversity, as well as the lack of adequate knowledge on the pathogenic determinants of Acinetobacter strains often hinder with pathogenesis studies for the development of better therapeutics to tackle this nosocomial pathogen. OBJECTIVES In this study, we comparatively analyzed the whole genome sequence of a virulent Acinetobacternosocomialis strain NCTC 8102. METHODS The genomic DNA of A. nosocomialis NCTC 8102 was isolated and sequenced using PacBio RS II platform. The sequenced genome was functionally annotated and gene prediction was carried out using the program, Glimmer 3. The phylogenetic analysis of the genome was performed using Mega 6 program and the comparative genome analysis was carried out by BLAST (Basic Local Alignment Search Tool). RESULTS The complete genome analysis depicted that the genome consists of a circular chromosome with an average G + C content of 38.7%. The genome comprises 3700 protein-coding genes, 96 RNA genes (18 rRNA, 74 tRNA and 4 ncRNA genes), and 91 pseudogenes. In addition, 6 prophage regions comprising 2 intact, 1 incomplete and 3 questionable ones and 18 genomic islands were identified in the genome, suggesting the possible occurrence of horizontal gene transfer in this strain. Comparative genome analysis of A. nosocomialis NCTC 8102 genome with the already sequenced A. nosocomialis strain SSA3 showed an average nucleotide identity of 99.0%. In addition, the number of prophages and genomic islands were higher in the A. nosocomialis NCTC 8102 genome compared to that of the strain SSA3. 14 of the genomic islands were unique to A. nosocomialis NCTC 8102 compared to strain SSA3 and they harbored genes which are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. CONCLUSION We sequenced the whole genome of A. nosocomialis strain NCTC 8102 followed by comparatively genome analysis. The study provides valuable information on the genetic features of A. nosocomialis strain and the data from this study would assist in further studies for the development of control measures for this nosocomial pathogen.
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Affiliation(s)
- Bindu Subhadra
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Surya Surendran
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Bo Ra Lim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Jong-Sung Yim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Dong Ho Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Kyungho Woo
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, South Korea.,BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, South Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, South Korea.
| | - Chul Hee Choi
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea.
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Fernández-Cuenca F, Tomás M, Caballero-Moyano FJ, Bou G, Pascual Á. Reporting antimicrobial susceptibilities and resistance phenotypes in Acinetobacter spp: a nationwide proficiency study. J Antimicrob Chemother 2019; 73:692-697. [PMID: 29244131 DOI: 10.1093/jac/dkx464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/07/2017] [Indexed: 01/30/2023] Open
Abstract
Objectives To evaluate the proficiency of Spanish microbiology laboratories with respect to the antimicrobial susceptibility testing (AST) of Acinetobacter spp. Methods Eight Acinetobacter spp. with different resistance mechanisms were sent to 48 Spanish centres which were asked to report: (i) the AST system used; (ii) MICs; (iii) breakpoints used (CLSI versus EUCAST); (iv) clinical category; and (v) resistance mechanisms inferred. Minor, major and very major errors (mE, ME and VME, respectively) were determined. Results The greatest percentages of discrepancies were: (i) by AST method: 18.5% Etest, 14.3% Vitek 2 and Sensititre; (ii) by breakpoints: 20.5% (CLSI) and 10.8% (EUCAST); and (iii) by antimicrobial agent: ampicillin/sulbactam (56.2% CLSI), minocycline (40.7% CLSI), tobramycin (38.7% CLSI, 16.8% EUCAST), imipenem (27.8% CLSI, 30.0% EUCAST) and meropenem (25.4% CLSI, 20.8% EUCAST). Categorical error rates: (i) by AST method ranged from 30.0% (Phoenix) to 100% (Sensititre and disc diffusion) for mE, 0.0% (Etest, Sensititre, disc diffusion) to 40% (Phoenix) for ME, and 0.0% (Sensititre and disc diffusion) to 30% (Phoenix) for VME; (ii) by breakpoints: mE (80.1% CLSI, 58.4% EUCAST), ME (3.5% CLSI, 12.4% EUCAST) and VME (16.4% CLSI, 29.2% EUCAST); and (iii) by antimicrobial agent: mE (100% levofloxacin/CLSI, 100% levofloxacin and meropenem/EUCAST), ME (35.3% colistin/CLSI, 25.0% colistin/EUCAST) and VME (64.7% colistin/CLSI, 86.7% gentamicin/EUCAST). Conclusions Clinical microbiology laboratories must improve their ability to determine antimicrobial susceptibilities of Acinetobacter spp. isolates. Higher discrepancies using CLSI when compared with EUCAST are mainly due to mE and to a much lesser extent to ME or VME.
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Affiliation(s)
- Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBIs), Sevilla, Spain
| | - María Tomás
- Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Francisco-Javier Caballero-Moyano
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Germán Bou
- Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBIs), Sevilla, Spain
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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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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: 10] [Impact Index Per Article: 1.7] [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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Li X, Tang Y, Lu X. Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1546-1553. [PMID: 29633221 DOI: 10.1007/s13361-018-1911-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ2 = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.
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Affiliation(s)
- Xiuyuan Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Legation Street 1#, Beijing, Dongcheng District, 100730, China
| | - Yanyan Tang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Legation Street 1#, Beijing, Dongcheng District, 100730, China
| | - Xinxin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Legation Street 1#, Beijing, Dongcheng District, 100730, China.
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Gautam V, Sharma M, Singhal L, Kumar S, Kaur P, Tiwari R, Ray P. MALDI-TOF mass spectrometry: An emerging tool for unequivocal identification of non-fermenting Gram-negative bacilli. Indian J Med Res 2018; 145:665-672. [PMID: 28948958 PMCID: PMC5644302 DOI: 10.4103/ijmr.ijmr_1105_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been instrumental in revolutionizing microbiological identification, especially in high-throughput laboratories. It has enabled the identification of organisms like non-fermenting Gram-negative bacilli (NFGNB), which has been a challenging task using conventional methods alone. In this study an attempt was made to validate MALDI-TOF MS for the identification of clinical isolates of each of the three most common NFGNB, other than Pseudomonas spp., taking molecular methods as the gold standard. METHODS One hundred and fifty clinical isolates of NFGNB, confirmed by molecular methods such as Acinetobacter baumannii[oxa-51 polymerase chain reaction (PCR)], Burkholderia cepacia complex (expanded multilocus sequence typing) and Stenotrophomonas maltophilia (species-specific PCR), were taken. Isolated colonies from fresh cultures of all 150 isolates were smeared onto ground steel plate, with and without formic acid extraction step. The identification was carried out using MALDI-TOF MS Biotyper database. RESULTS A concordance of 100 and 73.33 per cent was found between the molecular techniques and MALDI-TOF MS system in the identification of these isolates up to genus and species levels, respectively. Using a cut-off of 1.9 for reliable identification, rate of species identification rose to 82.66 per cent. Principal component analysis dendrogram and cluster analysis further increased discrimination of isolates. INTERPRETATION & CONCLUSIONS Our findings showed MALDI-TOF MS-based identification of NFGNB as a good, robust method for high-throughput laboratories.
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Affiliation(s)
- Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Megha Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Lipika Singhal
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Sunil Kumar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Parvinder Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Rupinder Tiwari
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Fernández-Cuenca F, Tomás M, Tormo N, Gimeno C, Bou G, Pascual Á. Reporting identification of Acinetobacter spp genomic species: A nationwide proficiency study in Spain. Enferm Infecc Microbiol Clin 2018; 37:89-92. [PMID: 29605096 DOI: 10.1016/j.eimc.2018.02.004] [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: 12/22/2017] [Revised: 02/01/2018] [Accepted: 02/07/2018] [Indexed: 11/25/2022]
Abstract
Acinetobacter baumannii is the most important genomic species of Acinetobacter from a clinical and epidemiological point of view. Nevertheless, genomic species other than A. baumannii are increasingly recognized as nosocomial pathogens. Molecular methods of identification (genotypic and proteomic assays) are more accurate and reliable and have greater discriminatory power than phenotypic methods. Eleven genomic species of Acinetobacter spp. (8 A. baumannii, 1 A. pittii, 1 A. nosocomialis and 1 A. lwoffii) with different antimicrobial resistance phenotypes and mechanisms of resistance to antimicrobial agents were sent to 48 participating Spanish centers to evaluate their ability for correct identification at the genomic species level. Identification of the genomic species was performed at the two Clinical Microbiology reference laboratories (Hospital Universitario Virgen Macarena, Seville, Spain; and Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain) by partial DNA sequencing of the rpoB gene and MALDI-TOF. The mean percentage of agreement was 76.1%. Fifty percent of CC-01 (A. pittii) and 50% of CC-02 (A. nosocomialis) identification results were reported as A. baumannii. Discrepancies by type of systems used for identification were: MicroScan WA (51.1%), Vitek 2 (19.5%), MALDI-TOF (18.0%), Phoenix (4.5%), Wider (3.8%) and API 20 NE (3.0%). In conclusion, clinical microbiology laboratories must improve their ability to correctly identify the most prevalent non A. baumannii genomic species.
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Affiliation(s)
- Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica y Medicina, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla IBIs, Sevilla, Spain.
| | - María Tomás
- Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Instituto de Investigación Biomédica (INIBIC) , A Coruña, Spain
| | - Nuria Tormo
- Servicio de Microbiología, Hospital General de Valencia, Valencia, Spain
| | - Concha Gimeno
- Servicio de Microbiología, Hospital General de Valencia, Valencia, Spain
| | - Germán Bou
- Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Instituto de Investigación Biomédica (INIBIC) , A Coruña, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica y Medicina, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPIRD12/0015), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla IBIs, Sevilla, Spain
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Comparison of clinical manifestations and antibiotic resistances among three genospecies of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. PLoS One 2018; 13:e0191748. [PMID: 29389980 PMCID: PMC5794090 DOI: 10.1371/journal.pone.0191748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/10/2018] [Indexed: 01/26/2023] Open
Abstract
The Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex has emerged as a high priority among hospital-acquired pathogens in intensive care units (ICUs), posing a challenge to infection management practices. In this study, the clinical characteristics, antimicrobial susceptibility patterns, and patients outcome among genospecies were retrospectively compared. Samples were taken from the tracheal secretions of 143 patients in the ICU. Genospecies of the ACB complex were discriminated by analysis of the 16S-23S rRNA gene intergenic spacer (ITS) sequence. Univariate and multiple variable logistic regression analyses were performed to identify risk factors for infection and mortality. Three genospecies were isolated: A. baumannii (73, 51.0%), A. nosocomialis (29, 20.3%), and A. pittii (41, 28.7%). The results showed that the distribution of infection and colonization among the three genospecies were the same, while A. baumannii was more resistant to common antibiotics than A. nosocomialis and A. pittii. Advanced age, a long stay in the ICU, acute physiology and chronic health evaluation (APACHE) II score, the use of a mechanical ventilator, and previous antibiotic use were risk factors for patient infection. The APACHE II score was a risk factor for mortality in patients with ACB complex isolated from tracheal secretions. Poor outcome of patients with ACB complex isolated from tracheal secretion appears to be related to the APACHE II score rather than genospecies.
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Harding CM, Hennon SW, Feldman MF. Uncovering the mechanisms of Acinetobacter baumannii virulence. Nat Rev Microbiol 2017; 16:91-102. [PMID: 29249812 DOI: 10.1038/nrmicro.2017.148] [Citation(s) in RCA: 541] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acinetobacter baumannii is a nosocomial pathogen that causes ventilator-associated as well as bloodstream infections in critically ill patients, and the spread of multidrug-resistant Acinetobacter strains is cause for concern. Much of the success of A. baumannii can be directly attributed to its plastic genome, which rapidly mutates when faced with adversity and stress. However, fundamental virulence mechanisms beyond canonical drug resistance were recently uncovered that enable A. baumannii and, to a limited extent, other medically relevant Acinetobacter species to successfully thrive in the health-care environment. In this Review, we explore the molecular features that promote environmental persistence, including desiccation resistance, biofilm formation and motility, and we discuss the most recently identified virulence factors, such as secretion systems, surface glycoconjugates and micronutrient acquisition systems that collectively enable these pathogens to successfully infect their hosts.
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Affiliation(s)
- Christian M Harding
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA.,VaxNewMo LLC, St. Louis, Missouri 63108, USA
| | - Seth W Hennon
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA.,VaxNewMo LLC, St. Louis, Missouri 63108, USA
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Genome characterization of two bile-isolated Vibrio fluvialis strains: an insight into pathogenicity and bile salt adaption. Sci Rep 2017; 7:11827. [PMID: 28928424 PMCID: PMC5605694 DOI: 10.1038/s41598-017-12304-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/06/2017] [Indexed: 12/26/2022] Open
Abstract
Vibrio fluvialis is recognized as an emerging pathogen. However, not much is known about the mechanism of its pathogenesis, and its adaptation to a special niche such as the gall bladder. Here we describe two V. fluvialis strains that cause acute cholecystitis. It is noteworthy that both strains were susceptible to all antibiotics tested, which is in contrast to previous studies, suggesting substantial genetic diversity among V. fluvialis isolates. In agreement with their survival and growth in the gall bladder, the genomes of strains 12605 and 3663 contain a considerable number of genes that confer resistance to bile, including toxR, ompU, tolC, cmeABC, rlpB, yrbK, rpoS, damX and gltK. Furthermore, integrative and conjugative elements (ICEs), virulence factors and prophage regions were also detected in strains 12605 and 3663, reflecting their flexibility in recombination during the evolution of pathogenicity. Comparative analysis of nine available genomes of V. fluvialis revealed a core genome consisting of 3,147 genes. Our results highlight the association of V. fluvialis with a rare disease profile and shed light on the evolution of pathogenesis and niche adaptation of V. fluvialis.
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Suttisunhakul V, Pumpuang A, Ekchariyawat P, Wuthiekanun V, Elrod MG, Turner P, Currie BJ, Phetsouvanh R, Dance DAB, Limmathurotsakul D, Peacock SJ, Chantratita N. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species. PLoS One 2017; 12:e0175294. [PMID: 28384252 PMCID: PMC5383291 DOI: 10.1371/journal.pone.0175294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species.
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Affiliation(s)
- Vichaya Suttisunhakul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Apinya Pumpuang
- Department of Clinical Pathology, Faculty of Medicine, Navamindradhiraj University, Bangkok, Thailand
| | - Peeraya Ekchariyawat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mindy G. Elrod
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Zoonotic and Emerging Infectious Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bart J. Currie
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia; Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sharon J. Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Jeong S, Hong JS, Kim JO, Kim KH, Lee W, Bae IK, Lee K, Jeong SH. Identification of Acinetobacter Species Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. Ann Lab Med 2017; 36:325-34. [PMID: 27139605 PMCID: PMC4855052 DOI: 10.3343/alm.2016.36.4.325] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 02/18/2016] [Accepted: 03/04/2016] [Indexed: 01/07/2023] Open
Abstract
Background Acinetobacter baumannii has a greater clinical impact and exhibits higher antimicrobial resistance rates than the non-baumannii Acinetobacter species. Therefore, the correct identification of Acinetobacter species is clinically important. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has recently become the method of choice for identifying bacterial species. The purpose of this study was to evaluate the ability of MALDI-TOF MS (Bruker Daltonics GmbH, Germany) in combination with an improved database to identify various Acinetobacter species. Methods A total of 729 Acinetobacter clinical isolates were investigated, including 447 A. baumannii, 146 A. nosocomialis, 78 A. pittii, 18 A. ursingii, 9 A. bereziniae, 9 A. soli, 4 A. johnsonii, 4 A. radioresistens, 3 A. gyllenbergii, 3 A. haemolyticus, 2 A. lwoffii, 2 A. junii, 2 A. venetianus, and 2 A. genomospecies 14TU. After 212 isolates were tested with the default Bruker database, the profiles of 63 additional Acinetobacter strains were added to the default database, and 517 isolates from 32 hospitals were assayed for validation. All strains in this study were confirmed by rpoB sequencing. Results The addition of the 63 Acinetobacter strains' profiles to the default Bruker database increased the overall concordance rate between MALDI-TOF MS and rpoB sequencing from 69.8% (148/212) to 100.0% (517/517). Moreover, after library modification, all previously mismatched 64 Acinetobacter strains were correctly identified. Conclusions MALDI-TOF MS enables the prompt and accurate identification of clinically significant Acinetobacter species when used with the improved database.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kosin University College of Medicine, Busan, Korea
| | - Jun Sung Hong
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Jung Ok Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Keon Han Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Woonhyoung Lee
- Department of Laboratory Medicine, Kosin University College of Medicine, Busan, Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, College of Medical and Life Science, Shilla University, Busan, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
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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: 59] [Impact Index Per Article: 7.4] [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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Nhu TQ, Park SB, Kim SW, Lee JS, Im SP, Lazarte JMS, Seo JP, Lee WJ, Kim JS, Jung TS. Matrix-assisted laser desorption ionization-time of flight mass spectrometry based identification of Edwardsiella ictaluri isolated from Vietnamese striped catfish (Pangasius hypothalamus). J Vet Sci 2016; 17:377-83. [PMID: 26726022 PMCID: PMC5037306 DOI: 10.4142/jvs.2016.17.3.377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/24/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022] Open
Abstract
Edwardsiella (E.) ictaluri is a major bacterial pathogen that affects commercially farmed striped catfish (Pangasius hypothalamus) in Vietnam. In a previous study, 19 strains of E. ictaluri collected from striped catfish were biochemically identified with an API-20E system. Here, the same 19 strains were used to assess the ability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS; applied using a MALDI Biotyper) to conduct rapid, easy and accurate identification of E. ictaluri. MALDI-TOF MS could directly detect the specific peptide patterns of cultured E. ictaluri colonies with high (> 2.0, indicating species-level identification) scores. MALDI Biotyper 3.0 software revealed that all of the strains examined in this study possessed highly similar peptide peak patterns. In addition, electrophoresis (SDS-PAGE) and subsequent immuno-blotting using a specific chicken antibody (IgY) against E. ictaluri revealed that the isolates had highly similar protein profiles and antigenic banding profiles. The results of this study suggest that E. ictaluri isolated from striped catfish in Vietnam have homologous protein compositions. This is important, because it indicates that MALDI-TOF MS analysis could potentially outperform the conventional methods of identifying E. ictaluri.
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Affiliation(s)
- Truong Quynh Nhu
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Seong Bin Park
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Si Won Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Jung Seok Lee
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Se Pyeong Im
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Jassy Mary S Lazarte
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | | | | | - Jae Sung Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
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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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32
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Yang Q, Rui Y. Two Multiplex Real-Time PCR Assays to Detect and Differentiate Acinetobacter baumannii and Non- baumannii Acinetobacter spp. Carrying blaNDM, blaOXA-23-Like, blaOXA-40-Like, blaOXA-51-Like, and blaOXA-58-Like Genes. PLoS One 2016; 11:e0158958. [PMID: 27391234 PMCID: PMC4938629 DOI: 10.1371/journal.pone.0158958] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 06/26/2016] [Indexed: 01/01/2023] Open
Abstract
Nosocomial infections caused by Acinetobacter spp. resistant to carbapenems are increasingly reported worldwide. Carbapenem-resistant Acinetobacter (CRA) is becoming a serious concern with increasing patient morbidity, mortality, and lengths of hospital stay. Therefore, the rapid detection of CRA is essential for epidemiological surveillance. Polymerase chain reaction (PCR) has been extensively used for the rapid identification of most pathogens. In this study, we have developed two multiplex real-time PCR assays to detect and differentiate A. baumannii and non-A. baumannii Acinetobacter spp, and common carbapenemase genes, including blaNDM, blaOXA-23-like, blaOXA-40-like, blaOXA-51-like, and blaOXA-58-like. We demonstrate the potential utility of these assays for the direct detection of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA in clinical specimens. Primers were specifically designed, and two multiplex real-time PCR assays were developed: multiplex real-time PCR assay1 for the detection of Acinetobacter baumannii 16S–23S rRNA internal transcribed spacer sequence, the Acinetobacter recA gene, and class-B-metalloenzyme-encoding gene blaNDM; and multiplex real-time PCR assay2 to detect class-D-oxacillinase-encoding genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like,and blaOXA-58-like). The assays were performed on an ABI Prism 7500 FAST Real-Time PCR System. CRA isolates were used to compare the assays with conventional PCR and sequencing. Known amounts of CRA cells were added to sputum and fecal specimens and used to test the multiplex real-time PCR assays. The results for target and nontarget amplification showed that the multiplex real-time PCR assays were specific, the limit of detection for each target was 10 copies per 20 μL reaction volume, the assays were linear over six log dilutions of the target genes (r2 > 0.99), and the Ct values of the coefficients of variation for intra- and interassay reproducibility were less than 5%. The multiplex real-time PCR assays showed 100% concordance with conventional PCR when tested against 400 CRA isolates and their sensitivity for the target DNA in sputum and fecal specimens was 102 CFU/mL. Therefore, these novel multiplex real-time PCR assays allow the sensitive and specific characterization and differentiation of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA, making them potential tools for the direct detection of CRA in clinical specimens and the surveillance of nosocomial infections.
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Affiliation(s)
- Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- * E-mail:
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33
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Regional differences and trends in antimicrobial susceptibility of Acinetobacter baumannii. Int J Antimicrob Agents 2016; 47:317-23. [DOI: 10.1016/j.ijantimicag.2016.01.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 12/12/2022]
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34
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The changing epidemiology of Acinetobacter spp. producing OXA carbapenemases causing bloodstream infections in Brazil: a BrasNet report. Diagn Microbiol Infect Dis 2015; 83:382-5. [DOI: 10.1016/j.diagmicrobio.2015.08.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 11/20/2022]
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35
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In Vitro Activity of Tigecycline Against Acinetobacter baumannii: Global Epidemiology and Resistance Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 897:1-14. [DOI: 10.1007/5584_2015_5001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Camoez M, Sierra JM, Dominguez MA, Ferrer-Navarro M, Vila J, Roca I. Automated categorization of methicillin-resistant Staphylococcus aureus clinical isolates into different clonal complexes by MALDI-TOF mass spectrometry. Clin Microbiol Infect 2015; 22:161.e1-161.e7. [PMID: 26482268 DOI: 10.1016/j.cmi.2015.10.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022]
Abstract
Early identification of methicillin-resistant Staphylococcus aureus (MRSA) dominant clones involved in infection and initiation of adequate infection control measures are essential to limit MRSA spread and understand MRSA population dynamics. In this study we evaluated the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) for the automated discrimination of the major MRSA lineages (clonal complexes, CC) identified in our hospital during a 20-year period (1990-2009). A collection of 82 well-characterized MRSA isolates belonging to the four main CCs (CC5, CC8, CC22 and CC398) was split into a reference set (n = 36) and a validation set (n = 46) to generate pattern recognition models using the ClinProTools software for the identification of MALDI-TOF/MS biomarker peaks. The supervised neural network (SNN) model showed the best performance compared with two other models, with sensitivity and specificity values of 100% and 99.11%, respectively. Eleven peaks (m/z range: 3278-6592) with the highest separation power were identified and used to differentiate all four CCs. Validation of the SNN model using ClinProTools resulted in a positive predictive value (PPV) of 99.6%. The specific contribution of each peak to the model was used to generate subtyping reference signatures for automated subtyping using the BioTyper software, which successfully classified MRSA isolates into their corresponding CCs with a PPV of 98.9%. In conclusion, we find this novel automated MALDI-TOF/MS approach to be a promising, powerful and reliable tool for S. aureus typing.
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Affiliation(s)
- M Camoez
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain
| | - J M Sierra
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain
| | - M A Dominguez
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain.
| | - M Ferrer-Navarro
- Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J Vila
- Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain; Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - I Roca
- Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain; Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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37
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Task force on management and prevention of Acinetobacter baumannii infections in the ICU. Intensive Care Med 2015; 41:2057-75. [DOI: 10.1007/s00134-015-4079-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/22/2015] [Indexed: 12/16/2022]
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38
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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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39
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Identification of NDM-1 in a Putatively Novel Acinetobacter Species ("NB14") Closely Related to Acinetobacter pittii. Antimicrob Agents Chemother 2015; 59:6657-60. [PMID: 26259796 DOI: 10.1128/aac.01455-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 08/04/2015] [Indexed: 11/20/2022] Open
Abstract
In this study, we describe the molecular characterization of a plasmid-located blaNDM-1 harbored by an Acinetobacter clinical isolate recovered from a patient in Turkey that putatively constitutes a novel Acinetobacter species, as shown by its distinct ARDRA (amplified 16S ribosomal DNA restriction analysis) profile and molecular sequencing techniques. blaNDM-1 was carried by a conjugative plasmid widespread among non-baumannii Acinetobacter isolates, suggesting its potential for dissemination before reaching more clinically relevant Acinetobacter species.
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40
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 770] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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41
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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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42
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Biswas I. Genetic tools for manipulating Acinetobacter baumannii genome: an overview. J Med Microbiol 2015; 64:657-669. [PMID: 25948809 DOI: 10.1099/jmm.0.000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial pathogen involved in a variety of infections ranging from minor soft-tissue infections to more severe infections such as ventilator-associated pneumonia and bacteraemia. A. baumannii has become resistant to most of the commonly used antibiotics and multidrug-resistant isolates are becoming a severe problem in the healthcare setting. In the past few years, whole-genome sequences of >200 A. baumannii isolates have been generated. Several methods and molecular tools have been used for genetic manipulation of various Acinetobacter spp. Here, we review recent developments of various genetic tools used for modification of the A. baumannii genome, including various ways to inactivate gene function, chromosomal integration and transposon mutagenesis.
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Affiliation(s)
- Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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43
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Liu YM, Lee YT, Kuo SC, Chen TL, Liu CP, Liu CE. Comparison between bacteremia caused by Acinetobacter pittii and Acinetobacter nosocomialis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:62-67. [PMID: 25735795 DOI: 10.1016/j.jmii.2015.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/30/2014] [Accepted: 01/19/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND/PURPOSE Patients with Acinetobacter pittii and Acinetobacter nosocomialis bacteremia have lower mortality rates than those with Acinetobacter baumannii bacteremia. However, it is unknown whether these organisms differ in outcomes of bacteremic patients. We conducted this study to answer this question. METHODS In this retrospective study conducted at a teaching hospital in Taiwan, we enrolled all 86 patients who had developed A. pittii bacteremia and those with A. nosocomialis bacteremia from 2000 to 2008 while matching for age, sex, Acute Physiology and Chronic Health Evaluation II score, and appropriate antimicrobial therapy. After adjustment, we accessed the clinical characteristics and 14- and 28-day mortalities. RESULTS We found that the patients with A. pittii bacteremia had multiple comorbidities less often and received invasive procedures less frequently. The 14-day mortality rate of patients with A. pittii or A. nosocomialis bacteremia was 14% and 7%, respectively, whereas their 28-day mortality rate was 17% and 9%, respectively. Using the mortality rate in patients with A. nosocomialis bacteremia as a reference, the odds ratios for the 14- and 28-day crude morality in those with A. pittii were 2.16 [95% confidence interval (CI), 0.77-6.05] and 2.06 (95% CI, 0.82-5.15), respectively, whereas the adjusted odds ratios for 14- and 28-day mortality were 1.89 (95% CI, 0.56-6.14) and 1.67 (95% CI, 0.59-4.78) respectively. CONCLUSION Our 8-year study showed that the mortality rate of A. pittii bacteremia was higher but the difference was not statistically significant.
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Affiliation(s)
- Yuag-Meng Liu
- Division of Infectious Diseases, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Tzu Lee
- Institutes of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Emergency Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shu-Chen Kuo
- Institutes of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan; Division of Infectious Diseases, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Te-Li Chen
- Institutes of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Infectious Diseases, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Infectious Diseases, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Chang-Pan Liu
- Division of Infectious Diseases, Department of Internal Medicine, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.
| | - Chun-Eng Liu
- Division of Infectious Diseases, Changhua Christian Hospital, Changhua, Taiwan.
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44
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[Frequency and antimicrobial resistance of Acinetobacter species in a university hospital of Buenos Aires City]. Rev Argent Microbiol 2015; 46:320-4. [PMID: 25576416 DOI: 10.1016/s0325-7541(14)70090-2] [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: 07/08/2014] [Accepted: 10/23/2014] [Indexed: 11/21/2022] Open
Abstract
Two-hundred Acinetobacter isolates belonging to 200 patients admitted to Hospital de Clínicas José de San Martín during the period March 2013-June 2014 were analyzed. The identification was performed by mass spectrometry and was confirmed by molecular methods. Susceptibility to antimicrobials was studied by the Vitek-2 system. A 94% correlation of both identification methods was found. Multidrug resistant Acinetobacter baumannii was the predominant genomic species (92.6%) in hospital-acquired infections, whereas Acinetobacter pitti and Acinetobacter nosocomialis accounted for 3.5% and 0.5% of the isolates recovered, respectively. In community-acquired infections a major predominance of the different genomic species was observed. Acinetobacter johnsonii and A. baumannii are the most frequent species, accounting for 45.9% of the isolates recovered. Resistance to carbapenems and minocycline was only observed in A. baumannii. Mass spectrophotometry was an effective tool for the identification of the different genomic species.
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45
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Lupo A, Vogt D, Seiffert SN, Endimiani A, Perreten V. Antibiotic resistance and phylogenetic characterization of Acinetobacter baumannii strains isolated from commercial raw meat in Switzerland. J Food Prot 2014; 77:1976-81. [PMID: 25364933 DOI: 10.4315/0362-028x.jfp-14-073] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The spread of antibiotic-resistant bacteria through food has become a major public health concern because some important human pathogens may be transferred via the food chain. Acinetobacter baumannii is one of the most life-threatening gram-negative pathogens; multidrug-resistant (MDR) clones of A. baumannii are spreading worldwide, causing outbreaks in hospitals. However, the role of raw meat as a reservoir of A. baumannii remains unexplored. In this study, we describe for the first time the antibiotic susceptibility and fingerprint (repetitive extragenic palindromic PCR [rep-PCR] profile and sequence types [STs]) of A. baumannii strains found in raw meat retailed in Switzerland. Our results indicate that A. baumannii was present in 62 (25.0%) of 248 (CI 95%: 19.7 to 30.9%) meat samples analyzed between November 2012 and May 2013, with those derived from poultry being the most contaminated (48.0% [CI 95%: 37.8 to 58.3%]). Thirty-nine strains were further tested for antibiotic susceptibility and clonality. Strains were frequently not susceptible (intermediate and/or resistant) to third- and fourth-generation cephalosporins for human use (i.e., ceftriaxone [65%], cefotaxime [32%], ceftazidime [5%], and cefepime [2.5%]). Resistance to piperacillin-tazobactam, ciprofloxacin, colistin, and tetracycline was sporadically observed (2.5, 2.5, 5, and 5%, respectively), whereas resistance to carbapenems was not found. The strains were genetically very diverse from each other and belonged to 29 different STs, forming 12 singletons and 6 clonal complexes (CCs), of which 3 were new (CC277, CC360, and CC347). RepPCR analysis further distinguished some strains of the same ST. Moreover, some A. baumannii strains from meat belonged to the clonal complexes CC32 and CC79, similar to the MDR isolates responsible for human infections. In conclusion, our findings suggest that raw meat represents a reservoir of MDR A. baumannii and may serve as a vector for the spread of these pathogens into both community and hospital settings.
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Affiliation(s)
- Agnese Lupo
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3010 Bern, Switzerland
| | - Debora Vogt
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Salome N Seiffert
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3010 Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3001 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, CH-3012 Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3010 Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3001 Bern, Switzerland.
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Evaluation of a loop-mediated isothermal amplification-based methodology to detect carbapenemase carriage in Acinetobacter clinical isolates. Antimicrob Agents Chemother 2014; 58:7538-40. [PMID: 25224010 DOI: 10.1128/aac.03870-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii is a major source of nosocomial infections worldwide and is mainly associated with the acquisition of OXA-type carbapenemases and, to a lesser extent, metallo-β-lactamases (MBLs). In this study, 82 nonepidemiologically related Acinetobacter strains carrying different types of OXA or MBL enzymes were tested using the Eazyplex system, a loop-mediated isothermal amplification (LAMP)-based method to rapidly detect carbapenemase carriage. The presence/absence of carbapenem-hydrolyzing enzymes was correctly determined for all isolates in <30 min.
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47
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Roca I, Mosqueda N, Altun B, Espinal P, Akova M, Vila J. Molecular characterization of NDM-1-producing Acinetobacter pittii isolated from Turkey in 2006. J Antimicrob Chemother 2014; 69:3437-8. [DOI: 10.1093/jac/dku306] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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48
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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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49
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Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Acinetobacter species. J Clin Microbiol 2014; 52:3095-100. [PMID: 24899038 DOI: 10.1128/jcm.01233-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker Biotyper) was able to accurately identify 98.6% (142/144) of Acinetobacter baumannii isolates, 72.4% (63/87) of A. nosocomialis isolates, and 97.6% (41/42) of A. pittii isolates. All Acinetobacter junii, A. ursingii, A. johnsonii, and A. radioresistens isolates (n = 28) could also be identified correctly by Bruker Biotyper.
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50
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Jalan R, Fernandez J, Wiest R, Schnabl B, Moreau R, Angeli P, Stadlbauer V, Gustot T, Bernardi M, Canton R, Albillos A, Lammert F, Wilmer A, Mookerjee R, Vila J, Garcia-Martinez R, Wendon J, Such J, Cordoba J, Sanyal A, Garcia-Tsao G, Arroyo V, Burroughs A, Ginès P. Bacterial infections in cirrhosis: a position statement based on the EASL Special Conference 2013. J Hepatol 2014; 60:1310-24. [PMID: 24530646 DOI: 10.1016/j.jhep.2014.01.024] [Citation(s) in RCA: 592] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/30/2013] [Accepted: 01/26/2014] [Indexed: 02/08/2023]
Abstract
Bacterial infections are very common and represent one of the most important reasons of progression of liver failure, development of liver-related complications, and mortality in patients with cirrhosis. In fact, bacterial infections may be a triggering factor for the occurrence of gastrointestinal bleeding, hypervolemic hyponatremia, hepatic encephalopathy, kidney failure, and development of acute-on-chronic liver failure. Moreover, infections are a very common cause of repeated hospitalizations, impaired health-related quality of life, and increased healthcare costs in cirrhosis. Bacterial infections develop as a consequence of immune dysfunction that occurs progressively during the course of cirrhosis. In a significant proportion of patients, infections are caused by gram-negative bacteria from intestinal origin, yet gram-positive bacteria are a frequent cause of infection, particularly in hospitalized patients. In recent years, infections caused by multidrug-resistant bacteria are becoming an important clinical problem in many countries. The reduction of the negative clinical impact of infections in patients with cirrhosis may be achieved by a combination of prophylactic measures, such as administration of antibiotics, to reduce the occurrence of infections in high-risk groups together with early identification and management of infection once it has developed. Investigation on the mechanisms of altered gut microflora, translocation of bacteria, and immune dysfunction may help develop more effective and safe methods of prevention compared to those that are currently available. Moreover, research on biomarkers of early infection may be useful in early diagnosis and treatment of infections. The current manuscript reports an in-depth review and a position statement on bacterial infections in cirrhosis.
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Affiliation(s)
- Rajiv Jalan
- Liver Failure Group, UCL Institute for Liver and Digestive Health, Royal Free Hospital, UK
| | - Javier Fernandez
- Liver Unit, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Reiner Wiest
- Department of Gastroenterology, UVCM, Inselspital, 3010 Bern, Switzerland
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Richard Moreau
- INSERM U773, Centre de Recherche Biomédicale Bichat-Beaujon CRB3, UMRS 773, Université Paris-Diderot Paris, Service d'Hépatologie, Hôpital Beaujon, APHP, Clichy, France
| | - Paolo Angeli
- Unit of Hepatic Emergencies and Liver Transplantation, Department of Medicine, University of Padova, Italy
| | - Vanessa Stadlbauer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Austria
| | - Thierry Gustot
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Mauro Bernardi
- Department of Medical and Surgical Sciences, University of Bologna, Italy
| | - Rafael Canton
- Department of Microbiology, Hospital Universitario Ramón y Cajal and Intituto Ramon y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Agustin Albillos
- Gastroenterology Service, University Hospital Ramon y Cajal, Madrid, Spain
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Alexander Wilmer
- Medical Intensive Care Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - Rajeshwar Mookerjee
- Liver Failure Group, UCL Institute for Liver and Digestive Health, Royal Free Hospital, UK
| | - Jordi Vila
- Department of Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Rita Garcia-Martinez
- Liver Unit, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Julia Wendon
- Institute of Liver Studies and Critical Care, Kings College London, Kings College Hospital, UK
| | - José Such
- Department of Clinical Medicine, Miguel Hernández University, Alicante, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Cordoba
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Arun Sanyal
- Charles Caravati Professor of Medicine, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Guadalupe Garcia-Tsao
- Department of Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Vicente Arroyo
- Liver Unit, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Andrew Burroughs
- The Royal Free Shelia Sherlock Liver Centre and University Department of Surgery, University College London and Royal Free Hospital, UK
| | - Pere Ginès
- Liver Unit, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.
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