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Pourcel C, Essoh C, Ouldali M, Tavares P. Acinetobacter baumannii satellite phage Aci01-2-Phanie depends on a helper myophage for its multiplication. J Virol 2024; 98:e0066724. [PMID: 38829140 PMCID: PMC11264900 DOI: 10.1128/jvi.00667-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
We report the discovery of a satellite-helper phage system with a novel type of dependence on a tail donor. The Acinetobacter baumannii satellite podovirus Aci01-2-Phanie (short name Phanie) uses a phage phi29-like DNA replication and packaging mode. Its linear 11,885 bp dsDNA genome bears 171 bp inverted terminal repeats (ITR). Phanie is related to phage DU-PP-III from Pectobacterium and to members of the Astrithrvirus from Salmonella enterica. Together, they form a new clade of phages with 27% to 30% identity over the whole genome. Detailed 3D protein structure prediction and mass spectrometry analyses demonstrate that Phanie encodes its capsid structural genes and genes necessary to form a short tail. However, our study reveals that Phanie virions are non-infectious unless they associate with the contractile tail of an unrelated phage, Aci01-1, to produce chimeric myoviruses. Following the coinfection of Phanie with myovirus Aci01-1, hybrid viral particles composed of Phanie capsids and Aci01-1 contractile tails are assembled together with Phanie and Aci01-1 particles.IMPORTANCEThere are few reported cases of satellite-helper phage interactions but many more may be yet undiscovered. Here we describe a new mode of satellite phage dependence on a helper phage. Phanie, like phage phi29, replicates its linear dsDNA by a protein primed-mechanism and protects it inside podovirus-like particles. However, these particles are defective, requiring the acquisition of the tail from a myovirus helper for production of infectious virions. The formation of chimeras between a phi29-like podovirus and a helper contractile tail reveals an unexpected association between very different bacterial viruses.
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Affiliation(s)
- Christine Pourcel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christiane Essoh
- Department of Biochemistry-Genetic, School of Biological Sciences, Université Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Anwer R. Molecular epidemiology and molecular typing methods of Acinetobacter baumannii: An updated review. Saudi Med J 2024; 45:458-467. [PMID: 38734425 PMCID: PMC11147555 DOI: 10.15537/smj.2024.45.5.20230886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant Acientobacter baumannii (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by Acientobacter baumannii (A. baumannii) and acquired resistance to antimicrobials. Nowadays, there is gradual shift from traditional typing methods to modern molecular methods to study molecular epidemiology and infection control. Molecular typing of A. baumannii strains has been revolutionized significantly in the last 2 decades. A few sequencing-based techniques have been proven as a breakthrough and opened new prospects, which have not been achieved by the traditional methods. In this review, discussed different pre-existing and recently used typing methods to explore the molecular epidemiology of A. baumannii pertaining in context with human infections.
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Affiliation(s)
- Razique Anwer
- From the Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University, Riyadh, Kingdom of Saudi Arabia.
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Xiong L, Deng C, Yang G, Shen M, Chen B, Tian R, Zha H, Wu K. Molecular epidemiology and antimicrobial resistance patterns of carbapenem-resistant Acinetobacter baumannii isolates from patients admitted at ICUs of a teaching hospital in Zunyi, China. Front Cell Infect Microbiol 2023; 13:1280372. [PMID: 38106474 PMCID: PMC10722174 DOI: 10.3389/fcimb.2023.1280372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundation for the development of infection prevention and control strategies. This study aimed to determine the antimicrobial susceptibility profile, the molecular epidemiology and conduct homology analysis on CRAB strains isolated from ICUs. Methods The sensitivity to various antimicrobials was determined using the minimum inhibitory concentration (MIC) method, Kirby-Bauer disk diffusion (KBDD), and E-test assays. Resistance genes were identified by polymerase chain reaction (PCR). Molecular typing was performed using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Results Among the 79 isolates collected, they exhibited high resistance to various antimicrobials but showed low resistance to levofloxacin, trimethoprim-sulfamethoxazole, and tetracyclines. Notably, all isolates of A. baumannii were identified as multidrug-resistant A. baumannii (MDR-AB). The bla OXA-51-like, adeJ, and adeG genes were all detected, while the detection rates of bla OXA-23-like (97.5%), adeB (93.67%), bla ADC (93.67%), qacEΔ1-sul1 (84.81%) were higher; most of the Ambler class A and class B genes were not detected. MLST analysis on the 79 isolates identified five sequence types (STs), which belonged to group 3 clonal complexes 369. ST1145Ox was the most frequently observed ST with a count of 56 out of 79 isolates (70.89%). MLST analysis for non-sensitive tigecycline isolates, which were revealed ST1145Ox and ST1417Ox as well. By using the MLVA assay, the 79 isolates could be grouped into a total of 64 distinct MTs with eleven clusters identified in them. Minimum spanning tree analysis defined seven different MLVA complexes (MCs) labeled MC1 to MC6 along with twenty singletons. The locus MLVA-AB_2396 demonstrated the highest Simpson's diversity index value at 0.829 among all loci tested in this study while also having one of the highest variety of tandem repeat species. Conclusion The molecular diversity and clonal affinities within the genomes of the CRAB strains were clearly evident, with the identification of ST1144Ox, ST1658Ox, and ST1646Oxqaq representing novel findings.
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Affiliation(s)
- Lin Xiong
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Chengmin Deng
- Scientific Research Center, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Guangwu Yang
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Meijing Shen
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Benhai Chen
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Rengui Tian
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - He Zha
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
- Scientific Research Center, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
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Busby EJ, Doyle RM, Leboreiro Babe C, Harris KA, Mack D, Méndez-Cervantes G, O’Sullivan DM, Pang V, Sadouki Z, Solanki P, Huggett JF, McHugh TD, Wey EQ. Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods. Microbiol Spectr 2023; 11:e0499522. [PMID: 37154773 PMCID: PMC10269802 DOI: 10.1128/spectrum.04995-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).
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Affiliation(s)
- Eloise J. Busby
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
| | - Ronan M. Doyle
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Clara Leboreiro Babe
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Kathryn A. Harris
- Virology Department, ESEL Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Damien Mack
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Vicky Pang
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Zahra Sadouki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Priya Solanki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, United Kingdom
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Emmanuel Q. Wey
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
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Maleki A, Kaviar VH, Koupaei M, Haddadi MH, Kalani BS, Valadbeigi H, Karamolahi S, Omidi N, Hashemian M, Sadeghifard N, Mohamadi J, Heidary M, Khoshnood S. Molecular typing and antibiotic resistance patterns among clinical isolates of Acinetobacter baumannii recovered from burn patients in Tehran, Iran. Front Microbiol 2022; 13:994303. [PMID: 36386699 PMCID: PMC9664937 DOI: 10.3389/fmicb.2022.994303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022] Open
Abstract
Acinetobacter baumannii (A. baumannii) is now considered a highly resistant pathogen to various types of antibiotics. Therefore, tracking the source of its prevalence and continuous control is crucial. This study aimed to determine antibiotic resistance and perform various molecular typing methods on clinical isolates of A. baumannii isolated from hospitalized burn patients in Shahid Motahari Burn Hospital, Tehran, Iran. Hospital isolates were confirmed by phenotypic and molecular methods. Then the sensitivity to different antibiotics was determined using the minimum inhibitory concentration (MIC) method. In order to perform molecular typing, three-locus dual assay multiplex polymerase chain reaction (PCR), multiple-locus variable-number tandem repeat analysis (MLVA), and multilocus sequence typing (MLST) methods were used. Among the 60 isolates collected, the frequencies of multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates were 90 and 10%, respectively. The most effective antibiotics were colistin with 100% and tigecycline with 83.33% sensitivity. Isolates were 100% resistant to piperacillin/tazobactam and cephalosporins, and 68.3% were resistant to carbapenem. The results of multiplex PCR showed five groups that international clone I (IC I) and IC II were the most common. The MLVA method identified 34 MLVA types (MTs), 5 clusters, and 25 singletons. Multilocus sequence typing results for tigecycline-resistant isolates showed seven different sequence types (STs). Increasing antibiotic resistance in A. baumannii isolates requires careful management to control and prevent the occurrence of the pre-antibiotic era. The results of this study confirm that the population structure of A. baumannii isolates has a high diversity. More extensive studies are needed in Iran to better understand the epidemiology of A. baumannii.
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Affiliation(s)
- Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Maryam Koupaei
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Behrooz Sadeghi Kalani
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Hassan Valadbeigi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Somayeh Karamolahi
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Nazanin Omidi
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Marziyeh Hashemian
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Jasem Mohamadi
- Department of Pediatrics, School of Medicine, Imam Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
- *Correspondence: Saeed Khoshnood, ; Mohsen Heidary,
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
- *Correspondence: Saeed Khoshnood, ; Mohsen Heidary,
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Homenta H, Julyadharma J, Susianti H, Noorhamdani N, Santosaningsih D. Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7100277. [PMID: 36288018 PMCID: PMC9607243 DOI: 10.3390/tropicalmed7100277] [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: 09/08/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (A. baumannii)-calcoaceticus complex (CRAb-cc) is an important pathogen causing nosocomial infections worldwide; however, molecular epidemiology of the A. baumannii-calcoaceticus complex in Indonesian hospitals is scarce. This study aimed to determine the clonal relatedness of CRAb-cc in two tertiary care hospitals in Malang and Manado in Indonesia. The CRAb-cc isolates from routine clinical cultures in two tertiary care hospitals in Malang and Manado were identified using the Vitek2® system (bioMérieux, Lyon, France). Multi-locus variable-number tandem-repeat analysis (MLVA) typing, multi-locus sequence typing (MLST), clonal complex (CC), and phylogenetic tree analysis were conducted for a subset of isolates. Seventy-three CRAb-cc isolates were collected. The CRAb-cc isolates were frequently found among lower-respiratory-tract specimens. We detected the MLVA type (MT) 1, MT3, and MT4 CRAB-cc isolates belonging to the sequence type (ST) 642, and CC1 was the predominant clone in this study. In conclusion, we identified the clonal relatedness of A. baumannii-calcoaceticus complex isolates in two tertiary care hospitals in Malang and Manado in Indonesia. Further study is required to investigate the clinical importance and distribution of ST642 in Indonesian hospitals for developing prevention and control measures.
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Affiliation(s)
- Heriyannis Homenta
- Doctoral Program in Medical Science, Faculty of Medicine, Universitas Brawijaya, Malang 65145, Indonesia
- Department of Clinical Microbiology, Faculty of Medicine, Sam Ratulangi University, Manado 95163, Indonesia
| | - Julyadharma Julyadharma
- Laboratory of Clinical Microbiology, Prof. Dr. R. D. Kandou Hospital, Manado 95163, Indonesia
| | - Hani Susianti
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
- Department of Clinical Pathology, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia
| | - Noorhamdani Noorhamdani
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
| | - Dewi Santosaningsih
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
- Department of Clinical Microbiology, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia
- Correspondence:
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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis. J Appl Genet 2021; 62:511-521. [PMID: 34105103 PMCID: PMC8357709 DOI: 10.1007/s13353-021-00640-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022]
Abstract
An optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation in the gene encoding the EmrA-homologue of E. coli, and antibiotic resistance patterns, in combination with three newly identified polymorphic regions in the genomes of A. baumannii clinical isolates. Differential analysis of two similarity matrices between different genotypes and resistance patterns allowed to distinguish three significant correlations (p < 0.05) between 172 bp DNA insertion combined with resistance to chloramphenicol and gentamycin. Interestingly, 45 and 55 bp DNA insertions within the CRISPR region were identified, and combined during analyses with resistance/susceptibility to trimethoprim/sulfamethoxazole. Moreover, 184 or 1374 bp DNA length polymorphisms in the genomic region located upstream of the GTP cyclohydrolase I gene, associated mainly with imipenem susceptibility, was identified. In addition, considerable nucleotide polymorphism of the gene encoding the gamma/tau subunit of DNA polymerase III, an enzyme crucial for bacterial DNA replication, was discovered. The differentiation analysis performed using the above described approach allowed us to monitor the distribution of A. baumannii isolates in different wards of the hospital in the time frame of several years, indicating that the optimized method may be useful in hospital epidemiological studies, particularly in identification of the source of primary infections.
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Kirtikliene T, Mierauskaitė A, Razmienė I, Kuisiene N. Multidrug-Resistant Acinetobacter baumannii Genetic Characterization and Spread in Lithuania in 2014, 2016, and 2018. Life (Basel) 2021; 11:life11020151. [PMID: 33669401 PMCID: PMC7920459 DOI: 10.3390/life11020151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial resistance to antimicrobial agents plays an important role in the treatment of bacterial infections in healthcare institutions. The spread of multidrug-resistant bacteria can occur during inter- and intra-hospital transmissions among patients and hospital personnel. For this reason, more studies must be conducted to understand how resistance occurs in bacteria and how it moves between hospitals by comparing data from different years and looking out for any patterns that might emerge. Multidrug-resistant (MDR) Acinetobacter spp. was studied at 14 healthcare institutions in Lithuania during 2014, 2016, and 2018 using samples from human bloodstream infections. In total, 194 isolates were collected and identified using MALDI-TOF and VITEK2 analyzers as Acinetobacter baumannii group bacteria. After that, the isolates were analyzed for the presence of different resistance genes (20 genes were analyzed) and characterized by using the Rep-PCR and MLVA (multiple-locus variable-number tandem repeat analysis) genotyping methods. The results of the study showed the relatedness of the different Acinetobacter spp. isolates and a possible circulation of resistance genes or profiles during the different years of the study. This study provides essential information, such as variability and diversity of resistance genes, genetic profiling, and clustering of isolates, to better understand the antimicrobial resistance patterns of Acinetobacter spp. These results can be used to strengthen the control of multidrug-resistant infections in healthcare institutions and to prevent potential outbreaks of this pathogen in the future.
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Affiliation(s)
- Tatjana Kirtikliene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-62156858
| | - Aistė Mierauskaitė
- National Public Health Surveillance Laboratory, Clinical Testing Department, LT-10257 Vilnius, Lithuania; (A.M.); (I.R.)
| | - Ilona Razmienė
- National Public Health Surveillance Laboratory, Clinical Testing Department, LT-10257 Vilnius, Lithuania; (A.M.); (I.R.)
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania;
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Santos MDV, Barros MPS, Silveira-Filho VDM, Mendes-Marques CL, Lima AVA, Silva MVD, Leal-Balbino TC, Silva MDPCD, Paiva PMG, Oliveira MBMD. Genetic and Biochemical Diversity of Clinical Acinetobacter baumannii and Pseudomonas aeruginosa Isolates in a Public Hospital in Brazil. Microb Drug Resist 2020; 27:509-517. [PMID: 32882147 DOI: 10.1089/mdr.2020.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Life-threatening bacterial infections are a major concern in health care services worldwide. This retrospective study aimed to demonstrate genetic and biochemical diversity in isolates of Acinetobacter baumannii and Pseudomonas aeruginosa from a public hospital in Brazil. A total of 63 isolates collected from different sites of infection and hospital sectors were characterized, and their susceptibility profile to antibiotics was assessed for 18 drugs belonging to 8 antimicrobial categories using the automated BACTEC system. Genetic diversity was assessed using the multiple locus variable number tandem repeat analysis. Among the isolates of A. baumannii, 83% were classified as extensively drug resistant (XDR), and 17 genotypic profiles were identified. About 67% of P. aeruginosa isolates were susceptible to antimicrobials and were distributed into 37 genotypic profiles, revealing genetic heterogeneity. This study has demonstrated the multicolonization of investigated pathogens and the high frequency (95.8%) of multidrug-resistant and XDR, as well as high genetic diversity, among the isolates supporting the continuous need to monitor these species in the hospital environment.
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Affiliation(s)
| | | | | | | | | | - Marcia Vanusa da Silva
- Department of Biochemistry, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Overexpression of bla OXA-58 Gene Driven by IS Aba3 Is Associated with Imipenem Resistance in a Clinical Acinetobacter baumannii Isolate from Vietnam. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7213429. [PMID: 32802871 PMCID: PMC7420922 DOI: 10.1155/2020/7213429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/02/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The aim of this study was to investigate genetic structures and expression of blaOXA-58 gene in five Acinetobacter baumannii clinical isolates recovered from two hospitals in southern Vietnam during 2012-2014. A. baumannii isolates were identified by automated microbiology systems and confirmed by PCR. All isolates were characterized as multidrug resistant by antimicrobial testing using the disk diffusion method. Four imipenem susceptible and one nonsusceptible isolates (MIC > 32 μg·ml−1) were identified by E-test. PCR amplification of blaOXA-58 gene upstream and downstream sequences revealed the presence of ISAba3 at both locations in one multidrug-resistant isolate. Semiquantitation of blaOXA-51 and blaOXA-58 gene expression was performed by the 2-ΔΔCt method. The blaOXA-51 gene expression of five isolates showed little difference, but the isolate bearing ISAba3-blaOXA-58-ISAba3 exhibited significantly higher blaOXA-58 mRNA level. Higher β-lactamases activity in periplasmic than cytoplasmic fraction was found in most isolates. The isolate overexpressing blaOXA-58 gene possessed very high periplasmic enzyme activity. In conclusion, the A. baumannii isolate bearing ISAba3-blaOXA-58 gene exhibited high resistance to imipenem, corresponding to an overexpression of blaOXA-58 gene and very high periplasmic β-lactamase activity.
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Farajzadeh Sheikh A, Savari M, Abbasi Montazeri E, Khoshnood S. Genotyping and molecular characterization of clinical Acinetobacter baumannii isolates from a single hospital in Southwestern Iran. Pathog Glob Health 2020; 114:251-261. [PMID: 32552452 PMCID: PMC7480470 DOI: 10.1080/20477724.2020.1765124] [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: 01/09/2023] Open
Abstract
ACINETOBACTER BAUMANNII (A. baumannii) is a pathogen responsible for nosocomial infections among the hospitalized patients. The aim of this study was to investigate genotyping and molecular characterization and to examine the biofilm formation ability of A. baumannii isolates. In total, 70 A. baumannii isolates were collected from patients admitted to Imam Khomeini Hospital in Ahvaz, Southwestern Iran. Minimum inhibitory concentrations (MIC) test was performed using Vitek 2 system. The presence of genes encoding metallo-β-lactamases, oxacillinases, and integrase and the biofilm formation ability were then evaluated. Multiple locus variable-number tandem repeat (VNTR) analysis (MLVA) typing and multiplex PCR were performed to determine the genetic relationships. The blaOXA-23-like gene had the highest prevalence. The frequency of genes encoding blaSPM, blaIMP, and blaVIM among MDR A. baumannii isolates were 12 (17.1%), 18 (25.7%), and 22 (31.4%), respectively. Moreover, 46 isolates (75.4%) harbored class I integron and 10 isolates (16.39%) carried class II integron. The number of weak, moderate and strong biofilm-producing isolates were 3 (4.3%), 7 (10%), and 55 (78.5%), respectively. The results showed that 70 A. baumannii isolates were grouped into 12 distinct MLVA types with five clusters and four singleton genotypes. In addition, 25 (35.7%) isolates were assigned to international clone (IC) variants, 37 (52.8%) isolates belonged to group 1 (IC II), and 8 (11.4%) isolates belonged to group 2 (IC I). Our findings revealed that the population structure of the A. baumannii isolates was genetically diverse. More focus on genetic variation and antibiotic resistance of A. baumannii isolates are recommended.
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Affiliation(s)
- Ahmad Farajzadeh Sheikh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Effat Abbasi Montazeri
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeed Khoshnood
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Khoshnood S, Savari M, Abbasi Montazeri E, Farajzadeh Sheikh A. Survey on Genetic Diversity, Biofilm Formation, and Detection of Colistin Resistance Genes in Clinical Isolates of Acinetobacter baumannii. Infect Drug Resist 2020; 13:1547-1558. [PMID: 32547124 PMCID: PMC7266307 DOI: 10.2147/idr.s253440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction Acinetobacter baumannii is an opportunistic pathogen responsible for nosocomial infections. The emergence of colistin-resistant A. baumannii is a significant threat to public health. The aim of this study was to investigate the molecular characterization and genotyping of clinical A. baumannii isolates in Southwestern Iran. Methods A total of 70 A. baumannii isolates were collected from patients admitted to Imam Khomeini Hospital in Ahvaz, Southwestern Iran. Minimum inhibitory concentration test was conducted by using Vitek 2 system. The presence of biofilm-forming genes and colistin resistance-related genes were evaluated by PCR. The isolates were also examined for their biofilm formation ability and the expression of pmrA and pmrB genes. Finally, multilocus sequence typing (MLST) and PCR-based sequence group were used to determine the genetic relationships of the isolates. Results Overall, 61 (87.1%) and 9 (12.8%) isolates were multidrug-resistant (MDR) and extensively drug-resistant (XDR), respectively. Colistin and tigecycline with 2 (2.8%) and 32 (45.7%) resistance rates had the highest effect. Among all the isolates, 55 (78.5%), 7 (10%), and 3 (4.3%) were strong, moderate, and weak biofilm producers, respectively. The frequency rates of biofilm-related genes were 64 (91.4%), 70 (100%), 56 (80%), and 22 (31.42%) for bap, ompA, csuE, and blaPER1, respectively. Overexpression of pmrA and pmrB genes was observed in two colistin-resistance isolates, but the expression of these genes did not change in colistin-sensitive isolates. Additionally, 37 (52.8%) and 8 (11.4%) isolates belonged to groups 1 (ICII) and 2 (IC I), respectively. MLST analysis revealed a total of nine different sequence types that six isolates belonged to clonal complex 92 (corresponding to ST801, ST118, ST138, ST 421, and ST735). Other isolates were belonging to ST133 and ST216, and two colistin-resistant (Ab4 and Ab41) isolates were belonging to ST387 and ST1812. Conclusion The present study revealed the presence of MDR and XDR A. baumannii isolates harboring biofilm genes and emergence of colistin-resistant isolates in Southwestern Iran. These isolates had high diversity, which was affirmed by typing techniques. The control measures and regular surveillance are urgently needed to preclude the spread of these isolates.
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Affiliation(s)
- Saeed Khoshnood
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Effat Abbasi Montazeri
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ahmad Farajzadeh Sheikh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19. INFORMATICS IN MEDICINE UNLOCKED 2020; 19:100356. [PMID: 32501423 PMCID: PMC7241407 DOI: 10.1016/j.imu.2020.100356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/24/2022] Open
Abstract
Motivation Recently, the outbreak of Coronavirus-Covid-19 has forced the World Health Organization to declare a pandemic status. A genome sequence is the core of this virus which interferes with the normal activities of its counterparts within humans. Analysis of its genome may provide clues toward the proper treatment of patients and the design of new drugs and vaccines. Microsatellites are composed of short genome subsequences which are successively repeated many times in the same direction. They are highly variable in terms of their building blocks, number of repeats, and their locations in the genome sequences. This mutability property has been the source of many diseases. Usually the host genome is analyzed to diagnose possible diseases in the victim. In this research, the focus is concentrated on the attacker's genome for discovery of its malicious properties. Results The focus of this research is the microsatellites of both SARS and Covid-19. An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. The Microsatellite discovery is based on an efficient indexing technique called K-Mer Hash Indexing. The method is called Fast Microsatellite Discovery (FMSD) and it is used for both SARS and Covid-19. A table composed of all microsatellites is reported. There are many differences between SARS and Covid-19, but there is an outstanding difference which requires further investigation. Availability FMSD is freely available at https://gitlab.com/FUM_HPCLab/fmsd_project, implemented in C on Linux-Ubuntu system. Software related contact: hossein_savari@mail.um.ac.ir.
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Abstract
Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.
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Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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Kumar S, Patil PP, Singhal L, Ray P, Patil PB, Gautam V. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates reveals the emergence of bla OXA-23 and bla NDM-1 encoding international clones in India. INFECTION GENETICS AND EVOLUTION 2019; 75:103986. [PMID: 31362071 DOI: 10.1016/j.meegid.2019.103986] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/09/2023]
Abstract
Acinetobacter baumannii is a nosocomial pathogen increasingly affecting the critically ill patients and represents a major public health challenge. Carbapenem-resistant A. baumannii (CRAB) is found to be associated with International Clones (ICs) and different classes of carbapenemases. The objective of the present study was to investigate the prevalence of carbapenem resistance genes, clonal relationship and genetic structure of clinical isolates of A. baumannii. In the present study, multi-locus sequence typing (MLSTOX) and analysis were carried out using Oxford scheme for 86 clinical isolates of CRAB along with 11 carbapenem sensitive A. baumannii (CSAB) collected over a period of two years (2014-2016) from two tertiary care hospitals of North India. We observed a high prevalence of the blaOXA-23-like (97.7%) among the CRAB followed by blaNDM-1 (29.1%) and blaOXA58-like (3.5%). Forty-seven Sequence Types (STs) were represented by all 97 isolates, out of which, 28 (59.6%) were novel STs that were assigned to 41 isolates. STs 451 (13%), 447 (7%), 195 (6%) and 848 (5%) were the most common STs. The majority of CRAB isolates (44.3%) belonged to the CC92, followed by the CC447 (15.1%), CC109 (9.3%) and CC110 (3.4%), which corresponds to the IC2, 8, 1 and 7 respectively. Phylogenetic and recombination analysis suggested two major and one minor lineage in the population. Further linkage disequilibrium analysis suggested clonal nature of the population as recombination was noticed at a low frequency, which was not enough to split the clonal relationship. The knowledge of genetic structure of CRAB from this study will be invaluable to illustrate epidemiology, surveillance and understanding its global diversity.
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Affiliation(s)
- Sunil Kumar
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India; Department of Biotechnology, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, Haryana 133207, India
| | - Prashant P Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India
| | - Lipika Singhal
- Government Medical College and Hospital, Sector -32B, Chandigarh 160030, India
| | - Pallab Ray
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India.
| | - Vikas Gautam
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
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Evaluation of Multilocus Variable-Number Tandem-Repeat (MLVA-8Orsay) for Typing of Carbapenem-Resistant Acinetobacter baumannii Isolated from Patients in Tehran, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.64402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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The Relationship Between Antibiotic Resistance Phenotypes and Biofilm Formation Capacity in Clinical Isolates of Acinetobacter baumannii. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.74315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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19
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Bahador A, Farshadzadeh Z, Raoofian R, Mokhtaran M, Pourakbari B, Pourhajibagher M, Hashemi FB. Association of virulence gene expression with colistin-resistance in Acinetobacter baumannii: analysis of genotype, antimicrobial susceptibility, and biofilm formation. Ann Clin Microbiol Antimicrob 2018; 17:24. [PMID: 29859115 PMCID: PMC5984448 DOI: 10.1186/s12941-018-0277-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/19/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acinetobacter baumannii causes difficult-to-treat nosocomial infections, which often lead to morbidity due to the development of antimicrobial drug resistance and expression of virulence genes. Data regarding the association of resistance to colistin, a last treatment option, and the virulence gene expression of A. baumannii is scarce. Methods We evaluated the MLVA genotype, antimicrobial resistance, and biofilm formation of 100 A. baumannii isolates from burn patients, and further compared the in vitro and in vivo expression of four virulence genes among five colistin-resistant A. baumannii (Cst-R-AB) isolates. Five Cst-R-AB isolates were tested; one from the present study, and four isolated previously. Results Our results showed that reduced expression of recA, along with increased in vivo expression of lpsB, dnaK, and blsA; are associated with colistin resistance among Cst-R-AB isolates. Differences in virulence gene expressions among Cst-R-AB isolates, may in part explain common discrepant in vitro vs. in vivo susceptibility data during treatment of infections caused by Cst-R-AB. Conclusions Our findings highlight the intricate relationship between colistin-resistance and virulence among A. baumannii isolates, and underscore the importance of examining the interactions between virulence and antimicrobial resistance toward efforts to control the spread of multidrug-resistant A. baumannii (MDR-AB) isolates, and also to reduce disease severity in burn patients with MDR-AB infection. Electronic supplementary material The online version of this article (10.1186/s12941-018-0277-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, 100 Poursina Ave., 100 Keshavarz Blvd, Tehran, 14167-53955, Iran.,Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Laser Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Farshadzadeh
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, 100 Poursina Ave., 100 Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran.,Innovative Research Center, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Masoumeh Mokhtaran
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, 100 Poursina Ave., 100 Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Babak Pourakbari
- Pediatrics Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Pourhajibagher
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, 100 Poursina Ave., 100 Keshavarz Blvd, Tehran, 14167-53955, Iran.,Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, 100 Poursina Ave., 100 Keshavarz Blvd, Tehran, 14167-53955, Iran.
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How Do You Design Undergraduate Genetics Laboratory Courses? Trends Genet 2018. [PMID: 29525438 DOI: 10.1016/j.tig.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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Farshadzadeh Z, Taheri B, Rahimi S, Shoja S, Pourhajibagher M, Haghighi MA, Bahador A. Growth Rate and Biofilm Formation Ability of Clinical and Laboratory-Evolved Colistin-Resistant Strains of Acinetobacter baumannii. Front Microbiol 2018; 9:153. [PMID: 29483899 PMCID: PMC5816052 DOI: 10.3389/fmicb.2018.00153] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022] Open
Abstract
Two different mechanisms of resistance to colistin in Acinetobacter baumannii have been described. The first involves the total loss of lipopolysaccharide (LPS) due to mutations in the lpxACD operon, which is involved in the lipid A biosynthesis pathway. The second entails the addition of ethanolamine to the lipid A of the LPS resulting from mutations in the PmrAB two-component system. To evaluate the impact of colistin resistance-associated mutations on antimicrobial resistance and virulence properties, four pairs of clinical and laboratory-evolved colistin-susceptible/colistin-resistant (ColS/ColR) A. baumannii isolates were used. Antimicrobial susceptibility, surface motility, in vitro and in vivo biofilm-forming capacity, in vitro and in vivo expression levels of biofilm-associated genes, and in vitro growth rate were analyzed in these strains. Growth rate, in vitro and in vivo biofilm formation ability, as well as expression levels of biofilm-associated gene were reduced in ColR LPS-deficient isolate (the lpxD mutant) when compared with its ColS partner, whereas there were not such differences between LPS-modified isolates (the pmrB mutants) and their parental isolates. Mutation in lpxD was accompanied by a greater reduction in minimum inhibitory concentrations of azithromycin, vancomycin, and rifampin than mutation in pmrB. Besides, loss of LPS was associated with a significant reduction in surface motility without any change in expression of type IV pili. Collectively, colistin resistance through loss of LPS causes a more considerable cost in biological features such as growth rate, motility, and biofilm formation capacity relative to LPS modification. Therefore, ColR LPS-modified strains are more likely to spread and transmit from one patient to another in hospital settings, which results in more complex treatment and control.
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Affiliation(s)
- Zahra Farshadzadeh
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behrouz Taheri
- Department of Medical Laboratory Sciences, School of Paramedicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Rahimi
- Department of Microbiology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Saeed Shoja
- Infectious and Tropical Disease Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad A Haghighi
- Department of Microbiology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Mitchell KE, Turton JF, Lloyd DH. Isolation and identification of Acinetobacter spp. from healthy canine skin. Vet Dermatol 2018; 29:240-e87. [PMID: 29430818 DOI: 10.1111/vde.12528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Acinetobacter species can exhibit widespread resistance to antimicrobial agents. They are already recognized as important nosocomial pathogens of humans, but are becoming increasingly recognized in opportunistic infections of animals. HYPOTHESIS/OBJECTIVES This study aimed to determine whether Acinetobacter spp. are carried on skin of healthy dogs and, if present, to identify the species. ANIMALS Forty dogs were sampled at veterinary practices and rescue centres. They were free from skin disease and receiving no systemic or topical treatments. METHODS Skin swab samples were collected from four sites on each dog and cultured. Acinetobacter spp. isolates were detected by biochemical tests and gas chromatography. The species was determined by sequencing the RNA polymerase β-subunit (rpoB) gene. Isolates were screened for OXA carbapenemase genes and class 1 integrons capable of carrying resistance genes, and subjected to antimicrobial susceptibility tests. RESULTS For 25% dogs sampled (10 of 40), Acinetobacter spp. were isolated at one or more skin sites. Thirteen Acinetobacter spp. isolates were recovered from 160 samples. The most frequently cultured was A. lwoffii (seven of 13), followed by A. baumannii (two of 13), A. junii (one of 13), A. calcoaceticus (one of 13), A. pittii (one of 13) and a novel Acinetobacter species (one of 13). Class 1 integrons and blaOXA-23-like were not detected. Isolates were susceptible to most antibiotics. CONCLUSIONS AND CLINICAL IMPORTANCE The study confirms that Acinetobacter spp. can survive on canine skin, where they may be potential reservoirs for infection. This highlights the importance of good hygiene in veterinary practice, adhering to aseptic principles in surgery, and treatment based on culture and susceptibility testing where possible.
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Affiliation(s)
- Kayleigh E Mitchell
- Fernside Veterinary Centre, 205 Shenley Road, Borehamwood, Hertfordshire, WD6 1AT, UK
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - David H Lloyd
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, Hawkshead Lane North Mymms, Hertfordshire, AL9 7TA, UK
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Saffari F, Monsen T, Karmostaji A, Azimabad FB, Widerström M. Significant spread of extensively drug-resistant Acinetobacter baumannii genotypes of clonal complex 92 among intensive care unit patients in a university hospital in southern Iran. J Med Microbiol 2017; 66:1656-1662. [PMID: 29058650 DOI: 10.1099/jmm.0.000619] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
PURPOSE Infections associated with Acinetobacter baumannii represent an increasing threat in healthcare settings. Therefore, we investigated the epidemiological relationship between clinical isolates of A. baumannii obtained from patients in a university hospital in Bandar Abbas in southern Iran. METHODOLOGY Sixty-four consecutive non-duplicate clinical isolates collected during 2014-2015 were subjected to susceptibility testing, clonal relationship analysis using PFGE, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST), and examined for the presence of carbapenemases and integrons. RESULTS Almost all A. baumannii isolates were extensively drug-resistant (XDR; 98 %) and carried an OXA carbapenemase gene (blaOXA-23-like; 98 %) and class 1 integrons (48 %). PFGE and MLST analysis identified three major genotypes, all belonging to clonal complex 92 (CC92): sequence type 848 (ST848) (n=23), ST451 (n=16) and ST195 (n=8). CC92 has previously been documented in the hospital setting in northern Iran, and ST195 has been reported in Arab States of the Persian Gulf. These data suggest national and global transmission of A. baumannii CC92. CONCLUSION This report demonstrates the occurrence and potential spread of closely related XDR genotypes of A. baumannii CC92 within a university hospital in southern Iran. These genotypes were found in the majority of the investigated isolates, showed high prevalence of blaOXA-23 and integron class 1, and were associated with stay in the intensive care unit. Very few treatment options remain for healthcare-adapted XDR A. baumannii, and hence effective measures are desperately needed to reduce the spread of these strains and resultant infections in the healthcare setting.
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Affiliation(s)
- Fereshteh Saffari
- Department of Microbiology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Afsaneh Karmostaji
- Infectious & Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Micael Widerström
- Department of Clinical Microbiology, Unit of Research, Education and Development Östersund, Umeå University, Umeå, Sweden
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A reliable combination method to identification and typing of epidemic and endemic clones among clinical isolates of Acinetobacter baumannii. INFECTION GENETICS AND EVOLUTION 2017; 54:501-507. [PMID: 28827174 DOI: 10.1016/j.meegid.2017.08.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/01/2017] [Accepted: 08/18/2017] [Indexed: 11/21/2022]
Abstract
The multi-drug resistant (MDR) Acinetobacter baumannii as an important nosocomial pathogen has emerged a global health concern in recent years. In this study, we applied three easier, faster, and cost-effective methods including PCR-based open reading frames (ORFs) typing, sequence typing of blaOXA-51-like and RAPD-PCR method to rapid typing of A. baumannii strains. Taken together in the present study the results of ORFs typing, PCR-sequencing of blaOXA-51-like genes and MLST sequence typing revealed there was a high prevalence (62%, 35/57) of ST2 as international and successful clone which detected among clinical isolates of multi-drug resistant A. baumannii with ORF pattern B and blaOXA-66 gene. Only 7% (4/57) of MDR isolates belonged to ST1 with ORF pattern A and blaOXA-69 gene. Interestingly, we detected singleton ST513 (32%, 18/57) that encoded blaOXA-90 and showed the ORF pattern H as previously isolated in Middle East. Moreover, our data showed RAPD-PCR method can detect divergent strains of the STs. The Cl-1, Cl-2, Cl-3, Cl-4, Cl-10, Cl-11, Cl-12, Cl-13 and Cl-14 belonged to ST2. While the Cl-6, Cl-7, Cl-8 and Cl-9 belonged to ST513. Only Cl-5 belonged to ST1. It seems that the combination of these methods have more discriminatory than any method separately and could be effectively applied to rapid detection of the clonal complex (CC) of A. baumannii strains without performing of MLST or PFGE.
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Plasmid borne Carbapenem-Hydrolyzing Class D β-Lactamases (CHDLs) and AdeABC efflux pump conferring carbapenem-tigecycline resistance among Acinetobacter baumannii isolates harboring TnAbaRs. Microb Pathog 2017; 104:310-317. [DOI: 10.1016/j.micpath.2017.01.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 12/18/2022]
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Acquisition of Tn6018-3′ CS regions increases colistin MICs against Acinetobacter baumannii isolates harboring new variants of AbaRs. Folia Microbiol (Praha) 2017; 62:373-379. [DOI: 10.1007/s12223-017-0507-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/14/2017] [Indexed: 01/03/2023]
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Tuan Anh N, Nga TVT, Tuan HM, Tuan NS, Y DM, Vinh Chau NV, Baker S, Duong HHT. Molecular epidemiology and antimicrobial resistance phenotypes of Acinetobacter baumannii isolated from patients in three hospitals in southern Vietnam. J Med Microbiol 2017; 66:46-53. [DOI: 10.1099/jmm.0.000418] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Nguyen Tuan Anh
- Diagnostic Department, Faculty of Nursing and Medical Technology, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Tran Vu Thieu Nga
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Huynh Minh Tuan
- Infection Control Department, University Medical Center, Ho Chi Minh City, Vietnam
| | - Nguyen Si Tuan
- Microbiology Department, Thong Nhat-Dong Nai General Hospital, Dong Nai Province, Vietnam
| | - Dao Minh Y
- Microbiology Department, Dong Nai General Hospital, Dong Nai Province, Vietnam
| | - Nguyen Van Vinh Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Centre for Tropical Medicine, Oxford University, Oxford, UK
- The Department of Medicine, The University of Cambridge, Cambridge, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho Huynh Thuy Duong
- Department of Genetics, Faculty of Biology, University of Science, Ho Chi Minh City, Vietnam
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Johnson JK, Robinson GL, Zhao L, Harris AD, Stine OC, Thom KA. Comparison of molecular typing methods for the analyses of Acinetobacter baumannii from ICU patients. Diagn Microbiol Infect Dis 2016; 86:345-350. [PMID: 27640081 DOI: 10.1016/j.diagmicrobio.2016.08.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 01/23/2023]
Abstract
Acinetobacter baumannii has emerged as an important cause of healthcare-associated infections causing great morbidity and mortality. Despite its clinical importance, it is still unknown which molecular typing method is the best to determine or confirm institutional outbreaks as well as to identify epidemiologically related isolates from different geographical areas. To determine the most discriminatory molecular typing method, we isolated A. baumannii from perianal swabs collected from intensive care unit (ICU) patients in a cohort study during 2002 and 2008. Strains from each year were analyzed by pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable-number tandem repeat analysis (MLVA). Genetic relatedness of the isolates was consistent between PFGE and MLST as well as between analyses of loci containing MLVA and MLST. Our data show that PFGE and MLVA are similar when discriminating between isolates and are both good methods to use when questioning whether two isolates are indistinguishable.
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Affiliation(s)
- J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD; Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD.
| | - Gwen L Robinson
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD
| | - LiCheng Zhao
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD
| | - Anthony D Harris
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
| | - O Colin Stine
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
| | - Kerri A Thom
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
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Imperi M, Pittiglio V, D'Avenio G, Gherardi G, Ciammaruconi A, Lista F, Pourcel C, Baldassarri L, Creti R. A new genotyping scheme based on MLVA for inter-laboratory surveillance of Streptococcus pyogenes. J Microbiol Methods 2016; 127:176-181. [PMID: 27302039 DOI: 10.1016/j.mimet.2016.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/24/2022]
Abstract
A newly developed MLVA seven-loci scheme for Streptococcus pyogenes is described. The method can be successfully applied by using both agarose gel with visual inspections of bands and Lab on Chip technology. The potential of the present MLVA has been tested on a collection of 100 clinical GAS strains representing the most common emm types found in high-income countries plus 18 published gap-free genomes, in comparison to PFGE and MLST. The MLVA analysis defined 30 MLVA types with ten out of the considered 15 emm types exhibiting multiple and specific MLVA types. In only one occasion the same MLVA profile was shared between isolates belonging to two different emm types. A robust congruency between the methods was observed, with MLVA discriminating within clonal complexes as defined by PFGE or MLST. This new MLVA scheme can be adopted as a quick, low-cost and reliable typing method to track the short-term diffusion of GAS clones in inter-laboratory-based surveillance.
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Affiliation(s)
- Monica Imperi
- Dept. of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Valentina Pittiglio
- Health Corps Italian Army, Department of Molecular Biology, Immunology and Experimental Medicine, Army Medical and Veterinary Research Center, Rome, Italy
| | - Giuseppe D'Avenio
- Dept. of Technology and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Andrea Ciammaruconi
- Health Corps Italian Army, Department of Molecular Biology, Immunology and Experimental Medicine, Army Medical and Veterinary Research Center, Rome, Italy
| | - Florigio Lista
- Health Corps Italian Army, Department of Molecular Biology, Immunology and Experimental Medicine, Army Medical and Veterinary Research Center, Rome, Italy
| | - Christine Pourcel
- I2BC, CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Lucilla Baldassarri
- Dept. of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Creti
- Dept. of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy.
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Milan A, Furlanis L, Cian F, Bressan R, Luzzati R, Lagatolla C, Deiana ML, Knezevich A, Tonin E, Dolzani L. Epidemic Dissemination of a Carbapenem-Resistant Acinetobacter baumannii Clone Carrying armA Two Years After Its First Isolation in an Italian Hospital. Microb Drug Resist 2016; 22:668-674. [PMID: 26990617 DOI: 10.1089/mdr.2015.0167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study describes the dissemination of a carbapenem-resistant Acinetobacter baumannii (CRAB) strain in a university hospital in Northeast Italy. Characterization of the outbreak strain was combined with a retrospective analysis of all CRAB isolates collected in the same hospital during the 5 years preceding the outbreak, with the aim of elucidating the origin of the epidemic spread. The outbreak strain was shown to belong to the International Clone II and carry the blaOXA-23 gene, flanked by two ISAba1 sequences in opposite orientation (Tn2006 arrangement). The epidemic clone harbored also the blaOXA-66 allele of the carbapenemase intrinsic to A. baumannii, the determinant of ArmA 16S rRNA methylase and a class 1 integron, with the aacA4, catB8, and aadA1 cassette array. Genotype analysis, performed by macrorestriction analysis and VRBA, revealed that isolates related to outbreak strain had been sporadically collected from inpatients in the 2 years preceding outbreak start. Carriage of blaOXA-66, armA, and the integron further supported relatedness of these isolates to the outbreak clone. Outbreak initially involved three medical wards, typically hosting elderly patients with a history of prolonged hospitalization. The study highlights the need to adopt strict infection control measures also when CRAB isolation appears to be a sporadic event.
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Affiliation(s)
- Annalisa Milan
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Linda Furlanis
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Franca Cian
- 2 Department of Laboratory Medicine, Microbiology CS, Azienda Ospedaliero-Universitaria "Ospedali Riuniti," Trieste, Italy
| | - Raffaela Bressan
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Roberto Luzzati
- 3 Division of Infective Diseases, Azienda Ospedaliero-Universitaria "Ospedali Riuniti," Trieste, Italy .,4 Department of Medical, Surgical and Health Sciences, University of Trieste , Trieste, Italy
| | | | - Maria Luisa Deiana
- 2 Department of Laboratory Medicine, Microbiology CS, Azienda Ospedaliero-Universitaria "Ospedali Riuniti," Trieste, Italy
| | - Anna Knezevich
- 2 Department of Laboratory Medicine, Microbiology CS, Azienda Ospedaliero-Universitaria "Ospedali Riuniti," Trieste, Italy
| | - Enrico Tonin
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Lucilla Dolzani
- 1 Department of Life Sciences, University of Trieste , Trieste, Italy
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Azimi L, Talebi M, Khodaei F, Najafi M, Lari AR. Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis typing of carbapenemases producing Acinetobacter baumannii isolated from burn patients. Burns 2016; 42:441-5. [DOI: 10.1016/j.burns.2015.08.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/17/2015] [Accepted: 08/16/2015] [Indexed: 10/22/2022]
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Lindquist MR, López-Núñez JC, Jones MA, Cox EJ, Pinkelman RJ, Bang SS, Moser BR, Jackson MA, Iten LB, Kurtzman CP, Bischoff KM, Liu S, Qureshi N, Tasaki K, Rich JO, Cotta MA, Saha BC, Hughes SR. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates. Appl Microbiol Biotechnol 2015; 99:9723-43. [PMID: 26272089 PMCID: PMC4628078 DOI: 10.1007/s00253-015-6852-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/12/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.
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Affiliation(s)
- Mitch R Lindquist
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Juan Carlos López-Núñez
- National Coffee Research Centre - Cenicafe, National Federation of Coffee Growers of Colombia - FNC, Cenicafé Planalto Km 4 vía Antigua Chinchiná, Manizales, Caldas, Colombia
| | - Marjorie A Jones
- 4160 Department of Chemistry, Illinois State University, 214 Julian Hall, Normal, IL, 61790-4160, USA
| | - Elby J Cox
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Rebecca J Pinkelman
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Sookie S Bang
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Bryan R Moser
- USDA, ARS, NCAUR, Bio-oils Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Jackson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Loren B Iten
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Cletus P Kurtzman
- USDA, ARS, NCAUR, Bacterial Foodborne Pathogens and Mycology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Siqing Liu
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth Tasaki
- Mitsubishi Chemical, USMC Research & Innovation, 410 Palos Verdes Blvd, Redondo Beach, CA, 90277, USA
| | - Joseph O Rich
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Cotta
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Badal C Saha
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA.
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Farshadzadeh Z, Hashemi FB, Rahimi S, Pourakbari B, Esmaeili D, Haghighi MA, Majidpour A, Shojaa S, Rahmani M, Gharesi S, Aziemzadeh M, Bahador A. Wide distribution of carbapenem resistant Acinetobacter baumannii in burns patients in Iran. Front Microbiol 2015; 6:1146. [PMID: 26539176 PMCID: PMC4611150 DOI: 10.3389/fmicb.2015.01146] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/05/2015] [Indexed: 11/14/2022] Open
Abstract
Antimicrobial resistance in carbapenem non-susceptible Acinetobacter baumannii (CNSAb) is a major public health concern globally. This study determined the antibiotic resistance and molecular epidemiology of CNSAb isolates from a referral burn center in Tehran, Iran. Sixty-nine CNSAb isolates were tested for susceptibility to antimicrobial agents using the E test methodology. Multiple locus variable number tandem repeat analysis (MLVA), Multilocus sequence typing (MLST) and multiplex PCR were performed. PCR assays tested for ambler classes A, B, and D β-lactamases. Detection of ISAba1, characterization of integrons, and biofilm formation were investigated. Fifty-three (77%) isolates revealed XDR phenotypes. High prevalence of blaOXA-23-like (88%) and blaPER-1 (54%) were detected. ISAba1 was detected upstream of blaADC, blaOXA-23-like and blaOXA51-like genes in, 97, 42, and 26% of isolates, respectively. Thirty-one (45%) isolates were assigned to international clone (IC) variants. MLVA identified 56 distinct types with six clusters and 53 singleton genotypes. Forty previously known MLST sequence types forming 5 clonal complexes were identified. The Class 1 integron (class 1 integrons) gene was identified in 84% of the isolates. The most prevalent (33%) cassette combination was aacA4-catB8-aadA1. The IC variants were predominant in the A. baumannii lineage with the ability to form strong biofilms. The XDR-CNSAb from burned patients in Iran is resistant to various antimicrobials, including tigecycline. This study shows wide genetic diversity in CNSAb. Integrating the new Iranian A. baumannii IC variants into the epidemiologic clonal and susceptibility profile databases can help effective global control measures against the XDR-CNSAb pandemic.
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Affiliation(s)
- Zahra Farshadzadeh
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Sara Rahimi
- Department of Microbiology, School of Medicine, Bushehr University of Medical Sciences Bushehr, Iran
| | - Babak Pourakbari
- Pediatrics Infectious Diseases Research Center, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Davoud Esmaeili
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences Tehran, Iran
| | - Mohammad A Haghighi
- Department of Microbiology, School of Medicine, Bushehr University of Medical Sciences Bushehr, Iran
| | - Ali Majidpour
- Anti-microbial Resistance Research Center, Iran University of Medical Sciences Tehran, Iran
| | - Saeed Shojaa
- Department of Microbiology, Faculty of Medicine, Hormozgan University of Medical Sciences Bandar Abbas, Iran
| | - Maryam Rahmani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Samira Gharesi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Masoud Aziemzadeh
- Department of Microbiology, School of Medicine, Bushehr University of Medical Sciences Bushehr, Iran
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
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Ciarroni S, Gallipoli L, Taratufolo MC, Butler MI, Poulter RTM, Pourcel C, Vergnaud G, Balestra GM, Mazzaglia A. Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide. PLoS One 2015; 10:e0135310. [PMID: 26262683 PMCID: PMC4532359 DOI: 10.1371/journal.pone.0135310] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/20/2015] [Indexed: 11/18/2022] Open
Abstract
The bacterial canker of kiwifruit by Pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many Actinidia spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.
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Affiliation(s)
- Serena Ciarroni
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - Lorenzo Gallipoli
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - Maria C. Taratufolo
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - Margi I. Butler
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Christine Pourcel
- Institute for Integrative Biology of the Cell, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- ENSTA ParisTech, Université Paris-Saclay, Palaiseau, France
| | - Giorgio M. Balestra
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - Angelo Mazzaglia
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
- * E-mail:
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Najar Peerayeh S, Karmostaji A. Molecular Identification of Resistance Determinants, Integrons and Genetic Relatedness of Extensively Drug Resistant Acinetobacter baumannii Isolated From Hospitals in Tehran, Iran. Jundishapur J Microbiol 2015; 8:e27021. [PMID: 26421140 PMCID: PMC4584074 DOI: 10.5812/jjm.27021v2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 05/01/2015] [Accepted: 05/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background: Acinetobacter baumannii has emerged as an important nosocomial pathogen. Hospital outbreaks of extensively drug resistant (XDR) A. baumannii are a great concern. Objectives: Aims of this study were to characterize the resistance determinants and genetic relatedness of (XDR) A. baumannii isolates in hospitals in Tehran, Iran. Materials and Methods: During a three-year study, clinical isolates of A. baumannii were collected from two hospitals in Tehran, Iran. Susceptibility testing to antibiotics was performed by disk diffusion method and XDR A. baumannii isolates were identified. Genes’ encoding for carbapenemase production and integrons were identified by PCR. MICs of imipenem and meropenem were determined by agar dilution. Multiple locus variable-number tandem repeat analysis (MLVA) typing was used to determine genetic relationships of XDR isolates. Results: Using PCR for amplification of blaOXA-51, 93.9% (123.131) of isolates were identified as A. baumannii and 24.4% (30.123) were XDR. These isolates were resistant to gentamicin, ciprofloxacin, amikacin, cotrimoxazole, cefepime, cefotaxime, aztreonam and ceftazidime. Thirty percent of the isolates were resistant to tigecycline. All isolates were susceptible to colistin and polymyxin-B, while 93.3% (28.30) possessed blaOXA-23-like and 6.7% (2.30) possessed blaOXA-24-like. All isolates possessed insertion sequence (ISAba1) in the upstream region of the OXA-23-like gene. Almost 96.7% (29.30) of the isolates were positive for class I integron and 43.3% (13.30) for class II. These isolates were also positive for class I. Class III integron was not detected. MLVA typing of XDR isolates showed seven clonally complexes and 16 singletons. Conclusions: The population structure of the A. baumannii isolates in our hospitals was genetically diverse. A significant association between XDR pattern and presence of class 1 integron (P < 0.001) was found indicating that many antibiotic resistance determinants are involved in development of XDR strains.
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Affiliation(s)
- Shahin Najar Peerayeh
- Department of Bacteriology, Faculty of Medical Sciences, University of Tarbiat Modares, Tehran, IR Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, IR Iran
- Corresponding author: Afsaneh Karmostaji, Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, IR Iran. Tel: +98-9177614512, Fax: +98-7636670724, E-mail:
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36
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Le Minh V, Thi Khanh Nhu N, Vinh Phat V, Thompson C, Huong Lan NP, Thieu Nga TV, Thanh Tam PT, Tuyen HT, Hoang Nhu TD, Van Hao N, Thi Loan H, Minh Yen L, Parry CM, Trung Nghia HD, Campbell JI, Hien TT, Thwaites L, Thwaites G, Van Vinh Chau N, Baker S. In vitro activity of colistin in antimicrobial combination against carbapenem-resistant Acinetobacter baumannii isolated from patients with ventilator-associated pneumonia in Vietnam. J Med Microbiol 2015; 64:1162-1169. [PMID: 26297024 PMCID: PMC4755130 DOI: 10.1099/jmm.0.000137] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acinetobacter baumannii has become one of the major infection threats in intensive care units (ICUs) globally. Since 2008, A. baumannii has been the leading cause of ventilator-associated pneumonia (VAP) in our ICU at an infectious disease hospital in southern Vietnam. The emergence of this pathogen in our setting is consistent with the persistence of a specific clone exhibiting resistance to carbapenems. Antimicrobial combinations may be a strategy to treat infections caused by these carbapenem-resistant A. baumannii. Therefore, we assessed potential antimicrobial combinations against local carbapenem-resistant A. baumannii by measuring in vitro interactions of colistin with four antimicrobials that are locally certified for treating VAP. We first performed antimicrobial susceptibility testing and multilocus variable number tandem repeat analysis (MLVA) genotyping on 74 A. baumannii isolated from quantitative tracheal aspirates from patients with VAP over an 18-month period. These 74 isolates could be subdivided into 21 main clusters by MLVA and >80 % were resistant to carbapenems. We selected 56 representative isolates for in vitro combination synergy testing. Synergy was observed in four (7 %), seven (13 %), 20 (36 %) and 38 (68 %) isolates with combinations of colistin with ceftazidime, ceftriaxone, imipenem and meropenem, respectively. Notably, more carbapenem-resistant A. baumannii isolates (36/43; 84 %) exhibited synergistic activity with a combination of colistin and meropenem than carbapenem-susceptible A. baumannii isolates (2/13; 15 %) (P = 0.023; Fisher's exact test). Our findings suggest that combinations of colistin and meropenem should be considered when treating carbapenem-resistant A. baumannii infections in Vietnam, and we advocate clinical trials investigating combination therapy for VAP.
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Affiliation(s)
- Vien Le Minh
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Division of Infectious Diseases, Department of Medicine, University of California San Francisco, CA, USA
| | - Nguyen Thi Khanh Nhu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Voong Vinh Phat
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne Thompson
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK
| | - Nguyen Phu Huong Lan
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Vu Thieu Nga
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Do Hoang Nhu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Hao
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Huynh Thi Loan
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Lam Minh Yen
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Christopher M Parry
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ho Dang Trung Nghia
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - James I Campbell
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK
| | - Tran Tinh Hien
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK
| | - Louise Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK
| | - Guy Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK
| | | | - Stephen Baker
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,London School of Hygiene and Tropical Medicine, London, UK.,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Hauck Y, Soler C, Gérôme P, Vong R, Macnab C, Appere G, Vergnaud G, Pourcel C. A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes. INFECTION GENETICS AND EVOLUTION 2015; 33:233-41. [PMID: 25965840 DOI: 10.1016/j.meegid.2015.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/04/2015] [Accepted: 05/08/2015] [Indexed: 11/17/2022]
Abstract
Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential.
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Affiliation(s)
- Yolande Hauck
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France
| | - Charles Soler
- Laboratoire de biologie clinique, HIA Percy, Clamart, France
| | - Patrick Gérôme
- Service de biologie médicale, HIA Desgenettes, 69275 Lyon cedex 03, France
| | - Rithy Vong
- Laboratoire de biologie clinique, HIA Percy, Clamart, France
| | | | | | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France; ENSTA ParisTech, Université Paris-Saclay, 91762 Palaiseau cedex, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay cedex, France.
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38
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Villalón P, Valdezate S, Cabezas T, Ortega M, Garrido N, Vindel A, Medina-Pascual MJ, Saez-Nieto JA. Endemic and epidemic Acinetobacter baumannii clones: a twelve-year study in a tertiary care hospital. BMC Microbiol 2015; 15:47. [PMID: 25887224 PMCID: PMC4352537 DOI: 10.1186/s12866-015-0383-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/11/2015] [Indexed: 11/22/2022] Open
Abstract
Background Nosocomial outbreaks of multidrug-resistant Acinetobacter baumannii are of worldwide concern. Using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and multiple locus variable number tandem repeat sequence (VNTR) analysis (MLVA), the present work examines the genetic diversity of the endemic and epidemic A. baumannii clones isolated in a single hospital over a twelve-year period. Results PFGE analysis of 405 A. baumannii-calcoaceticus complex isolates detected 15 A. baumannii endemic/epidemic PFGE types (EE1 to EE15) that grouped into five clusters: EE1-EE8, EE9, EE10, EE11 and EE12-EE15. The MLST sequence type (ST) distributions were: international clone II (ST-2) 60%, international clone III (ST-3) 26.7%, ST-15 6.7%, and ST-80 6.7%. MLVA-8Orsay returned 17 allelic profiles. The large (L) VNTR marker profiles were fully concordant with the detected STs, and concordant with 14 up to 15 PFGE types. Imipenem resistance was detected in five PFGE types; the prevalence of the blaOXA-58-like and blaOXA-40-like genes was 60% and 40% respectively. Conclusions PFGE proved to be a vital tool for analysis of the temporal and spatial distribution of the clones. MLST and the VNTR L-markers grouped the isolates into clonal clusters. The wide diversity of MLVA small (S)-markers, however, did not permit clustering. The present results demonstrate the persistence of several endemic PFGE types in the hospital, the involvement of some of them in outbreaks, and the inter hospital transmission of extensively drug-resistant ST-15 and ST-80.
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Affiliation(s)
- Pilar Villalón
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
| | - Sylvia Valdezate
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
| | - Teresa Cabezas
- Laboratorio de Biotecnología Hospital de Poniente El Ejido, Almería, Spain.
| | - Montserrat Ortega
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
| | - Noelia Garrido
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
| | - Ana Vindel
- Laboratorio de Infecciones Intrahospitalarias Servicio de Bacteriología, Centro Nacional de Microbiología Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - María J Medina-Pascual
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
| | - Juan A Saez-Nieto
- Laboratorio de Taxonomía, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda-Pozuelo km2, 28220, Madrid, Majadahonda, Spain.
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39
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Rafei R, Dabboussi F, Hamze M, Eveillard M, Lemarié C, Gaultier MP, Mallat H, Moghnieh R, Husni-Samaha R, Joly-Guillou ML, Kempf M. Molecular analysis of Acinetobacter baumannii strains isolated in Lebanon using four different typing methods. PLoS One 2014; 9:e115969. [PMID: 25541711 PMCID: PMC4277430 DOI: 10.1371/journal.pone.0115969] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/03/2014] [Indexed: 12/13/2022] Open
Abstract
This study analyzed 42 Acinetobacter baumannii strains collected between 2009-2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed.
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Affiliation(s)
- Rayane Rafei
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Fouad Dabboussi
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Monzer Hamze
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Matthieu Eveillard
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Marie-Pierre Gaultier
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Hassan Mallat
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | | | - Rola Husni-Samaha
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Marie-Laure Joly-Guillou
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Marie Kempf
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
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40
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Solomennyi A, Goncharov A, Zueva L. Extensively drug-resistant Acinetobacter baumannii belonging to the international clonal lineage I in a Russian burn intensive care unit. Int J Antimicrob Agents 2014; 45:525-8. [PMID: 25604276 DOI: 10.1016/j.ijantimicag.2014.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
Abstract
The high incidence of mortality in patients with severe burns can be attributed to bloodstream infections caused by drug-resistant microorganisms. Multilocus variable-number tandem repeat analysis (MLVA), multilocus sequence typing (MLST) and class 1 integron PCR amplification were performed to investigate an extensively drug-resistant Acinetobacter baumannii (XDR-AB) strain recovered from a blood culture of a patient admitted to a burn intensive care unit in St Petersburg (Russian Federation). This case study describes an XDR-AB strain of multilocus sequence type ST231 with a blaGES-12 gene cassette encoding a very potent ceftazidimase located inside of a composite class 1 integron. This is the first documented case of XDR-AB belonging to the international clonal lineage I in Russia.
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Affiliation(s)
- Aleksandr Solomennyi
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russian Federation.
| | - Artemiy Goncharov
- I.I. Mechnikov North-Western State Medical University, St Petersburg, Russian Federation
| | - Lyudmila Zueva
- I.I. Mechnikov North-Western State Medical University, St Petersburg, Russian Federation
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41
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Rafei R, Kempf M, Eveillard M, Dabboussi F, Hamze M, Joly-Guillou ML. Current molecular methods in epidemiological typing of Acinetobacter baumannii. Future Microbiol 2014; 9:1179-94. [DOI: 10.2217/fmb.14.63] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ABSTRACT The emergence of Acinetobacter baumannii during recent decades as an important nosocomial pathogen responsible of worldwide, intensively documented, outbreaks has resulted in a need for effective epidemiological typing methods. Throughout the years, many typing methods for A. baumannii epidemiological studies have been proposed from phenotypic to molecular methods. Currently, the use of phenotypic typing methods have declined considerably and been progressively replaced by molecular methods. In this review, we introduce the current molecular methods available for A. baumannii typing. Each method has its own advantages and disadvantages, and the selection of an appropriate genotyping method depends on studied objectives. This review sheds light on questions in different epidemiological settings and most molecular methods used to fit these objectives.
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Affiliation(s)
- Rayane Rafei
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Marie Kempf
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
| | - Matthieu Eveillard
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
| | - Fouad Dabboussi
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Monzer Hamze
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Marie-Laure Joly-Guillou
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
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42
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Dugat T, Chastagner A, Lagrée AC, Petit E, Durand B, Thierry S, Corbière F, Verheyden H, Chabanne L, Bailly X, Leblond A, Vourc'h G, Boulouis HJ, Maillard R, Haddad N. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants. Parasit Vectors 2014; 7:439. [PMID: 25228371 PMCID: PMC4262125 DOI: 10.1186/1756-3305-7-439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/02/2014] [Indexed: 11/26/2022] Open
Abstract
Background Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. Methods Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. Results From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. Conclusions Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-439) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Renaud Maillard
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France.
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Nhu NTK, Lan NPH, Campbell JI, Parry CM, Thompson C, Tuyen HT, Hoang NVM, Tam PTT, Le VM, Nga TVT, Nhu TDH, Van Minh P, Nga NTT, Thuy CT, Dung LT, Yen NTT, Van Hao N, Loan HT, Yen LM, Nghia HDT, Hien TT, Thwaites L, Thwaites G, Chau NVV, Baker S. Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious disease hospital in southern Vietnam. J Med Microbiol 2014; 63:1386-1394. [PMID: 25038137 PMCID: PMC4170484 DOI: 10.1099/jmm.0.076646-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ventilator-associated pneumonia (VAP) is a serious healthcare-associated infection that affects up to 30 % of intubated and mechanically ventilated patients in intensive care units (ICUs) worldwide. The bacterial aetiology and corresponding antimicrobial susceptibility of VAP is highly variable, and can differ between countries, national provinces and even between different wards in the same hospital. We aimed to understand and document changes in the causative agents of VAP and their antimicrobial susceptibility profiles retrospectively over an 11 year period in a major infectious disease hospital in southern Vietnam. Our analysis outlined a significant shift from Pseudomonas aeruginosa to Acinetobacter spp. as the most prevalent bacteria isolated from quantitative tracheal aspirates in patients with VAP in this setting. Antimicrobial resistance was common across all bacterial species and we found a marked proportional annual increase in carbapenem-resistant Acinetobacter spp. over a 3 year period from 2008 (annual trend; odds ratio 1.656, P = 0.010). We further investigated the possible emergence of a carbapenem-resistant Acinetobacter baumannii clone by multiple-locus variable number tandem repeat analysis, finding a blaOXA-23-positive strain that was associated with an upsurge in the isolation of this pathogen. We additionally identified a single blaNDM-1-positive A. baumannii isolate. This work highlights the emergence of a carbapenem-resistant clone of A. baumannii and a worrying trend of antimicrobial resistance in the ICU of the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Phu Huong Lan
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christopher M Parry
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne Thompson
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Minh Hoang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vien Minh Le
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, CA, USA.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Vu Thieu Nga
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Do Hoang Nhu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Van Minh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Thu Nga
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Cao Thu Thuy
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Le Thi Dung
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Nguyen Van Hao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Huynh Thi Loan
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Lam Minh Yen
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Louise Thwaites
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen Baker
- The London School of Hygiene and Tropical Medicine, London, UK.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Zaluga J, Stragier P, Van Vaerenbergh J, Maes M, De Vos P. Multilocus variable-number-tandem-repeats analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium. BMC Microbiol 2013; 13:126. [PMID: 23738754 PMCID: PMC3691591 DOI: 10.1186/1471-2180-13-126] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/24/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. RESULTS A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010-2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. CONCLUSIONS We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm.
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Affiliation(s)
- Joanna Zaluga
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000, Belgium
| | - Pieter Stragier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000, Belgium
| | - Johan Van Vaerenbergh
- Plant-Crop Protection, Institute for Agricultural and Fisheries Research, ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820, Belgium
| | - Martine Maes
- Plant-Crop Protection, Institute for Agricultural and Fisheries Research, ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000, Belgium
- BCCM/LMG Bacteria collection - Laboratory of Microbiology Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000, Belgium
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45
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N'guessan CA, Brisse S, Le Roux-Nio AC, Poussier S, Koné D, Wicker E. Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot. J Microbiol Methods 2013; 92:366-74. [PMID: 23376194 DOI: 10.1016/j.mimet.2013.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 11/25/2022]
Abstract
Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum phylotypes, and more specifically for the monitoring of the monomorphic ecotypes "Moko" (banana-pathogenic) and "brown rot" (potato-pathogenic under cool conditions). Screening of six R. solanacearum genome sequences lead to select 36 VNTR loci that were preliminarily amplified on 24 strains. From this step, 26 single-locus primer pairs were multiplexed, and applied to a worldwide collection of 337 strains encompassing the whole phylogenetic diversity, with revelation on a capillary-electrophoresis genotype. Four loci were monomorphic within all phylotypes and were not retained; the other loci were highly polymorphic but displayed a clear phylotype-specificity. Phylotype-specific MLVA schemes were thus defined, based on 13 loci for phylotype I, 12 loci for phylotype II, 11 loci for phylotype III and 6 for phylotype IV. MLVA typing was significantly more discriminative than egl-based sequevar typing, particularly on monomorphic "brown rot" ecotype (phylotype IIB/sequevar 1) and "Moko disease" clade 4 (Phylotype IIB/sequevar 4). Our results raise promising prospects for studies of population genetic structures and epidemiological monitoring.
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46
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Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis typing of Acinetobacter baumannii in China. J Clin Microbiol 2013; 51:1263-8. [PMID: 23345295 DOI: 10.1128/jcm.03108-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A panel of seven variable-number tandem-repeat (VNTR) markers was selected for Acinetobacter baumannii typing analysis (MLVA-7). Compared with pulsed-field gel electrophoresis (PFGE), MLVA-7 provided greater discrimination. We modified the criteria for MLVA complex assignments proposed previously, and a remarkable congruence between MLVA-7- and PFGE-based strain clustering was observed.
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47
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Stietz MS, Ramírez MS, Vilacoba E, Merkier AK, Limansky AS, Centrón D, Catalano M. Acinetobacter baumannii extensively drug resistant lineages in Buenos Aires hospitals differ from the international clones I-III. INFECTION GENETICS AND EVOLUTION 2013; 14:294-301. [PMID: 23313831 DOI: 10.1016/j.meegid.2012.12.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/17/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
As a way to contribute to the assessment of Acinetobacter baumannii clinical population structure, multi-locus sequence typing (MLST) was performed in a collection of 93 isolates from Buenos Aires (1983-2012) and Rosario (2006-2009) hospitals. Sequence types (STs) were achieved by Bartual (B) and Institut Pasteur (P) schemes. PFGE typing, antimicrobial susceptibility assays, and the amplification of the OXA carbapenemase genes most prevalent in our region, were also performed. e-Burst clustered the 25 STs(B) (15 novels) into 5 clonal complexes (CC) and 5 singletons, and grouped the 18 STs(P) (12 novels) into 3 CC and 4 singletons. Bartual scheme divided the CC79(P) into two groups. CC113(B)/CC79(P) prevailed in Buenos Aires at least in 1992-2009, being responsible for epidemic and for endemic infections and acquiring the XDR (extensively drug-resistant) pattern throughout the years. While, CC119(B)/CC79(P) was apparently present before the CC113(B)/CC79(P)domain. CC103(B)/CC15(P) was the second most prevalent CC. Interestingly, CC110(B)/ST25(P) apparently increased over the last years. Conversely, CC109(B)/CC1(P) (international clone I) predominated in Rosario, although the presence of CC113(B)/CC79(P), CC103(B)/CC15(P) and CC110(B)/ST25(P) was observed. Nineteen novel STs clustered in CC79(P), CC15(P), CC113(B), CC109(B) and CC103(B), suggesting their clonal expansion during persistence. PFGE typing proved transmission of strains intra- and inter-hospitals in each city. Except for one, all the recent isolates (2007-2012) harboured the blaOXA-23-like. All isolates were susceptible to colistin. Tigecycline MIC(90) was 1mg/L and the rifampicin MIC>512mg/l was found among isolates in three hospitals. In conclusion, the international clone II (CC92(B)/CC2(P)) was not found among our isolates. CC113(B)/CC79(P), CC103(B)/CC15(P), and ST25(P), suggested also as major components in the A. baumannii population together with the international clone I, were present in Buenos Aires and Rosario with different prevalence rate. Their recent isolates showed high distribution of the blaOXA-23-like as well as the XDR pattern.
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Affiliation(s)
- María Silvina Stietz
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPAM, UBA-CONICET), Facultad de Medicina, Argentina
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48
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Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents 2012; 41:11-9. [PMID: 23127486 DOI: 10.1016/j.ijantimicag.2012.09.008] [Citation(s) in RCA: 359] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/22/2022]
Abstract
The rapid expansion of Acinetobacter baumannii clinical isolates exhibiting resistance to carbapenems and most or all available antibiotics during the last decade is a worrying evolution. The apparent predominance of a few successful multidrug-resistant lineages worldwide underlines the importance of elucidating the mode of spread and the epidemiology of A. baumannii isolates in single hospitals, at a country-wide level and on a global scale. The evolutionary advantage of the dominant clonal lineages relies on the capability of the A. baumannii pangenome to incorporate resistance determinants. In particular, the simultaneous presence of divergent strains of the international clone II and their increasing prevalence in international hospitals further support the ongoing adaptation of this lineage to the hospital environment. Indeed, genomic and genetic studies have elucidated the role of mobile genetic elements in the transfer of antibiotic resistance genes and substantiate the rate of genetic alterations associated with acquisition in A. baumannii of various resistance genes, including OXA- and metallo-β-lactamase-type carbapenemase genes. The significance of single nucleotide polymorphisms and transposon mutagenesis in the evolution of A. baumannii has been also documented. Establishment of a network of reference laboratories in different countries would generate a more complete picture and a fuller understanding of the importance of high-risk A. baumannii clones in the international dissemination of antibiotic resistance.
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49
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Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R. Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. PHYTOPATHOLOGY 2012; 102:948-56. [PMID: 22957820 DOI: 10.1094/phyto-04-12-0078-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.
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Affiliation(s)
- Shuai Zhao
- Institut de Recherche pour le Developpement, Montpellier, France
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50
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Diversity of Acinetobacter baumannii in four French military hospitals, as assessed by multiple locus variable number of tandem repeats analysis. PLoS One 2012; 7:e44597. [PMID: 22984530 PMCID: PMC3440325 DOI: 10.1371/journal.pone.0044597] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/06/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Infections by A. calcoaceticus-A. baumannii (ACB) complex isolates represent a serious threat for wounded and burn patients. Three international multidrug-resistant (MDR) clones (EU clone I-III) are responsible for a large proportion of nosocomial infections with A. baumannii but other emerging strains with high epidemic potential also occur. METHODOLOGY/PRINCIPAL FINDINGS We automatized a Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) protocol and used it to investigate the genetic diversity of 136 ACB isolates from four military hospitals and one childrens hospital. Acinetobacter sp other than baumannii isolates represented 22.6% (31/137) with a majority being A. pittii. The genotyping protocol designed for A.baumannii was also efficient to cluster A. pittii isolates. Fifty-five percent of A. baumannii isolates belonged to the two international clones I and II, and we identified new clones which members were found in the different hospitals. Analysis of two CRISPR-cas systems helped define two clonal complexes and provided phylogenetic information to help trace back their emergence. CONCLUSIONS/SIGNIFICANCE The increasing occurrence of A. baumannii infections in the hospital calls for measures to rapidly characterize the isolates and identify emerging clones. The automatized MLVA protocol can be the instrument for such surveys. In addition, the investigation of CRISPR/cas systems may give important keys to understand the evolution of some highly successful clonal complexes.
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