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Gaetano AS, Semeraro S, Greco S, Greco E, Cain A, Perrone MG, Pallavicini A, Licen S, Fornasaro S, Barbieri P. Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant. Microorganisms 2024; 12:965. [PMID: 38792794 PMCID: PMC11124041 DOI: 10.3390/microorganisms12050965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.
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Affiliation(s)
- Anastasia Serena Gaetano
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Enrico Greco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Andrea Cain
- ACEGAS APS AMGA S.p.a., Via degli Alti Forni, 11, 34121 Trieste, Italy;
| | | | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Sabina Licen
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Stefano Fornasaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Pierluigi Barbieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
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De Blasiis MR, Sciurti A, Baccolini V, Isonne C, Ceparano M, Iera J, De Vito C, Marzuillo C, Villari P, Migliara G. Impact of antibiotic exposure on antibiotic-resistant Acinetobacter baumannii isolation in intensive care unit patients: a systematic review and meta-analysis. J Hosp Infect 2024; 143:123-139. [PMID: 37972711 DOI: 10.1016/j.jhin.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Acinetobacter baumannii (AB) poses a significant threat to critically ill patients in intensive care units (ICUs). Although an association between antibiotic exposure and resistant AB is reported in the literature, a synthesis of evidence in ICU patients is still lacking. AIM To summarize the evidence on the association between prior antibiotic exposure and the occurrence of resistant AB in ICU patients. METHODS Online databases were searched for cohort and case-control studies providing data on the association of interest. Carbapenem/multidrug-resistant AB isolation was compared with non-isolation; carbapenem/multidrug-resistant AB was compared with carbapenem/antibiotic-susceptible AB; and extensively drug-resistant AB isolation was compared with non-isolation. Each comparison was subjected to a restricted maximum likelihood random-effects meta-analysis per antibiotic class, estimating pooled ORs. Stratified meta-analyses were performed by study design, outcome type and association-measure adjustment. FINDINGS Overall, 25 high-quality studies were retrieved. Meta-analyses showed that carbapenem/multidrug-resistant AB isolation was associated with previous exposure to aminoglycosides, carbapenems, third-generation cephalosporines, glycylcyclines, and nitroimidazoles. Increased risk of isolation of carbapenem/multidrug-resistant AB isolation vs carbapenem/antibiotic-susceptible AB was shown for prior exposure to aminoglycosides, antipseudomonal penicillins, carbapenems, fluoroquinolones, glycopeptides, and penicillins. Third-generation cephalosporin exposure increased the risk of extensively drug-resistant AB isolation vs non-isolation. CONCLUSION This systematic review clarifies the role of antibiotic use in antibiotic-resistant AB spread in ICUs, although for some antibiotic classes the evidence is still uncertain due to the small number of adjusted analyses, methodological and reporting issues, and limited number of studies. Future studies need to be carried out with standardized methods and appropriate reporting of multivariable models.
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Affiliation(s)
- M R De Blasiis
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - A Sciurti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.
| | - V Baccolini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - C Isonne
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - M Ceparano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - J Iera
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy; Management and Health Laboratory, Institute of Management, Department EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - C De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - C Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - P Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - G Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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Kareem SM. Emergence of mcr- and fosA3-mediated colistin and fosfomycin resistance among carbapenem-resistant Acinetobacter baumannii in Iraq. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Balfousias T, Apostolopoulos A, Angelis S, Filippou D, Maris S. Pandrug-resistant Acinetobacter Baumannii Infection Identified in a Non-intensive Care Unit Patient: A Case Study. Cureus 2019; 11:e6321. [PMID: 31938612 PMCID: PMC6946043 DOI: 10.7759/cureus.6321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Acinetobacter baumannii is a major cause of hospital-acquired infections, particularly in patients treated in intensive care units (ICUs). It can be a causal agent of conditions like pneumonia, bacteremia, meningitis, soft-tissue, and urinary tract infections, and is associated with high mortality rates. We present a case of a 72-year-old male patient treated for fractured neck of femur who went on to develop an infection from a pandrug-resistant Acinetobacter baumannii isolated in blood and urine cultures during his hospitalization in trauma and orthopedic ward. The patient was operated on the second day following his injury with a cephalomedullary nail device and became febrile with rigors on day six. His clinical condition deteriorated over the next days and his inflammatory markers reached a peak value on day 10 post-injury. Acinetobacter baumannii was isolated from blood and urine cultures and a regimen combining rifampicin, tigecycline, and vancomycin in their maximum doses was initiated. The patient was discharged on day 26 post-injury. Before discharge, he had received the above-mentioned intravenous antibiotic regimen for 14 days. He had also been afebrile for six days and undergone three consecutive negative blood culture samples.
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Affiliation(s)
- Theodore Balfousias
- Orthopaedics, General Hospital Hellenic Red Cross Korgialenio Benakio, Athens, GRC
| | - Alexandros Apostolopoulos
- Orthopaedics, East Surrey Hospital Surrey and Sussex Healthcare National Health Service Trust, Redhill, GBR
| | - Stavros Angelis
- Orthopaedics, General Hospital Hellenic Red Cross Korgialenio Benakio, Athens, GRC
| | - Dimitrios Filippou
- Surgery, Medical School of National and Kapodistrian University of Athens, Athens, GRC
| | - Spyridon Maris
- Orhopaedics, General Hospital Hellenic Red Cross Korgialenio Benakio, Athens, GRC
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Atik TK, Atik B, Kilinç O, Bektöre B, Duran H, Selek BM, Ceken N, Baylan O, Özyurt M. Epidemiological evaluation of an Acinetobacter baumannii outbreak observed at an intensive care unit. Saudi Med J 2018; 39:767-772. [PMID: 30106413 PMCID: PMC6194996 DOI: 10.15537/smj.2018.8.22431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Objectives: To reveal the relationship between clinical and environmental isolates, analyzing both phenotypic and molecular aspects, in an Acinetobacter baumannii (A. baumannii) epidemic, and to use the epidemiological data to determine the source of the epidemic, to identify potential risk factors, and inform the effort to prevent and manage future epidemics. Methods: Acinetobacter baumannii was isolated from 5 clinical samples in Sultan Abdulhamid Han Training and Research hospital, Istanbul, Turkey, for a week period. To determine potential sources of infection we established cultures surveillance. Microbiological identification and antibiotic susceptibility testing of A. baumannii were performed using conventional methods and automated identification system. Multiplex polymerase chain reaction (PCR) and pulsed-field gel electrophoresis (PFGE) were used for carbapenemase gene screening and clonal relationship evaluation. Results: Among the environmental samples, bacterial growth was observed in 3 of the sample cultures. Clinical and environmental samples collected from patients X and Y had phenotypically similar antibiotic susceptibility patterns. The clinical and environmental isolates from patients X and Y comprised the first cluster (6 isolates), the isolates from patient Z formed the second cluster (2 isolates). Conclusion: We detected that all outbreak-related isolates contained the same OXA-type carbapenemase genes. Phenotypic similarity, based on the analysis of antimicrobial susceptibility patterns, was correlated with genotypic similarity. These results suggest that monitoring antimicrobial resistance patterns with daily culture surveillance follow-ups, coupled with the use of amplification based methods to detect that clonal relationships are important for the early identification of outbreaks and rapid deployment of proper countermeasures to halt the spread of the causative agent.
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Affiliation(s)
- Tuğba K. Atik
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Bülent Atik
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
- Address correspondence and reprint request to: Dr. Tuğba K. Atik, Department of Microbiology, Balıkesir Atatürk City hospital, Balıkesir, Turkey. E-mail: ORCID ID: orcid.org/0000-0002-2433-1977
| | - Osman Kilinç
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Bayhan Bektöre
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Hülya Duran
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Burak M. Selek
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Nihan Ceken
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Orhan Baylan
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
| | - Mustafa Özyurt
- From the Department of Microbiology (K. Atik, Kilinç), and from the Department of Anesthesiology and Reanimation clinic (Atik), Balıkesir Atatürk City hospital, from the Department of Microbiology (Duran, çeken), Balıkesir Public hospital, Balıkesir, from the Department of Microbiology (Bektöre), Kars Harakani Public hospital, Kars, and from the Department of Microbiology (selek, Baylan, özyurt), Sultan Abdulhamid Han Training and Research hospital, Health Sciences University, İstanbul, Turkey
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Lim CLL, Chua AQ, Teo JQM, Cai Y, Lee W, Kwa ALH. Importance of control groups when delineating antibiotic use as a risk factor for carbapenem resistance, extreme-drug resistance, and pan-drug resistance in Acinetobacter baumannii and Pseudomonas aeruginosa: A systematic review and meta-analysis. Int J Infect Dis 2018; 76:48-57. [PMID: 29870795 DOI: 10.1016/j.ijid.2018.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/10/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Carbapenem-resistant (CR), extremely drug-resistant (XDR), and pan-drug-resistant (PDR) Acinetobacter baumannii and Pseudomonas aeruginosa pose a huge clinical threat. This study reviews the impact of control groups on the association of antecedent antibiotic use and the acquisition of CR/XDR/PDR A. baumannii and P. aeruginosa. METHODS Studies investigating the role of antibiotics as a risk factor for CR/XDR/PDR A. baumannii and P. aeruginosa acquisition in adult hospitalized patients from 1950 to 2016 were identified in the databases. These were divided into two groups: antibiotic-resistant versus antibiotic-sensitive pathogens (group I); antibiotic-resistant versus no infection (group II). A random-effects model was performed. RESULTS Eighty-five studies (46 A. baumannii, 38 P. aeruginosa, and one of both) involving 22 396 patients were included. CR was investigated in 60 studies, XDR in 20 studies, and PDR in two studies. Prior antibiotic exposure was associated with significant acquisition of CR/XDR/PDR A. baumannii and P. aeruginosa in both groups I and II (p<0.05). Antibiotic classes implicated in both groups included aminoglycosides, carbapenems, glycopeptides, and penicillins. Cephalosporin use was not associated with resistance in either group. Fluoroquinolone exposure was only associated with resistance in group I but not group II. CONCLUSIONS Control groups play an important role in determining the magnitudes of risk estimates for risk factor studies, hence careful selection is necessary. Antibiotic exposure increases the acquisition of highly resistant A. baumannii and P. aeruginosa, thus appropriate antibiotic use is imperative.
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Affiliation(s)
- Cheryl Li Ling Lim
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
| | - Alvin Qijia Chua
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Jocelyn Qi Min Teo
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Yiying Cai
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Winnie Lee
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Outram Road, Singapore 169608, Singapore; Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857, Singapore; Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
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Bloodstream infections caused by Acinetobacter species with reduced susceptibility to tigecycline: clinical features and risk factors. Int J Infect Dis 2017; 62:26-31. [PMID: 28676346 DOI: 10.1016/j.ijid.2017.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/02/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION During recent decades, the rates of multidrug resistance, including resistance to carbapenems, have increased dramatically among Acinetobacter species. Tigecycline has activity against multidrug-resistant Acinetobacter spp, including carbapenem-resistant isolates. However, reports of tigecycline-resistant Acinetobacter spp are emerging from different parts of the world. The purpose of this study was to evaluate potential risk factors associated with tigecycline non-susceptible Acinetobacter bacteremia. METHODS The medical records of 152 patients with Acinetobacter bacteremia attending Samsung Medical Center between January 2010 and December 2014 were reviewed. Non-susceptibility to tigecycline was defined as a minimum inhibitory concentration (MIC) of tigecycline ≥4μg/ml. Cases were patients with tigecycline non-susceptible Acinetobacter bacteremia and controls were those with tigecycline-susceptible Acinetobacter bacteremia. RESULTS Of the 152 patients included in the study, 61 (40.1%) had tigecycline non-susceptible Acinetobacter bacteremia (case group). These patients were compared to 91 patients with tigecycline-susceptible Acinetobacter bacteremia (control group). The case group showed high resistance to other antibiotics (>90%) except colistin (6.6%) and minocycline (9.8%) when compared to the control group, which exhibited relatively low resistance to other antibiotics (<50%). Multivariate analysis showed that recent exposure to corticosteroids (minimum 20mg per day for more than 5 days within 2 weeks) (adjusted odds ratio (OR) 2.887, 95% confidence interval (CI) 1.170-7.126) and carbapenems (within 2 weeks) (adjusted OR 4.437, 95% CI 1.970-9.991) were significantly associated with tigecycline non-susceptible Acinetobacter bacteremia. Although prior exposure to tigecycline was more common in the case group than in the control group (9.8%, 6/61 vs. 2.2%, 2/91; p=0.046), this variable was found not to be a significant factor associated with tigecycline non-susceptibility after adjustment for other variables (adjusted OR 1.884, 95% CI 0.298-11.920; p=0.501). CONCLUSIONS These data suggest that tigecycline non-susceptible Acinetobacter spp have emerged and disseminated in the hospital in association with a recent exposure to carbapenems and an immunosuppressed state. This indicates that the rational use of antibiotics through a comprehensive antimicrobial stewardship program, especially in immunosuppressed patients, may be essential in limiting the emergence and spread of multidrug-resistant organisms such as tigecycline-resistant Acinetobacter spp, which are difficult to treat.
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Genomic and phenotypic characterization of the species Acinetobacter venetianus. Sci Rep 2016; 6:21985. [PMID: 26902269 PMCID: PMC4763211 DOI: 10.1038/srep21985] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
Crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. The potential use of microbes as bioremediation agents is one of the most promising fields in this area. Members of the species Acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement this process. Although a preliminary experimental characterization of the overall hydrocarbon degradation capability has been performed for five of them, to date, the genetic/genomic features underlying such molecular processes have not been identified. Here we have integrated genomic and phenotypic information for six A. venetianus strains, i.e. VE-C3, RAG-1T, LUH 13518, LUH 7437, LUH 5627 and LUH 8758. Besides providing a thorough description of the A. venetianus species, these data were exploited to infer the genetic features (presence/absence patterns of genes) and the short-term evolutionary events possibly responsible for the variability in n-alkane degradation efficiency of these strains, including the mechanisms of interaction with the fuel droplet and the subsequent catabolism of this pollutant.
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Inchai J, Liwsrisakun C, Theerakittikul T, Chaiwarith R, Khositsakulchai W, Pothirat C. Risk factors of multidrug-resistant, extensively drug-resistant and pandrug-resistant Acinetobacter baumannii ventilator-associated pneumonia in a Medical Intensive Care Unit of University Hospital in Thailand. J Infect Chemother 2015; 21:570-4. [PMID: 26026660 DOI: 10.1016/j.jiac.2015.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/23/2022]
Abstract
Ventilator-associated pneumonia (VAP) caused by Acinetobacter baumannii remains a significant cause of morbidity and mortality. Increasing antimicrobial resistance influences the selection of antibiotic treatment especially pandrug-resistant A. baumannii. A retrospective cohort study was conducted in the Medical Intensive Care Unit to identify the risk factors of VAP caused by multidrug-resistant A. baumannii (MDR-AB), extensively drug-resistant A. baumannii (XDR-AB) and pandrug-resistant A. baumannii (PDR-AB). All 337 adult patients with confirmed A. baumannii VAP were included. The incidence of MDR-AB, XDR-AB and PDR-AB were 72 (21.4%), 220 (65.3%) and 12 (3.6%), respectively. The risk factor for MDR-AB was prior use of carbapenems (OR 5.20; 95% CI 1.41-19.17). Risk factors for XDR-AB were the prior use of carbapenems (OR, 6.30; 95% CI, 1.80-21.97) and a high Sequential Organ Failure Assessment (SOFA) score (OR 1.35; 95% CI 1.07-1.71). In PDR-AB, the risk factors were the prior use of colistin (OR, 155.95; 95% CI, 8.00-3041.98), carbapenems (OR, 12.84; 95% CI, 1.60-103.20) and a high Simplified Acute Physiology Score (SAPS II) (OR 1.10; 95% CI 1.01-1.22). In conclusion, previous exposure to antibiotics and severity of VAP were risk factors of drug-resistant A. baumannii. Judicious use of carbapenems and colistin is recommended to prevent the antimicrobial-resistant strains of this organism.
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Affiliation(s)
- Juthamas Inchai
- Division of Pulmonary, Critical Care and Allergy, Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chalerm Liwsrisakun
- Division of Pulmonary, Critical Care and Allergy, Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Theerakorn Theerakittikul
- Division of Pulmonary, Critical Care and Allergy, Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Romanee Chaiwarith
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Chaicharn Pothirat
- Division of Pulmonary, Critical Care and Allergy, Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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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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Risk factors for nosocomial burn wound infection caused by multidrug resistant Acinetobacter baumannii. J Burn Care Res 2014; 35:e73-80. [PMID: 23799478 DOI: 10.1097/bcr.0b013e31828a493f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Acinetobacter baumannii infections in burn patients may lead to delays in wound healing, graft losses, and development of sepsis. Determining the risk factors for multidrug resistant A. baumannii (MDR-AB) infections is essential for infection control. In the present study, the authors aimed to evaluate risk factors for wound infections caused by A. baumannii in burn patients. The study was conducted at Dicle University Hospital Burn Center, from April 2011 to July 2012, to investigate the risk factors for MDR-AB infections. The data of both the case and control group patients and the result of wound cultures were recorded on a daily basis, on individual forms given for each patient, and analyzed. A total of 30 cases infected with MDR-AB, and 60 uninfected control patients, were included in the study. The mean age (±SD) was 7.7 ± 15.4 years in infected patients and 11.4 ± 16.5 years in uninfected patients. The mean total burn surface area was 13.5 ± 10.9% in uninfected patients and 34.7 ± 16.2% in infected patients. The mean total burn surface area, the abbreviated burn severity index, acute physiological and chronic health evaluation II score, day of admission to hospital, length of hospital stay, first excision day, prior usage of third-generation cephalosporins, and stay in intensive care unit of the infected patients were significantly higher (P < .001) than those of patients without infection. Univariate analysis found that high acute physiological and chronic health evaluation II score, first excision time of wound, invasive device usage, admission day to hospital, and prior usage of broad-spectrum antibiotics were risk factors for nosocomial infections. This study showed that multiple factors contribute to multidrug resistance in A. baumannii. A combination of an early diagnosis of wound infections, appropriate antimicrobial treatments, surgical debridement, and early wound closure may be effective in the management.
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Anti-multidrug-resistant Acinetobacter baumannii activity of DS-8587: In vitro activity and in vivo efficacy in a murine calf muscle infection model. J Infect Chemother 2014; 20:312-6. [DOI: 10.1016/j.jiac.2014.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/11/2014] [Accepted: 01/26/2014] [Indexed: 11/16/2022]
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Hojabri Z, Pajand O, Bonura C, Aleo A, Giammanco A, Mammina C. Molecular epidemiology of Acinetobacter baumannii in Iran: endemic and epidemic spread of multiresistant isolates. J Antimicrob Chemother 2014; 69:2383-7. [DOI: 10.1093/jac/dku045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chan MC, Chiu SK, Hsueh PR, Wang NC, Wang CC, Fang CT. Risk factors for healthcare-associated extensively drug-resistant Acinetobacter baumannii infections: a case-control study. PLoS One 2014; 9:e85973. [PMID: 24465819 PMCID: PMC3897568 DOI: 10.1371/journal.pone.0085973] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/03/2013] [Indexed: 02/06/2023] Open
Abstract
The emergence of extensively drug-resistant Acinetobacter baumannii (XDRAB) is a serious threat to hospitalized patients. From 2008 to 2010, surveillance detected 25 hospital-acquired infection (HAI) cases caused by XDRAB at a medical center in Taipei. The site of XDRAB infection was bloodstream (n = 8), urinary tract (n = 12), lower respiratory tract (n = 3), surgical site (n = 1), and cardiovascular (n = 1). The isolates were resistant to all currently available antibiotics except for colistin. The XDRAB isolates are genetically diverse, shown by pulsed-field gel electrophoresis, but 23 of 25 harbored class 1 integron with a 2.3-kb gene cassette. Most of these isolates carry OXA-23 (n = 21) and OXA-51-like carbapenemase genes (n = 25). To identify the risk factors, a case-control study was conducted. The 25 cases were compared with 100 controls randomly selected from hospitalized patients without XDRAB-HAIs, matched by the onset date, ward, and age, at a ratio of 1∶4. Prior use of imipenem, meropenem, piperacillin/tazobactam or fourth-generation cephalosporins (adjusted OR: 3.2, 95% CI: 1.03–10.2, P = 0.04) and >30 days bed-ridden (adjusted OR: 6.0, 95% CI: 1.3–27.6, P = 0.02) were found to be the independent risk factors for XDRAB-HAIs. These findings highlight that, even in the absence of clonal dissemination, XDRAB can emerge under the selective pressure of broad-spectrum antibiotics and causes subsequent HAIs in compromised hosts. An appropriate response to the XDRAB threat therefore should include a component of prudent use of broad-spectrum antibiotics active against gram-negative bacteria.
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Affiliation(s)
- Ming-Chin Chan
- Infection Control Office, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sheng-Kang Chiu
- Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ning-Chi Wang
- Infection Control Office, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Chien Wang
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- * E-mail: (CTF); (CCW)
| | - Chi-Tai Fang
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- * E-mail: (CTF); (CCW)
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15
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Ng TM, Teng CB, Lye DC, Apisarnthanarak A. A multicenter case-case control study for risk factors and outcomes of extensively drug-resistant Acinetobacter baumannii bacteremia. Infect Control Hosp Epidemiol 2013; 35:49-55. [PMID: 24334798 DOI: 10.1086/674387] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Extensively drug resistant (XDR) Acinetobacter baumannii infections are increasing. Knowledge of risk factors can help to prevent these infections. METHODS We designed a 1∶1∶1 case-case-control study to identify risk factors for XDR A. baumannii bacteremia in Singapore and Thailand. Case group 1 was defined as having infection due to XDR A. baumannii, and case group 2 was defined as having infection due to non-XDR A. baumannii. The control group comprised patients with blood cultures obtained to determine possible infection. RESULTS There were 93 patients in each group. Pitt bacteremia score (adjusted odds ratio [aOR], 2.570 [95% confidence interval (CI), 1.528-4.322]), central venous catheters (CVCs; aOR, 12.644 [95% CI, 2.143-74.620]), use of carbapenems (aOR, 54.391 [95% CI, 3.869-764.674]), and piperacillin-tazobactam (aOR, 55.035 [95% CI, 4.803-630.613]) were independently associated with XDR A. baumannii bacteremia. In case group 2, Pitt bacteremia score (aOR, 1.667 [95% CI, 1.265-2.196]) and third-generation cephalosporins (aOR, 2.965 [95% CI, 1.224-7.182]) were independently associated with non-XDR A. baumannii bacteremia. Concurrent infections (aOR, 3.527 [95% CI, 1.479-8.411]), cancer (aOR, 3.172 [95% CI, 1.135-8.865]), and respiratory source (aOR, 2.690 [95% CI, 1.160-6.239]) were associated with an increased risk of 30-day mortality. Survivors received more active empirical therapy (16.7% vs 9.6%; P = .157), had fewer cases of XDR bacteremia (45.8% vs 52.6%; P = .452), and received higher median definitive polymyxin B doses (840,000 units vs 700,000 units; P = .339) CONCLUSIONS: Use of CVC and broad spectrum antibiotics were unique risk factors of XDR A. baumannii bacteremia. Effective antimicrobial stewardship together with use of a CVC bundle may reduce the incidence of these infections. Risk factors of acquisition and mortality may help identify patients for early initiation of polymyxin B therapy.
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Affiliation(s)
- Tat Ming Ng
- Department of Pharmacy, Tan Tock Seng Hospital, Singapore
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Types and prevalence of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex in Northern Taiwan. Antimicrob Agents Chemother 2013; 58:201-4. [PMID: 24145535 DOI: 10.1128/aac.00779-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The frequency of the carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (CRACB) complex increases annually in our hospitals. However, the types and prevalence of carbapenemases among isolates still remain unclear. In this study, we identified and collected 672 carbapenem-resistant isolates from a medical center in Northern Taiwan between April and December of 2010. There were 577 genospecies 2 (Acinetobacter baumannii), 79 genospecies 13TU, and 16 genospecies 3 isolates. The isolates had an acquired blaOXA-24-like gene, which was confirmed by sequencing for the encoded OXA-72 carbapenemase, and were often associated with high-level carbapenem resistance. These CRACB complex isolates remained susceptible to colistin (100%). The genotyping of isolates was conducted using pulsed-field gel electrophoresis with ApaI digestion. In most clonally related groups, patients were from both branch hospitals. The results indicate that interhospital dissemination of clones occurred. This study provides updated data on the types and prevalence of the CRACB complex. In addition, it presents a warning on the emergence and spread of CRACB complex harboring blaOXA-24-like genes in northern Taiwan.
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Medina-Presentado JC, Seija V, Vignoli R, Pontet J, Robino L, Cordeiro NF, Bado I, García-Fulgueiras V, Berro M, Bazet C, Savio E, Rieppi G. Polyclonal endemicity of Acinetobacter baumannii in ventilated patients in an intensive care unit in Uruguay. Int J Infect Dis 2013; 17:e422-7. [PMID: 23415583 DOI: 10.1016/j.ijid.2012.12.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/21/2012] [Accepted: 12/31/2012] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES To identify the mechanisms responsible for respiratory infections by Acinetobacter baumannii in intubated patients and risk factors for digestive colonization and infection by A. baumannii. METHODS We conducted a prospective study in an intensive care unit (ICU) between May 2005 and November 2006, including 175 consecutive patients at the beginning of invasive ventilation (day 1). We performed pharyngeal and rectal swabs on days 1, 4, 7, 10, 13, and 16. Respiratory samples were taken on days 1 and 7, or on suspicion of ventilator-associated pneumonia (VAP). RESULTS We detected 62 patients with A. baumannii digestive colonization and 20 cases of A. baumannii lower respiratory infection (14 VAP and six purulent tracheobronchitis (PTB)). Digestive colonization by A. baumannii was an independent risk factor for lower respiratory tract infections with that microorganism (p<0.0001; relative risk 8.71, 95% confidence interval 2.73-27.77). Respiratory and rectal A. baumannii isolates from the same patients were compared by enterobacterial repetitive intergenic consensus (ERIC)-PCR; in 9/11 cases (eight VAP and one PTB) results suggested events of exogenous pneumonia with previous colonization, whereas the remaining two cases (two PTB) were suggestive of exogenous infection without previous colonization. CONCLUSIONS In our unit the pathogenesis of VAP by A. baumannii is mixed, most cases corresponding to exogenous pneumonia with previous colonization.
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Affiliation(s)
- Julio Cesar Medina-Presentado
- Cátedra de Enfermedades Infecciosas, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, Montevideo, 11600, Uruguay.
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Cao J, Song W, Gu B, Mei YN, Tang JP, Meng L, Yang CQ, Wang H, Zhou H. Correlation between carbapenem consumption and antimicrobial resistance rates of Acinetobacter baumannii in a university-affiliated hospital in China. J Clin Pharmacol 2013; 53:96-102. [PMID: 23400749 DOI: 10.1177/0091270011435988] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 12/17/2011] [Indexed: 11/16/2022]
Abstract
To investigate the correlation between carbapenem consumption and rates of antimicrobial resistance in Acinetobacter baumannii, carbapenem consumption was expressed as defined daily dose based on the World Health Organization (WHO) anatomical therapeutic chemical classification index. Clinical isolates from 2001-2009 were collected and analyzed using WHONET 5.4 software. Results show that the consumption of imipenem/cilastatin, meropenem, and total carbapenem is significantly correlated with imipenem resistance in A baumannii (r = 0.818, P = .007; r = 0.817, P = .007; r = 0.827, P = .006). Furthermore, total carbapenem consumption is significantly correlated with meropenem resistance in A baumannii (r = 0.900, P = .037). In addition, consumption of imipenem/cilastatin, meropenem, and total carbapenem is associated with A baumannii resistance to piperacillin-tazobactam, ceftazidime, cefepime, amikacin, and levofloxacin. These drugs are mainly β-lactams, aminoglycosides, and fluoroquinolones. The imipenem and meropenem resistance rates are significantly correlated with resistance rates to numerous antimicrobial drugs (eg, β-lactams, aminoglycosides, and fluoroquinolones) in A baumannii. Therefore, increased consumption of carbapenem may contribute to the development of resistance in A baumannii to imipenem, meropenem, and other antimicrobial drugs. Cross-resistance possibly occurs among imipenem/cilastatin and meropenem, as well as with β-lactams, aminoglycosides, and fluoroquinolones.
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Affiliation(s)
- Jia Cao
- Department of Pharmacy, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R., China.
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19
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D. Vaze N, L. Emery C, J. Hamilton R, D. Brooks A, G. Joshi S. Patient Demographics and Characteristics of Infection with Carbapenem-Resistant <i>Acinetobacter baumannii</i> in a Teaching Hospital from the United States. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aid.2013.31002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Jang IH, Park SD, Uh Y, Lee GS, Kim JB, Choi I. Molecular Characteristics of blaOXA-23-Producing Acinetobacter baumanniiIsolated from a University Hospital. ANNALS OF CLINICAL MICROBIOLOGY 2013. [DOI: 10.5145/acm.2013.16.3.126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- In-Ho Jang
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Soon Deok Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Gyu-sang Lee
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, Korea
| | - Jong-Bae Kim
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, Korea
| | - Il Choi
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sangi University, Wonju, Korea
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Fernández-Cuenca F, Tomás-Carmona M, Caballero-Moyano F, Bou G, Martínez-Martínez L, Vila J, Pachón J, Cisneros JM, Rodríguez-Baño J, Pascual Á. Actividad de 18 agentes antimicrobianos frente a aislados clínicos de Acinetobacter baumannii: segundo estudio nacional multicéntrico (proyecto GEIH-REIPI-Ab 2010). Enferm Infecc Microbiol Clin 2013; 31:4-9. [DOI: 10.1016/j.eimc.2012.06.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 01/14/2023]
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Chan JZM, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012; 12:302. [PMID: 23259572 PMCID: PMC3556118 DOI: 10.1186/1471-2180-12-302] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. RESULTS In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. CONCLUSION We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin's vision of classification becoming, as far as is possible, genealogical.
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Affiliation(s)
- Jacqueline Z-M Chan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Mihail R Halachev
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Chrystala Constantinidou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Mark J Pallen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Lee HY, Chang RC, Su LH, Liu SY, Wu SR, Chuang CH, Chen CL, Chiu CH. Wide spread of Tn2006 in an AbaR4-type resistance island among carbapenem-resistant Acinetobacter baumannii clinical isolates in Taiwan. Int J Antimicrob Agents 2012; 40:163-7. [PMID: 22743015 DOI: 10.1016/j.ijantimicag.2012.04.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/19/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022]
Abstract
Carbapenem resistance in Acinetobacter baumannii is a global problem. The purpose of this study was to elucidate current resistance mechanisms of imipenem-resistant A. baumannii (IRAB) in Taiwan and their correlation with patient outcomes. Acinetobacter baumannii clinical isolates from two teaching hospitals in Taiwan were collected in 2009 and were examined by Etest for determination of the minimum inhibitory concentrations (MICs) of imipenem, ceftazidime and ceftriaxone. Primers specific for carbapenemase genes and upstream regions were designed for PCR amplification. Bacterial isolates were genotyped by pulsed-field gel electrophoresis (PFGE). Clinical presentations of patients were analysed retrospectively. Upstream insertion sequence ISAba1 was found in 34 isolates that carried bla(OXA-23), including 28 with transposon Tn2006 (ISAba1-bla(OXA-23)-ISAba1) in an AbaR4-type resistance island and 6 with Tn2008 (ISAba1-bla(OXA-23)), as well as in 8 isolates carrying ISAba1-bla(OXA-51-like). All of these isolates expressed full resistance to imipenem (MIC>32 mg/L). Forty-one different PFGE genotypes were found among 62 isolates. Tn2006 was found in 19 genotypes (46.3%), which is more common than ISAba1-bla(OXA-51-like) (12.2%) (P=0.001). Prior use of carbapenems or extended-spectrum cephalosporins for ≥5 days was the only independent risk factor significantly associated with IRAB infection (odds ratio=361.175). Higher mortality was significantly associated with infection caused by IRAB and ISAba1-bla(OXA-23)-carrying strains compared with infection caused by imipenem-susceptible A. baumannii and ISAba1-bla(OXA-51-like)-carrying strains (P=0.009 and 0.027, respectively). Tn2006 is currently the most common imipenem resistance determinant, which showed a higher ability to spread among A. baumannii and was associated with a higher mortality in IRAB-infected patients.
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Affiliation(s)
- Hao-Yuan Lee
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
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Lee G, Lee JH, Lim K, Suh IB, Ryu SW, Eom YB, Kim SH, Park M, Kim JB. Prevalence of multidrug-resistant Acinetobacter baumannii producing OXA-23-like from a healthcare facility of Gangwon Province, South Korea. Int J Antimicrob Agents 2012; 39:452-3. [PMID: 22421331 DOI: 10.1016/j.ijantimicag.2012.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/11/2012] [Accepted: 01/11/2012] [Indexed: 10/28/2022]
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25
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Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2012; 65:455-78. [PMID: 21740228 DOI: 10.1146/annurev-micro-090110-102911] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
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Affiliation(s)
- Karen Bush
- Biology Department, Indiana University, Bloomington, Indiana 47401, USA.
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Netsvyetayeva I, Sikora M, Golas M, Swoboda-Kopec E, Walter de Walthoffen S, Dembicka O, Fraczek M, Mlynarczyk A, Pacholczyk M, Chmura A, Mlynarczyk G. Acinetobacter baumannii Multidrug-Resistant Strain Occurrence in Liver Recipients With Reference to Other High-Risk Groups. Transplant Proc 2011; 43:3116-20. [DOI: 10.1016/j.transproceed.2011.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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