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Tkalec KI, Hayes AJ, Lim KS, Lewis JM, Davies MR, Scott NE. Glycan-Tailored Glycoproteomic Analysis Reveals Serine is the Sole Residue Subjected to O-Linked Glycosylation in Acinetobacter baumannii. J Proteome Res 2024. [PMID: 38850255 DOI: 10.1021/acs.jproteome.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein glycosylation is a ubiquitous process observed across all domains of life. Within the human pathogen Acinetobacter baumannii, O-linked glycosylation is required for virulence; however, the targets and conservation of glycosylation events remain poorly defined. In this work, we expand our understanding of the breadth and site specificity of glycosylation within A. baumannii by demonstrating the value of strain specific glycan electron-transfer/higher-energy collision dissociation (EThcD) triggering for bacterial glycoproteomics. By coupling tailored EThcD-triggering regimes to complementary glycopeptide enrichment approaches, we assessed the observable glycoproteome of three A. baumannii strains (ATCC19606, BAL062, and D1279779). Combining glycopeptide enrichment techniques including ion mobility (FAIMS), metal oxide affinity chromatography (titanium dioxide), and hydrophilic interaction liquid chromatography (ZIC-HILIC), as well as the use of multiple proteases (trypsin, GluC, pepsin, and thermolysis), we expand the known A. baumannii glycoproteome to 33 unique glycoproteins containing 42 glycosylation sites. We demonstrate that serine is the sole residue subjected to glycosylation with the substitution of serine for threonine abolishing glycosylation in model glycoproteins. An A. baumannii pan-genome built from 576 reference genomes identified that serine glycosylation sites are highly conserved. Combined this work expands our knowledge of the conservation and site specificity of A. baumannii O-linked glycosylation.
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Affiliation(s)
- Kristian I Tkalec
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Kataleen S Lim
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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2
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Savin M, Sib E, Heinemann C, Eichel VM, Nurjadi D, Klose M, Andre Hammerl J, Binsker U, Mutters NT. Tracing clinically-relevant antimicrobial resistances in Acinetobacter baumannii-calcoaceticus complex across diverse environments: A study spanning clinical, livestock, and wastewater treatment settings. ENVIRONMENT INTERNATIONAL 2024; 186:108603. [PMID: 38547543 DOI: 10.1016/j.envint.2024.108603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/13/2024] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Acinetobacter baumannii has become a prominent nosocomial pathogen, primarily owing to its remarkable ability to rapidly acquire resistance to a wide range of antimicrobial agents and its ability to persist in diverse environments. However, there is a lack of data on the molecular epidemiology and its potential implications for public health of A. baumannii strains exhibiting clinically significant resistances that originate from non-clinical environments. Therefore, the genetic characteristics and resistance mechanisms of 80 A. baumannii-calcoaceticus (ABC) complex isolates, sourced from environments associated with poultry and pig production, municipal wastewater treatment plants (WWTPs), and clinical settings, were investigated. In total, our study classified 54 isolates into 29 previously described sequence types (STs), while 26 isolates exhibited as-yet-unassigned STs. We identified a broad range of A. baumannii STs originating from poultry and pig production environments (e.g., ST10, ST238, ST240, ST267, ST345, ST370, ST372, ST1112 according to Pasteur scheme). These STs have also been documented in clinical settings worldwide, highlighting their clinical significance. These findings also raise concerns about the potential zoonotic transmission of certain STs associated with livestock environments. Furthermore, we observed that clinical isolates exhibited the highest diversity of antimicrobial resistance genes (ARGs). In contrast to non-clinical isolates, clinical isolates typically carried a significantly higher number of ARGs, ranging from 10 to 15. They were also the exclusive carriers of biocide resistance genes and acquired carbapenemases (blaOXA-23, blaOXA-58, blaOXA-72, blaGIM-1, blaNDM-1). Additionally, we observed that clinical strains displayed an increased capacity for carrying plasmids and undergoing genetic transformation. This heightened capability could be linked to the intense selective pressures commonly found within clinical settings. Our study provides comprehensive insights into essential aspects of ABC isolates originating from livestock-associated environments and clinical settings. We explored their resistance mechanisms and potential implications for public health, providing valuable knowledge for addressing these critical issues.
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Affiliation(s)
- Mykhailo Savin
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany.
| | - Esther Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | | | - Vanessa M Eichel
- Section for Hospital Hygiene and Environmental Health, Center for Infectious Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases and Microbiology, University of Lübeck and University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Marian Klose
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrike Binsker
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
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3
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Jha NK, Gopu V, Sivasankar C, Singh SR, Devi PB, Murali A, Shetty PH. In vitro and in silico assessment of anti-biofilm and anti-quorum sensing properties of 2,4-Di-tert butylphenol against Acinetobacter baumannii. J Med Microbiol 2024; 73. [PMID: 38506718 DOI: 10.1099/jmm.0.001813] [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] [Indexed: 03/21/2024] Open
Abstract
Introduction. Acinetobacter baumannii is a nosocomial pathogen with a high potential to cause food-borne infections. It is designated as a critical pathogen by the World Health Organization due to its multi-drug resistance and mortalities reported. Biofilm governs major virulence factors, which promotes drug resistance in A. baumannii. Thus, a compound with minimum selection pressure on the pathogen can be helpful to breach biofilm-related virulence.Hypothesis/Gap Statement. To identify anti-biofilm and anti-virulent metabolites from extracts of wild Mangifera indica (mango) brine pickle bacteria that diminishes pathogenesis and resistance of A. baumannii.Aim. This study reports anti-biofilm and anti-quorum sensing (QS) efficacy of secondary metabolites from bacterial isolates of fermented food origin.Method. Cell-free supernatants (CFS) of 13 bacterial isolates from fermented mango brine pickles were screened for their efficiency in inhibiting biofilm formation and GC-MS was used to identify its metabolites. Anti-biofilm metabolite was tested on early and mature biofilms, pellicle formation, extra polymeric substances (EPS), cellular adherence, motility and resistance of A. baumannii. Gene expression and in silico studies were also carried out to validate the compounds efficacy.Results. CFS of TMP6b identified as Bacillus vallismortis, inhibited biofilm production (83.02 %). Of these, major compound was identified as 2,4-Di-tert-butyl phenol (2,4-DBP). At sub-lethal concentrations, 2,4-DBP disrupted both early and mature biofilm formation. Treatment with 2,4-DBP destructed in situ biofilm formed on glass and plastic. In addition, key virulence traits like pellicle (77.5 %), surfactant (95.3 %), EPS production (3-fold) and cell adherence (65.55 %) reduced significantly. A. baumannii cells treated with 2,4-DBP showed enhanced sensitivity towards antibiotics, oxide radicals and blood cells. Expression of biofilm-concomitant virulence genes like csuA/B, pgaC, pgaA, bap, bfmR, katE and ompA along with QS genes abaI, abaR significantly decreased. The in silico studies further validated the higher binding affinity of 2,4-DBP to the AbaR protein than the cognate ligand molecule.Conclusion. To our knowledge, this is the first report to demonstrate 2,4- DBP has anti-pathogenic potential alone and with antibiotics by in vitro, and in silico studies against A. baumannii. It also indicates its potential use in therapeutics and bio-preservatives.
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Affiliation(s)
- Nisha Kumari Jha
- Department of Food Science and Technology, Pondicherry University, Pondicherry-605014, India
| | - Venkadesaperumal Gopu
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chandran Sivasankar
- Department of Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan-54596, Republic of Korea
| | - Satya Ranjan Singh
- Department of Bioinformatics, Pondicherry University, Pondicherry-605014, India
| | - Palanisamy Bruntha Devi
- Department of Food Science and Technology, Pondicherry University, Pondicherry-605014, India
| | - Ayaluru Murali
- Department of Bioinformatics, Pondicherry University, Pondicherry-605014, India
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4
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Muzahid NH, Md Zoqratt MZH, Ten KE, Hussain MH, Su TT, Ayub Q, Tan HS, Rahman S. Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community. Sci Rep 2023; 13:12596. [PMID: 37537198 PMCID: PMC10400646 DOI: 10.1038/s41598-023-39642-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Acinetobacter species are widely known opportunistic pathogens causing severe community and healthcare-associated infections. One such emerging pathogen, Acinetobacter colistiniresistens, is known to exhibit intrinsic resistance to colistin. We investigated the molecular characteristics of A. colistiniresistens strain C-214, isolated from the fecal sample of a healthy community member, as part of a cohort study being conducted in Segamat, Malaysia. Comparison of the whole genome sequence of C-214 with other A. colistiniresistens sequences retrieved from the NCBI database showed 95% sequence identity or more with many of the genome sequences representing that species. Use of the Galleria mellonella killing assay showed that C-214 was pathogenic in this model infection system. The strain C-214 had a colistin and polymyxin B MIC of 32 and 16 mg/L, respectively. Besides, it was resistant to cefotaxime, amikacin, and tetracycline and showed moderate biofilm-producing ability. Different genes associated with virulence or resistance to major classes of antibiotics were detected. We observed mutations in lpxA/C/D in C-214 and other A. colistiniresistens strains as probable causes of colistin resistance, but the biological effects of these mutations require further investigation. This study provides genomic insights into A. colistiniresistens, a potentially pathogenic bacterium isolated from a community member and notes the public health threat it may pose.
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Affiliation(s)
- Nazmul Hasan Muzahid
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
| | | | - Kah Ern Ten
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Md Hamed Hussain
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Tin Tin Su
- South East Asia Community Observatory (SEACO), Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
- Monash University Malaysia Genomics Facility, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
- Monash University Malaysia Genomics Facility, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
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5
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Maharjan RP, Sullivan GJ, Adams F, Shah B, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short F, Parkhill J, Paulsen I, Barquist L, Eijkelkamp B, Cain A. DksA is a conserved master regulator of stress response in Acinetobacter baumannii. Nucleic Acids Res 2023; 51:6101-6119. [PMID: 37158230 PMCID: PMC10325922 DOI: 10.1093/nar/gkad341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.
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Affiliation(s)
- Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Felise G Adams
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Bhumika S Shah
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Victoria, Australia
| | - Natasha Delgado
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Liping Li
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Francesca L Short
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080Würzburg, Germany
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
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Timoshina OY, Kasimova AA, Shneider MM, Matyuta IO, Nikolaeva AY, Evseev PV, Arbatsky NP, Shashkov AS, Chizhov AO, Shelenkov AA, Mikhaylova YV, Slukin PV, Volozhantsev NV, Boyko KM, Knirel YA, Miroshnikov KA, Popova AV. Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii. Int J Mol Sci 2023; 24:ijms24109100. [PMID: 37240444 DOI: 10.3390/ijms24109100] [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: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage-bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents.
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Affiliation(s)
- Olga Y Timoshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Anastasia A Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Alena Y Nikolaeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander O Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey A Shelenkov
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Yulia V Mikhaylova
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Pavel V Slukin
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Nikolay V Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anastasia V Popova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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7
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Ren X, Palmer LD. Acinetobacter Metabolism in Infection and Antimicrobial Resistance. Infect Immun 2023:e0043322. [PMID: 37191522 DOI: 10.1128/iai.00433-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.
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Affiliation(s)
- Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Lauren D Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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8
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Traglia GM, Pasteran F, Escalante J, Nishimura B, Tuttobene MR, Subils T, Nuñez MR, Rivollier MG, Corso A, Tolmasky ME, Ramirez MS. Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic. BIOLOGY 2023; 12:358. [PMID: 36979049 PMCID: PMC10045941 DOI: 10.3390/biology12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND After the emergence of COVID-19, numerous cases of A. baumannii/SARS-CoV-2 co-infection were reported. Whether the co-infecting A. baumannii strains have distinctive characteristics remains unknown. METHODS AND RESULTS A. baumannii AMA_NO was isolated in 2021 from a patient with COVID-19. AMA166 was isolated from a mini-BAL used on a patient with pneumonia in 2016. Both genomes were similar, but they possessed 337 (AMA_NO) and 93 (AMA166) unique genes that were associated with biofilm formation, flagellar assembly, antibiotic resistance, secretion systems, and other functions. The antibiotic resistance genes were found within mobile genetic elements. While both strains harbored the carbapenemase-coding gene blaOXA-23, only the strain AMA_NO carried blaNDM-1. Representative functions coded for by virulence genes are the synthesis of the outer core of lipooligosaccharide (OCL5), biosynthesis and export of the capsular polysaccharide (KL2 cluster), high-efficiency iron uptake systems (acinetobactin and baumannoferrin), adherence, and quorum sensing. A comparative phylogenetic analysis including 239 additional sequence type (ST) 2 representative genomes showed high similarity to A. baumannii ABBL141. Since the degree of similarity that was observed between A. baumannii AMA_NO and AMA166 is higher than that found among other ST2 strains, we propose that they derive from a unique background based on core-genome phylogeny and comparative genome analysis. CONCLUSIONS Acquisition or shedding of specific genes could increase the ability of A. baumannii to infect patients with COVID-19.
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Affiliation(s)
- German Matias Traglia
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo 11200, Uruguay
| | - Fernando Pasteran
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Jenny Escalante
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Brent Nishimura
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Marisel R. Tuttobene
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario 2000, Argentina
| | - Tomás Subils
- Instituto de Procesos Biotecnológicos y Químicos de Rosario (IPROBYQ, CONICET-UNR), Rosario 2000, Argentina
| | - Maria Rosa Nuñez
- Laboratorio de Microbiología, Hospital Provincial Neuquén Dr. Castro Rendón, Neuquén 8300, Argentina
| | | | - Alejandra Corso
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
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9
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Noel HR, Petrey JR, Palmer LD. Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination. Ann N Y Acad Sci 2022; 1518:166-182. [PMID: 36316792 PMCID: PMC9771954 DOI: 10.1111/nyas.14918] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Jessica R. Petrey
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
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10
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Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
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Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
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11
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Balasubramanian D, López-Pérez M, Grant TA, Ogbunugafor CB, Almagro-Moreno S. Molecular mechanisms and drivers of pathogen emergence. Trends Microbiol 2022; 30:898-911. [DOI: 10.1016/j.tim.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022]
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12
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Hamidian M, Maharjan RP, Farrugia DN, Delgado NN, Dinh H, Short FL, Kostoulias X, Peleg AY, Paulsen IT, Cain AK. Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity. Microb Genom 2022; 8. [PMID: 35166651 PMCID: PMC8942024 DOI: 10.1099/mgen.0.000765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Acinetobacter baumannii is a critically important pathogen known for its widespread antibiotic resistance and ability to persist in hospital-associated environments. Whilst the majority of A. baumannii infections are hospital-acquired, infections from outside the hospital have been reported with high mortality. Despite this, little is known about the natural environmental reservoir(s) of A. baumannii and the virulence potential underlying non-clinical strains. Here, we report the complete genome sequences of six diverse strains isolated from environments such as river, soil, and industrial sites around the world. Phylogenetic analyses showed that four of these strains were unrelated to representative nosocomial strains and do not share a monophyletic origin, whereas two had sequence types belonging to the global clone lineages GC1 and GC2. Further, the majority of these strains harboured genes linked to virulence and stress protection in nosocomial strains. These genotypic properties correlated well with in vitro virulence phenotypic assays testing resistance to abiotic stresses, serum survival, and capsule formation. Virulence potential was confirmed in vivo, with most environmental strains able to effectively kill Galleria mellonella greater wax moth larvae. Using phenomic arrays and antibiotic resistance profiling, environmental and nosocomial strains were shown to have similar substrate utilisation patterns although environmental strains were distinctly more sensitive to antibiotics. Taken together, these features of environmental A. baumannii strains suggest the existence of a strain-specific distinct gene pools for niche specific adaptation. Furthermore, environmental strains appear to be equally virulent as contemporary nosocomial strains but remain largely antibiotic sensitive.
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Affiliation(s)
- Mohammad Hamidian
- The iThree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Daniel N Farrugia
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Natasha N Delgado
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Francesca L Short
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Xenia Kostoulias
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Anton Y Peleg
- Infection & Immunity Program Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.,Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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13
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Hu Y, Zheng J, Zhang J. Natural Transformation in Acinetobacter baumannii W068: A Genetic Analysis Reveals the Involvements of the CRP, XcpV, XcpW, TsaP, and TonB2. Front Microbiol 2022; 12:738034. [PMID: 35126321 PMCID: PMC8811193 DOI: 10.3389/fmicb.2021.738034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/14/2021] [Indexed: 01/25/2023] Open
Abstract
Acinetobacter baumannii is a serious threat to public health, and there is increasing attention to the development of antibiotic resistance in this bacterium. Natural transformation is a major horizontal gene transfer mechanism that can lead to antibiotic resistance. To better understand the mechanism of natural transformation in A. baumannii, we selected a clinical isolate that was transformable but had no visible extracellular type IV pili (T4P) filaments and then examined the effects of multiple single-gene knockouts on natural plasmid transformation. Among 33 candidate genes, 28 knockout mutants had severely or completely impaired transformability. Some of these genes had established roles in T4P biogenesis; DNA transfer across the outer membrane, periplasm, or inner membrane; and protection of intracellular single-stranded DNA (ssDNA). Other genes had no previously reported roles in natural transformation of A. baumannii, including competence activator cAMP receptor protein (CRP), a periplasmic protein that may function in T4P assembly (TonB2), a T4P secretin-associated protein (TsaP), and two type II secretion system (T2SS) minor pseudopilus assembly prime complex competent proteins (XcpV and XcpW). The deletion of the T2SS assembly platform protein X had no effect on transformation, and the minor pseudopilins were capable of initiating major pilin assembly. Thus, we speculate that XcpV and XcpW may function in DNA uptake with major pilin assembly, a non-T2SS-dependent mechanism and that a competence pseudopilus similar to T4P constituted the central part of the DNA uptake complex. These results may help guide future research on the alarming increase of antibiotic resistance in this pathogen.
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Affiliation(s)
- Yuan Hu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junjie Zheng
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Jianzhong Zhang,
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14
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The Molecular Basis of Acinetobacter baumannii Cadmium Toxicity and Resistance. Appl Environ Microbiol 2021; 87:e0171821. [PMID: 34495707 DOI: 10.1128/aem.01718-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Acinetobacter species are ubiquitous Gram-negative bacteria that can be found in water, in soil, and as commensals of the human skin. The successful inhabitation of Acinetobacter species in diverse environments is primarily attributable to the expression of an arsenal of stress resistance determinants, which includes an extensive repertoire of metal ion efflux systems. Metal ion homeostasis in the hospital pathogen Acinetobacter baumannii contributes to pathogenesis; however, insights into its metal ion transporters for environmental persistence are lacking. Here, we studied the impact of cadmium stress on A. baumannii. Our functional genomics and independent mutant analyses revealed a primary role for CzcE, a member of the cation diffusion facilitator (CDF) superfamily, in resisting cadmium stress. We also show that the CzcCBA heavy metal efflux system contributes to cadmium efflux. Collectively, these systems provide A. baumannii with a comprehensive cadmium translocation pathway from the cytoplasm to the periplasm and subsequently the extracellular space. Furthermore, analysis of the A. baumannii metallome under cadmium stress showed zinc depletion, as well as copper enrichment, both of which are likely to influence cellular fitness. Overall, this work provides new knowledge on the role of a broad arsenal of membrane transporters in A. baumannii metal ion homeostasis. IMPORTANCE Cadmium toxicity is a widespread problem, yet the interaction of this heavy metal with biological systems is poorly understood. Some microbes have evolved traits to proactively counteract cadmium toxicity, including Acinetobacter baumannii, which is notorious for persisting in harsh environments. Here, we show that A. baumannii utilizes a dedicated cadmium efflux protein in concert with a system that is primarily attuned to zinc efflux to efficiently overcome cadmium stress. The molecular characterization of A. baumannii under cadmium stress revealed how active cadmium efflux plays a key role in preventing the dysregulation of bacterial metal ion homeostasis, which appeared to be a primary means by which cadmium exerts toxicity upon the bacterium.
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Ma C, McClean S. Mapping Global Prevalence of Acinetobacter baumannii and Recent Vaccine Development to Tackle It. Vaccines (Basel) 2021; 9:vaccines9060570. [PMID: 34205838 PMCID: PMC8226933 DOI: 10.3390/vaccines9060570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/16/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022] Open
Abstract
Acinetobacter baumannii is a leading cause of nosocomial infections that severely threaten public health. The formidable adaptability and resistance of this opportunistic pathogen have hampered the development of antimicrobial therapies which consequently leads to very limited treatment options. We mapped the global prevalence of multidrug-resistant A. baumannii and showed that carbapenem-resistant A. baumannii is widespread throughout Asia and the Americas. Moreover, when antimicrobial resistance rates of Acinetobacter spp. exceed a threshold level, the proportion of A. baumannii isolates from clinical samples surges. Therefore, vaccines represent a realistic alternative strategy to tackle this pathogen. Research into anti-A. baumannii vaccines have enhanced in the past decade and multiple antigens have been investigated preclinically with varying results. This review summarises the current knowledge of virulence factors relating to A. baumannii–host interactions and its implication in vaccine design, with a view to understanding the current state of A. baumannii vaccine development and the direction of future efforts.
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16
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Novel Acinetobacter baumannii Myovirus TaPaz Encoding Two Tailspike Depolymerases: Characterization and Host-Recognition Strategy. Viruses 2021; 13:v13060978. [PMID: 34070371 PMCID: PMC8228797 DOI: 10.3390/v13060978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Acinetobacter baumannii, one of the most significant nosocomial pathogens, is capable of producing structurally diverse capsular polysaccharides (CPSs) which are the primary receptors for A. baumannii bacteriophages encoding polysaccharide-degrading enzymes. To date, bacterial viruses specifically infecting A. baumannii strains belonging to more than ten various capsular types (K types) were isolated and characterized. In the present study, we investigate the biological properties, genomic organization, and virus-bacterial host interaction strategy of novel myovirus TaPaz isolated on the bacterial lawn of A. baumannii strain with a K47 capsular polysaccharide structure. The phage linear double-stranded DNA genome of 93,703 bp contains 178 open reading frames. Genes encoding two different tailspike depolymerases (TSDs) were identified in the phage genome. Recombinant TSDs were purified and tested against the collection of A. baumannii strains belonging to 56 different K types. One of the TSDs was demonstrated to be a specific glycosidase that cleaves the K47 CPS by the hydrolytic mechanism.
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Álvarez-Pérez S, Tsuji K, Donald M, Van Assche A, Vannette RL, Herrera CM, Jacquemyn H, Fukami T, Lievens B. Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters. MICROBIAL ECOLOGY 2021; 81:990-1003. [PMID: 33404822 DOI: 10.1007/s00248-020-01671-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.
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Affiliation(s)
- Sergio Álvarez-Pérez
- Department of Microbial and Molecular Systems, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, B-3001, Leuven, Belgium.
- Department of Animal Health, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Kaoru Tsuji
- Center for Ecological Research, Kyoto University, Hirano 2, Otsu, Shiga, 520-2113, Japan
| | - Marion Donald
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Ado Van Assche
- Department of Microbial and Molecular Systems, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, B-3001, Leuven, Belgium
| | - Rachel L Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Hans Jacquemyn
- Biology Department, Laboratory of Plant Conservation and Population Biology, KU Leuven, B-3001, Leuven, Belgium
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Bart Lievens
- Department of Microbial and Molecular Systems, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, B-3001, Leuven, Belgium.
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18
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Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases. Sci Rep 2021; 11:7050. [PMID: 33782435 PMCID: PMC8007833 DOI: 10.1038/s41598-021-86400-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/08/2021] [Indexed: 11/08/2022] Open
Abstract
Treatments for 'superbug' infections are the focus for innovative research, as drug resistance threatens human health and medical practices globally. In particular, Acinetobacter baumannii (Ab) infections are repeatedly reported as difficult to treat due to increasing antibiotic resistance. Therefore, there is increasing need to identify novel targets in the development of different antimicrobials. Of particular interest is fatty acid synthesis, vital for the formation of phospholipids, lipopolysaccharides/lipooligosaccharides, and lipoproteins of Gram-negative envelopes. The bacterial type II fatty acid synthesis (FASII) pathway is an attractive target for the development of inhibitors and is particularly favourable due to the differences from mammalian type I fatty acid synthesis. Discrete enzymes in this pathway include two reductase enzymes: 3-oxoacyl-acyl carrier protein (ACP) reductase (FabG) and enoyl-ACP reductase (FabI). Here, we investigate annotated FabG homologs, finding a low-molecular weight 3-oxoacyl-ACP reductase, as the most likely FASII FabG candidate, and high-molecular weight 3-oxoacyl-ACP reductase (HMwFabG), showing differences in structure and coenzyme preference. To date, this is the second bacterial high-molecular weight FabG structurally characterized, following FabG4 from Mycobacterium. We show that ΔAbHMwfabG is impaired for growth in nutrient rich media and pellicle formation. We also modelled a third 3-oxoacyl-ACP reductase, which we annotated as AbSDR. Despite containing residues for catalysis and the ACP coordinating motif, biochemical analyses showed limited activity against an acetoacetyl-CoA substrate in vitro. Inhibitors designed to target FabG proteins and thus prevent fatty acid synthesis may provide a platform for use against multidrug-resistant pathogens including A. baumannii.
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Specific Interaction of Novel Friunavirus Phages Encoding Tailspike Depolymerases with Corresponding Acinetobacter baumannii Capsular Types. J Virol 2021; 95:JVI.01714-20. [PMID: 33268523 PMCID: PMC8092837 DOI: 10.1128/jvi.01714-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its «critical priority» category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types.
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CsrA Supports both Environmental Persistence and Host-Associated Growth of Acinetobacter baumannii. Infect Immun 2020; 88:IAI.00259-20. [PMID: 32989034 DOI: 10.1128/iai.00259-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/18/2020] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic and frequently multidrug-resistant Gram-negative bacterial pathogen that primarily infects critically ill individuals. Indirect transmission from patient to patient in hospitals can drive infections, supported by this organism's abilities to persist on dry surfaces and rapidly colonize susceptible individuals. To investigate how A. baumannii survives on surfaces, we cultured A. baumannii in liquid media for several days and then analyzed isolates that lost the ability to survive drying. One of these isolates carried a mutation that affected the gene encoding the carbon storage regulator CsrA. As we began to examine the role of CsrA in A. baumannii, we observed that the growth of ΔcsrA mutant strains was inhibited in the presence of amino acids. The ΔcsrA mutant strains had a reduced ability to survive drying and to form biofilms but an improved ability to tolerate increased osmolarity compared with the wild type. We also examined the importance of CsrA for A. baumannii virulence. The ΔcsrA mutant strains had a greatly reduced ability to kill Galleria mellonella larvae, could not replicate in G. mellonella hemolymph, and also had a growth defect in human serum. Together, these results show that CsrA is essential for the growth of A. baumannii on host-derived substrates and is involved in desiccation tolerance, implying that CsrA controls key functions involved in the transmission of A. baumannii in hospitals.
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A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development. Antimicrob Agents Chemother 2020; 64:AAC.00840-20. [PMID: 32718956 DOI: 10.1128/aac.00840-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/18/2020] [Indexed: 12/20/2022] Open
Abstract
Over the past two decades, Acinetobacter baumannii has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant A. baumannii as a priority 1 (critical) pathogen for research and development of new antibiotics. A key component in supporting this effort is accessibility to diverse and clinically relevant strains for testing. Here, we describe a panel of 100 diverse A. baumannii strains for use in this endeavor. Whole-genome sequencing was performed on 3,505 A. baumannii isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. Isolates were cultured from clinical samples at health care facilities around the world between 2001 and 2017. Core-genome multilocus sequence typing and high-resolution single nucleotide polymorphism (SNP)-based phylogenetic analyses were used to select a final panel of 100 strains that captured the genetic diversity of the collection. Comprehensive antibiotic susceptibility testing was also performed on all 100 isolates using 14 clinically relevant antibiotics. The final 100-strain diversity panel contained representative strains from 70 different traditional Pasteur scheme multilocus sequence types, including major epidemic clones. This diversity was also reflected in antibiotic susceptibility and antimicrobial resistance (AMR) gene content, with phenotypes ranging from pansensitive to panresistant, and over 100 distinct AMR gene alleles identified from 32 gene families. This panel provides the most diverse and comprehensive set of A. baumannii strains for use in developing solutions for combating antibiotic resistance. The panel and all available metadata, including genome sequences, will be available to industry and academic institutions and federal and other laboratories free of charge.
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Chung WY, Zhu Y, Mahamad Maifiah MH, Shivashekaregowda NKH, Wong EH, Abdul Rahim N. Novel antimicrobial development using genome-scale metabolic model of Gram-negative pathogens: a review. J Antibiot (Tokyo) 2020; 74:95-104. [PMID: 32901119 DOI: 10.1038/s41429-020-00366-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022]
Abstract
Antimicrobial resistance (AMR) threatens the effective prevention and treatment of a wide range of infections. Governments around the world are beginning to devote effort for innovative treatment development to treat these resistant bacteria. Systems biology methods have been applied extensively to provide valuable insights into metabolic processes at system level. Genome-scale metabolic models serve as platforms for constraint-based computational techniques which aid in novel drug discovery. Tools for automated reconstruction of metabolic models have been developed to support system level metabolic analysis. We discuss features of such software platforms for potential users to best fit their purpose of research. In this work, we focus to review the development of genome-scale metabolic models of Gram-negative pathogens and also metabolic network approach for identification of antimicrobial drugs targets.
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Affiliation(s)
- Wan Yean Chung
- School of Pharmacy, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Melbourne, 3800, VIC, Australia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), 53100, Jalan Gombak, Selangor, Malaysia
| | - Naveen Kumar Hawala Shivashekaregowda
- Center for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Eng Hwa Wong
- School of Medicine, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia.
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Acinetobacter baumannii NCIMB8209: a Rare Environmental Strain Displaying Extensive Insertion Sequence-Mediated Genome Remodeling Resulting in the Loss of Exposed Cell Structures and Defensive Mechanisms. mSphere 2020; 5:5/4/e00404-20. [PMID: 32727858 PMCID: PMC7392541 DOI: 10.1128/msphere.00404-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. A. baumannii arose from the Acinetobacter calcoaceticus-A. baumannii complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus, the study of nonclinical (“environmental”) A. baumannii isolates is necessary. We conducted here comparative genomic and virulence studies on A. baumannii NCMBI8209 isolated in 1943 from the microbiota responsible for the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the multidrug-resistant strains that are predominant nowadays. Our work provides insights on the adaptive strategies used by A. baumannii to escape from host defenses and may help the adoption of measures aimed to limit its further dissemination. Acinetobacter baumannii represents nowadays an important nosocomial pathogen of poorly defined reservoirs outside the clinical setting. Here, we conducted whole-genome sequencing analysis of the Acinetobacter sp. NCIMB8209 collection strain, isolated in 1943 from the aerobic degradation (retting) of desert guayule shrubs. Strain NCIMB8209 contained a 3.75-Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes indicated NCIMB8209 affiliation to A. baumannii, a result supported by the identification of a chromosomal blaOXA-51-like gene. Seven genomic islands lacking antimicrobial resistance determinants, 5 regions encompassing phage-related genes, and notably, 93 insertion sequences (IS) were found in this genome. NCIMB8209 harbors most genes linked to persistence and virulence described in contemporary A. baumannii clinical strains, but many of the genes encoding components of surface structures are interrupted by IS. Moreover, defense genetic islands against biological aggressors such as type 6 secretion systems or CRISPR-cas are absent from this genome. These findings correlate with a low capacity of NCIMB8209 to form biofilm and pellicle, low motility on semisolid medium, and low virulence toward Galleria mellonella and Caenorhabditis elegans. Searching for catabolic genes and concomitant metabolic assays revealed the ability of NCIMB8209 to grow on a wide range of substances produced by plants, including aromatic acids and defense compounds against external aggressors. All the above features strongly suggest that NCIMB8209 has evolved specific adaptive features to a particular environmental niche. Moreover, they also revealed that the remarkable genetic plasticity identified in contemporary A. baumannii clinical strains represents an intrinsic characteristic of the species. IMPORTANCEAcinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. A. baumannii arose from the Acinetobacter calcoaceticus-A. baumannii complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus, the study of nonclinical (“environmental”) A. baumannii isolates is necessary. We conducted here comparative genomic and virulence studies on A. baumannii NCMBI8209 isolated in 1943 from the microbiota responsible for the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the multidrug-resistant strains that are predominant nowadays. Our work provides insights on the adaptive strategies used by A. baumannii to escape from host defenses and may help the adoption of measures aimed to limit its further dissemination.
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Hubloher JJ, Zeidler S, Lamosa P, Santos H, Averhoff B, Müller V. Trehalose-6-phosphate-mediated phenotypic change in Acinetobacter baumannii. Environ Microbiol 2020; 22:5156-5166. [PMID: 32618111 DOI: 10.1111/1462-2920.15148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022]
Abstract
The stress protectant trehalose is synthesized in Acinetobacter baumannii from UPD-glucose and glucose-6-phosphase via the OtsA/OtsB pathway. Previous studies proved that deletion of otsB led to a decreased virulence, the inability to grow at 45°C and a slight reduction of growth at high salinities indicating that trehalose is the cause of these phenotypes. We have questioned this conclusion by producing ∆otsA and ∆otsBA mutants and studying their phenotypes. Only deletion of otsB, but not deletion of otsA or otsBA, led to growth impairments at high salt and high temperature. The intracellular concentrations of trehalose and trehalose-6-phosphate were measured by NMR or enzymatic assay. Interestingly, none of the mutants accumulated trehalose any more but the ∆otsB mutant with its defect in trehalose-6-phosphate phosphatase activity accumulated trehalose-6-phosphate. Moreover, expression of otsA in a ∆otsB background under conditions where trehalose synthesis is not induced led to growth inhibition and the accumulation of trehalose-6-phosphate. Our results demonstrate that trehalose-6-phosphate affects multiple physiological activities in A. baumannii ATCC 19606.
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Affiliation(s)
- Josephine Joy Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Sabine Zeidler
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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Antibiotics Act with vB_AbaP_AGC01 Phage against Acinetobacter baumannii in Human Heat-Inactivated Plasma Blood and Galleria mellonella Models. Int J Mol Sci 2020; 21:ijms21124390. [PMID: 32575645 PMCID: PMC7352404 DOI: 10.3390/ijms21124390] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Increasing multidrug resistance has led to renewed interest in phage-based therapy. A combination of the bacteriophages and antibiotics presents a promising approach enhancing the phage therapy effectiveness. First, phage candidates for therapy should be deeply characterized. Here we characterize the bacteriophage vB_AbaP_AGC01 that poses antibacterial activity against clinical Acinetobacter baumannii strains. Moreover, besides genomic and phenotypic analysis our study aims to analyze phage–antibiotic combination effectiveness with the use of ex vivo and in vivo models. The phage AGC01 efficiently adsorbs to A. baumannii cells and possesses a bacteriolytic lifecycle resulting in high production of progeny phages (317 ± 20 PFU × cell−1). The broad host range (50.27%, 93 out of 185 strains) against A. baumannii isolates and the inability of AGC01 to infect other bacterial species show its high specificity. Genomic analysis revealed a high similarity of the AGC01 genome sequence with that of the Friunavirus genus from a subfamily of Autographivirinae. The AGC01 is able to significantly reduce the A. baumannii cell count in a human heat-inactivated plasma blood model (HIP-B), both alone and in combination with antibiotics (gentamicin (GEN), ciprofloxacin (CIP), and meropenem (MER)). The synergistic action was observed when a combination of phage treatment with CIP or MER was used. The antimicrobial activity of AGC01 and phage-antibiotic combinations was confirmed using an in vivo larva model. This study shows the greatest increase in survival of G. mellonella larvae when the combination of phage (MOI = 1) and MER was used, which increased larval survival from 35% to 77%. Hence, AGC01 represents a novel candidate for phage therapy. Additionally, our study suggests that phages and antibiotics can act synergistically for greater antimicrobial effect when used as combination therapy.
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Singh M, De Silva PM, Al-Saadi Y, Switala J, Loewen PC, Hausner G, Chen W, Hernandez I, Castillo-Ramirez S, Kumar A. Characterization of Extremely Drug-Resistant and Hypervirulent Acinetobacter baumannii AB030. Antibiotics (Basel) 2020; 9:antibiotics9060328. [PMID: 32560407 PMCID: PMC7345994 DOI: 10.3390/antibiotics9060328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter baumannii is an important nosocomial bacterial pathogen. Multidrug-resistant isolates of A. baumannii are reported worldwide. Some A. baumannii isolates display resistance to nearly all antibiotics, making treatment of infections very challenging. As the need for new and effective antibiotics against A. baumannii becomes increasingly urgent, there is a need to understand the mechanisms of antibiotic resistance and virulence in this organism. In this work, comparative genomics was used to understand the mechanisms of antibiotic resistance and virulence in AB030, an extremely drug-resistant and hypervirulent strain of A. baumannii that is a representative of a recently emerged lineage of A. baumannii International Clone V. In order to characterize AB030, we carried out a genomic and phenotypic comparison with LAC-4, a previously described hyper-resistant and hypervirulent isolate. AB030 contains a number of antibiotic resistance- and virulence-associated genes that are not present in LAC-4. A number of these genes are present on mobile elements. This work shows the importance of characterizing the members of new lineages of A. baumannii in order to determine the development of antibiotic resistance and virulence in this organism.
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Affiliation(s)
- Manu Singh
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - P. Malaka De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Yasser Al-Saadi
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Wangxue Chen
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada;
| | - Ismael Hernandez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (I.H.); (S.C.-R.)
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (I.H.); (S.C.-R.)
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
- Correspondence:
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Mangas EL, Rubio A, Álvarez-Marín R, Labrador-Herrera G, Pachón J, Pachón-Ibáñez ME, Divina F, Pérez-Pulido AJ. Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation. Microb Genom 2020; 5. [PMID: 31626589 PMCID: PMC6927304 DOI: 10.1099/mgen.0.000309] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic bacterium that causes hospital-acquired infections with a high mortality and morbidity, since there are strains resistant to virtually any kind of antibiotic. The chase to find novel strategies to fight against this microbe can be favoured by knowledge of the complete catalogue of genes of the species, and their relationship with the specific characteristics of different isolates. In this work, we performed a genomics analysis of almost 2500 strains. Two different groups of genomes were found based on the number of shared genes. One of these groups rarely has plasmids, and bears clustered regularly interspaced short palindromic repeat (CRISPR) sequences, in addition to CRISPR-associated genes (cas genes) or restriction-modification system genes. This fact strongly supports the lack of plasmids. Furthermore, the scarce plasmids in this group also bear CRISPR sequences, and specifically contain genes involved in prokaryotic toxin–antitoxin systems that could either act as the still little known CRISPR type IV system or be the precursors of other novel CRISPR/Cas systems. In addition, a limited set of strains present a new cas9-like gene, which may complement the other cas genes in inhibiting the entrance of new plasmids into the bacteria. Finally, this group has exclusive genes involved in biofilm formation, which would connect CRISPR systems to the biogenesis of these bacterial resistance structures.
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Affiliation(s)
- Eugenio L Mangas
- Centro Andaluz de Biología del Desarrollo (CABD UPO-CSIC-JA), Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Alejandro Rubio
- Centro Andaluz de Biología del Desarrollo (CABD UPO-CSIC-JA), Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Rocío Álvarez-Marín
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Gema Labrador-Herrera
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Jerónimo Pachón
- Department of Medicine, University of Seville, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - María Eugenia Pachón-Ibáñez
- Department of Medicine, University of Seville, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Federico Divina
- School of Engineering, Pablo de Olavide University, Ctra. Utrera s/n, Seville, Spain
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD UPO-CSIC-JA), Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Seville, Spain
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Brovedan M, Repizo GD, Marchiaro P, Viale AM, Limansky A. Characterization of the diverse plasmid pool harbored by the blaNDM-1-containing Acinetobacter bereziniae HPC229 clinical strain. PLoS One 2019; 14:e0220584. [PMID: 31743332 PMCID: PMC6863613 DOI: 10.1371/journal.pone.0220584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter bereziniae is an environmental microorganism with increasing clinical incidence, and may thus provide a model for a bacterial species bridging the gap between the environment and the clinical setting. A. bereziniae plasmids have been poorly studied, and their characterization could offer clues on the causes underlying the leap between these two different habitats. Here we characterized the whole plasmid content of A. bereziniae HPC229, a clinical strain previously reported to harbor a 44-kbp plasmid, pNDM229, conferring carbapenem and aminoglycoside resistance. We identified five extra plasmids in HPC229 ranging from 114 to 1.3 kbp, including pAbe229-114 (114 kbp) encoding a MOBP111 relaxase and carrying heavy metal resistance, a bacteriophage defense BREX system and four different toxin-antitoxin (TA) systems. Two other replicons, pAbe229-15 (15.4 kbp) and pAbe229-9 (9.1 kbp), both encoding MOBQ1 relaxases and also carrying TA systems, were found. The three latter plasmids contained Acinetobacter Rep_3 superfamily replication initiator protein genes, and functional analysis of their transfer regions revealed the mobilizable nature of them. HPC229 also harbors two smaller plasmids, pAbe229-4 (4.4 kbp) and pAbe229-1 (1.3 kbp), the former bearing a ColE1-type replicon and a TA system, and the latter lacking known replication functions. Comparative sequence analyses against deposited Acinetobacter genomes indicated that the above five HPC229 plasmids were unique, although some regions were also present in other of these genomes. The transfer, replication, and adaptive modules in pAbe229-15, and the stability module in pAbe229-9, were bordered by sites potentially recognized by XerC/XerD site-specific tyrosine recombinases, thus suggesting a potential mechanism for their acquisition. The presence of Rep_3 and ColE1-based replication modules, different mob genes, distinct adaptive functions including resistance to heavy metal and other environmental stressors, as well as antimicrobial resistance genes, and a high content of XerC/XerD sites among HPC229 plasmids provide evidence of substantial links with bacterial species derived from both environmental and clinical habitats.
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Affiliation(s)
- Marco Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Guillermo D. Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Alejandro M. Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
| | - Adriana Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
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Chusri S, Chongsuvivatwong V, Silpapojakul K, Singkhamanan K, Hortiwakul T, Charernmak B, Doi Y. Clinical characteristics and outcomes of community and hospital-acquired Acinetobacter baumannii bacteremia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:796-806. [PMID: 31031096 DOI: 10.1016/j.jmii.2019.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 02/06/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022]
Abstract
PURPOSE We aimed to characterize clinical manifestations of the patients with bacteremia due to community-acquired Acinetobacter baumannii and evaluate the outcomes of these patients. METHODS We conducted a retrospective study to include adult patients with A. baumannii bacteremia and then classified them into two groups: community-acquired A. baumannii bacteremia and hospital-acquired A. baumannii bacteremia. Characteristics and outcomes between 2 groups were compared. The Galleria mellonella infection survival model was used to determine the virulence of A. baumannii in these 2 groups. RESULTS There were 63 patients with A. baumannii bacteremia: 21 patients with community-acquired (CA) bacteremia and 42 patients with hospital-acquired (HA) bacteremia. Three patients with CA bacteremia were excluded due to healthcare-associated risks of infection. The remaining 18 patients with CA bacteremia had carbapenem-susceptible A. baumannii (CA-CSAB). Among the 42 patients with HA bacteremia, 11 patients had carbapenem-susceptible A. baumannii (HA-CSAB) and 31 patients had carbapenem-resistant A. baumannii (HA-CRAB). The 30-day mortality rates of those with CA-CSAB did not differ from those with HA-CSAB bacteremia but were significantly lower than those with HA-CRAB (p = 0.003). The factors influencing 30-day mortality were infection with CRAB (p = 0.004), appropriate empirical antimicrobial therapy (p = 0.002), and higher Acute Physiology and Chronic Health Evaluation II score (p < 0.001). The G. mellonella assay showed no differences in survival rates among CA-CSAB, HA-CSAB, and HA-CRAB. CONCLUSIONS Patients with bacteremia due to CA-CSAB and HA-CSAB had similar outcomes. Similar virulences of CA-CSAB and HA-CSAB were confirmed with the G. mellonella infection model.
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Affiliation(s)
- Sarunyou Chusri
- Division of Infectious Disease, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | | | - Kachornsakdi Silpapojakul
- Division of Infectious Disease, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Thanaporn Hortiwakul
- Division of Infectious Disease, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Boonsri Charernmak
- Division of Infectious Disease, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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31
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Ly TDA, Kerbaj J, Edouard S, Hoang VT, Louni M, Dao TL, Benkouiten S, Badiaga S, Tissot-Dupont H, Raoult D, Brouqui P, Mediannikov O, Gautret P. The Presence of Acinetobacter baumannii DNA on the Skin of Homeless People and Its Relationship With Body Lice Infestation. Preliminary Results. Front Cell Infect Microbiol 2019; 9:86. [PMID: 31024857 PMCID: PMC6460902 DOI: 10.3389/fcimb.2019.00086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
The presence of Acinetobacter baumannii was demonstrated in body lice, however, little is known about the mechanism of natural lice infection. In 2013 and 2014, cross-sectional one-day studies were therefore performed within two Marseille homeless shelters to assess the presence of A. baumannii DNA on human skin, blood and in body lice collected from the same homeless individuals. All 332 participants completed questionnaires, were examined for dermatologic signs, and provided four skin samples (hair, neck, armpits, and pelvic belt), blood samples and body lice (if any). We developed a new real-time PCR tool targeting the ompA/motB gene for the detection of A. baumannii for all collected samples. Blood culture was also performed. Body lice were found in 24/325 (7.4%) of subjects. We showed a prevalence of A. baumannii DNA skin-carriage in 33/305 (10.8%) of subjects. No difference was found in A. baumannii DNA prevalence according to body sites. A strong association between body lice infestation (OR = 3.07, p = 0.029) and A. baumannii DNA skin-carriage was noted. In lice, A. baumannii DNA was detected in 59/219 arthropods (26.9%). All blood cultures and real-time PCR on blood samples were negative for A. baumannii. Lice probably get infected with A. baumannii while biting through the colonized skin and likely transmit the bacteria in their feces. We found no evidence that lice facilitate the invasion of A. baumannii into the blood stream. Further investigations are needed to compare phenotypic and genotypic features of A. baumannii isolates from human skin and lice from the same individuals.
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Affiliation(s)
- Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | | | - Sophie Edouard
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, MEPHI, Marseille, France
| | - Van Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Department of Pneumology, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Meriem Louni
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Thi Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Department of Pneumology, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Samir Benkouiten
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Sekene Badiaga
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, Service des urgences CHU Hôpital Nord, Marseille, France
| | - Herve Tissot-Dupont
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, MEPHI, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, MEPHI, Marseille, France
| | - Philippe Brouqui
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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32
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Liang R, Zou X, Wu Y, Ma Z, Deng M, Deng C. WITHDRAWN: Pneumonia: A Case Report on Largely Emerging and Severe Infectious Disease from Southeast China and Literature Review. Respir Med Case Rep 2019. [DOI: 10.1016/j.rmcr.2019.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Meumann EM, Anstey NM, Currie BJ, Piera KA, Kenyon JJ, Hall RM, Davis JS, Sarovich DS. Genomic epidemiology of severe community-onset Acinetobacter baumannii infection. Microb Genom 2019; 5. [PMID: 30806611 PMCID: PMC6487312 DOI: 10.1099/mgen.0.000258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Acinetobacter baumannii causes severe, fulminant, community-acquired pneumonia (CAP) in tropical and subtropical regions. We compared the population structure, virulence and antimicrobial resistance determinants of northern Australian community-onset A. baumannii strains with local and global strains. We performed whole-genome sequencing on 55 clinical and five throat colonization A. baumannii isolates collected in northern Australia between 1994 and 2016. Clinical isolates included CAP (n=41), healthcare-associated pneumonia (n=7) and nosocomial bloodstream (n=7) isolates. We also included 93 publicly available international A. baumannii genome sequences in the analyses. Patients with A. baumannii CAP were almost all critically unwell; 82 % required intensive care unit admission and 18 % died during their inpatient stay. Whole-genome phylogenetic analysis demonstrated that community-onset strains were not phylogenetically distinct from nosocomial strains. Some non-multidrug-resistant local strains were closely related to multidrug-resistant strains from geographically distant locations. Pasteur sequence type (ST)10 was the dominant ST and accounted for 31/60 (52 %) northern Australian strains; the remainder belonged to a diverse range of STs. The most recent common ancestor for ST10 was estimated to have occurred in 1738 (95 % highest posterior density, 1626–1826), with evidence of multiple introduction events between Australia and Southeast Asia between then and the present day. Virulence genes associated with biofilm formation and the type 6 secretion system (T6SS) were absent in many strains, and were not associated with in-hospital mortality. All strains were susceptible to gentamicin and meropenem; none carried an AbaR resistance island. Our results suggest that international dissemination of A. baumannii is occurring in the community on a contemporary timescale. Genes associated with biofilm formation and the T6SS may not be required for survival in community niches. The relative contributions of host and bacterial factors to the clinical severity of community-onset A. baumannii infection require further investigation.
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Affiliation(s)
- Ella M Meumann
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Nicholas M Anstey
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Kim A Piera
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia
| | - Johanna J Kenyon
- 3School of Biomedical Sciences, Queensland University of Technology, Brisbane 4001, Australia
| | - Ruth M Hall
- 4School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Joshua S Davis
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,5Department of Infectious Diseases, John Hunter Hospital and the University of Newcastle, Newcastle 2305, Australia
| | - Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,6Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4072, Australia
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Zhu Y, Zhao J, Maifiah MHM, Velkov T, Schreiber F, Li J. Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling. mSystems 2019; 4:e00157-18. [PMID: 30746493 PMCID: PMC6365644 DOI: 10.1128/msystems.00157-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/08/2019] [Indexed: 02/04/2023] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic pathogen over the past decades, with a high incidence in nosocomial infections. Discovered in the late 1940s but abandoned in the 1970s, polymyxins (i.e., polymyxin B and colistin) have been revived as the last-line therapy against Gram-negative "superbugs," including MDR A. baumannii. Worryingly, resistance to polymyxins in A. baumannii has been increasingly reported, urging the development of novel antimicrobial therapies to rescue this last-line class of antibiotics. In the present study, we integrated genome-scale metabolic modeling with multiomics data to elucidate the mechanisms of cellular responses to colistin treatment in A. baumannii. A genome-scale metabolic model, iATCC19606, was constructed for strain ATCC 19606 based on the literature and genome annotation, containing 897 genes, 1,270 reactions, and 1,180 metabolites. After extensive curation, prediction of growth on 190 carbon sources using iATCC19606 achieved an overall accuracy of 84.3% compared to Biolog experimental results. Prediction of gene essentiality reached a high accuracy of 86.1% and 82.7% compared to two transposon mutant libraries of AB5075 and ATCC 17978, respectively. Further integrative modeling with our correlative transcriptomics and metabolomics data deciphered the complex regulation on metabolic responses to colistin treatment, including (i) upregulated fluxes through gluconeogenesis, the pentose phosphate pathway, and amino acid and nucleotide biosynthesis; (ii) downregulated TCA cycle and peptidoglycan and lipopolysaccharide biogenesis; and (iii) altered fluxes over respiratory chain. Our results elucidated the interplay of multiple metabolic pathways under colistin treatment in A. baumannii and provide key mechanistic insights into optimizing polymyxin combination therapy. IMPORTANCE Combating antimicrobial resistance has been highlighted as a critical global health priority. Due to the drying drug discovery pipeline, polymyxins have been employed as the last-line therapy against Gram-negative "superbugs"; however, the detailed mechanisms of antibacterial killing remain largely unclear, hampering the improvement of polymyxin therapy. Our integrative modeling using the constructed genome-scale metabolic model iATCC19606 and the correlative multiomics data provide the fundamental understanding of the complex metabolic responses to polymyxin treatment in A. baumannii at the systems level. The model iATCC19606 may have a significant potential in antimicrobial systems pharmacology research in A. baumannii.
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Affiliation(s)
- Yan Zhu
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jinxin Zhao
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Mohd Hafidz Mahamad Maifiah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Jian Li
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
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Traglia G, Chiem K, Quinn B, Fernandez JS, Montaña S, Almuzara M, Mussi MA, Tolmasky ME, Iriarte A, Centrón D, Ramírez MS. Genome sequence analysis of an extensively drug-resistant Acinetobacter baumannii indigo-pigmented strain depicts evidence of increase genome plasticity. Sci Rep 2018; 8:16961. [PMID: 30446709 PMCID: PMC6240043 DOI: 10.1038/s41598-018-35377-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/29/2018] [Indexed: 01/02/2023] Open
Abstract
Acinetobacter baumannii is a multidrug resistant nosocomial pathogen that shows an outstanding ability to undergo genetic exchange, thereby acquiring different traits that contribute to its success. In this work, we identified genetic features of an indigo-pigmented A. baumannii strain (Ab33405) that belongs to the clonal complex CC113B/CC79P. Ab33405 possesses a high number of genes coding for antibiotic resistance and virulence factors that may contribute to its survival, not only in the human host, but also in the hospital environment. Thirteen genes conferring resistance to different antibiotic families (trimethoprim, florfenicol, β-lactams, aminoglycosides and sulfonamide) as well as the adeIJK genes and the capsule locus (KL) and outer core locus (OCL) were identified. Ab33405 includes 250 unique genes and a significant number of elements associated with Horizontal Gene Transfer, such as insertion sequences and transposons, genomic islands and prophage sequences. Also, the indigo-pigmented uncommon phenotype that could be associated with the monooxygenase or dioxygenase enzyme coded for by the iacA gene within the iac cluster was probably conferred by insertion of a 18-kb DNA fragment into the iacG gene belonging to this cluster. The Ab33405 genome includes all type VI secretion system genes and killing assays showed the ability of Ab33045 to kill Escherichia coli. In addition, Ab33405 can modulate susceptibility antibiotics when exposed to blue light.
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Affiliation(s)
- German Traglia
- Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Kevin Chiem
- Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Brettni Quinn
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Jennifer S Fernandez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Sabrina Montaña
- Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriología, Hospital Interzonal de Agudos Eva Perón, San Martín Buenos Aires, Argentina
| | - María Alejandra Mussi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI- CONICET), Rosario, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Andres Iriarte
- Laboratorio de Biología Computacional, Dpto. de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Daniela Centrón
- Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA.
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36
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Catabolic activity and biofilm formation of foodborne Listeria monocytogenes strains. J Verbrauch Lebensm 2018. [DOI: 10.1007/s00003-018-1169-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Complete Genome Sequencing of Acinetobacter baumannii Strain K50 Discloses the Large Conjugative Plasmid pK50a Encoding Carbapenemase OXA-23 and Extended-Spectrum β-Lactamase GES-11. Antimicrob Agents Chemother 2018; 62:AAC.00212-18. [PMID: 29463529 DOI: 10.1128/aac.00212-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii strains appeared as serious emerging nosocomial pathogens in clinical environments and especially in intensive care units (ICUs). A. baumannii strain K50, recovered from a hospitalized patient in Kuwait, exhibited resistance to carbapenems and additionally to ciprofloxacin, chloramphenicol, sulfonamides, amikacin, and gentamicin. Genome sequencing revealed that the strain possesses two plasmids, pK50a (79.6 kb) and pK50b (9.5 kb), and a 3.75-Mb chromosome. A. baumannii K50 exhibits an average nucleotide identity (ANI) of 99.98% to the previously reported Iraqi clinical isolate AA-014, even though the latter strain lacked plasmid pK50a. Strain K50 belongs to sequence type 158 (ST158) (Pasteur scheme) and ST499 (Oxford scheme). Plasmid pK50a is a member of the Aci6 (replication group 6 [RG6]) group of Acinetobacter plasmids and carries a conjugative transfer module and two antibiotic resistance gene regions. The transposon Tn2008 carries the carbapenemase gene blaOXA-23, whereas a class 1 integron harbors the resistance genes blaGES-11, aacA4, dfrA7, qacEΔ1, and sul1, conferring resistance to all β-lactams and reduced susceptibility to carbapenems and resistance to aminoglycosides, trimethoprim, quaternary ammonium compounds, and sulfamethoxazole, respectively. The class 1 integron is flanked by MITEs (miniature inverted-repeat transposable elements) delimiting the element at its insertion site.
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Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Front Genet 2018; 9:121. [PMID: 29692801 PMCID: PMC5902709 DOI: 10.3389/fgene.2018.00121] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/26/2018] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.
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Affiliation(s)
- Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Erol Kavvas
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
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Hernandez-Morales AC, Lessor LL, Wood TL, Migl D, Mijalis EM, Cahill J, Russell WK, Young RF, Gill JJ. Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity. J Virol 2018; 92:e01064-17. [PMID: 29298884 PMCID: PMC5827379 DOI: 10.1128/jvi.01064-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/06/2017] [Indexed: 01/08/2023] Open
Abstract
The increased prevalence of drug-resistant, nosocomial Acinetobacter infections, particularly from pathogenic members of the Acinetobacter calcoaceticus-baumannii complex, necessitates the exploration of novel treatments such as phage therapy. In the present study, we characterized phage Petty, a novel podophage that infects multidrug-resistant Acinetobacter nosocomialis and Acinetobacter baumannii Genome analysis reveals that phage Petty is a 40,431-bp ϕKMV-like phage, with a coding density of 92.2% and a G+C content of 42.3%. Interestingly, the lysis cassette encodes a class I holin and a single-subunit endolysin, but it lacks canonical spanins to disrupt the outer membrane. Analysis of other ϕKMV-like genomes revealed that spaninless lysis cassettes are a feature of phages infecting Acinetobacter within this subfamily of bacteriophages. The observed halo surrounding Petty's large clear plaques indicated the presence of a phage-encoded depolymerase capable of degrading capsular exopolysaccharides (EPS). The product of gene 39, a putative tail fiber, was hypothesized to possess depolymerase activity based on weak homology to previously reported phage tail fibers. The 101.4-kDa protein gene product 39 (gp39) was cloned and expressed, and its activity against Acinetobacter EPS in solution was determined. The enzyme degraded purified EPS from its host strain A. nosocomialis AU0783, reducing its viscosity, and generated reducing ends in solution, indicative of hydrolase activity. Given that the accessibility to cells within a biofilm is enhanced by degradation of EPS, phages with depolymerases may have enhanced diagnostic and therapeutic potential against drug-resistant Acinetobacter strains.IMPORTANCE Bacteriophage therapy is being revisited as a treatment for difficult-to-treat infections. This is especially true for Acinetobacter infections, which are notorious for being resistant to antimicrobials. Thus, sufficient data need to be generated with regard to phages with therapeutic potential, if they are to be successfully employed clinically. In this report, we describe the isolation and characterization of phage Petty, a novel lytic podophage, and its depolymerase. To our knowledge, it is the first phage reported to be able to infect both A. baumannii and A. nosocomialis The lytic phage has potential as an alternative therapeutic agent, and the depolymerase could be used for modulating EPS both during infections and in biofilms on medical equipment, as well as for capsular typing. We also highlight the lack of predicted canonical spanins in the phage genome and confirm that, unlike the rounding of lambda lysogens lacking functional spanin genes, A. nosocomialis cells infected with phage Petty lyse by bursting. This suggests that phages like Petty employ a different mechanism to disrupt the outer membrane of Acinetobacter hosts during lysis.
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Affiliation(s)
- A C Hernandez-Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - L L Lessor
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - T L Wood
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - D Migl
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - E M Mijalis
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J Cahill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - W K Russell
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - R F Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J J Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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40
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Shah BS, Ashwood HE, Harrop SJ, Farrugia DN, Paulsen IT, Mabbutt BC. Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii. PLoS One 2018; 13:e0191610. [PMID: 29352301 PMCID: PMC5774825 DOI: 10.1371/journal.pone.0191610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022] Open
Abstract
With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB. This dehydratase belongs to the ‘extended’ short-chain dehydrogenase/reductase (SDR) family, related in fold to previously characterised enzymes CapE and FlaA1. Our 2.65Å resolution structure of Ab-WbjB shows a hexamer, organised into a trimer of chain pairs, with coenzyme NADP+ occupying each chain. Specific active-site interactions between each coenzyme and a lysine quaternary group of a neighbouring chain interconnect adjacent dimers, so stabilising the hexameric form. We show UDP-GlcNAc to be a specific substrate for Ab-WbjB, with binding evident by ITC (Ka = 0.23 μmol-1). The sequence of Ab-WbjB shows variation from the consensus active-site motifs of many SDR enzymes, demonstrating a likely catalytic role for a specific threonine sidechain (as an alternative to tyrosine) in the canonical active site chemistry of these epimerases.
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Affiliation(s)
- Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Heather E. Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Stephen J. Harrop
- School of Physics, The University of New South Wales, Sydney, Australia
| | - Daniel N. Farrugia
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- * E-mail:
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41
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Mittal J, Szymczak WA, Robbins N, Harris C, Nori P. An unusual cause of community-acquired pneumonia. IDCases 2017; 11:41-43. [PMID: 29318108 PMCID: PMC5751873 DOI: 10.1016/j.idcr.2017.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 11/29/2022] Open
Abstract
A. baumannii community-acquired pneumonia incidence and prevalence is unknown in temperate regions. It potentially has a rapidly progressive course and poor outcome. Progression of disease may be due to immune dysfunction in certain hosts. Studies are conflicting on the role and regimen of antibiotics on disease progression.
We present a case of fatal community-acquired pneumonia (CAP) due to Acinetobacter baumannii, which is rarely reported in the northeastern United States. Previously reported cases originate from tropical and subtropical climates, and infection tends to have an aggressive course with a poor outcome. Appropriate antimicrobial therapy is crucial; however, the associated systemic inflammatory response may overwhelm host defenses, especially in patients with certain co-morbidities.
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Affiliation(s)
- Jaimie Mittal
- Albert Einstein College of Medicine and Montefiore Medical Center, Department of Internal Medicine, Division of Infectious Diseases, Bronx, NY, USA
| | - Wendy A Szymczak
- Albert Einstein College of Medicine and Montefiore Medical Center, Department of Pathology, Bronx, NY, USA
| | - Noah Robbins
- Albert Einstein College of Medicine and Montefiore Medical Center, Department of Internal Medicine, Division of Infectious Diseases, Bronx, NY, USA
| | - Carol Harris
- Albert Einstein College of Medicine and Jacobi Medical Center, Department of Internal Medicine, Division of Infectious Diseases, Bronx, NY, USA
| | - Priya Nori
- Albert Einstein College of Medicine and Montefiore Medical Center, Department of Internal Medicine, Division of Infectious Diseases, Bronx, NY, USA
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Novel Fri1-like Viruses Infecting Acinetobacter baumannii-vB_AbaP_AS11 and vB_AbaP_AS12-Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy. Viruses 2017; 9:v9070188. [PMID: 28714913 PMCID: PMC5537680 DOI: 10.3390/v9070188] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 01/25/2023] Open
Abstract
Acinetobacter baumannii is a gram-negative, non-fermenting aerobic bacterium which is often associated with hospital-acquired infections and known for its ability to develop resistance to antibiotics, form biofilms, and survive for long periods in hospital environments. In this study, we present two novel viruses, vB_AbaP_AS11 and vB_AbaP_AS12, specifically infecting and lysing distinct multidrug-resistant clinical A. baumannii strains with K19 and K27 capsular polysaccharide structures, respectively. Both phages demonstrate rapid adsorption, short latent periods, and high burst sizes in one-step growth experiments. The AS11 and AS12 linear double-stranded DNA genomes of 41,642 base pairs (bp) and 41,402 bp share 86% nucleotide sequence identity with the most variable regions falling in host receptor–recognition genes. These genes encode tail spikes possessing depolymerizing activities towards corresponding capsular polysaccharides which are the primary bacterial receptors. We described AS11 and AS12 genome organization and discuss the possible regulation of transcription. The overall genomic architecture and gene homology analyses showed that the phages are new representatives of the recently designated Fri1virus genus of the Autographivirinae subfamily within the Podoviridae family.
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Hassan KA, Pederick VG, Elbourne LDH, Paulsen IT, Paton JC, McDevitt CA, Eijkelkamp BA. Zinc stress induces copper depletion in Acinetobacter baumannii. BMC Microbiol 2017; 17:59. [PMID: 28284195 PMCID: PMC5346208 DOI: 10.1186/s12866-017-0965-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/24/2017] [Indexed: 12/18/2022] Open
Abstract
Background The first row transition metal ions zinc and copper are essential to the survival of many organisms, although in excess these ions are associated with significant toxicity. Here, we examined the impact of zinc and copper stress on Acinetobacter baumannii, a common opportunistic pathogen. Results We show that extracellular zinc stress induces a copper-specific depletion phenotype in A. baumannii ATCC 17978. Supplementation with copper not only fails to rescue this phenotype, but further exacerbates the copper depletion. Extensive analysis of the A. baumannii ATCC 17978 genome identified 13 putative zinc/copper resistance efflux pumps. Transcriptional analyses show that four of these transporters are responsive to zinc stress, five to copper stress and seven to the combination of zinc and copper stress, thereby revealing a likely foundation for the zinc-induced copper starvation in A. baumannii. In addition, we show that zinc and copper play crucial roles in management of oxidative stress and the membrane composition of A. baumannii. Further, we reveal that zinc and copper play distinct roles in macrophage-mediated killing of this pathogen. Conclusions Collectively, this study supports the targeting of metal ion homeostatic mechanisms as an effective antimicrobial strategy against multi-drug resistant bacterial pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0965-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Victoria G Pederick
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
| | - Bart A Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
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Phylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species. Appl Microbiol Biotechnol 2016; 101:367-379. [PMID: 27734121 DOI: 10.1007/s00253-016-7866-0] [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] [Received: 03/30/2016] [Revised: 08/31/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
Abstract
A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.
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Patamatamkul S, Klungboonkrong V, Praisarnti P, Jirakiat K. A case-control study of community-acquired Acinetobacter baumannii pneumonia and melioidosis pneumonia in northeast Thailand: an emerging fatal disease with unique clinical features. Diagn Microbiol Infect Dis 2016; 87:79-86. [PMID: 27789057 DOI: 10.1016/j.diagmicrobio.2016.10.014] [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] [Received: 08/10/2016] [Accepted: 10/08/2016] [Indexed: 10/20/2022]
Abstract
Acinetobacter baumannii is the emerging cause of severe and often fatal gram-negative, community-acquired pneumonia (CAP-AB) in Thailand. Due to its rarity, its specific clinical features are ill defined. In this retrospective study, we compared the demographic data, risk factors, clinical characteristics, radiographic pattern, and microbiological data between CAP-AB and Burkholderia pseudomallei CAP (CAP-BP) to identify the clinical features and risk factors of CAP-AB. CAP-AB was associated with a more productive cough and a shorter duration of symptoms, while CAP-BP was associated with more musculoskeletal symptoms. The white blood cell and neutrophil counts were significantly lower in the CAP-AB group. Gram staining of the sputum revealed a significantly higher amount of bacteria in the CAP-AB group. Lobar infiltration and unilateral right lung involvement were the most common radiographic patterns in the CAP-AB group. CAP-AB is associated with severe pneumonia and has unique clinical features that distinguish it from CAP-BP.
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Affiliation(s)
- Samadhi Patamatamkul
- Faculty of Medicine, Suddhavej Hospital, Mahasarakham University, Mueang Maha Sarakham, Mahasarakham 44000, Thailand.
| | - Voravan Klungboonkrong
- Faculty of Medicine, Suddhavej Hospital, Mahasarakham University, Mueang Maha Sarakham, Mahasarakham 44000, Thailand
| | - Pakawas Praisarnti
- Faculty of Medicine, Suddhavej Hospital, Mahasarakham University, Mueang Maha Sarakham, Mahasarakham 44000, Thailand
| | - Kittitouch Jirakiat
- Faculty of Medicine, Suddhavej Hospital, Mahasarakham University, Mueang Maha Sarakham, Mahasarakham 44000, Thailand
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Hassan A, Naz A, Obaid A, Paracha RZ, Naz K, Awan FM, Muhmmad SA, Janjua HA, Ahmad J, Ali A. Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics 2016; 17:732. [PMID: 27634541 PMCID: PMC5025611 DOI: 10.1186/s12864-016-2951-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/19/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. RESULTS The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. CONCLUSION The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
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Affiliation(s)
- Afreenish Hassan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Anam Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Ayesha Obaid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Faryal Mehwish Awan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Syed Aun Muhmmad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
- Department of Computer Science and Information Technology, Stratford University, Falls Church, VA 22043 USA
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
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A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones. INFECTION GENETICS AND EVOLUTION 2016; 42:41-5. [PMID: 27125687 DOI: 10.1016/j.meegid.2016.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/21/2016] [Accepted: 04/24/2016] [Indexed: 01/12/2023]
Abstract
A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings.
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Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene. Antimicrob Agents Chemother 2016; 60:3032-40. [PMID: 26953198 DOI: 10.1128/aac.00124-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/02/2016] [Indexed: 11/20/2022] Open
Abstract
The species Acinetobacter baumannii is one of the most important multidrug-resistant human pathogens. To determine its virulence and antibiotic resistance determinants, the genome of the nosocomial blaNDM-1-positive A. baumannii strain R2090 originating from Egypt was completely sequenced. Genome analysis revealed that strain R2090 is highly related to the community-acquired Australian A. baumannii strain D1279779. The two strains belong to sequence type 267 (ST267). Isolate R2090 harbored the chromosomally integrated transposon Tn125 carrying the carbapenemase gene blaNDM-1 that is not present in the D1279779 genome. To test the transferability of the metallo-β-lactamase (MBL) gene region, the clinical isolate R2090 was mated with the susceptible A. baumannii recipient CIP 70.10, and the carbapenem-resistant derivative R2091 was obtained. Genome sequencing of the R2091 derivative revealed that it had received an approximately 66-kb region comprising the transposon Tn125 embedding the blaNDM-1 gene. This region had integrated into the chromosome of the recipient strain CIP 70.10. From the four known mechanisms for horizontal gene transfer (conjugation, outer membrane vesicle-mediated transfer, transformation, and transduction), conjugation could be ruled out, since strain R2090 lacks any plasmid, and a type IV secretion system is not encoded in its chromosome. However, strain R2090 possesses three putative prophages, two of which were predicted to be complete and therefore functional. Accordingly, it was supposed that the transfer of the resistance gene region from the clinical isolate R2090 to the recipient occurred by general transduction facilitated by one of the prophages present in the R2090 genome. Hence, phage-mediated transduction has to be taken into account for the dissemination of antibiotic resistance genes within the species A. baumannii.
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Hrenovic J, Goic-Barisic I, Kazazic S, Kovacic A, Ganjto M, Tonkic M. Carbapenem-resistant isolates of Acinetobacter baumannii in a municipal wastewater treatment plant, Croatia, 2014. Euro Surveill 2016; 21:30195. [DOI: 10.2807/1560-7917.es.2016.21.15.30195] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/14/2016] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is an emerging hospital pathogen. Whereas A. baumannii isolated from patients or hospitals has been reported, there are few data regarding propagation of viable A. baumannii in the natural environment. This study investigates the occurrence and antimicrobial susceptibility of viable A. baumannii in municipal wastewater and its persistence through the wastewater treatment process. A total of 21 A. baumannii isolates were recovered at a secondary type of municipal wastewater treatment plant in Zagreb, Croatia: 15 from raw influent wastewater and six from final effluent. All isolates were carbapenem- and multidrug-resistant. Among 14 isolates tested for bla
OXA genes, all harboured the constitutive bla
OXA-51-like gene, while the acquired bla
OXA-23-like and bla
OXA-40-like genes were found in 10 and three isolates respectively. Six A. baumannii isolates recovered from effluent wastewater multiplied and survived in sterilised effluent wastewater up to 50 days. These findings support the idea that multidrug-resistant A. baumannii can occur and have the ability to survive in the environment.
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Affiliation(s)
- Jasna Hrenovic
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia
| | - Ivana Goic-Barisic
- University Hospital Centre Split, Department of Clinical Microbiology and University of Split School of Medicine, Split, Croatia
| | - Snjezana Kazazic
- Ruđer Boskovic Institute, Division of Physical Chemistry, Zagreb, Croatia
| | - Ana Kovacic
- Institute of Public Health of Split and Dalmatia County, Split, Croatia
| | - Marin Ganjto
- Zagreb Wastewater - Management and Operation Ltd., Zagreb, Croatia
| | - Marija Tonkic
- University Hospital Centre Split, Department of Clinical Microbiology and University of Split School of Medicine, Split, Croatia
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Chiang MH, Sung WC, Lien SP, Chen YZ, Lo AFY, Huang JH, Kuo SC, Chong P. Identification of novel vaccine candidates against Acinetobacter baumannii using reverse vaccinology. Hum Vaccin Immunother 2016; 11:1065-73. [PMID: 25751377 DOI: 10.1080/21645515.2015.1010910] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Acinetobacter baumannii (Ab) is a global emerging bacterium causing nosocomial infections such as pneumonia, meningitis, bacteremia and soft tissue infections especially in intensive care units. Since Ab is resistant to almost all conventional antibiotics, it is now one of the 6 top-priorities of the dangerous microorganisms listed by the Infectious Disease Society of America. The development of vaccine is one of the most promising and cost-effective strategies to prevent infections. In this study, we identified potential protective vaccine candidates using reverse vaccinology. We have analyzed 14 on-line available Ab genome sequences and found 2752 homologous core genes. Using information obtained from immuno-proteomic experiments, published proteomic information and the bioinformatics PSORTb v3.0 software to predict the location of extracellular and/or outer membrane proteins, 77 genes were identified and selected for further studies. After excluding those antigens have been used as vaccine candidates reported by the in silico search-engines of PubMed and Google Scholar, 13 proteins could potentially be vaccine candidates. We have selected and cloned the genes of 3 antigens that were further expressed and purified. These antigens were found to be highly immunogenic and conferred partial protection (60%) in a pneumonia animal model. The strategy described in the present study incorporates the advantages of reverse vaccinology, bioinformatics and immuno-proteomic platform technologies and is easy to perform to identify novel immunogens for multi-component vaccines development.
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Affiliation(s)
- Ming-Hsien Chiang
- a Vaccine R&D Center; National Institute of Infectious Diseases and Vaccinology ; National Health Research Institutes ; Zhunan Town , Taiwan
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