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Soontarach R, Srimanote P, Arechanajan B, Nakkaew A, Voravuthikunchai SP, Chusri S. Characterization of a novel bacteriophage endolysin (LysAB1245) with extended lytic activity against distinct capsular types associated with Acinetobacter baumannii resistance. PLoS One 2024; 19:e0296453. [PMID: 38165983 PMCID: PMC10760713 DOI: 10.1371/journal.pone.0296453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
Capsular polysaccharides are considered as major virulence factors associated with the ability of multidrug-resistant (MDR) Acinetobacter baumannii to cause severe infections. In this study, LysAB1245, a novel bacteriophage-encoded endolysin consisting of a lysozyme-like domain from phage T1245 was successfully expressed, purified, and evaluated for its antibacterial activity against distinct capsular types associated with A. baumannii resistance. The results revealed a broad spectrum activity of LysAB1245 against all clinical MDR A. baumannii isolates belonging to capsular type (KL) 2, 3, 6, 10, 47, 49, and 52 and A. baumannii ATCC 19606. At 2 h following the treatment with 1.7 unit/reaction of LysAB1245, more than 3 log reduction in the numbers of bacterial survival was observed. In addition, LysAB1245 displayed rapid bactericidal activity within 30 min (nearly 3 log CFU/mL of bacterial reduction). Thermostability assay indicated that LysAB1245 was stable over a broad range of temperature from 4 to 70°C, while pH sensitivity assay demonstrated a wide range of pH from 4.5 to 10.5. Furthermore, both minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of LysAB1245 against all MDR A. baumannii isolates and A. baumannii ATCC 19606 were 4.21 μg/mL (0.1 unit/reaction). Conclusively, these results suggest that LysAB1245 possesses potential application for the treatment of nosocomial MDR A. baumannii infections.
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Affiliation(s)
- Rosesathorn Soontarach
- Faculty of Science, Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla, Thailand
- Faculty of Medicine, Department of Internal Medicine, Division of Infectious Diseases, Prince of Songkla University, Songkhla, Thailand
| | - Potjanee Srimanote
- Faculty of Allied Health Sciences, Graduate in Biomedical Sciences, Thammasat University, Pathum Thani, Thailand
| | - Buppa Arechanajan
- Faculty of Allied Health Sciences, Graduate in Biomedical Sciences, Thammasat University, Pathum Thani, Thailand
| | - Alisa Nakkaew
- Faculty of Science, Division of Biological Science, Program in Molecular Biology and Bioinformatics, Prince of Songkla University, Songkhla, Thailand
| | | | - Sarunyou Chusri
- Faculty of Medicine, Department of Internal Medicine, Division of Infectious Diseases, Prince of Songkla University, Songkhla, Thailand
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Wiradiputra MRD, Thirapanmethee K, Khuntayaporn P, Wanapaisan P, Chomnawang MT. Comparative genotypic characterization related to antibiotic resistance phenotypes of clinical carbapenem-resistant Acinetobacter baumannii MTC1106 (ST2) and MTC0619 (ST25). BMC Genomics 2023; 24:689. [PMID: 37978344 PMCID: PMC10655397 DOI: 10.1186/s12864-023-09734-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prevalence of Acinetobacter baumannii in nosocomial infections and its remarkable ability to develop antimicrobial resistance have been a critical issue in hospital settings. Here, we examined the genomic features related to resistance phenotype displayed by carbapenem-resistant A. baumannii (CRAB) MTC1106 (ST2) and MTC0619 (ST25). RESULTS Resistome analysis of both strains revealed that MTC1106 possessed higher numbers of antimicrobial resistance genes compared to MTC0619. Some of those genetic determinants were present in accordance with the susceptibility profile of the isolates. The predicted ISAba1 region upstream of blaOXA-23 gene was related to carbapenem resistance since this IS element was well-characterized to mediate overexpression of carbapenemase genes and eventually provided capability to confer resistance. Unlike MTC0619 strain, which only carried class B and D β-lactamase genes, MTC1106 strain also possessed blaTEM-1D, a class A β-lactamase. Regarding to aminoglycosides resistance, MTC0619 contained 5 related genes in which all of them belonged to three groups of aminoglycosides modifying enzyme (AME), namely, N-acetyltransferase (AAC), O-nucleotidyltransferase (ANT), and O-phosphotransferase (APH). On the other hand, MTC1106 lacked only the AAC of which found in MTC0619, yet it also carried an armA gene encoding for 16S rRNA methyltransferase. Two macrolides resistance genes, mph(E) and msr(E), were identified next to the armA gene of MTC1106 isolate in which they encoded for macrolide 2'-phosphotransferase and ABC-type efflux pump, respectively. Besides acquired resistance genes, some chromosomal genes and SNPs associated with resistance to fluoroquinolones (i.e. gyrA and parC) and colistin (i.e. pmrCAB, eptA, and emrAB) were observed. However, gene expression analysis suggested that the genetic determinants significantly contributing to low-level colistin resistance remained unclear. In addition, similar number of efflux pumps genes were identified in both lineages with only the absence of adeC, a part of adeABC RND-type multidrug efflux pump in MTC0619 strain. CONCLUSIONS We found that MTC1106 strain harbored more antimicrobial resistance genes and showed higher resistance to antibiotics than MTC0619 strain. Regarding genomic characterization, this study was likely the first genome comparative analysis of CARB that specifically included isolates belonging to ST2 and ST25 which were widely spread in Thailand. Taken altogether, this study suggests the importance to monitor the resistance status of circulating A. baumannii clones and identify genes that may contribute to shifting the resistance trend among isolates.
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Affiliation(s)
- Made Rai Dwitya Wiradiputra
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Biopharmaceutical Sciences Program, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Krit Thirapanmethee
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Piyatip Khuntayaporn
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Pagakrong Wanapaisan
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
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Doughty EL, Liu H, Moran RA, Hua X, Ba X, Guo F, Chen X, Zhang L, Holmes M, van Schaik W, McNally A, Yu Y. Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 37:100780. [PMID: 37693864 PMCID: PMC10485671 DOI: 10.1016/j.lanwpc.2023.100780] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 09/12/2023]
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations. Methods A three-month cross-sectional observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 5068 samples were collected from the hospital environment (n = 3985), patients (n = 964) and staff (n = 119). CRAB isolates were obtained from 10.5% of these samples (n = 532). All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing. Findings The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.6%) sampling occasions but from patients on only 72/299 (24.1%) occasions. CRAB was spread to adjacent bed units and rooms, and following re-location of patients within the ICU. We also observed three horizontal gene transfer events between CRAB strains in the ICU, involving three different plasmids. Interpretation The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology and the unique challenges in containing the spread of CRAB in ICUs where this important multidrug-resistant pathogen is endemic. Funding This work was undertaken as part of the DETECTIVE research project funded by the Medical Research Council (MR/S013660/1), National Natural Science Foundation of China (81861138054, 32011530116, 31970128, 31770142), Zhejiang Province Medical Platform Backbone Talent Plan (2020RC075), and the National Key Research and Development Program of China grant (2018YFE0102100). W.v.S was also supported by a Wolfson Research Merit Award (WM160092).
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Affiliation(s)
- Emma L. Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Haiyang Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Feng Guo
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Xiangping Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
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Timoshina OY, Kasimova AA, Shneider MM, Arbatsky NP, Shashkov AS, Shelenkov AA, Mikhailova YV, Popova AV, Hall RM, Knirel YA, Kenyon JJ. Loss of a Branch Sugar in the Acinetobacter baumannii K3-Type Capsular Polysaccharide Due To Frameshifts in the gtr6 Glycosyltransferase Gene Leads To Susceptibility To Phage APK37.1. Microbiol Spectr 2023; 11:e0363122. [PMID: 36651782 PMCID: PMC9927144 DOI: 10.1128/spectrum.03631-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
The type of capsular polysaccharide (CPS) on the cell surface of Acinetobacter baumannii can determine the specificity of lytic bacteriophage under consideration for therapeutic use. Here, we report the isolation of a phage on an extensively antibiotic resistant ST2 A. baumannii isolate AB5001 that carries the KL3 CPS biosynthesis gene cluster predicting a K3-type CPS. As the phage did not infect isolates carrying KL3 or KL22 and known to produce K3 CPS, the structure of the CPS isolated from A. baumannii AB5001 was determined. AB5001 produced a variant CPS form, K3-v1, that lacks the β-d-GlсpNAc side chain attached to the d-Galp residue in the K3 structure. Inspection of the KL3 sequence in the genomes of AB5001 and other phage-susceptible isolates with a KL3 locus revealed single-base deletions in gtr6, causing loss of the Gtr6 glycosyltransferase that adds the missing d-GlсpNAc side chain to the K3 CPS. Hence, the presence of this sugar profoundly restricts the ability of the phage to digest the CPS. The 41-kb linear double-stranded DNA (dsDNA) phage genome was identical to the genome of a phage isolated on a K37-producing isolate and thus was named APK37.1. APK37.1 also infected isolates carrying KL116. Consistent with this, K3-v1 resembles the K37 and K116 structures. APK37.1 is a Friunavirus belonging to the Autographiviridae family. The phage-encoded tail spike depolymerase DpoAPK37.1 was not closely related to Dpo encoded by other sequenced Friunaviruses, including APK37 and APK116. IMPORTANCE Lytic bacteriophage have potential for the treatment of otherwise untreatable extensively antibiotic-resistant bacteria. For Acinetobacter baumannii, most phage exhibit specificity for the type of capsular polysaccharide (CPS) produced on the cell surface. However, resistance can arise via mutations in CPS genes that abolish this phage receptor. Here, we show that single-base deletions in a CPS gene result in alteration of the final structure rather than deletion of the capsule layer and hence affect the ability of a newly reported podophage to infect strains producing the K3 CPS.
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Affiliation(s)
- Olga Y. Timoshina
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A. Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M. Shneider
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P. Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S. Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Anastasiya V. Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Ruth M. Hall
- School of Life and Environmental Science, University of Sydney, Sydney, Australia
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Johanna J. Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
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Mohamad F, Alzahrani RR, Alsaadi A, Alrfaei BM, Yassin AEB, Alkhulaifi MM, Halwani M. An Explorative Review on Advanced Approaches to Overcome Bacterial Resistance by Curbing Bacterial Biofilm Formation. Infect Drug Resist 2023; 16:19-49. [PMID: 36636380 PMCID: PMC9830422 DOI: 10.2147/idr.s380883] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
The continuous emergence of multidrug-resistant pathogens evoked the development of innovative approaches targeting virulence factors unique to their pathogenic cascade. These approaches aimed to explore anti-virulence or anti-infective therapies. There are evident concerns regarding the bacterial ability to create a superstructure, the biofilm. Biofilm formation is a crucial virulence factor causing difficult-to-treat, localized, and systemic infections. The microenvironments of bacterial biofilm reduce the efficacy of antibiotics and evade the host's immunity. Producing a biofilm is not limited to a specific group of bacteria; however, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus biofilms are exemplary models. This review discusses biofilm formation as a virulence factor and the link to antimicrobial resistance. In addition, it explores insights into innovative multi-targeted approaches and their physiological mechanisms to combat biofilms, including natural compounds, phages, antimicrobial photodynamic therapy (aPDT), CRISPR-Cas gene editing, and nano-mediated techniques.
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Affiliation(s)
- F Mohamad
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Raghad R Alzahrani
- Nanomedicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ahlam Alsaadi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Bahauddeen M Alrfaei
- Stem Cells and Regenerative Medicine, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Eldeen B Yassin
- College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Manal M Alkhulaifi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia,Manal M Alkhulaifi, P.O. Box 55670, Riyadh, 11544, Tel +966 (11) 805-1685, Email
| | - Majed Halwani
- Nanomedicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,Correspondence: Majed Halwani, P.O. Box 3660, Mail Code 1515 (KAIMRC), Riyadh, 11481, Tel +966 (11) 429-4433, Fax +966 (11) 429-4440, Email ;
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6
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Soontarach R, Nwabor OF, Voravuthikunchai SP. Interaction of lytic phage T1245 with antibiotics for enhancement of antibacterial and anti-biofilm efficacy against multidrug-resistant Acinetobacter baumannii. BIOFOULING 2022; 38:994-1005. [PMID: 36606321 DOI: 10.1080/08927014.2022.2163479] [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: 04/29/2022] [Revised: 11/15/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Biofilms associated with multidrug-resistant (MDR) Acinetobacter baumannii on medical devices remain a big clinical problem. Antibiotic susceptibility tests were performed with eight commonly employed antibiotics against clinical isolates. The effects of antibiotics in combination with well-characterized lytic phage T1245 were studied to assess their antibacterial and anti-biofilm efficacy. Ceftazidime, colistin, imipenem, and meropenem significantly reduced bacterial density up to approximately 80% when combined with phage T1245, compared with control. Phage T1245 in combination with ceftazidime, colistin, and meropenem at subinhibitory concentrations demonstrated significant reduction in biomass and bacterial viability of 3-day established biofilms, compared with antibiotic alone. In addition, electron microscopy further confirmed the disruption of biofilm structure and cell morphology upon treatment with phage T1245 and antibiotics, including ceftazidime, colistin, and meropenem. Combined treatment of phage T1245 with these antibiotics could be employed for the management of A. baumannii infections and eradication of the bacterial biofilms.
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Affiliation(s)
- Rosesathorn Soontarach
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Natural Product Research Center of Excellence, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla, Thailand
| | - Ozioma Forstinus Nwabor
- Natural Product Research Center of Excellence, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Natural Product Research Center of Excellence, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla, Thailand
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Cahill SM, Hall RM, Kenyon JJ. An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus. Microb Genom 2022; 8. [PMID: 36214673 DOI: 10.1099/mgen.0.000878] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several novel non-antibiotic therapeutics for the critical priority bacterial pathogen, Acinetobacter baumannii, rely on specificity to the cell-surface capsular polysaccharide (CPS). Hence, prediction of CPS type deduced from genes in whole genome sequence data underpins the development and application of these therapies. In this study, we provide a comprehensive update to the A. baumannii K locus reference sequence database for CPS typing (available in Kaptive v. 2.0.1) to include 145 new KL, providing a total of 237 KL reference sequences. The database was also reconfigured for compatibility with the updated Kaptive v. 2.0.0 code that enables prediction of 'K type' from special logic parameters defined by detected combinations of KL and additional genes outside the K locus. Validation of the database against 8994 publicly available A. baumannii genome assemblies from NCBI databases identified the specific KL in 73.45 % of genomes with perfect, very high or high confidence. Poor sequence quality or the presence of insertion sequences were the main reasons for lower confidence levels. Overall, 17 KL were overrepresented in available genomes, with KL2 the most common followed by the related KL3 and KL22. Substantial variation in gene content of the central portion of the K locus, that usually includes genes specific to the CPS type, included 34 distinct groups of genes for synthesis of various complex sugars and >400 genes for forming linkages between sugars or adding non-sugar substituents. A repertoire of 681 gene types were found across the 237 KL, with 88.4 % found in <5 % of KL.
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Affiliation(s)
- Sarah M Cahill
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
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Soontarach R, Srimanote P, Enright MC, Blundell-Hunter G, Dorman MJ, Thomson NR, Taylor PW, Voravuthikunchai SP. Isolation and Characterisation of Bacteriophage Selective for Key Acinetobacter baumannii Capsule Chemotypes. Pharmaceuticals (Basel) 2022; 15:443. [PMID: 35455440 PMCID: PMC9027227 DOI: 10.3390/ph15040443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Nineteen bacteriophages against five main capsular types of multidrug-resistant Acinetobacter baumannii were isolated from tertiary care hospital sewage. Eight representative phages from each capsular type were characterized and tested for their biological properties. The biological features revealed that phages T1245, T444, and T515 had a large burst size of more than 420 pfu/mL, together with a short latent period lasting less than 6 min, and were readily adsorbed to a bacterial host within 10 min. Moreover, these phages demonstrated host specificity and stability over a broad range of temperatures (-20 to 60 °C) and pH (5.0-9.0). A whole-genome analysis of six lytic and two temperate phages revealed high genomic similarity with double-stranded DNA between 40 and 50 kb and G + C content of 38-39%. The protein compositions disclosed the absence of toxin-coding genes. The phylogenic results, together with morphological micrographs, confirmed that three selected phages (T1245, T444, and T515) belong to the Podoviridae family within the order Caudovirales. The biological data and bioinformatics analysis indicated that these novel A. baumannii phages possess important enzymes, including depolymerase and endolysin, which could be further developed as promising alternative antibacterial agents to control A. baumannii infections.
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Affiliation(s)
- Rosesathorn Soontarach
- Division of Biological Science, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Songkhla 90110, Thailand;
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla 90110, Thailand
| | - Potjanee Srimanote
- Graduate Program, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani 12121, Thailand;
| | - Mark C. Enright
- Department of Life Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK;
| | | | - Matthew J. Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; (M.J.D.); (N.R.T.)
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; (M.J.D.); (N.R.T.)
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Peter W. Taylor
- School of Pharmacy, University College London, London WC1N 1AX, UK; (G.B.-H.); (P.W.T.)
| | - Supayang P. Voravuthikunchai
- Division of Biological Science, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Songkhla 90110, Thailand;
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Prince of Songkla University, Songkhla 90110, Thailand
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Chukamnerd A, Singkhamanan K, Chongsuvivatwong V, Palittapongarnpim P, Doi Y, Pomwised R, Sakunrang C, Jeenkeawpiam K, Yingkajorn M, Chusri S, Surachat K. Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand. Comput Struct Biotechnol J 2022; 20:545-558. [PMID: 36284706 PMCID: PMC9582705 DOI: 10.1016/j.csbj.2021.12.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/25/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the blaOXA-23 gene, while certain isolates harbored the blaNDM-1 or blaIMP-14 genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., armA, aph(6)-Id, and aph(3″)-Ib), fosfomycin resistance gene (abaF), and tetracycline resistance genes (tet(B) and tet(39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the ompA, adeF, pgaA, lpxA, and bfmR genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology, Fujita Health University, Aichi, Japan
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Mingkwan Yingkajorn
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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10
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Kamuyu G, Ercoli G, Ramos-Sevillano E, Willcocks S, Kewcharoenwong C, Kiratisin P, Taylor PW, Wren BW, Lertmemongkolchai G, Stabler RA, Brown JS. Strain Specific Variations in Acinetobacter baumannii Complement Sensitivity. Front Immunol 2022; 13:853690. [PMID: 35812377 PMCID: PMC9258041 DOI: 10.3389/fimmu.2022.853690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/27/2022] [Indexed: 12/02/2022] Open
Abstract
The complement system is required for innate immunity against Acinetobacter baumannii, an important cause of antibiotic resistant systemic infections. A. baumannii strains differ in their susceptibility to the membrane attack complex (MAC) formed from terminal complement pathway proteins, but the reasons for this variation remain poorly understood. We have characterized in detail the complement sensitivity phenotypes of nine A. baumannii clinical strains and some of the factors that might influence differences between strains. Using A. baumannii laboratory strains and flow cytometry assays, we first reconfirmed that both opsonization with the complement proteins C3b/iC3b and MAC formation were inhibited by the capsule. There were marked differences in C3b/iC3b and MAC binding between the nine clinical A. baumannii strains, but this variation was partially independent of capsule composition or size. Opsonization with C3b/iC3b improved neutrophil phagocytosis of most strains. Importantly, although C3b/iC3b binding and MAC formation on the bacterial surface correlated closely, MAC formation did not correlate with variations between A. baumannii strains in their levels of serum resistance. Genomic analysis identified only limited differences between strains in the distribution of genes required for serum resistance, but RNAseq data identified three complement-resistance genes that were differentially regulated between a MAC resistant and two MAC intermediate resistant strains when cultured in serum. These data demonstrate that clinical A. baumannii strains vary in their sensitivity to different aspects of the complement system, and that the serum resistance phenotype was influenced by factors in addition to the amount of MAC forming on the bacterial surface.
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Affiliation(s)
- Gathoni Kamuyu
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, United Kingdom
| | - Giuseppe Ercoli
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, United Kingdom
| | - Elisa Ramos-Sevillano
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chidchamai Kewcharoenwong
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Cellular and Molecular Immunology Unit, Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peter W. Taylor
- School of Pharmacy, University College London, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ganjana Lertmemongkolchai
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Cellular and Molecular Immunology Unit, Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Richard A. Stabler
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jeremy S. Brown
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, United Kingdom
- *Correspondence: Jeremy S. Brown,
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11
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Roberts T, Silisouk J, Sengdatka D, Sibounheuang B, Seljuk R, Vang X, Sengduangphachanh A, Davong V, Vongsouvath M, Malou N, Ferreyra C, Ashley EA, Simpson AJH. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac006. [PMID: 35146428 PMCID: PMC8826549 DOI: 10.1093/jacamr/dlac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/06/2022] [Indexed: 11/14/2022] Open
Abstract
Background There is a need for simple microbiology diagnostics to enable antimicrobial resistance surveillance in low- and middle-income countries. Objectives To investigate the field utility of InTray COLOREX plates for urine culture and ESBL detection. Methods Clinical urine samples from Mahosot Hospital, Vientiane, Lao PDR were inoculated onto chromogenic media and InTray COLOREX Screen plates between June and August 2020. Urine and isolates from other clinical specimens were inoculated onto COLOREX ESBL plates. A simulated field study investigating the field utility of the InTray COLOREX plates was also completed. Results In total, 355 urine samples were inoculated onto standard chromogenic agar and InTray COLOREX Screen plates, and 154 urine samples and 54 isolates from other clinical specimens on the COLOREX ESBL plates. Growth was similar for the two methods (COLOREX Screen 41%, standard method 38%) with 20% discordant results, mainly due to differences in colony counts or colonial appearance. Contamination occurred in 13% of samples, with the COLOREX Screen plates showing increased contamination rates, potentially due to condensation. ESBL producers were confirmed from 80% of isolates from the COLOREX ESBL plates, and direct plating provided rapid detection of presumptive ESBL producers. Burkholderia pseudomallei also grew well on the ESBL plates, a relevant finding in this melioidosis-endemic area. Conclusions The InTray COLOREX Screen and ESBL plates were simple to use and interpret, permitting rapid detection of uropathogens and ESBLs, and have the potential for easy transport and storage from field sites and use in laboratories with low capacity.
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Affiliation(s)
- Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Corresponding author. E-mail:
| | - Joy Silisouk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Davanh Sengdatka
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Bountoy Sibounheuang
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Ranoy Seljuk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Xao Vang
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Amphonesavanh Sengduangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | | | | | - Elizabeth A. Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J. H. Simpson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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12
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Fedrigo NH, Xavier DE, Cerdeira L, Fuga B, Marini PVB, Shinohara DR, Carrara-Marroni FE, Lincopan N, Tognim MCB. Genomic insights of Acinetobacter baumannii ST374 reveal wide and increasing resistome and virulome. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105148. [PMID: 34801753 DOI: 10.1016/j.meegid.2021.105148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/23/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
WGS-based surveillance has significantly improved the ability to track global spread and emergence of multidrug-resistant clones of clinically relevant pathogens. In this study, we performed the genomic characterization and comparative analysis of an Acinetobacter baumannii (strain Ac56) belonging to the sequence type ST374, which was isolated for the first time in Brazil, in 1996. Genomic analysis of Ac56 predicted a total of 5373 genes, with 3012 being identical across nine genomes of A. baumannii isolates of ST374 from European, Asian, North and South American countries. GoeBURST analysis grouped ST374 lineages into clonal complex CC3 (international clone IC-III). Resistome analysis of ST374 clone predicted genes associated with resistance to heavy metals and clinically relevant beta-lactams and aminoglycosides antibiotics. In this regard, in two closely related A. baumannii strains, the intrinsic blaADC gene was linked to the insertion sequence ISAba1; including the Ac56 strain, where it has been possibly associated with intermediate susceptibility to meropenem. Other four carbapenem-resistant A. baumannii strains carried the ISAba1/blaOXA-23 gene array, which was associated with the transposon Tn2008 or with Tn2006 in an AbaR4-type resistance island. While most virulence genes were shared for A. baumannii strains of ST374, three isolates from Thailand harbored KL49 capsular loci, previously identified in the hypervirulent A. baumannii LAC-4 strain. Analysis of thirty-four predicted plasmids showed eight major groups, of which GR-6 (LN-1) and GR-2 (LN-2) were prevalent. All strains, including the earliest isolate Ac56 harbored at least one complete prophage, whereas none CRISPR-associated (cas) gene was detected. In summary, genomic data of A. baumannii ST374 reveal a potential of this lineage to become a successful clone.
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Affiliation(s)
| | | | - Louise Cerdeira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | - Floristher Elaine Carrara-Marroni
- Department of Pathology, Clinical and Toxicological Analysis, University Hospital, State University of Londrina, Londrina, Paraná, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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13
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:934-943. [DOI: 10.1093/jac/dkac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 12/26/2021] [Indexed: 11/14/2022] Open
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14
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Zafer MM, Hussein AFA, Al-Agamy MH, Radwan HH, Hamed SM. Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel bla ADC-257. Front Microbiol 2021; 12:736982. [PMID: 34880837 PMCID: PMC8645854 DOI: 10.3389/fmicb.2021.736982] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
Acinetobacter baumannii has become a major challenge to clinicians worldwide due to its high epidemic potential and acquisition of antimicrobial resistance. This work aimed at investigating antimicrobial resistance determinants and their context in four extensively drug-resistant (XDR) NDM-producing A. baumannii clinical isolates collected between July and October 2020 from Kasr Al-Ainy Hospital, Cairo, Egypt. A total of 20 A. baumannii were collected and screened for acquired carbapenemases (blaNDM, blaVIM and blaIMP) using PCR. Four NDM producer A. baumannii isolates were identified and selected for whole-genome sequencing, in silico multilocus sequence typing, and resistome analysis. Antimicrobial susceptibility profiles were determined using disk diffusion and broth microdilution tests. All blaNDM-positive A. baumannii isolates were XDR. Three isolates belonged to high-risk international clones (IC), namely, IC2 corresponding to ST570Pas/1701Oxf (M20) and IC9 corresponding to ST85Pas/ST1089Oxf (M02 and M11). For the first time, we report blaNDM-1 gene on the chromosome of an A. baumannii strain that belongs to sequence type ST164Pas/ST1418Oxf. Together with AphA6, blaNDM-1 was bracketed by two copies of ISAba14 in ST85Pas isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel blaADC allele (blaADC-257) with an upstream ISAba1 element was identified in M19 (ST/CC164Pas and ST1418Oxf/CC234Oxf). blaADC genes harbored by M02 and M11 were uniquely interrupted by IS1008. Tn2006-associated blaOXA-23 was carried by M20. blaOXA-94 genes were preceded by ISAba1 element in M02 and M11. AbGRI3 was carried by M20 hosting the resistance genes aph(3`)-Ia, aac(6`)-Ib`, catB8, ant(3``)-Ia, sul1, armA, msr(E), and mph(E). Nonsynonymous mutations were identified in the quinolone resistance determining regions (gyrA and parC) of all isolates. Resistance to colistin in M19 was accompanied by missense mutations in lpxACD and pmrABC genes. The current study provided an insight into the genomic background of XDR phenotype in A. baumannii recovered from patients in Egypt. WGS revealed strong association between resistance genes and diverse mobile genetic elements with novel insertion sites and genetic organizations.
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Affiliation(s)
- Mai M Zafer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Amira F A Hussein
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed H Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Hesham H Radwan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
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15
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Koong J, Johnson C, Rafei R, Hamze M, Myers GSA, Kenyon JJ, Lopatkin AJ, Hamidian M. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 2021; 7. [PMID: 34874246 PMCID: PMC8767349 DOI: 10.1099/mgen.0.000705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
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Affiliation(s)
- Jonathan Koong
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Claire Johnson
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences. Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Allison J Lopatkin
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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16
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Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. Antibiotics (Basel) 2021; 10:antibiotics10091054. [PMID: 34572636 PMCID: PMC8468411 DOI: 10.3390/antibiotics10091054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Resistance to the last-line antibiotics against invasive Gram-negative bacterial infection is a rising concern in public health. Multidrug resistant (MDR) Acinetobacter baumannii Aci46 can resist colistin and carbapenems with a minimum inhibitory concentration of 512 µg/mL as determined by microdilution method and shows no zone of inhibition by disk diffusion method. These phenotypic characteristics prompted us to further investigate the genotypic characteristics of Aci46. Next generation sequencing was applied in this study to obtain whole genome data. We determined that Aci46 belongs to Pasture ST2 and is phylogenetically clustered with international clone (IC) II as the predominant strain in Thailand. Interestingly, Aci46 is identical to Oxford ST1962 that previously has never been isolated in Thailand. Two plasmids were identified (pAci46a and pAci46b), neither of which harbors any antibiotic resistance genes but pAci46a carries a conjugational system (type 4 secretion system or T4SS). Comparative genomics with other polymyxin and carbapenem-resistant A. baumannii strains (AC30 and R14) identified shared features such as CzcCBA, encoding a cobalt/zinc/cadmium efflux RND transporter, as well as a drug transporter with a possible role in colistin and/or carbapenem resistance in A. baumannii. Single nucleotide polymorphism (SNP) analyses against MDR ACICU strain showed three novel mutations i.e., Glu229Asp, Pro200Leu, and Ala138Thr, in the polymyxin resistance component, PmrB. Overall, this study focused on Aci46 whole genome data analysis, its correlation with antibiotic resistance phenotypes, and the presence of potential virulence associated factors.
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17
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Kamuyu G, Suen Cheng Y, Willcocks S, Kewcharoenwong C, Kiratisin P, Taylor PW, Wren BW, Lertmemongkolchai G, Stabler RA, Brown J. Sequential Vaccination With Heterologous Acinetobacter baumannii Strains Induces Broadly Reactive Antibody Responses. Front Immunol 2021; 12:705533. [PMID: 34394105 PMCID: PMC8363311 DOI: 10.3389/fimmu.2021.705533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/08/2021] [Indexed: 12/11/2022] Open
Abstract
Antibody therapy may be an alternative treatment option for infections caused by the multi-drug resistant (MDR) bacterium Acinetobacter baumannii. As A. baumannii has multiple capsular serotypes, a universal antibody therapy would need to target conserved protein antigens rather than the capsular polysaccharides. We have immunized mice with single or multiple A. baumannii strains to induce antibody responses to protein antigens, and then assessed whether these responses provide cross-protection against a collection of genetically diverse clinical A. baumannii isolates. Immunized mice developed antibody responses to multiple protein antigens. Flow cytometry IgG binding assays and immunoblots demonstrated improved recognition of both homologous and heterologous clinical strains in sera from mice immunized with multiple strains compared to a single strain. The capsule partially inhibited bacterial recognition by IgG and the promotion of phagocytosis by human neutrophils. However, after immunization with multiple strains, serum antibodies to protein antigens promoted neutrophil phagocytosis of heterologous A. baumannii strains. In an infection model, mice immunized with multiple strains had lower bacterial counts in the spleen and liver following challenge with a heterologous strain. These data demonstrate that antibodies targeting protein antigens can improve immune recognition and protection against diverse A. baumannii strains, providing support for their use as an antibody therapy.
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Affiliation(s)
- Gathoni Kamuyu
- Centre for Inflammation and Tissue Repair, University College London (UCL) Respiratory, London, United Kingdom
| | - Yat Suen Cheng
- Centre for Inflammation and Tissue Repair, University College London (UCL) Respiratory, London, United Kingdom
| | - Sam Willcocks
- London School of Hygiene and Tropical Medicine, Infectious and Tropical Disease, Department of Infection Biology, London, United Kingdom
| | - Chidchamai Kewcharoenwong
- Cellular and Molecular Immunology Unit, Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, Thailand
| | - Peter W Taylor
- School of Pharmacy, University College London, London, United Kingdom
| | - Brendan W Wren
- London School of Hygiene and Tropical Medicine, Infectious and Tropical Disease, Department of Infection Biology, London, United Kingdom
| | - Ganjana Lertmemongkolchai
- Cellular and Molecular Immunology Unit, Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Richard A Stabler
- London School of Hygiene and Tropical Medicine, Infectious and Tropical Disease, Department of Infection Biology, London, United Kingdom
| | - Jeremy Brown
- Centre for Inflammation and Tissue Repair, University College London (UCL) Respiratory, London, United Kingdom
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18
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OmpA Protein-Deficient Acinetobacter baumannii Outer Membrane Vesicles Trigger Reduced Inflammatory Response. Pathogens 2021; 10:pathogens10040407. [PMID: 33807410 PMCID: PMC8066360 DOI: 10.3390/pathogens10040407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Multidrug resistant Acinetobacter baumannii shows a growing number of nosocomial infections worldwide during the last decade. The outer membrane vesicles (OMVs) produced by this bacterium draw increasing attention as a possible treatment target. OMVs have been implicated in the reduction of antibiotic level in the surrounding environment, transfer of virulence factors into the host cells, and induction of inflammatory response. Although the evidence on the involvement of OMVs in A. baumannii pathogenesis is currently growing, their role during inflammation is insufficiently explored. It is likely that bacteria, by secreting OMVs, can expand the area of their exposure and prepare surrounding matrix for infection. Here, we investigated the impact of A. baumannii OMVs on activation of macrophages in vitro. We show that OmpA protein present in A. baumannii OMVs substantially contributes to the proinflammatory response in J774 murine macrophages and to the cell death in both lung epithelium cells and macrophages. The loss of OmpA protein in OMVs, obtained from A. baumannii ∆ompA mutant, resulted in the altered expression of genes coding for IL-6, NLRP3 and IL-1β proinflammatory molecules in macrophages in vitro. These results imply that OmpA protein in bacterial OMVs could trigger a more intense proinflammatory response.
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19
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Khuntayaporn P, Kanathum P, Houngsaitong J, Montakantikul P, Thirapanmethee K, Chomnawang MT. Predominance of international clone 2 multidrug-resistant Acinetobacter baumannii clinical isolates in Thailand: a nationwide study. Ann Clin Microbiol Antimicrob 2021; 20:19. [PMID: 33743736 PMCID: PMC7980754 DOI: 10.1186/s12941-021-00424-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/14/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii has emerged as one of the common multidrug resistance pathogens causing hospital-acquired infections. This study was conducted to elucidate the distribution of antimicrobial resistance genes in the bacterial population in Thailand. Multidrug-resistant A. baumannii (MDR A. baumannii) isolates were characterized phenotypically, and the molecular epidemiology of clinical isolates in 11 tertiary hospitals was investigated at a country-wide level. METHODS A total of 135 nonrepetitive MDR A. baumannii isolates collected from tertiary care hospitals across 5 regions of Thailand were examined for antibiotic susceptibility, resistance genes, and sequence types. Multilocus sequence typing (MLST) was performed to characterize the spread of regional lineages. RESULTS ST2 belonging to IC2 was the most dominant sequence type in Thailand (65.19%), and to a lesser extent, there was also evidence of the spread of ST164 (10.37%), ST129 (3.70%), ST16 (2.96%), ST98 (2.96%), ST25 (2.96%), ST215 (2.22%), ST338 (1.48%), and ST745 (1.48%). The novel sequence types ST1551, ST1552, ST1553, and ST1557 were also identified in this study. Among these, the blaoxa-23 gene was by far the most widespread in MDR A. baumannii, while the blaoxa-24/40 and blaoxa-58 genes appeared to be less dominant in this region. The results demonstrated that the predominant class D carbapenemase was blaOXA-23, followed by the class B carbapenemase blaNDM-like, while the mcr-1 gene was not observed in any isolate. Most of the MDR A. baumannii isolates were resistant to ceftazidime (99.23%), gentamicin (91.85%), amikacin (82.96%), and ciprofloxacin (97.78%), while all of them were resistant to carbapenems. The results suggested that colistin could still be effective against MDR A. baumannii in this region. CONCLUSION This is the first molecular epidemiological analysis of MDR A. baumannii clinical isolates at the national level in Thailand to date. Studies on the clonal relatedness of MDR A. baumannii isolates could generate useful data to understand the local epidemiology and international comparisons of nosocomial outbreaks.
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Affiliation(s)
- Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand
| | - Pohnvipa Kanathum
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand
| | - Jantana Houngsaitong
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand
| | - Preecha Montakantikul
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri Ayudthya Rd, Rajathevi, Bangkok, 10400, Thailand.
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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