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Carascal MB, Macalalad LS, Petronio-Santos JA, Destura RV, Rivera WL. Loop-mediated isothermal amplification assay detects multiple alleles of bla OXA-51-like genes in Acinetobacter baumannii and other Gram-negative bacteria despite primer-template mismatches. Heliyon 2024; 10:e35653. [PMID: 39170108 PMCID: PMC11337129 DOI: 10.1016/j.heliyon.2024.e35653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
The known intrinsic and polymorphic bla OXA-51-like genes of Acinetobacter baumannii were recently reported in other non-A. baumannii Gram-negative pathogens. Accurate detection of this potentially transferrable carbapenemase gene in the clinical setting is critical. This study developed a loop-mediated isothermal amplification (LAMP) assay targetting multiple alleles of bla OXA-51-like genes. Specifically, an alignment-based primer design, in silico primer screening, and in vitro assay confirmation were conducted. Both in silico and in vitro results revealed the tolerance of the LAMP assay to up to five primer-template mismatches outside the 3'-end primer regions. Within 90 min, the LAMP assay also detected the gene targets in other Gram-negative bacteria with known and novel bla OXA-51-like genes. Finally, it showed a superior limit of detection (as low as 101 CFU/mL) compared with polymerase chain reaction, and high specificity against non-targets. This study developed a highly adaptable LAMP assay to monitor bla OXA-51-like genes in the clinical setting and provided important insights into LAMP primer design and screening.
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Affiliation(s)
- Mark B. Carascal
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
- Clinical and Translational Research Institute, The Medical City, Ortigas Avenue, Pasig City 1605, Philippines
| | - Lawrence S. Macalalad
- Clinical and Translational Research Institute, The Medical City, Ortigas Avenue, Pasig City 1605, Philippines
| | - Joy Ann Petronio-Santos
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
- Biological Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Raul V. Destura
- Clinical and Translational Research Institute, The Medical City, Ortigas Avenue, Pasig City 1605, Philippines
- Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, City of Manila 1159, Philippines
| | - Windell L. Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
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Hu L, Zhang XT, Zeng X, Xiong LX, Ai Q, Liu CJ, Yang WW, Wu Y, Guo X, Li GQ, Liu L. ISAba1-mediated intrinsic chromosomal oxacillinase amplification confers carbapenem resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2024; 64:107258. [PMID: 38914142 DOI: 10.1016/j.ijantimicag.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 05/19/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Tandem amplification of carbapenemase genes increases gene copy number and enhances carbapenem resistance. These amplifications are often heterogeneous, transient, and located on plasmids, which also contribute to heteroresistance. Amplification of encoding genes is especially important for enzymes with low hydrolysis activity, which are often overlooked. Here, we reported an intrinsic oxacillinase oxaAb amplification flanked by ISAba1. The amplification is in the chromosome and contains up to 25 repeats. We provided genomic, transcriptomic, and proteomic evidence that the amplification resulted in oxacillinase overproduction. Notably, no point mutations of oxaAb were found during the amplification process. Strains of Acinetobacter baumannii with intrinsic amplified or external transformed ISAba1-oxaAb exhibited higher meropenem hydrolysis activity. Furthermore, the number of repeats in the amplification decreased gradually over a period of 21 d cultured with carbapenem withdrawal. However, upon re-exposure to meropenem, the ISAba1 flanked oxaAb responded rapidly, with repeat numbers reaching or exceeding pre-carbapenem withdrawal levels within 24 h. Taken together, these findings suggest that ISAba1-mediated gene amplification and overproduction of intrinsic low-activity oxacillinase oxaAb resulted in carbapenem resistance.
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Affiliation(s)
- Limiao Hu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiao-Tuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xi Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Lu-Xi Xiong
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Qi Ai
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Cai-Juan Liu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Wei-Wei Yang
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yuan Wu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.
| | - Xuemin Guo
- Meizhou People's Hospital, Meizhou, China; Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translation Research of Hakka Population, Meizhou, China.
| | - Guo-Qing Li
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China; Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, China.
| | - Logen Liu
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, China; Clinical Research Center, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.
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Klamer ZL, June CM, Wawrzak Z, Taracila MA, Grey JA, Benn AMI, Russell CP, Bonomo RA, Powers RA, Leonard DA, Szarecka A. Structural and Dynamic Features of Acinetobacter baumannii OXA-66 β-Lactamase Explain Its Stability and Evolution of Novel Variants. J Mol Biol 2024; 436:168603. [PMID: 38729259 PMCID: PMC11198252 DOI: 10.1016/j.jmb.2024.168603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
OXA-66 is a member of the OXA-51 subfamily of class D β-lactamases native to the Acinetobacter genus that includes Acinetobacter baumannii, one of the ESKAPE pathogens and a major cause of drug-resistant nosocomial infections. Although both wild type OXA-66 and OXA-51 have low catalytic activity, they are ubiquitous in the Acinetobacter genomes. OXA-51 is also remarkably thermostable. In addition, newly emerging, single and double amino acid variants show increased activity against carbapenems, indicating that the OXA-51 subfamily is growing and gaining clinical significance. In this study, we used molecular dynamics simulations, X-ray crystallography, and thermal denaturation data to examine and compare the dynamics of OXA-66 wt and its gain-of-function variants: I129L (OXA-83), L167V (OXA-82), P130Q (OXA-109), P130A, and W222L (OXA-234). Our data indicate that OXA-66 wt also has a high melting temperature, and its remarkable stability is due to an extensive and rigid hydrophobic bridge formed by a number of residues around the active site and harbored by the three loops, P, Ω, and β5-β6. Compared to the WT enzyme, the mutants exhibit higher flexibility only in the loop regions, and are more stable than other robust carbapenemases, such as OXA-23 and OXA-24/40. All the mutants show increased rotational flexibility of residues I129 and W222, which allows carbapenems to bind. Overall, our data support the hypothesis that structural features in OXA-51 and OXA-66 promote evolution of multiple highly stable variants with increased clinical relevance in A. baumannii.
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Affiliation(s)
- Zachary L Klamer
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Joshua A Grey
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Alyssa M I Benn
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Departments of Pharmacology, Biochemistry, and Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA.
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - Agnieszka Szarecka
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
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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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Harmer CJ, Nigro SJ, Hall RM. Acinetobacter baumannii GC2 Sublineage Carrying the aac( 6')- Im Amikacin, Netilmicin, and Tobramycin Resistance Gene Cassette. Microbiol Spectr 2023; 11:e0120423. [PMID: 37409961 PMCID: PMC10434200 DOI: 10.1128/spectrum.01204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/09/2023] [Indexed: 07/07/2023] Open
Abstract
The aminoglycoside antibiotics amikacin, gentamicin, and tobramycin are important therapeutic options for Acinetobacter iinfections. Several genes that confer resistance to one or more of these antibiotics are prevalent in the globally distributed resistant clones of Acinetobacter baumannii, but the aac(6')-Im (aacA16) gene (amikacin, netilmicin, and tobramycin resistance), first reported in isolates from South Korea, has rarely been reported since. In this study, GC2 isolates (1999 to 2002) from Brisbane, Australia, carrying aac(6')-Im and belonging to the ST2:ST423:KL6:OCL1 type were identified and sequenced. The aac(6')-Im gene and surrounds have been incorporated into one end of the IS26-bounded AbGRI2 antibiotic resistance island and are accompanied by a characteristic 70.3-kbp deletion of adjacent chromosome. The compete genome of the 1999 isolate F46 (RBH46) includes only two copies of ISAba1 (in AbGRI1-3 and upstream of ampC) but later isolates, which differ from one another by <10 single nucleotide differences (SND), carry two to seven additional shared copies. Several complete GC2 genomes with aac(6')-Im in an AbGRI2 island (2004 to 2017; several countries) found in GenBank and two additional Australian A. baumannii isolates (2006) carry different gene sets, KL2, KL9, KL40, or KL52, at the capsule locus. These genomes include ISAba1 copies in a different set of shared locations. The distribution of SND between F46 and AYP-A2, a 2013 ST2:ST208:KL2:OCL1 isolate from Victoria, Australia, revealed that a 640-kbp segment that includes KL2 and the AbGRI1 resistance island replaces the corresponding region in F46. Over 1,000 A. baumannii draft genomes also include aac(6')-Im, indicating that it is currently globally disseminated and significantly underreported. IMPORTANCE Aminoglycosides are important therapeutic options for treatment of Acinetobacter infections. Here, we show that a little-known aminoglycoside resistance gene, aac(6')-Im (aacA16), that confers amikacin, netilmicin, and tobramycin resistance has been circulating undetected for many years in a sublineage of A. baumannii global clone 2 (GC2), generally with a second aminoglycoside resistance gene, aacC1, which confers resistance to gentamicin. These two genes are commonly found together in GC2 complete and draft genomes and globally distributed. One isolate appears to be ancestral, as its genome contains few ISAba1 copies, providing insight into the original source of this insertion sequence (IS), which is abundant in most GC2 isolates. Tracking ISAba1 spread can provide a simple means to track the development and ongoing evolution as well as the dissemination of specific lineages and detect the formation of many sublineages. The complete ancestral genome will provide an essential base point for tracking this process.
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Affiliation(s)
- Christopher J. Harmer
- School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
| | - Steven J. Nigro
- School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
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Li J, Li Y, Cao X, Zheng J, Zhang Y, Xie H, Li C, Liu C, Shen H. Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database. Front Microbiol 2023; 14:1174200. [PMID: 37323896 PMCID: PMC10267304 DOI: 10.3389/fmicb.2023.1174200] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Objective To use genomic analysis to identify Acinetobacter spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (blaOXA) among Acinetobacter species globally. Methods Genomes of global Acinetobacter spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of blaOXAs across Acinetobacter spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the blaOXA genes in Acinetobacter spp. Average-nucleotide identification (ANI) was performed to re-type the Acinetobacter spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of Acinetobacter baumannii strain. Results A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 blaOXA variants were identified from the genomes of 5,893 Acinetobacter spp.; blaOXA-23 (n = 3,168, 53.8%) and blaOXA-66 (2,630, 44.6%) were the most frequent blaOXAs, accounting for 52.6% (3,489/6639), and the co-carriage of blaOXA-23 and blaOXA-66 was seen in 2223 (37.7%) strains. The 282 blaOXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was blaOXA-51-family carbapenem-hydrolyzing enzymes composed of 108 blaOXA variants. Overall, 4,923 A. baumannii were identified out of the 6,639 Acinetobacter spp. strains and 291 distinct STs were identified among the 4,904 blaOXA-carrying A. baumannii. The most prevalent ST was ST2 (n = 3,023, 61.6%) followed by ST1 (n = 228, 4.6%). Conclusion OXA-like carbapenemases were the main blaOXA-type β-lactamase spread widely across Acinetobacter spp. Both blaOXA-23 and blaOXA-66 were the predominant blaOXAs, among all A. baumannii strains, with ST2 (belonging to CC2) being the main clone disseminated globally.
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Affiliation(s)
- Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yang Li
- Department of Nosocomial Infection Control, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jie Zheng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yan Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
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Karah N, Mateo-Estrada V, Castillo-Ramírez S, Higgins PG, Havenga B, Khan W, Domingues S, Da Silva GJ, Poirel L, Nordmann P, Ambrosi C, Ma C, McClean S, Quiroga MP, Alvarez VE, Centron D, Zarrilli R, Kenyon JJ, Russo TA, Evans BA, Opazo-Capurro A, Rafei R, Hamze M, Daoud Z, Ahmad I, Rather PN, Hall RM, Wilharm G, Uhlin BE. The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace. FEMS MICROBES 2023; 4:xtad009. [PMID: 37333444 PMCID: PMC10132847 DOI: 10.1093/femsmc/xtad009] [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: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 06/20/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-resistant strains. Here we introduce Ab-web (https://www.acinetobacterbaumannii.no), the first online platform for sharing expertise on A. baumannii. Ab-web is a species-centric knowledge hub, initially with 10 articles organized into two main sections, 'Overview' and 'Topics', and three themes, 'epidemiology', 'antibiotic resistance', and 'virulence'. The 'workspace' section provides a spot for colleagues to collaborate, build, and manage joint projects. Ab-web is a community-driven initiative amenable to constructive feedback and new ideas.
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Affiliation(s)
- Nabil Karah
- Corresponding author. Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden. E-mail:
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, México
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, D-50935 Cologne, Germany
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, 7602 Stellenbosch, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, 7602 Stellenbosch, South Africa
| | - Sara Domingues
- Faculty of Pharmacy, University of Coimbra, 3000-458 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Gabriela Jorge Da Silva
- Faculty of Pharmacy, University of Coimbra, 3000-458 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Laurent Poirel
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, 1700 Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, 1700 Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS, 00166 Rome, Italy
| | - Chaoying Ma
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield D04 V1W8, Dublin 4, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield D04 V1W8, Dublin 4, Ireland
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), 1245 Ayacucho (C1111AAI), Buenos Aires, Argentina
| | - Verónica E Alvarez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), 1245 Ayacucho (C1111AAI), Buenos Aires, Argentina
| | - Daniela Centron
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), 1245 Ayacucho (C1111AAI), Buenos Aires, Argentina
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, 80138 Naples, Italy
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health,, Queensland University of Technology, Brisbane City QLD 4000, Australia
| | - Thomas A Russo
- Veterans Administration Western NY, Healthcare System, epartment of Medicine, Jacobs School of Medicine and Biomedical Sciences, University Buffalo, Buffalo, NY 14260, United States
| | - Benjamin A Evans
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andres Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Ziad Daoud
- College of Medicine, Central Michigan University, Mount Pleasant, MI 48859, United States
- Department of Clinical Microbiology, Michigan Health Clinics, Saginaw, MI 48604, United States
| | - Irfan Ahmad
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Punjab 54600, Pakistan
| | - Philip N Rather
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30307, United States
- Research Service, Department of Veterans Affairs, Atlanta Veterans Affairs (VA) Medical Center, Decatur, GA 30033, United States
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gottfried Wilharm
- Robert Koch Institute, Project Group P2 (Acinetobacter baumannii—Biology of a Nosocomial Pathogen), Burgstr 37, 38855 Wernigerode, Germany
| | - Bernt Eric Uhlin
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
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8
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Muntean AA, Muntean MM, Oueslati S, Bonnin R, Naas T, Popa MI. Comment on Mitteregger et al. A Variant Carbapenem Inactivation Method (CIM) for Acinetobacter baumannii Group with Shortened Time-to-Result: rCIM-A. Pathogens 2022, 11, 482. Pathogens 2022; 11:pathogens11070751. [PMID: 35889996 PMCID: PMC9317618 DOI: 10.3390/pathogens11070751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Andrei-Alexandru Muntean
- Cantacuzino National Medical Military Institute for Research and Developement, Carol Davila University of Medicine and Pharmacy, 050096 Bucharest, Romania; (A.-A.M.); (M.-M.M.)
| | - Madalina-Maria Muntean
- Cantacuzino National Medical Military Institute for Research and Developement, Carol Davila University of Medicine and Pharmacy, 050096 Bucharest, Romania; (A.-A.M.); (M.-M.M.)
| | - Saoussen Oueslati
- University of Paris-Saclay, Kremlin-Bicetre Hospital, 94270 Le Kremlin-Bicêtre, France;
| | - Remy Bonnin
- University of Paris-Saclay, Kremlin Bicetre Hospital, Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France; (R.B.); (T.N.)
| | - Thierry Naas
- University of Paris-Saclay, Kremlin Bicetre Hospital, Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France; (R.B.); (T.N.)
| | - Mircea Ioan Popa
- Cantacuzino National Medical Military Institute for Research and Developement, Carol Davila University of Medicine and Pharmacy, 050096 Bucharest, Romania; (A.-A.M.); (M.-M.M.)
- Correspondence:
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9
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Gao Y, Li H, Chen H, Zhang J, Wang R, Wang Z, Wang H. Origin, Phylogeny, and Transmission of the Epidemic Clone ST208 of Carbapenem-Resistant Acinetobacter baumannii on a Global Scale. Microbiol Spectr 2022; 10:e0260421. [PMID: 35638783 PMCID: PMC9241911 DOI: 10.1128/spectrum.02604-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic pathogen that has become a global threat. The dissemination of global clone 2 (GC2) CRAB has been well documented. Oxford sequence type (ST) 208 is one of the most prevalent lineages of A. baumannii GC2; however, its evolution and phylogeny are unclear. We collected 45 representative ST208 isolates from 14 cities in China between 1999 and 2018. Moreover, 411 ST208 genome sequences were downloaded from the GenBank database for comparison. The global ST208 phylogeny showed that ST208 might have originated from North America and subsequently evolved into two clades. Notably, the widespread OXA-23-producing ST208 A. baumannii was correlated with the transposon structure and dynamics of replicative transposition, and the Tn2009 tandem structure of five copies of blaOXA-23 and potential circular intermediate of Tn2009 were first detected. Furthermore, 15 Chinese ST208 isolates carried GR25 pABTJ1-like plasmids, which contained blaOXA-23 and have only been found in China in the last decade. In conclusion, our work suggests that replicative transposition contributes to the evolution and transmission of OXA-23-producing ST208 A. baumannii and highlights the new challenges posed by the epidemiological surveillance of globally distributed clonal groups via whole genome sequencing. IMPORTANCE ST208 as one of the most prevalent lineages of CRAB has caused several difficult-to-treat infections and outbreaks around the world. However, few studies have focused on evaluating the genetic background differences of ST208 A. baumannii isolated from very distant geographic regions. A comprehensive genomic analysis of 456 clinical strains of ST208 A. baumannii from a wide temporal and geographic range was performed in this study. Moreover, the mechanisms leading to the horizontal transfer of blaOXA-23 in ST208 A. baumannii are poorly understood. We first describe experimental evidence of the potential circular intermediate of Tn2009, and the Tn2009 tandem structure of five copies of blaOXA-23 was first detected. The interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems highlights the essential need to enhance epidemiologic surveillance.
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Affiliation(s)
- Yue Gao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Jiangang Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Zhiren Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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10
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Chan KW, Liu CY, Wong HY, Chan WC, Wong KY, Chen S. Specific Amino Acid Substitutions in OXA-51-Type β-Lactamase Enhance Catalytic Activity to a Level Comparable to Carbapenemase OXA-23 and OXA-24/40. Int J Mol Sci 2022; 23:ijms23094496. [PMID: 35562886 PMCID: PMC9105447 DOI: 10.3390/ijms23094496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
The chromosomal blaOXA-51-type gene encodes carbapenem-hydrolyzing class D β-lactamases (CHDLs), specific variants shown to mediate carbapenem resistance in the Gram-negative bacterial pathogen Acinetobacter baumannii. This study aims to characterize the effect of key amino acid substitutions in OXA-51 variants of carbapenem-hydrolyzing class D β-lactamases (CHDLs) on substrate catalysis. Mutational and structural analyses indicated that each of the L167V, W222G, or I129L substitutions contributed to an increase in catalytic activity. The I129L mutation exhibited the most substantial effect. The combination of W222G and I129L substitutions exhibited an extremely strong catalytic enhancement effect in OXA-66, resulting in higher activity than OXA-23 and OXA-24/40 against carbapenems. These findings suggested that specific arrangement of residues in these three important positions in the intrinsic OXA-51 type of enzyme can generate variants that are even more active than known CHDLs. Likewise, mutation leading to the W222M change also causes a significant increase in the catalytic activity of OXA-51. blaOXA-51 gene in A. baumannii may likely continue to evolve, generating mutant genes that encode carbapenemase with extremely strong catalytic activity.
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Affiliation(s)
- Kwan-Wai Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; (K.-W.C.); (H.-Y.W.); (W.-C.C.); (K.-Y.W.)
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong;
| | - Chen-Yu Liu
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong;
| | - Ho-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; (K.-W.C.); (H.-Y.W.); (W.-C.C.); (K.-Y.W.)
| | - Wai-Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; (K.-W.C.); (H.-Y.W.); (W.-C.C.); (K.-Y.W.)
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; (K.-W.C.); (H.-Y.W.); (W.-C.C.); (K.-Y.W.)
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong;
- Correspondence: ; Tel.: +852-3442-5782
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11
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Abouelfetouh A, Mattock J, Turner D, Li E, Evans BA. Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase. Microb Genom 2022; 8. [PMID: 35104206 PMCID: PMC8942029 DOI: 10.1099/mgen.0.000752] [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: 01/08/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. Fifty-four carbapenem-resistant isolates from Alexandria Main University Hospital (AMUH), Alexandria, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. The core-gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. Multilocus sequence typing (MLST) sequence type (ST) and antibiotic-resistance genes were identified. The majority of Egyptian isolates belonged to one of three major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and STPAS158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried bla NDM-1 and one carried bla NDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CCPAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the USA military. The carbapenem-resistant A. baumannii population in AMUH is very diverse, and indicates an endemic circulating population, including a region-specific lineage. A major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.
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Affiliation(s)
- Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | | | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol, UK
| | - Erica Li
- Norwich Medical School, University of East Anglia, Norwich, UK
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12
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Harmer CJ, Lebreton F, Stam J, McGann PT, Hall RM. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1851-1855. [PMID: 35403193 PMCID: PMC9244215 DOI: 10.1093/jac/dkac115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives To examine the causes of antibiotic resistance in the extensively resistant global clone 1 (GC1) Acinetobacter baumannii isolate MRSN 56 recovered at a US military treatment facility. Methods MRSN 56 was sequenced using MinION (Oxford Nanopore) and the reads combined with available Illumina MiSeq data using Unicycler. Acquired resistance genes were identified using ABRicate and their environment examined. ISAba1 and ISAba125 copies were located. Results MRSN 56 is ST1IP:ST231Ox:KL1:OCL1 and the complete genome includes four small plasmids, none of which carry resistance genes. The acquired resistance genes were found at four locations in the chromosome in addition to AbaR28 (aphA1, aacC1, aadA1, sul1) in comM. Tn2006 (oxa23, carbapenem resistance) was both in AbaR4 and alone elsewhere. Two copies of Tn7 (dfrA1, sat, aadA1) were identified. One was associated with a 22 852 bp adjacent segment [tetA(B), sul2] derived from the AbGRI1 island, and this novel configuration was designated Tn7+. Tn7+ was incorporated in the position preferred by Tn7, downstream of glmS, by transposition using a sequence in AbGRI1 resembling the Tn7 terminal inverted repeats. Tn7 was found at a secondary site. Fluoroquinolone resistance appears to involve a mutation in gyrA combined with inactivation by ISAba1 of the marR gene in the mar operon and constitutive expression of marA from the promoter internal to ISAba1. Conclusions MRSN 56 represents a new sublineage of GC1 lineage 1 with novel features that had not been detected previously. The involvement of the mar operon in fluoroquinolone resistance has not been noted previously.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Francois Lebreton
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Stam
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick T McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Woon JJ, Teh CSJ, Chong CW, Abdul Jabar K, Ponnampalavanar S, Idris N. Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolated from the Intensive Care Unit in a Tertiary Teaching Hospital in Malaysia. Antibiotics (Basel) 2021; 10:antibiotics10111340. [PMID: 34827278 PMCID: PMC8615160 DOI: 10.3390/antibiotics10111340] [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: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has now become a global sentinel event. CRAB infections often instigate severe clinical complications and are potentially fatal, especially for debilitated patients. The present study aimed to conduct molecular characterization on CRAB isolated from patients in the intensive care unit from 2015 to 2016 and determine the risk factors associated with patients’ mortality. One hundred CRAB isolates were retrospectively selected and included in this study. Antimicrobial susceptibility testing showed that all isolates remained susceptible to colistin, even though 62% of them conferred resistance to all other classes of antibiotics tested. OXA carbapenemase gene was found to be the predominant carbapenemase gene, with 99% of the isolates coharbouring blaOXA-23-like and blaOXA-51-like carbapenemase genes. All isolates were carrying intact CarO genes, with the presence of various degree of nucleotide insertion, deletion and substitution. Overall, PFGE subtyped the isolates into 13 distinct pulsotypes, with the presence of 2 predominant pulsotypes. Univariate analysis implied that age, infection/colonization by CRAB, ethnicity, comorbidity and CRAB specimen source were significantly associated with in-hospital mortality. Multivariate analysis identified a higher risk of mortality for patients who are of Chinese ethnicity with diabetes as an underlying disease. As CRAB infection could lead to high rate of mortality, comprehensive infection control measures are needed to minimize the spread of this pathogen.
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Affiliation(s)
- Jia Jie Woon
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Subang Jaya 47500, Malaysia
- Correspondence: (C.W.C.); (N.I.); Tel.: +60-379-676-671 (N.I.)
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Sasheela Ponnampalavanar
- Department of Infectious Diseases, University of Malaya Medical Centre, Kuala Lumpur 50603, Malaysia;
| | - Nuryana Idris
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
- Correspondence: (C.W.C.); (N.I.); Tel.: +60-379-676-671 (N.I.)
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14
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Javkar K, Rand H, Hoffmann M, Luo Y, Sarria S, Thirunavukkarasu N, Pillai CA, McGann P, Johnson JK, Strain E, Pop M. Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance. Front Microbiol 2021; 12:714284. [PMID: 34659144 PMCID: PMC8518998 DOI: 10.3389/fmicb.2021.714284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
Carbapenems-one of the important last-line antibiotics for the treatment of gram-negative infections-are becoming ineffective for treating Acinetobacter baumannii infections. Studies have identified multiple genes (and mechanisms) responsible for carbapenem resistance. In some A. baumannii strains, the presence/absence of putative resistance genes is not consistent with their resistance phenotype-indicating the genomic factors underlying carbapenem resistance in A. baumannii are not fully understood. Here, we describe a large-scale whole-genome genotype-phenotype association study with 349 A. baumannii isolates that extends beyond the presence/absence of individual antimicrobial resistance genes and includes the genomic positions and pairwise interactions of genes. Ten known resistance genes exhibited statistically significant associations with resistance to imipenem, a type of carbapenem: blaOXA-23, qacEdelta1, sul1, mphE, msrE, ant(3")-II, aacC1, yafP, aphA6, and xerD. A review of the strains without any of these 10 genes uncovered a clade of isolates with diverse imipenem resistance phenotypes. Finer resolution evaluation of this clade revealed the presence of a 38.6 kbp conserved chromosomal region found exclusively in imipenem-susceptible isolates. This region appears to host several HTH-type DNA binding transcriptional regulators and transporter genes. Imipenem-susceptible isolates from this clade also carried two mutually exclusive plasmids that contain genes previously known to be specific to imipenem-susceptible isolates. Our analysis demonstrates the utility of using whole genomes for genotype-phenotype correlations in the context of antibiotic resistance and provides several new hypotheses for future research.
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Affiliation(s)
- Kiran Javkar
- Department of Computer Science, University of Maryland, College Park, MD, United States.,Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, United States
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States
| | - Saul Sarria
- Center for Veterinary Medicine, United States Food and Drug Administration, Department of Health and Human Services, Laurel, MD, United States
| | - Nagarajan Thirunavukkarasu
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States
| | - Christine A Pillai
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States
| | - Patrick McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Errol Strain
- Center for Veterinary Medicine, United States Food and Drug Administration, Department of Health and Human Services, Laurel, MD, United States
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, United States
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15
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O'Donnell JN, Putra V, Lodise TP. Treatment of patients with serious infections due to carbapenem-resistant Acinetobacter baumannii: How viable are the current options? Pharmacotherapy 2021; 41:762-780. [PMID: 34170571 DOI: 10.1002/phar.2607] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 11/07/2022]
Abstract
This review critically appraises the published microbiologic and clinical data on the treatment of patients with carbapenem-resistant Acinetobacter baumannii infections. Despite being recognized as an urgent threat pathogen by the CDC and WHO, optimal treatment of patients with serious CRAB infections remains ill-defined. Few commercially available agents exhibit reliable in vitro activity against CRAB. Historically, polymyxins have been the most active agents in vitro, though interpretations of susceptibility data are difficult given issues surrounding MIC testing methodologies and lack of correlation between MICs and clinical outcomes. Most available preclinical and clinical data involve use of polymyxins, tetracyclines, and sulbactam, alone and in combination. As the number of viable treatment options is limited, combination therapy with a polymyxin is often used for patients with CRAB infections, despite the significant risk of nephrotoxicity. However, no treatment regimen has been found to reduce mortality, which exceeds 40% across most studies, or substantially improve clinical response. While some newer agents, such as eravacycline and cefiderocol, have demonstrated in vitro activity, clinical efficacy has not been fully established. New agents with clinically relevant activity against CRAB isolates and favorable toxicity profiles are sorely needed.
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Affiliation(s)
- J Nicholas O'Donnell
- Department of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Vibert Putra
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Thomas P Lodise
- Department of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
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16
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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