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Gutiérrez K, Vásquez-Mendoza A, Rodríguez C. An outbreak of severe or lethal infections by a multidrug-resistant Acinetobacter baumannii ST126 strain carrying a plasmid with bla NDM-1 and bla OXA-58 carbapenemases. Diagn Microbiol Infect Dis 2024; 110:116428. [PMID: 39094238 DOI: 10.1016/j.diagmicrobio.2024.116428] [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: 02/08/2024] [Revised: 06/22/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
Acinetobacter baumannii poses a significant health threat because of its frequent implications in hospital outbreaks and multidrug resistance (MDR). Here, we studied four A. baumannii isolates recovered during a hospital outbreak of severe or fatal cases to elucidate their diversity and factors contributing to their increased virulence and antibiotic resistance. The isolates were identified using MALDI-ToF and characterized using comparative genomics, PCR, and antimicrobial susceptibility tests. They were classified as ST126 and exhibited fewer than five chromosomal single-nucleotide variants and the same extrachromosomal content, indicating that they are a single strain (A. baumannii AB01). A. baumannii AB01 showed an MDR phenotype that could be linked to the carriage of parC and gyrA mutations, efflux transporters, aminoglycoside resistance genes, a class C beta-lactamase, and three carbapenemases, some of which are encoded on a 72 kb plasmid. ST126 is infrequent and has not been reported in Latin America, and our genomic data indicate a plausible origin for A. baumannii AB01 within the Pan Pacific region.
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Affiliation(s)
- Karla Gutiérrez
- Laboratorio Clínico, Hospital Clínica Bíblica, San José, Costa Rica
| | | | - César Rodríguez
- CIET & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
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Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A, Sulimani MM, Ben Taarit S, Reichardt S, Hokamp K, Westermann AJ, Kröger C. Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO. Nucleic Acids Res 2024:gkae668. [PMID: 39149883 DOI: 10.1093/nar/gkae668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.
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Affiliation(s)
- Fergal J Hamrock
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Daniel Ryan
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
| | - Ali Shaibah
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Anna S Ershova
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aalap Mogre
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Maha M Sulimani
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Safa Ben Taarit
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Alexander J Westermann
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Marino A, Augello E, Stracquadanio S, Bellanca CM, Cosentino F, Spampinato S, Cantarella G, Bernardini R, Stefani S, Cacopardo B, Nunnari G. Unveiling the Secrets of Acinetobacter baumannii: Resistance, Current Treatments, and Future Innovations. Int J Mol Sci 2024; 25:6814. [PMID: 38999924 PMCID: PMC11241693 DOI: 10.3390/ijms25136814] [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: 06/01/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Acinetobacter baumannii represents a significant concern in nosocomial settings, particularly in critically ill patients who are forced to remain in hospital for extended periods. The challenge of managing and preventing this organism is further compounded by its increasing ability to develop resistance due to its extraordinary genomic plasticity, particularly in response to adverse environmental conditions. Its recognition as a significant public health risk has provided a significant impetus for the identification of new therapeutic approaches and infection control strategies. Indeed, currently used antimicrobial agents are gradually losing their efficacy, neutralized by newer and newer mechanisms of bacterial resistance, especially to carbapenem antibiotics. A deep understanding of the underlying molecular mechanisms is urgently needed to shed light on the properties that allow A. baumannii enormous resilience against standard therapies. Among the most promising alternatives under investigation are the combination sulbactam/durlobactam, cefepime/zidebactam, imipenem/funobactam, xeruborbactam, and the newest molecules such as novel polymyxins or zosurabalpin. Furthermore, the potential of phage therapy, as well as deep learning and artificial intelligence, offer a complementary approach that could be particularly useful in cases where traditional strategies fail. The fight against A. baumannii is not confined to the microcosm of microbiological research or hospital wards; instead, it is a broader public health dilemma that demands a coordinated, global response.
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Affiliation(s)
- Andrea Marino
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, ARNAS Garibaldi Hospital, 95122 Catania, Italy
| | - Egle Augello
- Department of Biomedical and Biotechnological Science, Section of Pharmacology, University of Catania, 95123 Catania, Italy
- Clinical Toxicology Unit, University Hospital of Catania, 95123 Catania, Italy
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Carlo Maria Bellanca
- Department of Biomedical and Biotechnological Science, Section of Pharmacology, University of Catania, 95123 Catania, Italy
- Clinical Toxicology Unit, University Hospital of Catania, 95123 Catania, Italy
| | - Federica Cosentino
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, ARNAS Garibaldi Hospital, 95122 Catania, Italy
| | - Serena Spampinato
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, ARNAS Garibaldi Hospital, 95122 Catania, Italy
| | - Giuseppina Cantarella
- Department of Biomedical and Biotechnological Science, Section of Pharmacology, University of Catania, 95123 Catania, Italy
| | - Renato Bernardini
- Department of Biomedical and Biotechnological Science, Section of Pharmacology, University of Catania, 95123 Catania, Italy
- Clinical Toxicology Unit, University Hospital of Catania, 95123 Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Bruno Cacopardo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, ARNAS Garibaldi Hospital, 95122 Catania, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, ARNAS Garibaldi Hospital, 95122 Catania, Italy
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Tobin LA, Cain AK, Djordjevic SP, Hamidian M. Transposons Carrying the aacC2e Aminoglycoside and blaTEM Beta-Lactam Resistance Genes in Acinetobacter. Microb Drug Resist 2024; 30:273-278. [PMID: 38593463 DOI: 10.1089/mdr.2023.0299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
This study examines the genetic contexts and evolutionary steps responsible for the formation of the widely spread transposon Tn6925 carrying blaTEM and aacC2e, which confers resistance to beta-lactam and aminoglycoside antibiotics in Gram-negative bacteria. The blaTEM-1 and aacC2e genes were found in several transposons. They were first observed within an IS26 bounded 3.7 kb transposon (Tn6925) on several Acinetobacter baumannii plasmids located within a 4.7 kb dif module. Truncated and expanded variations of Tn6925 were found across other A. baumannii plasmids, as well as in other Gram-negative bacteria (including Vibrio cholerae). Moreover, blaTEM-1 and aacC2e were in much larger resistance-heavy transposons including the ISAba1-bounded 24.6 kb (here called Tn6927), found in an A. baumannii chromosome. A novel ISKpn12-bounded transposon was also observed to contain blaTEM and aacC2e which was found interrupting Tn5393 along with an IS26 pseudo-compound transposon to form a 24.9 kb resistance island in an Acinetobacter pittii plasmid. Multiple mobile genetic elements are involved in the formation of transposon structures that circulate blaTEM and aacC2e. Among these, IS26 and ISAba1 appear to have played a major role in the formation and spread of these elements in the Acinetobacter species.
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Affiliation(s)
- Liam A Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
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McLeod SM, O'Donnell JP, Narayanan N, Mills JP, Kaye KS. Sulbactam-durlobactam: a β-lactam/β-lactamase inhibitor combination targeting Acinetobacter baumannii. Future Microbiol 2024; 19:563-576. [PMID: 38426849 PMCID: PMC11229585 DOI: 10.2217/fmb-2023-0248] [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: 11/08/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Sulbactam-durlobactam is a pathogen-targeted β-lactam/β-lactamase inhibitor combination that has been approved by the US FDA for the treatment of hospital-acquired and ventilator-associated bacterial pneumonia caused by susceptible isolates of Acinetobacter baumannii-calcoaceticus complex (ABC) in patients 18 years of age and older. Sulbactam is a penicillin derivative with antibacterial activity against Acinetobacter but is prone to hydrolysis by β-lactamases encoded by contemporary isolates. Durlobactam is a diazabicyclooctane β-lactamase inhibitor with activity against Ambler classes A, C and D serine β-lactamases that restores sulbactam activity both in vitro and in vivo against multidrug-resistant ABC. Sulbactam-durlobactam is a promising alternative therapy for the treatment of serious Acinetobacter infections, which can have high rates of mortality.
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Affiliation(s)
- Sarah M McLeod
- Innoviva Specialty Therapeutics, Inc., an affiliate of Entasis Therapeutics Inc., 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - John P O'Donnell
- Innoviva Specialty Therapeutics, Inc., an affiliate of Entasis Therapeutics Inc., 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Navaneeth Narayanan
- Rutgers University Ernest Mario School of Pharmacy, Department of Pharmacy Practice & Administration, Piscataway, NJ 08901, USA
| | - John P Mills
- Division of Allergy, Immunology & Infectious Diseases, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Keith S Kaye
- Division of Allergy, Immunology & Infectious Diseases, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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Tobin LA, Jarocki VM, Kenyon J, Drigo B, Donner E, Djordjevic SP, Hamidian M. Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains. Appl Environ Microbiol 2024; 90:e0165423. [PMID: 38206028 PMCID: PMC10885009 DOI: 10.1128/aem.01654-23] [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: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.
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Affiliation(s)
- Liam A. Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Veronica M. Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Johanna Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- UniSA STEM, University of South Australia, Mawson Lakes, SA, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
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El-Soudany I, Attia N, Emad R, Rezk S. The Effect of Citric and Ascorbic Acids as Anti-Biofilm and Anti-Capsular Agents on Multidrug-Resistant Acinetobacter baumannii. Med Princ Pract 2024; 33:281-290. [PMID: 38359804 PMCID: PMC11175600 DOI: 10.1159/000537852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE Acinetobacter baumannii (A. baumannii) is an opportunistic bacterium with multiple virulence factors, including capsule and biofilm, and is known for its high drug resistance. Anti-virulence natural substances have been suggested as novel alternatives to conventional antibiotics. We aimed to evaluate the effect of citric and ascorbic acids as anti-biofilm and anti-capsular agents against multidrug-resistant (MDR) A. baumannii clinical isolates. MATERIALS AND METHODS Twenty-eight A. baumannii MDR isolates were collected from different clinical sources. The minimum inhibitory concentration (MIC) of each agent was estimated. Biofilm formation and capsule were investigated phenotypically in the absence and presence of both agents at ½ and ¼ MICs. The presence of 14 adhesive and nonadhesive virulence genes was investigated. RESULTS Phenotypically, all the isolates were biofilm producers and were capsulated. The MIC of citric acid ranged from 1.25 to 2.5 mg/mL, while that of ascorbic acid was 3 mg/mL for all isolates. Both agents showed significant reduction in biofilm and capsular thinning. Ascorbic acid showed a dose-dependent effect in both biofilm reduction and capsule thinning unlike citric acid. Four genes, papG23, sfa1, fyuA, and cvaC, were absent among all isolates, while iutA was present in 100% of isolates. Other genes showed different distributions among the isolates. These virulence genes were not correlated to the anti-biofilm effect of both agents. Ascorbic acid was observed to have a better effect than citric acid. This can provide a clue for a better treatment regimen including ascorbic acid against MDR A. baumannii infections.
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Affiliation(s)
- Ingy El-Soudany
- Microbiology and Immunology Department, Pharos University in Alexandria, Alexandria, Egypt
| | - Nancy Attia
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Shahinda Rezk
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
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