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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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2
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Dessenne C, Ménart B, Acket S, Dewulf G, Guerardel Y, Vidal O, Rossez Y. Lipidomic analyses reveal distinctive variations in homeoviscous adaptation among clinical strains of Acinetobacter baumannii, providing insights from an environmental adaptation perspective. Microbiol Spectr 2024; 12:e0075724. [PMID: 39254344 PMCID: PMC11448061 DOI: 10.1128/spectrum.00757-24] [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: 03/22/2024] [Accepted: 08/07/2024] [Indexed: 09/11/2024] Open
Abstract
Acinetobacter baumannii is known for its antibiotic resistance and is increasingly found outside of healthcare settings. To survive colder temperatures, bacteria, including A. baumannii, adapt by modifying glycerophospholipids (GPL) to maintain membrane flexibility. This study examines the lipid composition of six clinical A. baumannii strains, including the virulent AB5075, at two temperatures. At 18°C, five strains consistently show an increase in palmitoleic acid (C16:1), while ABVal2 uniquely shows an increase in oleic acid (C18:1). LC-HRMS2 analysis identifies shifts in GPL and glycerolipid composition between 18°C and 37°C, highlighting variations in phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) lipids. ABVal2 shows increased PE with C18:1 and C16:1 at 18°C, but no change in PG, in contrast to other strains that show increased PE and PG with C16:1. Notably, although A. baumannii typically lacks FabA, a key enzyme for unsaturated fatty acid synthesis, this enzyme was found in both ABVal2 and ABVal3. In addition, ABVal2 contains five candidate desaturases that may contribute to its lipid profile. The study also reveals variations in strain motility and biofilm formation over temperature. These findings enhance our understanding of A. baumannii's physiological adaptations, survival strategies and ecological fitness in different environments.IMPORTANCEAcinetobacter baumannii, a bacterium known for its resistance to antibiotics, is a concern in healthcare settings. This study focused on understanding how this bacterium adapts to different temperatures and how its lipid composition changes. Lipids are the building blocks of cell membranes. By studying these changes, scientists can gain insights into how the bacterium survives and behaves in various environments. This understanding improves our understanding of its global dissemination capabilities. The results of the study contribute to our broader understanding of how Acinetobacter baumannii works, which is important for developing strategies to combat its impact on patient health.
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Affiliation(s)
- Clara Dessenne
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Benoît Ménart
- Centre Hospitalier de valenciennes, Laboratoire de Biologie Hygiène-service de Microbiologie, Valenciennes, France
| | - Sébastien Acket
- Université de technologie de Compiègne, UPJV, UMR CNRS 7025, Enzyme and Cell Engineering, Centre de recherche Royallieu, Compiègne Cedex, Compiègne, France
| | - Gisèle Dewulf
- Centre Hospitalier de valenciennes, Laboratoire de Biologie Hygiène-service de Microbiologie, Valenciennes, France
| | - Yann Guerardel
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Olivier Vidal
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Yannick Rossez
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Université de technologie de Compiègne, UPJV, UMR CNRS 7025, Enzyme and Cell Engineering, Centre de recherche Royallieu, Compiègne Cedex, Compiègne, France
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3
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024; 22:598-616. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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4
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Mohamed RAE, Moustafa NM, Mahmoud FM, Elsaadawy YS, Aziz HSA, Gaber SAB, Hussin AM, Seadawy MG. Whole-genome sequencing of two multidrug-resistant acinetobacter baumannii strains isolated from a neonatal intensive care unit in Egypt: a prospective cross-sectional study. BMC Microbiol 2024; 24:362. [PMID: 39306657 PMCID: PMC11415996 DOI: 10.1186/s12866-024-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Acinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium. OBJECTIVES This study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt. METHODS Following the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed. RESULTS Two isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them. CONCLUSIONS A low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.
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Affiliation(s)
- Rania Alam Eldin Mohamed
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nouran Magdy Moustafa
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Basic Medical Science Department, College of Medicine, Dar Al Uloom University, Riyadh, Saudi Arabia
| | - Fatma Mostafa Mahmoud
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yara Said Elsaadawy
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Heba Sherif Abdel Aziz
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | | | | | - Mohamed G Seadawy
- Biodefense Center for Infectious and Emerging Diseases, Ministry of Defense, Cairo, Egypt
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5
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Koncz M, Stirling T, Hadj Mehdi H, Méhi O, Eszenyi B, Asbóth A, Apjok G, Tóth Á, Orosz L, Vásárhelyi BM, Ari E, Daruka L, Polgár TF, Schneider G, Zalokh SA, Számel M, Fekete G, Bohár B, Nagy Varga K, Visnyovszki Á, Székely E, Licker MS, Izmendi O, Costache C, Gajic I, Lukovic B, Molnár S, Szőcs-Gazdi UO, Bozai C, Indreas M, Kristóf K, Van der Henst C, Breine A, Pál C, Papp B, Kintses B. Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens. Cell 2024:S0092-8674(24)01027-4. [PMID: 39332413 DOI: 10.1016/j.cell.2024.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/15/2024] [Accepted: 09/04/2024] [Indexed: 09/29/2024]
Abstract
Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.
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Affiliation(s)
- Mihály Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary
| | - Tamás Stirling
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Hiba Hadj Mehdi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Bálint Eszenyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - András Asbóth
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary
| | - Gábor Apjok
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ákos Tóth
- National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - László Orosz
- Department of Medical Microbiology, University of Szeged, Szent-Györgyi Albert Medical School, Dom tér 10, 6720 Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Eszter Ari
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Tamás Ferenc Polgár
- Institute of Biophysics, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Theoretical Medicine Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Sif Aldin Zalokh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Mónika Számel
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Bohár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, 10th Floor Commonwealth Building Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Karolina Nagy Varga
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ádám Visnyovszki
- South-Pest Central Hospital National Institute of Hematology and Infectious Diseases, Nagyvárad tér 1, 1097 Budapest, Hungary; Doctoral School of Interdisciplinary Medical Sciences, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Edit Székely
- George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, Str. Gheorghe Marinescu 38, 540142 Targu Mures, Romania; County Emergency Clinical Hospital of Targu Mures, Str. Dr. Gh. Marinescu 50, 540136 Targu Mures, Romania
| | - Monica-Sorina Licker
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Oana Izmendi
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania; Doctoral School, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania
| | - Carmen Costache
- Department of Microbiology, University of Medicine and Pharmacy "Iuliu Hatieganu" Cluj-Napoca, Str. Victor Babes 8, 400347 Cluj-Napoca, Romania
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia
| | - Bojana Lukovic
- Academy of Applied Studies Belgrade, College of Health Sciences, Bulevar Zorana Djindjica 152a, Belgrade, Serbia
| | - Szabolcs Molnár
- Emergency County Hospital Miercurea-Ciuc, Str. Doctor Dénes László 2, 530173 Miercurea Ciuc, Romania
| | | | - Csilla Bozai
- County Emergency Hospital Satu Mare, Str. Ravensburg 1-3, 440192 Satu Mare, Romania
| | - Marina Indreas
- Bacau County Emergency Hospital, Str. Haret Spiru 2-4, 600114 Bacau, Romania
| | - Katalin Kristóf
- Institute of Laboratory Medicine, Semmelweis University, Üllői út 78/b, 1083 Budapest, Hungary
| | - Charles Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Anke Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary; National Laboratory for Health Security, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary.
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Gheorghe-Barbu I, Surleac M, Barbu IC, Paraschiv S, Bănică LM, Rotaru LI, Vrâncianu CO, Niță Lazăr M, Oțelea D, Chifiriuc MC. Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania. Heliyon 2024; 10:e33372. [PMID: 39035534 PMCID: PMC11259834 DOI: 10.1016/j.heliyon.2024.e33372] [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: 04/06/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.
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Affiliation(s)
- Irina Gheorghe-Barbu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Marius Surleac
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | - Ilda Czobor Barbu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Simona Paraschiv
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | | | - Liviu-Iulian Rotaru
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Corneliu Ovidiu Vrâncianu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 296 Splaiul Independentei, District 6, 060031 Bucharest, Romania
| | - Mihai Niță Lazăr
- National Institute for Research and Development for Industrial Ecology, Bucharest, Romania
| | - Dan Oțelea
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Romanian Academy, Bucharest, Romania
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7
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Singh S, Singh S, Trivedi M, Dwivedi M. An insight into MDR Acinetobacter baumannii infection and its pathogenesis: Potential therapeutic targets and challenges. Microb Pathog 2024; 192:106674. [PMID: 38714263 DOI: 10.1016/j.micpath.2024.106674] [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: 10/19/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Acinetobacter baumannii is observed as a common species of Gram-negative bacteria that exist in soil and water. Despite being accepted as a typical component of human skin flora, it has become an important opportunistic pathogen, especially in healthcare settings. The pathogenicity of A. baumannii is attributed to its virulence factors, which include adhesins, pili, lipopolysaccharides, outer membrane proteins, iron uptake systems, autotransporter, secretion systems, phospholipases etc. These elements provide the bacterium the ability to cling to and penetrate host cells, get past the host immune system, and destroy tissue. Its infection is a major contributor to human pathophysiological conditions including pneumonia, bloodstream infections, urinary tract infections, and surgical site infections. It is challenging to treat infections brought on by this pathogen since this bacterium has evolved to withstand numerous drugs and further emergence of drug-resistant A. baumannii results in higher rates of morbidity and mortality. The long-term survival of this bacterium on surfaces of medical supplies and hospital furniture facilitates its frequent spread in humans from one habitat to another. There is a need for urgent investigations to find effective drug targets for A. baumannii as well as designing novel drugs to reduce the survival and spread of infection. In the current review, we represent the specific features, pathogenesis, and molecular intricacies of crucial drug targets of A. baumannii. This would also assist in proposing strategies and alternative therapies for the prevention and treatment of A. baumannii infections and their spread.
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Affiliation(s)
- Sukriti Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Sushmita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India; Research Cell, Amity University Uttar Pradesh, Lucknow, 226028, India.
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8
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Luo TL, Martin MJ, Kovalchuk V, Kondratiuk V, Trapaidze N, Metreveli M, Hulseberg CE, Dao HD, Kwak YI, Maybank R, Musich TA, Scherer MR, Bennett JW, Mc Gann PT, Lebreton F. Detection of carbapenemase producing Acinetobacter baumannii ST19 from Georgia and Ukraine carrying bla OXA-23, bla OXA-72, and/or bla NDM-5, December 2019 to June 2023. Euro Surveill 2024; 29:2400259. [PMID: 38873796 PMCID: PMC11177571 DOI: 10.2807/1560-7917.es.2024.29.24.2400259] [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: 04/26/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
In 2003-2023, amid 5,436 Acinetobacter baumannii isolates collected globally through the Multidrug-Resistant Organism Repository and Surveillance Network, 97 were ST19PAS, 34 of which carbapenem-resistant. Strains (n = 32) sampled after 2019 harboured either bla OXA-23, bla OXA-72, and/or bla NDM-5. Phylogenetic analysis of the 97 isolates and 11 publicly available ST19 genomes revealed three sub-lineages of carbapenemase-producing isolates from mainly Ukraine and Georgia, including an epidemic clone carrying all three carbapenemase genes. Infection control and global surveillance of carbapenem-resistant A. baumannii remain important.
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Affiliation(s)
- Ting L Luo
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Melissa J Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Valentyn Kovalchuk
- Department of Microbiology, National Pirogov Memorial Medical University, Vinnytsia, Ukraine
| | - Viacheslav Kondratiuk
- Department of Emergency and Military Medicine, National Pirogov Memorial Medical University, Vinnytsia, Ukraine
| | - Nino Trapaidze
- US Army Medical Research Directorate - Europe & Middle East, Tbilisi, Georgia
| | - Magda Metreveli
- US Army Medical Research Directorate - Europe & Middle East, Tbilisi, Georgia
| | | | - Henry D Dao
- Landstuhl Regional Medical Center, Landstuhl, Germany
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Thomas A Musich
- US Army Medical Research Directorate - Europe & Middle East, Tbilisi, Georgia
| | - Matthew R Scherer
- US Army Medical Research Directorate - Europe & Middle East, Tbilisi, Georgia
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Patrick T Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States
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9
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Wang R, Liu Y, Zhang Y, Yu S, Zhuo H, Huang Y, Lyu J, Lin Y, Zhang X, Mi Z, Liu Y. Identification and characterization of the capsule depolymerase Dpo27 from phage IME-Ap7 specific to Acinetobacter pittii. Front Cell Infect Microbiol 2024; 14:1373052. [PMID: 38808067 PMCID: PMC11130378 DOI: 10.3389/fcimb.2024.1373052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/11/2024] [Indexed: 05/30/2024] Open
Abstract
Among the Acinetobacter genus, Acinetobacter pittii stands out as an important opportunistic infection causative agent commonly found in hospital settings, which poses a serious threat to human health. Recently, the high prevalence of carbapenem-resistant A. pittii isolates has created significant therapeutic challenges for clinicians. Bacteriophages and their derived enzymes are promising therapeutic alternatives or adjuncts to antibiotics effective against multidrug-resistant bacterial infections. However, studies investigating the depolymerases specific to A. pittii strains are scarce. In this study, we identified and characterized a capsule depolymerase, Dpo27, encoded by the bacteriophage IME-Ap7, which targets A. pittii. A total of 23 clinical isolates of Acinetobacter spp. were identified as A. pittii (21.91%, 23/105), and seven A. pittii strains with various K locus (KL) types (KL14, KL32, KL38, KL111, KL163, KL207, and KL220) were used as host bacteria for phage screening. The lytic phage IME-Ap7 was isolated using A. pittii 7 (KL220) as an indicator bacterium and was observed for depolymerase activity. A putative tail fiber gene encoding a polysaccharide-degrading enzyme (Dpo27) was identified and expressed. The results of the modified single-spot assay showed that both A. pittii 7 and 1492 were sensitive to Dpo27, which was assigned the KL220 type. After incubation with Dpo27, A. pittii strain was susceptible to killing by human serum; moreover, the protein displayed no hemolytic activity against erythrocytes. Furthermore, the protein exhibited sustained activity across a wide pH range (5.0-10.0) and at temperatures between 20 and 50°C. In summary, the identified capsule depolymerase Dpo27 holds promise as an alternative treatment for combating KL220-type A. pittii infections.
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Affiliation(s)
- Rentao Wang
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yannan Liu
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Yaqian Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shijun Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hailong Zhuo
- Department of Transfusion Medicine, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jinhui Lyu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiqiang Mi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Youning Liu
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, China
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10
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Kakaraskoska Boceska B, Vilken T, Xavier BB, Kostyanev T, Lin Q, Lammens C, Ellis S, O'Brien S, da Costa RMA, Cook A, Russell N, Bielicki J, Riddell A, Stohr W, Walker AS, Berezin EN, Roilides E, De Luca M, Romani L, Ballot D, Dramowski A, Wadula J, Lochindarat S, Boonkasidecha S, Namiiro F, Ngoc HTB, Tran MD, Cressey TR, Preedisripipat K, Berkley JA, Musyimi R, Zarras C, Nana T, Whitelaw A, da Silva CB, Jaglal P, Ssengooba W, Saha SK, Islam MS, Mussi-Pinhata MM, Carvalheiro CG, Piddock LJV, Heath PT, Malhotra-Kumar S, Sharland M, Glupczynski Y, Goossens H. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nat Commun 2024; 15:3947. [PMID: 38729951 PMCID: PMC11087563 DOI: 10.1038/s41467-024-48296-z] [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: 11/27/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Biljana Kakaraskoska Boceska
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | | | - Aislinn Cook
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Neal Russell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Julia Bielicki
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
- Paediatric Research Centre, University of Basel Children's Hospital, Basel, Switzerland
| | - Amy Riddell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Wolfgang Stohr
- MRC Clinical Trials Unit, University College London, London, UK
| | | | | | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Paediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Maia De Luca
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Lorenza Romani
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Daynia Ballot
- Department of Pediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Flavia Namiiro
- Mulago Specialized Women's and Neonatal Hospital, Kampala, Uganda
| | | | | | - Tim R Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Robert Musyimi
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Cely Barreto da Silva
- Infection Control and Prevention Service, Santa Casa de Sao Paulo, Sao Paulo, Brazil
| | - Prenika Jaglal
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Kampala, Uganda
| | - Samir K Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | | | | | | | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Paul T Heath
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Michael Sharland
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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11
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Harmer CJ, Cahill SM, Kenyon JJ, Hall RM. Aminoglycoside resistance genes in early members of the Acinetobacter baumannii ST78A (SMAL, Italian clone) reside in an IS26-bounded island in the chromosome. J Antimicrob Chemother 2024; 79:1014-1018. [PMID: 38530861 PMCID: PMC11062947 DOI: 10.1093/jac/dkae064] [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: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The Acinetobacter baumannii isolate called SMAL, previously used to determine the structures of capsular polysaccharide and lipooligosaccharide, was recovered in Pavia, Italy in 2002 among the collection of aminoglycoside-resistant isolates designated as SMAL type. This type was later called the Italian clone, then ST78. ST78 isolates are now widely distributed. OBJECTIVES To establish the resistance gene complement and the location and structure of acquired resistance regions in early members of the Italian/ST78 clone. METHODS The draft genome of SMAL2002 was assembled from Illumina MiSeq reads. Contigs containing resistance genes were joined and located in the chromosome using PCR with custom primers. The resistance profile was determined using disc diffusion. RESULTS SMAL2002 is an ST78A isolate and includes three aminoglycoside resistance genes, aadB (gentamicin, kanamycin, tobramycin) aphA1 (kanamycin, neomycin) and aac(6')-Ian (amikacin, kanamycin, tobramycin). The aadB gene cassette is incorporated at a secondary site in a relative of the aphA1-containing, IS26-bounded pseudo-compound transposon, PTn6020. The aac(6')-Ian gene is in an adjacent IS26-bounded structure that includes sul2 (sulphonamide) and floR (florfenicol) resistance genes. The two pseudo-compound transposons overlap and are in the chromosomal hutU gene flanked by an 8 bp target site duplication. Although aac(6')-Ian was not noticed previously, the same genes and structures were found in several available draft genomes of early ST78A isolates. CONCLUSIONS This study highlights the importance of correlating resistance profiles with resistance gene content. The location of acquired resistance genes in the SMAL2002 chromosome represents the original location in the ST78A lineage of ST78.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2008, Australia
| | - Sarah M Cahill
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2008, Australia
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12
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Anwer R. Molecular epidemiology and molecular typing methods of Acinetobacter baumannii: An updated review. Saudi Med J 2024; 45:458-467. [PMID: 38734425 PMCID: PMC11147555 DOI: 10.15537/smj.2024.45.5.20230886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant Acientobacter baumannii (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by Acientobacter baumannii (A. baumannii) and acquired resistance to antimicrobials. Nowadays, there is gradual shift from traditional typing methods to modern molecular methods to study molecular epidemiology and infection control. Molecular typing of A. baumannii strains has been revolutionized significantly in the last 2 decades. A few sequencing-based techniques have been proven as a breakthrough and opened new prospects, which have not been achieved by the traditional methods. In this review, discussed different pre-existing and recently used typing methods to explore the molecular epidemiology of A. baumannii pertaining in context with human infections.
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Affiliation(s)
- Razique Anwer
- From the Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University, Riyadh, Kingdom of Saudi Arabia.
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13
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Findlay J, Bianco G, Boattini M, Nordmann P. In vivo development of cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii associated with the downregulation of a TonB-dependent siderophore receptor, PiuA. J Antimicrob Chemother 2024; 79:928-930. [PMID: 38297993 PMCID: PMC10984935 DOI: 10.1093/jac/dkae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Jacqueline Findlay
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Gabriele Bianco
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Torino, Turin, Italy
| | - Matteo Boattini
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Torino, Turin, Italy
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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14
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Sykes EME, Mateo-Estrada V, Engelberg R, Muzaleva A, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Khan IUH, Castillo-Ramírez S, Kumar A. Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-human Acinetobacter baumannii. mSphere 2024; 9:e0074123. [PMID: 38440986 PMCID: PMC10964423 DOI: 10.1128/msphere.00741-23] [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: 11/29/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative, opportunistic pathogen that causes infections in the immunocompromised. With a high incidence of muti-drug resistance, carbapenem-resistant A. baumannii is designated as a priority 1 pathogen by the WHO. The current literature has expertly characterized clinical isolates of A. baumannii. As the challenge of these infections has recently been classified as a One Health issue, we set out to explore the diversity of isolates from human and non-clinical sources, such as agricultural surface water, urban streams, various effluents from wastewater treatment plants, and food (tank milk); and, importantly, these isolates came from a wide geographic distribution. Phylogenomic analysis considering almost 200 isolates showed that our diverse set is well-differentiated from the main international clones of A. baumannii. We discovered novel sequence types in both hospital and non-clinical settings and five strains that overexpress the resistance-nodulation-division efflux pump adeIJK without changes in susceptibility reflected by this overexpression. Furthermore, we detected a bla ADC-79 in a non-human isolate despite its sensitivity to all antibiotics. There was no significant differentiation between the virulence profiles of clinical and non-clinical isolates in the Galleria mellonella insect model of virulence, suggesting that virulence is neither dependent on geographic origin nor isolation source. The detection of antibiotic resistance and virulence genes in non-human strains suggests that these isolates may act as a genetic reservoir for clinical strains. This endorses the notion that in order to combat multi-drug-resistant infection caused by A. baumannii, a One Health approach is required, and a deeper understanding of non-clinical strains must be achieved.IMPORTANCEThe global crisis of antibiotic resistance is a silent one. More and more bacteria are becoming resistant to all antibiotics available for treatment, leaving no options remaining. This includes Acinetobacter baumannii. This Gram-negative, opportunistic pathogen shows a high frequency of multi-drug resistance, and many strains are resistant to the last-resort drugs carbapenem and colistin. Research has focused on strains of clinical origin, but there is a knowledge gap regarding virulence traits, particularly how A. baumannii became the notorious pathogen of today. Antibiotic resistance and virulence genes have been detected in strains from animals and environmental locations such as grass and soil. As such, A. baumannii is a One Health concern, which includes the health of humans, animals, and the environment. Thus, in order to truly combat the antibiotic resistance crisis, we need to understand the antibiotic resistance and virulence gene reservoirs of this pathogen under the One Health continuum.
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Affiliation(s)
- Ellen M. E. Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Raelene Engelberg
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Muzaleva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ömer Akineden
- Dairy Sciences, Institute of Veterinary Food Science, Justus-Liebig, University of Giessen, Giessen, Germany
| | - Izhar U. H. Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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15
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Zheng C, Li D, Wang Y, Wang L, Huang Y, Yao J. Risk factors and genetic characteristics of the carriage of hypervirulent and carbapenem-resistant Acinetobacter baumannii among pregnant women. Front Microbiol 2024; 15:1351722. [PMID: 38572236 PMCID: PMC10987950 DOI: 10.3389/fmicb.2024.1351722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) and its emerging evolutionary branch toward hypervirulence have been neglected in pregnancy. Methods From September 2020 to August 2021, an active surveillance culture program encompassed 138 randomly selected pregnant women, with five subjected to sample collection at two different time points. The clinical characterization was explored through statistical analysis. Whole-genome sequencing, a Galleria mellonella infection model, and a global database were used to investigate the genetic characterization, pathogenicity, evolutionary history, and phylogenetic relationships of the isolates. Results Of the 41 CRAB isolates obtained, they were divided into four ClustersRS and an orphan pattern. ClusterRS 1 (n = 31), with eight complex types in pregnancy, was also the dominant ClusterRS globally, followed by ClusterRS 13 (n = 5), identified as hypervirulent KL49 CRAB, exhibiting phylogeographical specificity to Guangdong. A maternal carriage CRAB rate of 26.09% (36/138) was revealed, with half of the isolates representing novel complex types, prominently including CT3071, as the first KL7 isolates identified in Shenzhen. Both KL49 and KL7 isolates were most commonly found in the same participant, suggesting potential intraspecific competition as a possible reason for CRAB infection without carriers during pregnancy. The independent risk factors for carriers were revealed for the first time, including advanced maternal age, gestational diabetes mellitus, and Group B Streptococcus infection. Conclusion The significant carriage rate and enhanced virulence of CRAB during pregnancy emphasize the imperative for routine surveillance to forestall dissemination within this high-risk group, especially in Guangdong for ClusterRS 13 isolates.
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Affiliation(s)
- Chao Zheng
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
- Bacteriology and Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Disease, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
- School of Materials and Environmental Engineering, Shenzhen Polytechnic University, Shenzhen, China
| | - Defeng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Yinglan Wang
- Department of Obstetrics and Gynecology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Lisheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Yuting Huang
- Bacteriology and Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Disease, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
- Department of Head and Neck Surgery, Cancer Hospital Chinese Academy of Medical Sciences Shenzhen Center, Shenzhen, China
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
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16
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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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Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems 2024; 9:e0060623. [PMID: 38189271 PMCID: PMC10878099 DOI: 10.1128/msystems.00606-23] [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: 06/11/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Acinetobacter baumannii causes severe infections in humans, resists multiple antibiotics, and survives in stressful environmental conditions due to modulations of its complex transcriptional regulatory network (TRN). Unfortunately, our global understanding of the TRN in this emerging opportunistic pathogen is limited. Here, we apply independent component analysis, an unsupervised machine learning method, to a compendium of 139 RNA-seq data sets of three multidrug-resistant A. baumannii international clonal complex I strains (AB5075, AYE, and AB0057). This analysis allows us to define 49 independently modulated gene sets, which we call iModulons. Analysis of the identified A. baumannii iModulons reveals validating parallels to previously defined biological operons/regulons and provides a framework for defining unknown regulons. By utilizing the iModulons, we uncover potential mechanisms for a RpoS-independent general stress response, define global stress-virulence trade-offs, and identify conditions that may induce plasmid-borne multidrug resistance. The iModulons provide a model of the TRN that emphasizes the importance of transcriptional regulation of virulence phenotypes in A. baumannii. Furthermore, they suggest the possibility of future interventions to guide gene expression toward diminished pathogenic potential.IMPORTANCEThe rise in hospital outbreaks of multidrug-resistant Acinetobacter baumannii infections underscores the urgent need for alternatives to traditional broad-spectrum antibiotic therapies. The success of A. baumannii as a significant nosocomial pathogen is largely attributed to its ability to resist antibiotics and survive environmental stressors. However, there is limited literature available on the global, complex regulatory circuitry that shapes these phenotypes. Computational tools that can assist in the elucidation of A. baumannii's transcriptional regulatory network architecture can provide much-needed context for a comprehensive understanding of pathogenesis and virulence, as well as for the development of targeted therapies that modulate these pathways.
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Affiliation(s)
- Nitasha D. Menon
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Nicholas Dillon
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Biological Sciences, University of Texas at Dallas, Dallas, Texas, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yujiro Hirose
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
| | - Bipin G. Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Geetha B. Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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18
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Wang M, Ge L, Chen L, Komarow L, Hanson B, Reyes J, Cober E, Alenazi T, Zong Z, Xie Q, Liu Z, Li L, Yu Y, Gao H, Kanj SS, Figueroa J, Herc E, Cordova E, Weston G, Ananth Tambyah P, Garcia-Diaz J, Kaye KS, Dhar S, Munita JM, Salata RA, Vilchez S, Stryjewski ME, Villegas Botero MV, Iovleva A, Evans SR, Baum K, Hill C, Kreiswirth BN, Patel R, Paterson DL, Arias CA, Bonomo RA, Chambers HF, Fowler VG, Satlin MJ, van Duin D, Doi Y. Clinical Outcomes and Bacterial Characteristics of Carbapenem-resistant Acinetobacter baumannii Among Patients From Different Global Regions. Clin Infect Dis 2024; 78:248-258. [PMID: 37738153 PMCID: PMC10874260 DOI: 10.1093/cid/ciad556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (CRAb) is 1 of the most problematic antimicrobial-resistant bacteria. We sought to elucidate the international epidemiology and clinical impact of CRAb. METHODS In a prospective observational cohort study, 842 hospitalized patients with a clinical CRAb culture were enrolled at 46 hospitals in five global regions between 2017 and 2019. The primary outcome was all-cause mortality at 30 days from the index culture. The strains underwent whole-genome analysis. RESULTS Of 842 cases, 536 (64%) represented infection. By 30 days, 128 (24%) of the infected patients died, ranging from 1 (6%) of 18 in Australia-Singapore to 54 (25%) of 216 in the United States and 24 (49%) of 49 in South-Central America, whereas 42 (14%) of non-infected patients died. Bacteremia was associated with a higher risk of death compared with other types of infection (40 [42%] of 96 vs 88 [20%] of 440). In a multivariable logistic regression analysis, bloodstream infection and higher age-adjusted Charlson comorbidity index were independently associated with 30-day mortality. Clonal group 2 (CG2) strains predominated except in South-Central America, ranging from 216 (59%) of 369 in the United States to 282 (97%) of 291 in China. Acquired carbapenemase genes were carried by 769 (91%) of the 842 isolates. CG2 strains were significantly associated with higher levels of meropenem resistance, yet non-CG2 cases were over-represented among the deaths compared with CG2 cases. CONCLUSIONS CRAb infection types and clinical outcomes differed significantly across regions. Although CG2 strains remained predominant, non-CG2 strains were associated with higher mortality. Clinical Trials Registration. NCT03646227.
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Affiliation(s)
- Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China,Shanghai, China
| | - Lizhao Ge
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Lauren Komarow
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Blake Hanson
- Center for Infectious Diseases and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, USA
| | - Thamer Alenazi
- College of Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Qing Xie
- Department of Infectious Disease, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Zhengyin Liu
- Infectious Disease Section, Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hainv Gao
- Department of Infectious Diseases, Shulan Hangzhou Hospital, Hangzhou, China
| | - Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jairo Figueroa
- Department of Infectious Diseases, Hospital Universitario Erasmo Meoz ESE, Cúcuta, Colombia
| | - Erica Herc
- Division of Infectious Diseases, Department of Medicine, Henry Ford Hospital, Detroit, Michigan, USA
| | - Ezequiel Cordova
- Infectious Diseases Unit, Hospital Cosme Argerich de Buenos Aires, Buenos Aires, Argentina
| | - Gregory Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Paul Ananth Tambyah
- Infectious Diseases Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Julia Garcia-Diaz
- Division of Infectious Diseases, Ochsner Medical Center, New Orleans, Louisiana, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Division of Allergy, Immunology and Infectious Diseases, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Sorabh Dhar
- Division of Infectious Disease, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Jose M Munita
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina, Facultad de Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Robert A Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Samuel Vilchez
- Center for Infectious Disease Research, Department of Microbiology and Parasitology, School of Medicine, National Autonomous University of Nicaragua, Leon, Nicaragua
| | - Martin E Stryjewski
- Department of Medicine and Division of Infectious Diseases, Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Argentina
| | | | - Alina Iovleva
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott R Evans
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China,Shanghai, China
- Department of Biostatics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Keri Baum
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - David L Paterson
- Department of Infectious Diseases, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cesar A Arias
- Division of Infectious Diseases, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Western Reserve University VA Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Henry F Chambers
- Department of Medicine, University of California SanFrancisco, San Francisco, California, USA
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - David van Duin
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Yohei Doi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
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19
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Müller C, Reuter S, Wille J, Xanthopoulou K, Stefanik D, Grundmann H, Higgins PG, Seifert H. A global view on carbapenem-resistant Acinetobacter baumannii. mBio 2023; 14:e0226023. [PMID: 37882512 PMCID: PMC10746149 DOI: 10.1128/mbio.02260-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Carbapenem-resistant Acinetobacter baumannii are of increasing public health importance, as they are resistant to last-line antibiotics. International clones with well-characterized resistance genes dominate globally; however, locally, other lineages with different properties may be of importance to consider. This study investigated isolates from a broad geographic origin from 114 hospitals in 47 countries and from five world regions ensuring the greatest possible diversity in an organism known for its propensity for clonal epidemic spread and reflecting the current global epidemiology of carbapenem-resistant A. baumannii. In Latin America, a lineage different from other geographic regions circulates, with a different resistance gene profile. This knowledge is important to adjust local infection prevention measures. In a global world with migration and increasing use of antimicrobials, multidrug-resistant bacteria will continue to adapt and challenge our healthcare systems worldwide.
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Affiliation(s)
- Carina Müller
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Danuta Stefanik
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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20
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Fernández-Vázquez JL, Hernández-González IL, Castillo-Ramírez S, Jarillo-Quijada MD, Gayosso-Vázquez C, Mateo-Estrada VE, Morfín-Otero R, Rodríguez-Noriega E, Santos-Preciado JI, Alcántar-Curiel MD. Pandrug-resistant Acinetobacter baumannii from different clones and regions in Mexico have a similar plasmid carrying the blaOXA-72 gene. Front Cell Infect Microbiol 2023; 13:1278819. [PMID: 38192399 PMCID: PMC10773864 DOI: 10.3389/fcimb.2023.1278819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii is a common hospital-acquired pathogen. The increase in antibiotic resistance is commonly due to the acquisition of mobile genetic elements carrying antibiotic resistance genes. To comprehend this, we analyzed the resistome and virulome of Mexican A. baumannii multidrug-resistant isolates. Methods Six clinical strains of A. baumannii from three Mexican hospitals were sequenced using the Illumina platform, the genomes were assembled with SPAdes and annotated with Prokka. Plasmid SPAdes and MobRecon were used to identify the potential plasmid sequences. Sequence Type (ST) assignation under the MLST Oxford scheme was performed using the PubMLST database. Homologous gene search for known virulent factors was performed using the virulence factor database VFDB and an in silico prediction of the resistome was conducted via the ResFinder databases. Results The six strains studied belong to different STs and clonal complexes (CC): two strains were ST208 and one was ST369; these two STs belong to the same lineage CC92, which is part of the international clone (IC) 2. Another two strains were ST758 and one was ST1054, both STs belonging to the same lineage CC636, which is within IC5. The resistome analysis of the six strains identified between 7 to 14 antibiotic resistance genes to different families of drugs, including beta-lactams, aminoglycosides, fluoroquinolones and carbapenems. We detected between 1 to 4 plasmids per strain with sizes from 1,800 bp to 111,044 bp. Two strains from hospitals in Mexico City and Guadalajara had a plasmid each of 10,012 bp pAba78r and pAba79f, respectively, which contained the bla OXA-72 gene. The structure of this plasmid showed the same 13 genes in both strains, but 4 of them were inverted in one of the strains. Finally, the six strains contain 49 identical virulence genes related to immune response evasion, quorum-sensing, and secretion systems, among others. Conclusion Resistance to carbapenems due to pAba78r and pAba79f plasmids in Aba pandrug-resistant strains from different geographic areas of Mexico and different clones was detected. Our results provide further evidence that plasmids are highly relevant for the horizontal transfer of antibiotic resistance genes between different clones of A. baumannii.
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Affiliation(s)
- José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ismael Luis Hernández-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ma Dolores Jarillo-Quijada
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Eréndira Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - José Ignacio Santos-Preciado
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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21
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Bulach D, Carter GP, Li L, Al-Hashem G, Rotimi VO, Albert MJ. The whole-genome molecular epidemiology of sequential isolates of Acinetobacter baumannii colonizing the rectum of patients in an adult intensive care unit of a tertiary hospital. Microbiol Spectr 2023; 11:e0219123. [PMID: 37843271 PMCID: PMC10715177 DOI: 10.1128/spectrum.02191-23] [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: 05/24/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen that colonizes and infects debilitated patients in the ICU. There is very little information on the genomic characteristics of colonizing strains. This information is important to understand the evolution of lineages of A. baumannii that develop resistance while patients receive antibiotic treatment in the ICU. Our study demonstrated different patterns of colonization of the rectum of ICU patients with different STs of A. baumannii while one ST colonized all patients. Some STs carried more antibiotic resistance genes compared to others. However, there was a correlation between ST and a particular resistance gene profile. Our results further elucidate the dynamics of enteric colonization of this opportunistic pathogen.
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Affiliation(s)
- Dieter Bulach
- Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lucy Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ghayda Al-Hashem
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
| | - Vincent O. Rotimi
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
| | - M. John Albert
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
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22
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Odih EE, Sunmonu GT, Okeke IN, Dalsgaard A. NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital. Microbiol Spectr 2023; 11:e0238123. [PMID: 37796014 PMCID: PMC10714947 DOI: 10.1128/spectrum.02381-23] [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: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a leading cause of hospital-associated infections globally. A. baumannii reservoirs outside hospital settings are still unknown, and their occurrence in the environment is linked to clinical and anthropogenic activities. Although the risk of transmission of A. baumannii from environmental sources to humans is not fully understood, these sources pose significant risks for the continued dissemination of A. baumannii and their resistance traits. This study provides evidence that diverse and clinically relevant A. baumannii strains, many of which are resistant to carbapenems, are constantly being discharged into the environment through inadequately treated hospital wastewater. We further elucidate potential transmission routes between the environment and clinical infections and demonstrate the high prevalence of carbapenem resistance genes on highly mobile transposons among these strains. Our findings highlight the pressing need to address hospital wastewater as a crucial factor in curtailing the spread of carbapenem-resistant A. baumannii.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Gabriel Temitope Sunmonu
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Lupo A, Valot B, Saras E, Drapeau A, Robert M, Bour M, Haenni M, Plésiat P, Madec JY, Potron A. Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades. Sci Rep 2023; 13:21854. [PMID: 38071225 PMCID: PMC10710421 DOI: 10.1038/s41598-023-49268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The Acinetobacter baumannii clonal lineage ST25 has been identified in humans and animals and found associated with outbreaks globally. To highlight possible similarities among ST25 A. baumannii of animal and human origins and to gather clues on the dissemination and evolution of the ST25 lineage, we conducted a phylogenetic analysis on n = 106 human and n = 35 animal A. baumannii ST25 genomes, including 44 sequenced for this study. Resistance genes and their genetic background were analyzed, as well. ST25 genomes are clustered into four clades: two are widespread in South America, while the other two are largely distributed in Europe, Asia and America. One particular clade was found to include the most recent strains and the highest number of acquired antibiotic resistance genes. OXA-23-type carbapenemase was the most common. Other resistance genes such as blaNDM-1, blaPER-7, and armA were found embedded in complex chromosomal regions present in human isolates. Genomic similarity among multidrug resistant ST25 isolates of either animal or human origin was revealed, suggesting cross-contaminations between the two sectors. Tracking the clonal complex ST25 between humans and animals should provide new insights into the mode of dissemination of these bacteria, and should help defining strategies for preserving global health.
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Affiliation(s)
- Agnese Lupo
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France.
| | - Benoît Valot
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Marine Robert
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Maxime Bour
- CNR de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Patrick Plésiat
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Anaïs Potron
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
- CNR de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
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Huang Y, Ali MR, Li W, Wang W, Dai Y, Lu H, He Z, Li Y, Sun B. Epidemiological characteristics of multidrug-resistant Acinetobacter baumannii ST369 in Anhui, China. mSystems 2023; 8:e0073123. [PMID: 37655924 PMCID: PMC10654100 DOI: 10.1128/msystems.00731-23] [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: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a major health threat due to its antibiotic resistance and ability to cause nosocomial infections. Epidemiological studies indicated that the majority of globally prevalent ST369 clones originated from China, indicating a significant impact on public health in the country. In this study, we conducted whole-genome sequencing, comparative genomics, and Galleria mellonella infection model on eight A. baumannii ST369 isolates collected from a provincial hospital in China to comprehensively understand the organism. We identified two mutations (G540A and G667D) on the wzc gene that can affect bacterial virulence and viscosity. We confirmed their impact on resistance and virulence. We also investigated the potential involvement of AB46_0125 and AB152_03903 proteins in virulence. This finding provides a theoretical reference for further research on A. baumannii ST369 clinical isolates with similar mutations.
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Affiliation(s)
- Yi Huang
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Md Roushan Ali
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wanying Wang
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Yuanyuan Dai
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Huaiwei Lu
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhien He
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yujie Li
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Migliaccio A, Bray J, Intoccia M, Stabile M, Scala G, Jolley KA, Brisse S, Zarrilli R. Phylogenomics of Acinetobacter species and analysis of antimicrobial resistance genes. Front Microbiol 2023; 14:1264030. [PMID: 37928684 PMCID: PMC10620307 DOI: 10.3389/fmicb.2023.1264030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Non-baumannii Acinetobacter species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 Acinetobacter spp. isolates, which included 798 non-baumannii Acinetobacter genomes, in order to define the concordance of classification and discriminatory power of 7-gene MLST, 53-gene MLST, and single-nucleotide polymorphism (SNPs) phylogenies. Methods Phylogenies were performed on Pasteur Multilocus Sequence Typing (MLST) or ribosomal Multilocus Sequence Typing (rMLST) concatenated alleles, or SNPs extracted from core genome alignment. Results The Pasteur MLST scheme was able to identify and genotype 72 species in the Acinetobacter genus, with classification results concordant with the ribosomal MLST scheme. The discriminatory power and genotyping reliability of the Pasteur MLST scheme were assessed in comparison to genome-wide SNP phylogeny on 535 non-baumannii Acinetobacter genomes assigned to Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter seifertii, and Acinetobacter lactucae (heterotypic synonym of Acinetobacter dijkshoorniae), which were the most clinically relevant non-baumannii species of the A. baumannii group. The Pasteur MLST and SNP phylogenies were congruent at Robinson-Fould and Matching cluster tests and grouped genomes into four and three clusters in A. pittii, respectively, and one each in A. seifertii. Furthermore, A. lactucae genomes were grouped into one cluster within A. pittii genomes. The SNP phylogeny of A. nosocomialis genomes showed a heterogeneous population and did not correspond to the Pasteur MLST phylogeny, which identified two recombinant clusters. The antimicrobial resistance genes belonging to at least three different antimicrobial classes were identified in 91 isolates assigned to 17 distinct species in the Acinetobacter genus. Moreover, the presence of a class D oxacillinase, which is a naturally occurring enzyme in several Acinetobacter species, was found in 503 isolates assigned to 35 Acinetobacter species. Conclusion In conclusion, Pasteur MLST phylogeny of non-baumannii Acinetobacter isolates coupled with in silico detection of antimicrobial resistance makes it important to study the population structure and epidemiology of Acinetobacter spp. isolates.
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Affiliation(s)
| | - James Bray
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Michele Intoccia
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Stabile
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
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Moreno-Manjón J, Castillo-Ramírez S, Jolley KA, Maiden MCJ, Gayosso-Vázquez C, Fernández-Vázquez JL, Mateo-Estrada V, Giono-Cerezo S, Alcántar-Curiel MD. Acinetobacter baumannii IC2 and IC5 Isolates with Co-Existing blaOXA-143-like and blaOXA-72 and Exhibiting Strong Biofilm Formation in a Mexican Hospital. Microorganisms 2023; 11:2316. [PMID: 37764160 PMCID: PMC10536109 DOI: 10.3390/microorganisms11092316] [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: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the blaOXA-143-like family (not previously described in Mexico), the blaOXA-72 and the blaOXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital.
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Affiliation(s)
- Julia Moreno-Manjón
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
- Laboratorio de Bacteriología Médica, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico; (S.C.-R.); (V.M.-E.)
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK; (K.A.J.); (M.C.J.M.)
| | - Martin C. J. Maiden
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK; (K.A.J.); (M.C.J.M.)
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
| | - José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico; (S.C.-R.); (V.M.-E.)
| | - Silvia Giono-Cerezo
- Laboratorio de Bacteriología Médica, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
| | - María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
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27
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Vasconcellos L, Silva SV, da Costa LV, de Miranda RVDSL, Dos Reis CMF, Braga LMPDS, Silva C, Conceição G, Mattoso J, Silva IB, Forsythe SJ, Midlej V, Boas MHSV, Brandão MLL. Phenotypical and molecular characterization of Acinetobacter spp. isolated from a pharmaceutical facility. Lett Appl Microbiol 2023; 76:ovad101. [PMID: 37660241 DOI: 10.1093/lambio/ovad101] [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: 06/26/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Characterizing microorganisms according to different criteria is useful when investigating sources of microbiological contamination in the pharmaceutical industry. The aim of this study was to characterize 38 Acinetobacter baumannii complex strains isolated from a biopharmaceutical industry by 16S rRNA sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS), multilocus sequence typing (MLST), antimicrobial susceptibility profile, biofilm formation, and sensibility to disinfectants. Thirty-three (86.9%) strains were identified by 16S rRNA gene sequencing as A. seifertii/pitti/nosocomialis/lactucae, four (10.5%) as A. baumannii, and one (2.6%) as A. vivianii/courvalini. MALDI-TOF/MS did not identify one strain, and incorrectly identified 30/37 (81.1%) strains as A. baumannii. Strains were assigned to 12 different STs, of which nine were newly defined in this study (STs 2091-2099). Twenty-six (68.4%) strains showed resistance to amikacin and gentamicin. Thirty-three (86.8%) strains were classified as moderately or strongly adherent on polystyrene. Alcohol 70%/15 min and quaternary ammonium 0.08%/20 min were not able to eliminate the biofilm formed, but sodium hypochlorite 0.1%/15 min was efficient. In conclusion, improved methods are needed to improve the identification of Acinetobacter strains in pharmaceutical industries. This organism is of particular concern as it forms recalcitrant biofilms, leading to persistence in the manufacturing environment and increased risk of product contamination.
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Affiliation(s)
- Luiza Vasconcellos
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Samara Verly Silva
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Luciana Veloso da Costa
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Rebeca Vitoria da Silva Lage de Miranda
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | | | | | - Claudiane Silva
- Laboratory of Cellular Ultrastructure, IOC/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Greice Conceição
- Department of Quality Control, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Josiane Mattoso
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Igor Barbosa Silva
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | | | - Victor Midlej
- Laboratory of Cellular Ultrastructure, IOC/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
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Mansouri M, Sadeghpoor M, Abdollahi M, Vafaei AJ, Jalali Nadoushan M, Rasooli I. Synergistic immunoprotection by Oma87 and Bap against Acinetobacter baumannii sepsis model. Int Immunopharmacol 2023; 122:110650. [PMID: 37454632 DOI: 10.1016/j.intimp.2023.110650] [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: 05/20/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Acinetobacter baumannii is the leading cause of nosocomial infection. A surface protein commonly known as biofilm associate protein (Bap) has been identified in a bloodstream isolate of A. baumannii. Bap of A. baumannii is involved in intercellular adhesion within the mature biofilm. Outer membrane protein Acinetobacter 87 kDa (Oma87) or β-barrel assembly machinery A (BamA) has been introduced as an immunogenic outer membrane protein via in silico reverse vaccinology. Current research examines the synergistic effect of immunization of mice with both recombinant proteins viz., Oma87 and Bap. Antibodies were raised to the proteins. The mice were challenged with A. baumannii ATCC 19606 and the bacterial burden was enumerated in the mice's livers, spleens, and lungs followed by histological examination. IgG levels significantly increased, and a significant (p < 0.0001) difference was observed between bacterial burdens in the internal organs of the actively and passively immunized groups. Female BALB/c mice weighing 20-25 g, were divided into 4 groups of 14 mice each viz., control, Oma87, Bap, Oma87-Bap groups. The proteins were individually immunogenic, but the combination of both proteins had a synergistic protection property. This is further supported by the histological examination. Based on the results, the combination of Oma87 and Bap may be considered a promising vaccine candidate against A. baumannii .
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Affiliation(s)
- Mobina Mansouri
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Masoomeh Sadeghpoor
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Marziyeh Abdollahi
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Amir Javad Vafaei
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | | | - Iraj Rasooli
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran; Molecular Microbiology Research Center and Department of Biology, Shahed University, Tehran, Iran.
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Naderi G, Asadian M, Seifi A, Ghourchian S, Talebi M, Rahbar M, Abdollahi A, Douraghi M. Dissemination of the Acinetobacter baumannii isolates belonging to global clone 2 containing AbGRI resistance islands in a referral hospital. Microbiol Spectr 2023; 11:e0537322. [PMID: 37638730 PMCID: PMC10581056 DOI: 10.1128/spectrum.05373-22] [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: 01/05/2023] [Accepted: 05/16/2023] [Indexed: 08/29/2023] Open
Abstract
Acinetobacter baumannii strains belonging to global clone 2 (GC2) contain resistance islands (AbGRIs), which are composed of genes conferring resistance to older and newer antibiotics. Here, to locate these genes in AbGRIs, the GC2 strains from Tehran, Iran were examined. Among the 170 A. baumannii, 90 isolates were identified as GC2. Of the genes that confer resistance to older antibiotics, tetA(B), tetR(B) (tetracyclines), strA, and strB (aminoglycosides) were located in AbGRI1 of 65 GC2 isolates (72.2%). Of the other aminoglycosides, the aphA1b was located in AbGRI2-12b (63.6%), AbGRI2-12a (21.2%), or AbGRI2-1 (15.1%). The aacC1 and aadA1 genes were co-located within AbGRI2-1 (5.5%). The armA was located in AbGRI3-4 (77.7%) and AbGRI3ABI221 (22.2%). Of sulfonamides, the sul1 was located within AbGRI2-1 (5.5%). Of beta-lactams, the blaTEM was located in AbGRI2-12b (42%), AbGRI2-12a (14%), AbGRI2-1 (10%), or AbGRI2ABI257 (34%). The oxa23 gene conferring resistance to newer antibiotics (carbapenems) was located in AbaR4 (81.1%); of them, the AbaR4 was located within AbGRI1 in 45.2% of the isolates. This study showed that the GC2 isolates, which contained at least one AbGRI, disseminate in the hospital. Hence, it is likely that the AbGRIs play a significant role in conferring resistance to older and newer antibiotics in GC2 isolates from Iran. IMPORTANCE The majority of Acinetobacter baumannii isolates that are resistant to multiple antibiotics belong to one of the two major global clones, namely global clone 1 (GC1) and global clone 2 (GC2). The resistance islands, which contain variable assortments of transposons, integrons, and specific resistance genes, have been characterized in the genome of these GCs. In GC2 A. baumannii, the chromosomally located A. baumannii genomic resistance islands (AbGRIs) carry the genes conferring resistance to older and newer antibiotics. In this context, we tested whether GC2 isolates collected from a referral hospital carry the AbGRIs containing these genes. This study provided evidence for the circulation of the GC2 A. baumannii strains harboring AbGRI resistance islands between different wards of a referral hospital.
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Affiliation(s)
- Ghazal Naderi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahla Asadian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Seifi
- Department of Infectious Diseases, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sedigheh Ghourchian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Iranian Reference Health Laboratory Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Shelenkov A, Akimkin V, Mikhaylova Y. International Clones of High Risk of Acinetobacter Baumannii-Definitions, History, Properties and Perspectives. Microorganisms 2023; 11:2115. [PMID: 37630675 PMCID: PMC10459012 DOI: 10.3390/microorganisms11082115] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named 'international clones of high risk' (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
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Sheck E, Romanov A, Shapovalova V, Shaidullina E, Martinovich A, Ivanchik N, Mikotina A, Skleenova E, Oloviannikov V, Azizov I, Vityazeva V, Lavrinenko A, Kozlov R, Edelstein M. Acinetobacter Non- baumannii Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1301. [PMID: 37627721 PMCID: PMC10451542 DOI: 10.3390/antibiotics12081301] [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: 07/17/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Acinetobacter species other than A. baumannii are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates. METHODS Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016-2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific blaOXA-51-like gene was used as a means of differentiating A. baumannii from Anb species, and the partial sequencing of the rpoB gene was used as a reference method for Anb species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim-sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in Acinetobacter-acquired carbapenemase genes (blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like, blaNDM, blaIMP, and blaVIM) was assessed using real-time PCR. RESULTS In total, 234 isolates were identified as belonging to 14 Anb species. These comprised 6.2% of Acinetobacter spp. and 0.7% of all bacterial isolates from the observations. Among the Anb species, the most abundant were A. pittii (42.7%), A. nosocomialis (13.7%), the A. calcoaceticus/oleivorans group (9.0%), A. bereziniae (7.7%), and A. geminorum (6.0%). Notably, two environmental species, A. oleivorans and A. courvalinii, were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in Anb species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of A. bereziniae, A. johnsonii, A. nosocomialis, A. oleivorans, A. pittii, and A. ursingii were resistant to carbapenems. A. bereziniae was more frequently resistant to sulbactam, aminoglycosides, trimethoprim-sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of A. bereziniae, A. johnsonii, A. pittii were found to carry carbapenemase genes (blaOXA-58-like and blaNDM, either alone or in combination). The overall accuracy rates of the species-level identification of Anb isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively. CONCLUSIONS This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical Anb isolates.
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Affiliation(s)
- Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Andrey Romanov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Valeria Shapovalova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elvira Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Alexey Martinovich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Natali Ivanchik
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Anna Mikotina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elena Skleenova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vladimir Oloviannikov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vera Vityazeva
- Republican Children’s Hospital, 185000 Petrozavodsk, Republic of Karelia, Russia
| | - Alyona Lavrinenko
- Shared Resource Laboratory, Karaganda Medical University, 100008 Karaganda, Kazakhstan
| | - Roman Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Mikhail Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
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Artuso I, Poddar H, Evans BA, Visca P. Genomics of Acinetobacter baumannii iron uptake. Microb Genom 2023; 9:mgen001080. [PMID: 37549061 PMCID: PMC10483418 DOI: 10.1099/mgen.0.001080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Iron is essential for growth in most bacteria due to its redox activity and its role in essential metabolic reactions; it is a cofactor for many bacterial enzymes. The bacterium Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen. A. baumannii responds to low iron availability imposed by the host through the exploitation of multiple iron-acquisition strategies, which are likely to deliver iron to the cell under a variety of environmental conditions, including human and animal infection. To date, six different gene clusters for active iron uptake have been described in A. baumannii , encoding protein systems involved in (i) ferrous iron uptake (feo ); (ii) haem uptake (hemT and hemO ); and (iii) synthesis and transport of the baumannoferrin(s) (bfn ), acinetobactin (bas /bau ) and fimsbactin(s) (fbs ) siderophores. Here we describe the structure, distribution and phylogeny of iron-uptake gene clusters among >1000 genotypically diverse A. baumannii isolates, showing that feo , hemT , bfn and bas /bau clusters are very prevalent across the dataset, whereas the additional haem-uptake system hemO is only present in a portion of the dataset and the fbs gene cluster is very rare. Since the expression of multiple iron-uptake clusters can be linked to virulence, the presence of the additional haem-uptake system hemO may have contributed to the success of some A. baumannii clones.
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Affiliation(s)
- Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Harsh Poddar
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Benjamin A. Evans
- Norwich Medical School, University of East Anglia, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
- Fondazione Santa Lucia IRCCS, Via Ardeatina, 306/354, 00179 Rome, Italy
- National Biodiversity Future Centre, Palermo 90133, Italy
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Dong X, Yang Y. Acinetobacter entericus sp. nov., isolated from the gut of plastic-eating insect larvae Zophobas atratus. Int J Syst Evol Microbiol 2023; 73. [PMID: 37609852 DOI: 10.1099/ijsem.0.006006] [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: 08/24/2023] Open
Abstract
A Gram-negative, non-motile and rod-shaped strain, BIT-DXN8T, was isolated from the gut of plastic-eating insect larvae Zophobas atratus. The taxonomic position of this new isolate was examined by using a polyphasic approach. A preliminary analysis based on the 16S rRNA gene sequence (1411 bp) indicated that the most similar strain to BIT-DXN8T was Acinetobacter bouvetii DSM 14964T (98.5%), followed by Acinetobacter haemolyticus CIP 64.3T (98.2%) and Acinetobacter pullicarnis S23T (98.2%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (fusA, gyrB, recA, rplB and rpoB) and genome sequences, placed strain BIT-DXN8T in a separate lineage among the genus Acinetobacter of the family Moraxellaceae. The average nucleotide identity and digital DNA-DNA hybridization values of the strain when compared to all other species within the genus Acinetobacter were below 96 and 70 %, respectively. The physiological and biochemical tests confirm the affiliation of strain BIT-DXN8T to the present species within the genus Acinetobacter, but with some specific phenotypic differences. Therefore, strain BIT-DXN8T is considered to represent a novel species, for which the name Acinetobacter entericus sp. nov. is proposed. The type strain is BIT-DXN8T (=CCTCC AB 2022117T=KCTC 92696T).
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Affiliation(s)
- Xuena Dong
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yu Yang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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Longjam LA, Tsering DC, Das D. Molecular Characterization of Class A-ESBLs, Class B-MBLs, Class C-AmpC, and Class D-OXA Carbapenemases in MDR Acinetobacter baumannii Clinical Isolates in a Tertiary Care Hospital, West Bengal, India. Cureus 2023; 15:e43656. [PMID: 37600436 PMCID: PMC10435264 DOI: 10.7759/cureus.43656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 08/22/2023] Open
Abstract
Background Acinetobacter calcoaceticus baumannii (ACB) complex has become a major concern nowadays because of its increasing involvement in several severe infections associated with catheter-related bloodstream and urinary tract infections, ventilator-associated pneumonia, cerebrospinal shunt-related meningitis, and wound infections. Multiple drug-resistant (MDR) ACB cases have been described with an increasing trend where at least it is resistant to a minimum of three antimicrobial groups. The mortality rate associated with A. baumannii is significantly higher than all Acinetobacter spp. isolates with the most prevalence seen in India and Thailand. The rapid spread of high resistance to most potent antimicrobial drugs is due to its ability to incorporate resistance determinants despite multifactorial reasons such as alteration in permeability of cell membrane by either losing expression of outer membrane porins or excess production of efflux pumps. This study aims to characterize resistance determinants responsible for MDR at the genetic level and emphasizes the use of genotyping in routine diagnosis as genotype analysis is reliable and valid. Methodology A total of 289 ACB complex clinical isolates were included in this study. The study for species-level identification of A. baumannii was conducted at the Department of Microbiology, IQ City Medical College Hospital, Durgapur, West Bengal. In addition, the detection of encoded genes associated with class A-extended spectrum beta-lactamases (i.e., CTX-M, KPC, SHV, and TEM genes), class B-metallo-β-lactamases (i.e., IMP, NDM, and VIM genes), Class C-AmpC cephalosporinase, and classD-OXA carbapenemases (i.e., blaOXA-10/11, blaOXA-24, blaOXA-48, blaOXA-58, blaOXA-143, and blaOXA-235 was done using real-time polymerase chain reaction. Results All 289 non-repetitive ACB complex clinical isolates were confirmed as A. baumannii, of which 277 (96%) isolates were MDR. There were no findings of blaCTX-M, blaKPC, blaSHV, blaTEM, blaIMP, blaVIM, blaAmpC, blaOXA-10/11, blaOXA-24, blaOXA-48, blaOXA-58, blaOXA-143, and blaOXA-235 genes in our study. However, there were four (1.44%) positive findings of the blaNDM gene. All MDR isolates (n = 277) were positive for the blaOXA-51 gene. In addition, blaOXA-23 was positive in 269 (97.12%) isolates. Conclusions The oxacillinase production corresponding to blaOXA-23 and blaOXA-51 were the most prevalent antibiotic resistance determinants among MDR A. baumannii in our study. Four (1.44%) isolates had the multiple genes blaOXA-51, blaOXA-23, and blaNDM that shows the coexistence of diverse genetic elements involved in MDR A. baumannii, resulting in total resistance except for a few potent drugs such as colistin and tigecycline. Genotyping is helpful in determining the contribution of the isolates in understanding their association with encoded genes, which, in turn, helps in designing effective surveillance and control strategies in the management of such MDR isolates.
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Affiliation(s)
- Langamba A Longjam
- Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok, IND
| | - Dechen C Tsering
- Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok, IND
| | - Dipmala Das
- Microbiology, IQ City Medical College and Hospital, Durgapur, IND
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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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Findlay J, Nordmann P, Bouvier M, Kerbol A, Poirel L. Dissemination of ArmA- and OXA-23-co-producing Acinetobacter baumannii Global Clone 2 in Switzerland, 2020-2021. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04643-4. [PMID: 37470894 DOI: 10.1007/s10096-023-04643-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Following the observation of an increased number of isolation of OXA-23- and ArmA-producing Acinetobacter baumannii at the national level, our aim was to evaluate whether some given clone(s) might actually be spreading and/or emerging in Switzerland. To evaluate this possibility, our study investigated and characterized all A. baumannii isolates harboring both the blaOXA-23 and armA genes that had been collected at the Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) from 2020 to 2021. Most isolates were obtained from infections rather than colonization with the majority being obtained from respiratory specimens. Pulsed-field gel electrophoresis (PFGE) analysis of 56 isolates identified nine profiles. Then, whole-genome sequencing that was performed on a subset of 11 isolates including at least one representative isolate of each PFGE profile identified three STs; one each of ST25 and ST1902, and nine ST2 (a member of Global Clone 2 (GC-2). The blaOXA-23 gene was always found embedded within Tn2006 structures, as commonly described with GC-2 (ST2) isolates. Susceptibility testing showed that most of those isolates, despite being highly resistant to all carbapenems and all aminoglycosides, remained susceptible to colistin (94.6%), sulbactam-durlobactam (87.5%), and cefiderocol (83.9% or 91.1% according to EUCAST or CLSI breakpoints, respectively). Overall, this study identified that the A. baumannii co-producing OXA-23 and ArmA are increasing in incidence in Switzerland, largely due to the dissemination of the high-risk GC-2. This highlights the importance of the monitoring of such MDR A. baumannii strains, in order to contribute to reduce their potential further spread.
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Affiliation(s)
- Jacqueline Findlay
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Maxime Bouvier
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Auriane Kerbol
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland.
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland.
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Hamed SM, Elkhatib WF, Brangsch H, Gesraha AS, Moustafa S, Khater DF, Pletz MW, Sprague LD, Neubauer H, Wareth G. Acinetobacter baumannii Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt. Antibiotics (Basel) 2023; 12:1149. [PMID: 37508245 PMCID: PMC10376554 DOI: 10.3390/antibiotics12071149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 A. baumannii clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of blaOXA-51-like genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (STOxf 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, blaOXA-23 was carried by most of the isolates (69.6%), followed by ISAba1-amplified blaADC (56.5%), blaNDM-1 and blaGES-11 (21.7% each), and blaGES-35 (2.2%) genes. A significant correlation was found between carbapenem resistance and carO mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both blaOXA-23- and blaGES-11. Amikacin resistance was most probably mediated by armA, aac(6')-Ib9, and aph(3')-VI, most commonly coexisting in GC2 isolates. No mutations were found in pmrABC or lpxACD operons in the colistin-resistant isolates. Tigecycline resistance was associated with adeS (N268Y) and baeS (A436T) mutations. While the lineage-specific distribution of some genes (e.g., blaADC and blaOXA-51-like alleles) was evident, some resistance genes, such as blaOXA-23 and sul1, were found in all GCs. The data generated here highlight the contribution of five GCs in A. baumannii infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene blaOXA-23 in isolates encompassing all GCs.
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Affiliation(s)
- Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Walid F Elkhatib
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Cairo 11566, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, Suez 43727, Egypt
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Ahmed S Gesraha
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta 31511, Egypt
| | - Shawky Moustafa
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Dalia F Khater
- Tanta Laboratory, Animal Health Research Institute, Agricultural Research Center, Tanta 31511, Egypt
| | - Mathias W Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany
| | - Lisa D Sprague
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany
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Iruegas R, Pfefferle K, Göttig S, Averhoff B, Ebersberger I. Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii. PLoS Genet 2023; 19:e1010646. [PMID: 37498819 PMCID: PMC10374093 DOI: 10.1371/journal.pgen.1010646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/06/2023] [Indexed: 07/29/2023] Open
Abstract
The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes coinciding with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein feature architectures. Using type IVa pili (T4aP) as an example, we show that three pilus components, among them the pilus tip adhesin ComC, vary in their Pfam domain annotation within the genus Acinetobacter. In most pathogenic Acinetobacter isolates, ComC displays a von Willebrand Factor type A domain harboring a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. All three genes are part of an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise functions have been adjusted by modifying individual components on the domain level.
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Affiliation(s)
- Ruben Iruegas
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Katharina Pfefferle
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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Sykes EME, Mateo-Estrada V, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Khan IIU, Castillo-Ramírez S, Kumar A. Emergence of ADC-5 Cephalosporinase in environmental Acinetobacter baumannii from a German tank milk with a novel Sequence Type. Access Microbiol 2023; 5:acmi000485.v3. [PMID: 37424542 PMCID: PMC10323797 DOI: 10.1099/acmi.0.000485.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Bacteria resistant to antibiotics arguably pose the greatest threat to human health in the twenty-first century. One such bacterium that typifies antibiotic resistance is Acinetobacter baumannii . Frequently, hospital strains of A. baumannii display multidrug resistant (MDR) or extensively drug resistant (XDR) phenotypes, often requiring the use of last resort antibiotics for treatment. In addition to hospital settings, A. baumannii has been isolated from many highly divergent sources including wastewater treatment plant effluent, soil, and agricultural run-off with global distribution. However, such isolates remain poorly characterized. In this study, we characterized a strain of A. baumannii, AB341-IK15, isolated from bulk tank milk in Germany that demonstrated resistance to ceftazidime and intermediate resistance to ceftriaxone and piperacillin/tazobactam. Further genetic characterization identified an ADC-5 cephalosporinase, first incidence in an environmental isolate; and an OXA-408 oxacillinase that may contribute to this phenotype. Interestingly, AB341-IK15 is of a novel sequence type. This research underscores the importance of studying isolates of A. baumannii of non-clinical origin to understand the antibiotic resistance and virulence potential of environmental isolates of A. baumannii as well to understand the diversity of this species.
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Affiliation(s)
- Ellen M. E. Sykes
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ömer Akineden
- Institute of Veterinary Food Science, University of Giessen, Giessen, Germany
| | - Izhar I. U. Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, Canada
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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Odih EE, Oaikhena AO, Underwood A, Hounmanou YMG, Oduyebo OO, Fadeyi A, Aboderin AO, Ogunleye VO, Argimón S, Akpunonu VN, Oshun PO, Egwuenu A, Okwor TJ, Ihekweazu C, Aanensen DM, Dalsgaard A, Okeke IN. High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020. mSphere 2023; 8:e0009823. [PMID: 37067411 PMCID: PMC10286719 DOI: 10.1128/msphere.00098-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Phillip O. Oshun
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | | | - David M. Aanensen
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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Busby EJ, Doyle RM, Leboreiro Babe C, Harris KA, Mack D, Méndez-Cervantes G, O’Sullivan DM, Pang V, Sadouki Z, Solanki P, Huggett JF, McHugh TD, Wey EQ. Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods. Microbiol Spectr 2023; 11:e0499522. [PMID: 37154773 PMCID: PMC10269802 DOI: 10.1128/spectrum.04995-22] [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: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).
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Affiliation(s)
- Eloise J. Busby
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
| | - Ronan M. Doyle
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Clara Leboreiro Babe
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Kathryn A. Harris
- Virology Department, ESEL Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Damien Mack
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Vicky Pang
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Zahra Sadouki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Priya Solanki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, United Kingdom
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Emmanuel Q. Wey
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
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Tiseo G, Giordano C, Leonildi A, Riccardi N, Galfo V, Limongi F, Nicastro M, Barnini S, Falcone M. Salvage therapy with sulbactam/durlobactam against cefiderocol-resistant Acinetobacter baumannii in a critically ill burn patient: clinical challenges and molecular characterization. JAC Antimicrob Resist 2023; 5:dlad078. [PMID: 37325251 PMCID: PMC10265591 DOI: 10.1093/jacamr/dlad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are associated with high mortality rates. The optimal treatment regimen for CRAB has not been defined. Cefiderocol has been recently introduced in the armamentarium against CRAB but there is concern about treatment-emergent resistance. Since mortality rates in CRAB infections remain high, further antibiotic options are needed. Methods We report a case of severe infection by CRAB resistant to both colistin and cefiderocol treated with sulbactam/durlobactam and describe the molecular features of the strain. Susceptibility to cefiderocol was detected by disc diffusion according to EUCAST breakpoints. Susceptibility to sulbactam/durlobactam was determined by Etest according to preliminary breakpoints provided by Entasis Therapeutics. Whole Genome Sequencing (WGS) of the CRAB isolate was performed. Results A burn patient with ventilator-associated pneumonia by CRAB resistant to colistin and cefiderocol received sulbactam/durlobactam as compassionate use. She was alive after 30 days from the end of therapy. Complete microbiological eradication of CRAB was achieved. The isolate harboured blaADC-30, blaOXA-23 and blaOXA-66. A missense mutation in PBP3 was detected. The isolate harboured a mutation in the TonB-dependent siderophore receptor gene piuA that showed a frameshift mutation causing a premature stop codon (K384fs). Moreover, the fepA gene, which is orthologous to pirA, was interrupted by a transposon insertion P635-ISAba125 (IS30 family). Conclusions Further treatment options for severe infections by CRAB resistant to all available antibiotics are urgently needed. Sulbactam/durlobactam may be a future option against MDR A. baumannii.
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Affiliation(s)
- Giusy Tiseo
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Cesira Giordano
- Microbiology Unit, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | | | - Niccolò Riccardi
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Valentina Galfo
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Federica Limongi
- Department of Anaesthesia and Critical Care Medicine, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - Manuela Nicastro
- Department of Anaesthesia and Critical Care Medicine, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - Simona Barnini
- Microbiology Unit, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
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Bala A, Uhlin BE, Karah N. Insights into the genetic contexts of sulfonamide resistance among early clinical isolates of Acinetobacter baumannii. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 112:105444. [PMID: 37210019 DOI: 10.1016/j.meegid.2023.105444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Since the late 1930s, resistance to sulfonamides has been accumulating across bacterial species including Acinetobacter baumannii, an opportunistic pathogen increasingly implicated the spread of antimicrobial resistance worldwide. Our study aimed to explore events involved in the acquisition of sulfonamide resistance genes, particularly sul2, among the earliest available isolates of A. baumannii. The study utilized the genomic data of 19 strains of A. baumannii isolated before 1985. The whole genomes of 5 clinical isolates obtained from the Culture Collection University of Göteborg (CCUG), Sweden, were sequenced using the Illumina MiSeq system. Acquired resistance genes, insertion sequence elements and plasmids were detected using ResFinder, ISfinder and Plasmidseeker, respectively, while sequence types (STs) were assigned using the PubMLST Pasteur scheme. BLASTn was used to verify the occurrence of sul genes and to map their genetic surroundings. The sul1 and sul2 genes were detected in 4 and 9 isolates, respectively. Interestingly, sul2 appeared thirty years earlier than sul1. The sul2 gene was first located in the genomic island GIsul2 located on a plasmid, hereafter called NCTC7364p. With the emergence of international clone 1, the genetic context of sul2 evolved toward transposon Tn6172, which was also plasmid-mediated. Sulfonamide resistance in A. baumannii was efficiently acquired and transferred vertically, e.g., among the ST52 and ST1 isolates, as well as horizontally among non-related strains by means of a few efficient transposons and plasmids. Timely acquisition of the sul genes has probably contributed to the survival skill of A. baumannii under the high antimicrobial stress of hospital settings.
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Affiliation(s)
- Anju Bala
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden.
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Nabil Karah
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden.
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Álvarez VE, Quiroga MP, Centrón D. Identification of a Specific Biomarker of Acinetobacter baumannii Global Clone 1 by Machine Learning and PCR Related to Metabolic Fitness of ESKAPE Pathogens. mSystems 2023:e0073422. [PMID: 37184409 DOI: 10.1128/msystems.00734-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Since the emergence of high-risk clones worldwide, constant investigations have been undertaken to comprehend the molecular basis that led to their prevalent dissemination in nosocomial settings over time. So far, the complex and multifactorial genetic traits of this type of epidemic clones have allowed only the identification of biomarkers with low specificity. A machine learning algorithm was able to recognize unequivocally a biomarker for early and accurate detection of Acinetobacter baumannii global clone 1 (GC1), one of the most disseminated high-risk clones. A support vector machine model identified the U1 sequence with a length of 367 nucleotides that matched a fragment of the moaCB gene, which encodes the molybdenum cofactor biosynthesis C and B proteins. U1 differentiates specifically between A. baumannii GC1 and non-GC1 strains, becoming a suitable biomarker capable of being translated into clinical settings as a molecular typing method for early diagnosis based on PCR as shown here. Since the metabolic pathways of Mo enzymes have been recognized as putative therapeutic targets for ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens, our findings highlight that machine learning can also be useful in knowledge gaps of high-risk clones and provides noteworthy support to the literature to identify relevant nosocomial biomarkers for other multidrug-resistant high-risk clones. IMPORTANCE A. baumannii GC1 is an important high-risk clone that rapidly develops extreme drug resistance in the nosocomial niche. Furthermore, several strains have been identified worldwide in environmental samples, exacerbating the risk of human interactions. Early diagnosis is mandatory to limit its dissemination and to outline appropriate antibiotic stewardship schedules. A region with a length of 367 bp (U1) within the moaCB gene that is not subjected to lateral genetic transfer or to antibiotic pressures was successfully found by a support vector machine model that predicts A. baumannii GC1 strains. At the same time, research on the group of Mo enzymes proposed this metabolic pathway related to the superbug's metabolism as a potential future drug target site for ESKAPE pathogens due to its central role in bacterial fitness during infection. These findings confirm that machine learning used for the identification of biomarkers of high-risk lineages can also serve to identify putative novel therapeutic target sites.
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Affiliation(s)
- Verónica Elizabeth Álvarez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), 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), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), 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), Ciudad Autónoma de Buenos Aires, Argentina
- Nodo de Bioinformática. Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), 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), Ciudad Autónoma de Buenos Aires, Argentina
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Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
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Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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47
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Muzahid NH, Hussain MH, Huët MAL, Dwiyanto J, Su TT, Reidpath D, Mustapha F, Ayub Q, Tan HS, Rahman S. Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia. Microb Genom 2023; 9. [PMID: 37018035 PMCID: PMC10210948 DOI: 10.1099/mgen.0.000977] [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: 04/06/2023] Open
Abstract
Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections around the world. However, little is known about the persistence and dynamics of A. baumannii in a healthy community. This study investigated the role of the community as a prospective reservoir for A. baumannii and explored possible links between hospital and community isolates. A total of 12 independent A. baumannii strains were isolated from human faecal samples from the community in Segamat, Malaysia, in 2018 and 2019. Another 15 were obtained in 2020 from patients at the co-located tertiary public hospital. The antimicrobial resistance profile and biofilm formation ability were analysed, and the relatedness of community and hospital isolates was determined using whole-genome sequencing (WGS). Antibiotic profile analysis revealed that 12 out of 15 hospital isolates were MDR, but none of the community isolates were MDR. However, phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) and a pangenome analysis of core genes showed clustering between four community and two hospital strains. Such clustering of strains from two different settings based on their genomes suggests that these strains could persist in both. WGS revealed 41 potential resistance genes on average in the hospital strains, but fewer (n=32) were detected in the community strains. In contrast, 68 virulence genes were commonly seen in strains from both sources. This study highlights the possible transmission threat to public health posed by virulent A. baumannii present in the gut of asymptomatic individuals in the community.
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Affiliation(s)
- Nazmul Hasan Muzahid
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Md Hamed Hussain
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | - Jacky Dwiyanto
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Tin Tin Su
- South East Asia Community Observatory (SEACO) and Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Daniel Reidpath
- South East Asia Community Observatory (SEACO) and Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Faizah Mustapha
- Department of Pathology, Hospital Segamat, Jalan Genuang, Bandar Putra, 85000, Segamat, Johor, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
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48
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Strateva TV, Sirakov I, Stoeva TJ, Stratev A, Peykov S. Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients. Microorganisms 2023; 11:microorganisms11040875. [PMID: 37110301 PMCID: PMC10141887 DOI: 10.3390/microorganisms11040875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is designated as an urgent public health threat, both due to its remarkable multidrug resistance and propensity for clonal spread. This study aimed to explore the phenotypic and molecular characteristics of antimicrobial resistance in CRAB isolates (n = 73) from intensive care unit (ICU) patients in two university hospitals in Bulgaria (2018–2019). The methodology included antimicrobial susceptibility testing, PCR, whole-genome sequencing (WGS), and phylogenomic analysis. The resistance rates were as follows: imipenem, 100%; meropenem, 100%; amikacin, 98.6%; gentamicin, 89%; tobramycin, 86.3%; levofloxacin, 100%; trimethoprim–sulfamethoxazole, 75.3%; tigecycline, 86.3%; colistin, 0%; and ampicillin–sulbactam, 13.7%. All isolates harbored blaOXA-51-like genes. The frequencies of distribution of other antimicrobial resistance genes (ARGs) were: blaOXA-23-like, 98.6%; blaOXA-24/40-like, 2.7%; armA, 86.3%; and sul1, 75.3%. The WGS of selected extensively drug-resistant A. baumannii (XDR-AB) isolates (n = 3) revealed the presence of OXA-23 and OXA-66 carbapenem-hydrolyzing class D β-lactamases in all isolates, and OXA-72 carbapenemase in one of them. Various insertion sequencies, such as ISAba24, ISAba31, ISAba125, ISVsa3, IS17, and IS6100, were also detected, providing increased ability for horizontal transfer of ARGs. The isolates belonged to the widespread high-risk sequence types ST2 (n = 2) and ST636 (n = 1) (Pasteur scheme). Our results show the presence of XDR-AB isolates, carrying a variety of ARGs, in Bulgarian ICU settings, which highlights the crucial need for nationwide surveillance, especially in the conditions of extensive antibiotic usage during COVID-19.
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Mangioni D, Fox V, Chatenoud L, Bolis M, Bottino N, Cariani L, Gentiloni Silverj F, Matinato C, Monti G, Muscatello A, Teri A, Terranova L, Piatti A, Gori A, Grasselli G, Stocchetti N, Alteri C, Bandera A. Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (CRAB) in Mechanically Ventilated COVID-19 Patients and Impact of Infection Control Measures on Reducing CRAB Circulation during the Second Wave of the SARS-CoV-2 Pandemic in Milan, Italy. Microbiol Spectr 2023; 11:e0020923. [PMID: 36976013 PMCID: PMC10100775 DOI: 10.1128/spectrum.00209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
COVID-19 has significantly affected hospital infection prevention and control (IPC) practices, especially in intensive care units (ICUs). This frequently caused dissemination of multidrug-resistant organisms (MDROs), including carbapenem-resistant Acinetobacter baumannii (CRAB). Here, we report the management of a CRAB outbreak in a large ICU COVID-19 hub Hospital in Italy, together with retrospective genotypic analysis by whole-genome sequencing (WGS). Bacterial strains obtained from severe COVID-19 mechanically ventilated patients diagnosed with CRAB infection or colonization between October 2020 and May 2021 were analyzed by WGS to assess antimicrobial resistance and virulence genes, along with mobile genetic elements. Phylogenetic analysis in combination with epidemiological data was used to identify putative transmission chains. CRAB infections and colonization were diagnosed in 14/40 (35%) and 26/40 (65%) cases, respectively, with isolation within 48 h from admission in 7 cases (17.5%). All CRAB strains belonged to Pasteur sequence type 2 (ST2) and 5 different Oxford STs and presented blaOXA-23 gene-carrying Tn2006 transposons. Phylogenetic analysis revealed the existence of four transmission chains inside and among ICUs, circulating mainly between November and January 2021. A tailored IPC strategy was composed of a 5-point bundle, including ICU modules' temporary conversion to CRAB-ICUs and dynamic reopening, with limited impact on ICU admission rate. After its implementation, no CRAB transmission chains were detected. Our study underlies the potentiality of integrating classical epidemiological studies with genomic investigation to identify transmission routes during outbreaks, which could represent a valuable tool to ensure IPC strategies and prevent the spread of MDROs. IMPORTANCE Infection prevention and control (IPC) practices are of paramount importance for preventing the spread of multidrug-resistant organisms (MDROs) in hospitals, especially in the intensive care unit (ICU). Whole-genome sequencing (WGS) is seen as a promising tool for IPC, but its employment is currently still limited. COVID-19 pandemics have posed dramatic challenges in IPC practices, causing worldwide several outbreaks of MDROs, including carbapenem-resistant Acinetobacter baumannii (CRAB). We present the management of a CRAB outbreak in a large ICU COVID-19 hub hospital in Italy using a tailored IPC strategy that allowed us to contain CRAB transmission while preventing ICU closure during a critical pandemic period. The analysis of clinical and epidemiological data coupled with retrospective genotypic analysis by WGS identified different putative transmission chains and confirmed the effectiveness of the IPC strategy implemented. This could be a promising approach for future IPC strategies.
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Affiliation(s)
- Davide Mangioni
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Valeria Fox
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Matteo Bolis
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Nicola Bottino
- Department of Anaesthesia, Critical Care and Emergency, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Lisa Cariani
- Microbiology Laboratory, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | - Caterina Matinato
- Microbiology Laboratory, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Gianpaola Monti
- Department of Anesthesia and Intensive Care, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Antonio Teri
- Microbiology Laboratory, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Leonardo Terranova
- Department of Internal Medicine, Respiratory Unit and Adult Cystic Fibrosis Center, Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Piatti
- Medical Direction, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Giacomo Grasselli
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
- Department of Anaesthesia, Critical Care and Emergency, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Nino Stocchetti
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
- Department of Anaesthesia and Critical Care, Neuroscience Intensive Care Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
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50
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Healthcare-Associated Bloodstream Infections Due to Multidrug-Resistant Acinetobacter baumannii in COVID-19 Intensive Care Unit: A Single-Center Retrospective Study. Microorganisms 2023; 11:microorganisms11030774. [PMID: 36985347 PMCID: PMC10056625 DOI: 10.3390/microorganisms11030774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Healthcare-associated infections are an emerging cause of morbidity and mortality in COVID-19 intensive care units (ICUs) worldwide, especially those caused by multidrug-resistant (MDR) pathogens. The objectives of this study were to assess the incidence of bloodstream infections (BSIs) among critically ill COVID-19 patients and to analyze the characteristics of healthcare-associated BSIs due to MDR Acinetobacter baumannii in an COVID-19 ICU. A single-center retrospective study was conducted at a tertiary hospital during a 5-month period. The detection of carbapenemase genes was performed by PCR and genetic relatedness by pulsed-field gel electrophoresis (PFGE) and multilocus-sequence typing. A total of 193 episodes were registered in 176 COVID-19 ICU patients, with an incidence of 25/1000 patient-days at risk. A. baumannii was the most common etiological agent (40.3%), with a resistance to carbapenems of 100%. The blaOXA-23 gene was detected in ST2 isolates while the blaOXA-24 was ST636-specific. PFGE revealed a homogeneous genetic background of the isolates. The clonal spread of OXA-23-positive A. baumannii is responsible for the high prevalence of MDR A. baumannii BSIs in our COVID-19 ICU. Further surveillance of resistance trends and mechanisms is needed along with changes in behavior to improve the implementation of infection control and the rational use of antibiotics.
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