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Tagueha AD, D’Agostini C, Scribano D, Fiorilla C, Limongi D, Fillo S, Corrent L, Lipari M, Lista F, Nencioni L, Palamara AT, Ambrosi C. A decade of genomic and phenotypic adaptation of carbapenem-resistant Acinetobacter baumannii. Front Cell Infect Microbiol 2025; 15:1527488. [PMID: 40370403 PMCID: PMC12075148 DOI: 10.3389/fcimb.2025.1527488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 04/08/2025] [Indexed: 05/16/2025] Open
Abstract
Introduction Acinetobacter baumannii exhibits high genomic plasticity, enabling it to acquire virulence factors and antibiotic resistance (AR). Understanding its evolutionary adaptations is crucial for developing effective therapeutic strategies. Methods Thirty clinical isolates collected from two distinct time periods, defined as older (2010-2013), and recent (2022-2023),- were compared phenotypically (antibiotic resistance, growth, biofilm formation, desiccation tolerance, invasiveness) and genotypically (whole-genome sequencing). Results All isolates displayed an extensively drug-resistant phenotype. Overall, respiratory isolates harbored a higher content of antibiotic-resistant genes (ARGs), with older isolates showing 12.5% increases in the average number of ARGs compared to recent urine isolates (P = 0.02). More than 50% of the strains with faster growth, stronger biofilm formation, and increased lung cell invasiveness were recent respiratory isolates, while over 70% of older isolates showed greater desiccation tolerance and bladder cell invasiveness. Eleven virulence factor genes were shared between old and recent respiratory isolates, and eight were common between recent urinary and respiratory strains with no overlap among urinary isolates. Statistically significant positive correlations were observed between fast-growing and strong biofilm-forming respiratory isolates as well as their lung cell invasiveness. Conversely, negative correlations were found between collection time, isolation site, and host cell invasiveness. Analysis of macrocolony types revealed no link to phenotypic behavior. Conclusion Significant genetic variability was found between past and recent isolates. Older isolates had more genes involved in adhesion and nutrient uptake, while recent respiratory strains demonstrated increased biofilm formation and invasiveness, reflecting adaptation to clinical pressures. These findings highlight the dynamic evolution of A. baumannii, providing insights for future therapeutic strategies and infection control.
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Affiliation(s)
- Astri D. Tagueha
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Cartesio D’Agostini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- Laboratory of Clinical Microbiology, Policlinico Tor Vergata, Rome, Italy
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carlotta Fiorilla
- Laboratory of Clinical Microbiology, Policlinico Tor Vergata, Rome, Italy
| | - Dolores Limongi
- Department of Promotion of Human Sciences and Quality of Life, San Raffaele Open University, Rome, Italy
- Laboratory of Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Roma, Rome, Italy
| | - Silvia Fillo
- Scientific Department, Army Medical Center, Defense Institute for Biomedical Sciences, Rome, Italy
| | - Luca Corrent
- Scientific Department, Army Medical Center, Defense Institute for Biomedical Sciences, Rome, Italy
| | - Martina Lipari
- Scientific Department, Army Medical Center, Defense Institute for Biomedical Sciences, Rome, Italy
| | - Florigio Lista
- Scientific Department, Army Medical Center, Defense Institute for Biomedical Sciences, Rome, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Cecilia Ambrosi
- Department of Promotion of Human Sciences and Quality of Life, San Raffaele Open University, Rome, Italy
- Laboratory of Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Roma, Rome, Italy
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2
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Ahmed SF, Gulick AM. The structural basis of substrate selectivity of the acinetobactin biosynthetic adenylation domain, BasE. J Biol Chem 2025; 301:108413. [PMID: 40096888 PMCID: PMC12005286 DOI: 10.1016/j.jbc.2025.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 03/01/2025] [Accepted: 03/12/2025] [Indexed: 03/19/2025] Open
Abstract
Siderophores are small molecule natural products that are often produced by enzymes called nonribosomal peptide synthetases that many pathogenic bacteria produce to adapt to low iron conditions. Nonribosomal peptide synthetase bioengineering could lead to the production of siderophore analogs with the potential to interrupt this unique bacterial iron uptake system, endowing the molecules with antimicrobial properties. Acinetobacter baumannii produces the catecholate siderophore acinetobactin to scavenge iron, a nutrient essential for several metabolic processes. Previous studies have reported synthetic analogs of acinetobactin that disrupt iron acquisition by A. baumannii, resulting in inhibition of bacterial growth. To foster a long-term goal of using a chemoenzymatic approach to produce additional analogs, we have targeted the adenylation domain BasE for the incorporation of alternate substrates. Here, we report a structure-guided approach to investigate the substrate selectivity of BasE for non-native aryl substrates. Using targeted mutagenesis in the active site of BasE, we generated mutants that catalyze the activation of alternate substrates with catalytic efficiencies comparable to the WT enzyme with its natural substrate 2,3-dihydroxybenzoic acid. We further solved structures of these mutants bound to the non-native substrates that illustrate an expanded binding pocket that support the improved promiscuity of BasE. Motivated to develop an approach to produce analogs of acinetobactin, including molecules that could block iron uptake or be readily conjugated to antibiotic cargo, our work aims to develop a structure-guided approach for using catecholate siderophore pathways to incorporate alternate substrates.
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Affiliation(s)
- Syed Fardin Ahmed
- Department of Structural Biology, University at Buffalo, Buffalo, New York, United States
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, Buffalo, New York, United States.
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3
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Ahmed SF, Balutowski A, Yang J, Wencewicz TA, Gulick AM. Expanding the Substrate Selectivity of the Fimsbactin Biosynthetic Adenylation Domain, FbsH. ACS Chem Biol 2024; 19:2451-2461. [PMID: 39513969 PMCID: PMC11661926 DOI: 10.1021/acschembio.4c00512] [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: 07/25/2024] [Revised: 10/02/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.
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Affiliation(s)
- Syed Fardin Ahmed
- Department
of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
| | - Adam Balutowski
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Jinping Yang
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Timothy A. Wencewicz
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Andrew M. Gulick
- Department
of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
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4
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Ahmed SF, Balutowski A, Yang J, Wencewicz TA, Gulick AM. Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605314. [PMID: 39091846 PMCID: PMC11291136 DOI: 10.1101/2024.07.26.605314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report on structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early-stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.
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Affiliation(s)
- Syed Fardin Ahmed
- Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203, United States
| | - Adam Balutowski
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Jinping Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Andrew M. Gulick
- Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203, United States
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5
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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: 0.5] [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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Bisaro F, Shuman HA, Feldman MF, Gebhardt MJ, Pukatzki S. Acinetobacter baumannii ATCC 17978 encodes a microcin system with antimicrobial properties for contact-independent competition. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001346. [PMID: 37289493 PMCID: PMC10333792 DOI: 10.1099/mic.0.001346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that persists in the hospital environment and causes various clinical infections, primarily affecting immunocompromised patients. A. baumannii has evolved a wide range of mechanisms to compete with neighbouring bacteria. One such competition strategy depends on small secreted peptides called microcins, which exert antimicrobial effects in a contact-independent manner. Here, we report that A. baumannii ATCC 17978 (AB17978) encodes the class II microcin 17 978 (Mcc17978) with antimicrobial activity against closely related Acinetobacter, and surprisingly, also Escherichia coli strains. We identified the genetic locus encoding the Mcc17978 system in AB17978. Using classical bacterial genetic approaches, we determined that the molecular receptor of Mcc17978 in E. coli is the iron-catecholate transporter Fiu, and in Acinetobacter is Fiu's homolog, PiuA. In bacteria, the Ferric uptake regulator (Fur) positively regulates siderophore systems and microcin systems under iron-deprived environments. We found that the Mcc17978 system is upregulated under low-iron conditions commonly found in the host environment and identified a putative Fur binding site upstream of the mcc17978 gene. When we tested the antimicrobial activity of Mcc17978 under different levels of iron availability, we observed that low iron levels not only triggered transcriptional induction of the microcin, but also led to enhanced microcin activity. Taken together, our findings suggest that A. baumannii may utilize microcins to compete with other microbes for resources during infection.
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Affiliation(s)
- Fabiana Bisaro
- Department of Biology, The City College, City University of New York, New York, NY 10031, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis MO 63110, USA
| | - Howard A. Shuman
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
- Present address: P.O. Box 1088, Sheffield, MA 01257, USA
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis MO 63110, USA
| | - Michael J. Gebhardt
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Stefan Pukatzki
- Department of Biology, The City College, City University of New York, New York, NY 10031, USA
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7
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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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Variants of Tn 6924, a Novel Tn 7 Family Transposon Carrying the blaNDM Metallo-β-Lactamase and 14 Copies of the aphA6 Amikacin Resistance Genes Found in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0174521. [PMID: 35019774 PMCID: PMC8754128 DOI: 10.1128/spectrum.01745-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is primarily due to the global spread of two main clones that carry oxa23, oxa24, and oxa58. However, new carbapenem-resistant clones are emerging that are also resistant to a wide range of antibiotics. Strains belonging to ST85IP (Institut Pasteur) carry the blaNDM metallo-β-lactamase carbapenem resistance gene. Here, we completed the genome sequence of an ST85IP strain, Cl300, recovered in 2015 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. Cl300 is highly resistant to meropenem and amikacin, and consistent with this, a copy of the blaNDM carbapenem and 14 copies of the aphA6 amikacin resistance genes were found in the genome. Cl300 also contains the sul2 sulfonamide and the msr(E) macrolide resistance genes. All aphA6 copies and blaNDM are in a novel 76-kb Tn7 family transposon designated Tn6924. Like Tn7, Tn6924 is bounded by 29-bp inverted repeats with additional TnsB binding sites at each end. Several variants of Tn6924 were found in a set of diverse strains, including ST85IP strains as well as members of global clones 1 and 2. sul2 and msr(E) are in a 13.0-kb pseudocompound transposon (PCT) bounded by IS1008. ST85s represent a diverse group of strains, particularly in their antibiotic resistance gene content and the K and OC surface polysaccharide loci. Acquisition of Tn6924 by members of global clones indicates the significance of this transposon in spreading two clinically significant resistance genes, blaNDM and aphA6. IMPORTANCE To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the blaNDM gene. Here, we completed the genome sequence of an ST85 strain and showed that blaNDM and 14 copies of the aphA6 amikacin resistance genes are in Tn6924, a novel Tn7 family transposon. Analysis of all publicly available ST85s predicted that all strains in the main lineage carry a variant of Tn6924. Variants of Tn6924 were also found in other clones, including GC1 and GC2. Tn6924 is an important mobile element given that it carries two clinically important resistance genes (blaNDM and aphA6) and has spread to other clones. Therefore, outbreaks caused by ST85s should be studied and tracked.
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Tn6553, a Tn7-family transposon encoding putative iron uptake functions found in Acinetobacter. Arch Microbiol 2022; 204:678. [PMID: 36289115 PMCID: PMC9605922 DOI: 10.1007/s00203-022-03291-0] [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: 08/25/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2022]
Abstract
Acinetobacter baumannii is an opportunistic pathogen that has become difficult to eradicate mainly because of its high level of antibiotic resistance. Other features that contribute to this organism's success are the ability to compete for nutrients and iron. Recently, several novel Tn7-family transposons that encode synthesis and transport of siderophore and iron uptake systems were characterised. Here, another Tn7-type transposon (named Tn6553) is described. Tn6553 contains a set of iron utilisation genes with a transposition module related to Tn7. Tn7-family transposons that carry iron uptake systems facilitate the spread of these functions in Acinetobacter strains. Given that Tn7 is known to transpose efficiently into its preferred target site, finding siderophore functions on Tn7 family transposons is important in the context of dissemination of virulence genes amongst Acinetobacter strains.
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10
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Cargo Genes of Tn 7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes. mBio 2021; 12:e0293821. [PMID: 34872347 PMCID: PMC8649781 DOI: 10.1128/mbio.02938-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities in a gene-sharing network demonstrates how transposons function as a conduit of genes between phylogenetically distant hosts. Comparative analysis of the cargo genes reveals significant enrichment of mobile genetic elements (MGEs) nested within Tn7-like transposons, such as insertion sequences and toxin-antitoxin modules, and of genes involved in recombination, anti-MGE defense, and antibiotic resistance. More unexpectedly, cargo also includes genes encoding central carbon metabolism enzymes. Twenty-two Tn7-like transposons carry both an anti-MGE defense system and antibiotic resistance genes, illustrating how bacteria can overcome these combined pressures upon acquisition of a single transposon. This work substantially expands the distribution of Tn7-like transposons, defines their evolutionary relationships, and provides a large-scale functional classification of prokaryotic genes mobilized by transposition.
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11
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Koong J, Johnson C, Rafei R, Hamze M, Myers GSA, Kenyon JJ, Lopatkin AJ, Hamidian M. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 2021; 7. [PMID: 34874246 PMCID: PMC8767349 DOI: 10.1099/mgen.0.000705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
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Affiliation(s)
- Jonathan Koong
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Claire Johnson
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences. Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Allison J Lopatkin
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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