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Dhurve G, Behera SR, Kodetham G, Siddavattam D. Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer. Microbiol Spectr 2024:e0081724. [PMID: 39101807 DOI: 10.1128/spectrum.00817-24] [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: 04/02/2024] [Accepted: 06/20/2024] [Indexed: 08/06/2024] Open
Abstract
The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells. IMPORTANCE Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.
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Affiliation(s)
- Ganeshwari Dhurve
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sandhya Rani Behera
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Gopinath Kodetham
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Mancilla-Rojano J, Flores V, Cevallos MA, Ochoa SA, Parra-Flores J, Arellano-Galindo J, Xicohtencatl-Cortes J, Cruz-Córdova A. A bioinformatic approach to identify confirmed and probable CRISPR-Cas systems in the Acinetobacter calcoaceticus- Acinetobacter baumannii complex genomes. Front Microbiol 2024; 15:1335997. [PMID: 38655087 PMCID: PMC11035748 DOI: 10.3389/fmicb.2024.1335997] [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: 11/09/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction The Acinetobacter calcoaceticus-Acinetobacter baumannii complex, or Acb complex, consists of six species: Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii, and Acinetobacter lactucae. A. baumannii is the most clinically significant of these species and is frequently related to healthcare-associated infections (HCAIs). Clustered regularly interspaced short palindromic repeat (CRISPR) arrays and associated genes (cas) constitute bacterial adaptive immune systems and function as variable genetic elements. This study aimed to conduct a genomic analysis of Acb complex genomes available in databases to describe and characterize CRISPR systems and cas genes. Methods Acb complex genomes available in the NCBI and BV-BRC databases, the identification and characterization of CRISPR-Cas systems were performed using CRISPRCasFinder, CRISPRminer, and CRISPRDetect. Sequence types (STs) were determined using the Oxford scheme and ribosomal multilocus sequence typing (rMLST). Prophages were identified using PHASTER and Prophage Hunter. Results A total of 293 genomes representing six Acb species exhibited CRISPR-related sequences. These genomes originate from various sources, including clinical specimens, animals, medical devices, and environmental samples. Sequence typing identified 145 ribosomal multilocus sequence types (rSTs). CRISPR-Cas systems were confirmed in 26.3% of the genomes, classified as subtypes I-Fa, I-Fb and I-Fv. Probable CRISPR arrays and cas genes associated with CRISPR-Cas subtypes III-A, I-B, and III-B were also detected. Some of the CRISPR-Cas systems are associated with genomic regions related to Cap4 proteins, and toxin-antitoxin systems. Moreover, prophage sequences were prevalent in 68.9% of the genomes. Analysis revealed a connection between these prophages and CRISPR-Cas systems, indicating an ongoing arms race between the bacteria and their bacteriophages. Furthermore, proteins associated with anti-CRISPR systems, such as AcrF11 and AcrF7, were identified in the A. baumannii and A. pittii genomes. Discussion This study elucidates CRISPR-Cas systems and defense mechanisms within the Acb complex, highlighting their diverse distribution and interactions with prophages and other genetic elements. This study also provides valuable insights into the evolution and adaptation of these microorganisms in various environments and clinical settings.
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Affiliation(s)
- Jetsi Mancilla-Rojano
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico, Mexico
| | - Víctor Flores
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Miguel A. Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara A. Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico, Mexico
| | - Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - José Arellano-Galindo
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gomez, Mexico, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico, Mexico
| | - Ariadnna Cruz-Córdova
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico, Mexico
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Ilyas M, Purkait D, Atmakuri K. Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. Brief Funct Genomics 2024; 23:55-68. [PMID: 36528816 DOI: 10.1093/bfgp/elac051] [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: 09/13/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.
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Affiliation(s)
- Mohd Ilyas
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Dyuti Purkait
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
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Prajapati A, Yogisharadhya R, Mohanty NN, Mendem SK, Chanda MM, Siddaramappa S, Shivachandra SB. Comparative genome analysis of Pasteurella multocida strains of porcine origin. Genome 2024; 67:13-23. [PMID: 37639729 DOI: 10.1139/gen-2023-0021] [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: 08/31/2023]
Abstract
Pasteurella multocida causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters. In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.
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Affiliation(s)
- Awadhesh Prajapati
- ICAR - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, Karnataka, India
| | - Revanaiah Yogisharadhya
- ICAR - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, Karnataka, India
| | - Nihar Nalini Mohanty
- CCS - National Institute of Animal Health (NIAH), Baghpat 250609, Uttar Pradesh, India
| | - Suresh Kumar Mendem
- ICAR - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, Karnataka, India
| | - Mohammed Mudassar Chanda
- ICAR - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, Karnataka, India
| | - Shivakumara Siddaramappa
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru 560100, Karnataka, India
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Marutescu LG, Popa M, Gheorghe-Barbu I, Barbu IC, Rodríguez-Molina D, Berglund F, Blaak H, Flach CF, Kemper MA, Spießberger B, Wengenroth L, Larsson DGJ, Nowak D, Radon K, de Roda Husman AM, Wieser A, Schmitt H, Pircalabioru Gradisteanu G, Vrancianu CO, Chifiriuc MC. Wastewater treatment plants, an "escape gate" for ESCAPE pathogens. Front Microbiol 2023; 14:1193907. [PMID: 37293232 PMCID: PMC10244645 DOI: 10.3389/fmicb.2023.1193907] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
Antibiotics are an essential tool of modern medicine, contributing to significantly decreasing mortality and morbidity rates from infectious diseases. However, persistent misuse of these drugs has accelerated the evolution of antibiotic resistance, negatively impacting clinical practice. The environment contributes to both the evolution and transmission of resistance. From all anthropically polluted aquatic environments, wastewater treatment plants (WWTPs) are probably the main reservoirs of resistant pathogens. They should be regarded as critical control points for preventing or reducing the release of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic-resistance genes (ARGs) into the natural environment. This review focuses on the fate of the pathogens Enterococcus faecium, Staphylococcus aureus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp. (ESCAPE) in WWTPs. All ESCAPE pathogen species, including high-risk clones and resistance determinants to last-resort antibiotics such as carbapenems, colistin, and multi-drug resistance platforms, were detected in wastewater. The whole genome sequencing studies demonstrate the clonal relationships and dissemination of Gram-negative ESCAPE species into the wastewater via hospital effluents and the enrichment of virulence and resistance determinants of S. aureus and enterococci in WWTPs. Therefore, the efficiency of different wastewater treatment processes regarding the removal of clinically relevant ARB species and ARGs, as well as the influence of water quality factors on their performance, should be explored and monitored, along with the development of more effective treatments and appropriate indicators (ESCAPE bacteria and/or ARGs). This knowledge will allow the development of quality standards for point sources and effluents to consolidate the WWTP barrier role against the environmental and public health AR threats.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Marcela Popa
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Ilda Czobor Barbu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Daloha Rodríguez-Molina
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology – IBE, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Fanny Berglund
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Hetty Blaak
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Merel Aurora Kemper
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Beate Spießberger
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Laura Wengenroth
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
| | - D. G. Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Dennis Nowak
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
| | - Katja Radon
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Andreas Wieser
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Heike Schmitt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Gratiela Pircalabioru Gradisteanu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Romanian Academy of Sciences, Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- The Romanian Academy, Bucharest, Romania
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Ren X, Palmer LD. Acinetobacter Metabolism in Infection and Antimicrobial Resistance. Infect Immun 2023:e0043322. [PMID: 37191522 DOI: 10.1128/iai.00433-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.
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Affiliation(s)
- Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Lauren D Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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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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Peykov S, Strateva T. Whole-Genome Sequencing-Based Resistome Analysis of Nosocomial Multidrug-Resistant Non-Fermenting Gram-Negative Pathogens from the Balkans. Microorganisms 2023; 11:microorganisms11030651. [PMID: 36985224 PMCID: PMC10051916 DOI: 10.3390/microorganisms11030651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas aeruginosa and Acinetobacter baumannii, are among the major opportunistic pathogens involved in the global antibiotic resistance epidemic. They are designated as urgent/serious threats by the Centers for Disease Control and Prevention and are part of the World Health Organization’s list of critical priority pathogens. Also, Stenotrophomonas maltophilia is increasingly recognized as an emerging cause for healthcare-associated infections in intensive care units, life-threatening diseases in immunocompromised patients, and severe pulmonary infections in cystic fibrosis and COVID-19 individuals. The last annual report of the ECDC showed drastic differences in the proportions of NFGNB with resistance towards key antibiotics in different European Union/European Economic Area countries. The data for the Balkans are of particular concern, indicating more than 80% and 30% of invasive Acinetobacter spp. and P. aeruginosa isolates, respectively, to be carbapenem-resistant. Moreover, multidrug-resistant and extensively drug-resistant S. maltophilia from the region have been recently reported. The current situation in the Balkans includes a migrant crisis and reshaping of the Schengen Area border. This results in collision of diverse human populations subjected to different protocols for antimicrobial stewardship and infection control. The present review article summarizes the findings of whole-genome sequencing-based resistome analyses of nosocomial multidrug-resistant NFGNBs in the Balkan countries.
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Affiliation(s)
- Slavil Peykov
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8, Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- BioInfoTech Laboratory, Sofia Tech Park, 111, Tsarigradsko Shosse Blvd., 1784 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
| | - Tanya Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
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Ababneh Q, Al Sbei S, Jaradat Z, Syaj S, Aldaken N, Ababneh H, Inaya Z. Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance. PeerJ 2023; 11:e14709. [PMID: 36718445 PMCID: PMC9884047 DOI: 10.7717/peerj.14709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23, and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
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Affiliation(s)
- Qutaiba Ababneh
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Sara Al Sbei
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Ziad Jaradat
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Sebawe Syaj
- Department of General Surgery and Urology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Neda’a Aldaken
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Hamza Ababneh
- Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Zeina Inaya
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
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Shayea RH, Ali MR. Whole-genome Study of Carbapenem-resistant Acinetobacter baumannii Virulence and Resistance. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2023. [DOI: 10.30699/ijmm.17.1.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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11
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Intensification in Genetic Information and Acquisition of Resistant Genes in Genome of Acinetobacter baumannii: A Pan-Genomic Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3186343. [PMID: 36605106 PMCID: PMC9810410 DOI: 10.1155/2022/3186343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/02/2022] [Accepted: 12/03/2022] [Indexed: 12/29/2022]
Abstract
Acinetobacter baumannii (A. baumannii) attributes 26% of the mortality rate in hospitalized patients, and the percentage can rise to 46 in patients admitted to ICU as it is a major cause of ventilator-associated pneumonia. It has been nominated as the critical priority organism by WHO for which new therapeutic drugs are urgently required. To understand the genomic identification of different strains, antimicrobial resistance patterns, and epidemiological typing of organisms, whole-genome sequencing (WGS) analysis provides insight to explore new epitopes to develop new drugs against the organism. Therefore, the study is aimed at investigating the whole genome sequence of A. baumannii strains to report the new intensifications in its genomic profile. The genome sequences were retrieved from the NCBI database system. Pan-genome BPGA (Bacterial Pan-genome Analysis Tool) was used to analyze the core, pan, and species-specific genome analysis. The pan and core genome curves were extrapolated using the empirical power law equation f(x) = a.xb and the exponential equation f1(x) = c.e (d.x). To identify the resistant genes with resistant mutations against antibiotics, ResFinder and Galaxy Community hub bioinformatics tools were used. According to pan-genome analysis, there were 2227 core genes present in each species of the A. baumannii genome. Furthermore, the number of accessory genes ranged from 1182 to 1460, and the unique genes in the genome were 931. There were 325 exclusively absent genes in the genome of Acinetobacter baumannii. The pan-genome analysis showed that there is a 5-fold increase in the genome of A. baumannii in 5 years, and the genome is still open. There is the addition of multiple unique genes; among them, genes participating in the function of information and processing are increased.
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Kumkar SN, Kamble EE, Chavan NS, Dhotre DP, Pardesi KR. Diversity of resistant determinants, virulence factors, and mobile genetic elements in Acinetobacter baumannii from India: A comprehensive in silico genome analysis. Front Cell Infect Microbiol 2022; 12:997897. [PMID: 36519127 PMCID: PMC9742364 DOI: 10.3389/fcimb.2022.997897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction The frequency of infections associated with multidrug resistant A. baumannii has risen substantially in India. The use of next-generation sequencing (NGS) techniques combined with comparative genomics has great potential for tracking, monitoring, and ultimately controlling the spread of this troublesome pathogen. Here, we investigated the whole genome sequences of 47 A. baumannii from India. Methods In brief, A. baumannii genomes were analyzed for the presence of antibiotic resistance genes (ARGs), virulence factors genes (VFGs), and mobile genetic elements (MGEs) using various in silico tools. The AbaR-type resistance islands (AbaRIs) were detected by examining the genetic environment of the chromosomal comM gene. Multilocus sequence types were determined using the Pasteur scheme. The eBURST and whole genome SNPs-based phylogenetic analysis were performed to analyze genetic diversity between A. baumannii genomes. Results and discussion A larger number of A. baumannii isolates belonging to the ST2 genotype was observed. The SNPs-based phylogenetic analysis showed a diversity between compared genomes. The predicted resistome showed the presence of intrinsic and acquired ARGs. The presence of plasmids, insertion sequences, and resistance islands carrying putative ARGs conferring resistance to antibiotics, quaternary ammonium compounds, and heavy metals was predicted in 43 (91%) genomes. The presence of putative VFGs related to adherence, biofilm formation and iron uptake was observed in the study. Overall, the comprehensive genome analysis in this study provides an essential insight into the resistome, virulome and mobilome of A. baumannii isolates from India.
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Affiliation(s)
- Shital N. Kumkar
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra State, India
| | - Ekta E. Kamble
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra State, India
| | - Nikeeta S. Chavan
- National Centre for Cell Science, Savitribai Phule Pune University Pune, Maharashtra State, India
| | - Dhiraj P. Dhotre
- National Centre for Cell Science, Savitribai Phule Pune University Pune, Maharashtra State, India,*Correspondence: Dhiraj P. Dhotre, ; Karishma R. Pardesi,
| | - Karishma R. Pardesi
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra State, India,*Correspondence: Dhiraj P. Dhotre, ; Karishma R. Pardesi,
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Khongfak S, Thummeepak R, Leungtongkam U, Tasanapak K, Thanwisai A, Sitthisak S. Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329. PeerJ 2022; 10:e13718. [PMID: 35855908 PMCID: PMC9288165 DOI: 10.7717/peerj.13718] [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: 05/05/2022] [Accepted: 06/21/2022] [Indexed: 01/17/2023] Open
Abstract
Acinetobacter baumannii is a major cause of nosocomial infection, and the incidence of extensively drug-resistant A. baumannii (XDRAB) infections has dramatically increased worldwide. In this study, we aimed to explore the complete genome sequence of XDRAB 329, ST1166/98 (Oxford/Pasteur), which is an outbreak clone from a hospital in Thailand. Whole-genome sequencing (WGS) was performed using short-read Illumina and long-read PacBio sequencing, and a conjugation assay of its plasmid was performed. The complete genome sequence of A. baumannii AB329 revealed a circular chromosome 3,948,038 bp in length with 39% GC content. Antibiotic resistance genes (ARGs), including beta-lactam resistance (bla OXA-51, bla ADC-25, bla OXA-23, bla TEM-1D), aminoglycoside resistance (aph(3')-Ia, aph(3″)-Ib, aph(6)-Id, armA), tetracycline resistance (tet(B), tet (R)), macrolide resistance (mph(E), msr(E)), and efflux pumps, were found. Mobile genetic elements (MGEs) analysis of A. baumannii AB329 revealed two plasmids (pAB329a and pAB329b), three prophages, 19 genomic islands (GIs), and 33 insertion sequences (ISs). pAB329a is a small circular plasmid of 8,731 bp, and pAB329b is a megaplasmid of 82,120 bp. aph(3')-VIa was detected in pAB329b, and a major facilitator superfamily (MFS) transporter was detected in the prophage. Acinetobacter baumannii resistance island 4 (AbaR4) harboring tetracycline and aminoglycoside resistance was detected in the genome of A. baumannii AB329. pAB329b, which belongs to Rep-type GR6 (plasmid lineage LN_1), is a conjugative plasmid with the ability to transfer an aminoglycoside resistance gene to sodium azide-resistant A. baumannii. This study provides insights into the features of the MGEs of XDRAB, which are the main reservoir and source of dissemination of ARGs.
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Affiliation(s)
- Supat Khongfak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
| | - Rapee Thummeepak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
| | - Udomluk Leungtongkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
| | - Kannipa Tasanapak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok, Thailand
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Comparative genome analysis of Pasteurella multocida serogroup B:2 strains causing haemorrhagic septicaemia (HS) in bovines. Gene 2022; 826:146452. [PMID: 35339640 DOI: 10.1016/j.gene.2022.146452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
Pasteurella multocida, a Gram-negative bacterium with ubiquitous nature, is known to affect wide range of host species worldwide with varied clinical manifestations including haemorrhagic septicaemia (HS) in bovines. Although, HS causing P. multocida strains were identified and characterized by conventional tools and PCR assays, diverse strains are indistinguishable by these tools in the face of disease outbreaks. In this study, draft genomes of three virulent P. multocida serotype B:2 strains (NIVEDIPm32, NIVEDIPm34 and NIVEDIPm35) were analyzed following whole genome sequencing, assembly, annotation and compared them with existing global genomes (n = 43) of bovine origin in the database. Three draft genomes of NIVEDIPm strains consisted of 40-52 contigs with GC content of ∼40.4%. The genome size and predicted genes content was ∼2.3 Mb and 2181-2189, respectively. Besides, the presence of various mobile genetic elements, antimicrobial resistance genes and biofilm related genes suggested their vital roles in virulence; further, adaptation to the host immune system as well as host pathogen interaction. Multi locus sequence analysis based on RIRDC scheme showed the presence of ST122 in all the three strains. wgMLST based phylogenic analysis suggested that HS causing Indian virulent field strains differed geographically and showed diversity from existing HS vaccine strain P52. The phylogenetic tree revealed that North Indian strains share high similarity with strains of Pakistan than South Indian Strain. Notably, a high divergence of SNPs between the HS causing circulating virulent strains of India and current HS vaccine strain P52 suggested an imminent need for relook in to HS vaccination strategy for livestock in India.
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Durand BARN, Yahiaoui Martinez A, Baud D, François P, Lavigne JP, Dunyach-Remy C. Comparative genomics analysis of two Helcococcus kunzii strains co-isolated with Staphylococcus aureus from diabetic foot ulcers. Genomics 2022; 114:110365. [PMID: 35413435 DOI: 10.1016/j.ygeno.2022.110365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/01/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Helcococcus kunzii is a commensal Gram-positive bacterial species recovered from the human skin microbiota and considered as an opportunistic pathogen. Although little is known about its clinical significance, its increased abundance has been reported in infected wounds, particularly in foot ulcers in persons with diabetes. This species is usually detected in mixed cultures from human specimens and frequently isolated with Staphylococcus aureus. Modulation of staphylococci virulence by H. kunzii has been shown in an infection model of Caenorhabditis elegans. The aim of this study was to compare the genomes of two H. kunzii strains isolated from foot ulcers -isolate H13 and H10 showing high or low impact on S. aureus virulence, respectively- and the H. kunzii ATCC51366 strain. Whole genome analyses revealed some differences between the two strains: length (2.06 Mb (H13) and 2.05 Mb (H10) bp), GC content (29.3% (H13) and 29.5% (H10)) and gene content (1,884 (H13) and 1,786 (H10) predicted genes). The core-proteome phylogenies within the genus characterised H. kunzii H13 and H10 as genetically similar to their ancestor. The main differences between the strains were mainly in sugar-associated transporters and various hypothetical proteins. Five targets were identified as potentially involved in S. aureus virulence modulation in both genomes: the two-component iron export system and three autoinducer-like proteins. Moreover, H13 strain harbours a prophage inserted in 1,261,110-1,295,549 (attL-attR), which is absent in H10 strain. The prophage PhiCD38_2 was previously reported for its ability to modulate secretion profile, reinforcing the autoinducer-like hypothesis. In the future, transcriptomics or metaproteomics approaches could be performed to better characterize the H13 strain and possibly identify the underlying mechanism for S. aureus virulence modulation.
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Affiliation(s)
- Benjamin A R N Durand
- Bacterial Virulence and Chronic Infections, INSERM U1047, University of Montpellier, Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, 30908 Nîmes, France
| | - Alex Yahiaoui Martinez
- Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, University of Montpellier, 30029 Nîmes, France
| | - Damien Baud
- Department of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Patrice François
- Department of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Jean-Philippe Lavigne
- Bacterial Virulence and Chronic Infections, INSERM U1047, University of Montpellier, Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, 30908 Nîmes, France.
| | - Catherine Dunyach-Remy
- Bacterial Virulence and Chronic Infections, INSERM U1047, University of Montpellier, Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, 30908 Nîmes, France
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Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species. Microbiol Spectr 2022; 10:e0126421. [PMID: 35446150 PMCID: PMC9241875 DOI: 10.1128/spectrum.01264-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.
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Outer Membrane Vesicles of Acinetobacter baumannii DS002 Are Selectively Enriched with TonB-Dependent Transporters and Play a Key Role in Iron Acquisition. Microbiol Spectr 2022; 10:e0029322. [PMID: 35266817 PMCID: PMC9045253 DOI: 10.1128/spectrum.00293-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Outer membrane vesicles (OMVs) of Acinetobacter baumannii DS002 carry proteins which perform selective biological functions. The proteins involved in cell wall/membrane biogenesis and inorganic ion transport and metabolism occupied a significant portion of the 302 proteins associated with OMVs. Interestingly, the TonB-dependent transporters (TonRs), linked to the active transport of nutrients across the energy-deprived outer membrane, are predominant among proteins involved in inorganic ion transport and metabolism. The OMVs of DS002 contain TonRs capable of transporting iron complexed to catecholate, hydroximate, and mixed types of siderophores. Consistent with this observation, the OMVs were firmly bound to ferric-enterobactin (55Fe-Ent) and successfully transported iron into A. baumannii DS002 cells grown under iron-limiting conditions. In addition to the TonRs, OMVs also carry proteins known to promote pathogenesis, immune evasion, and biofilm formation. Our findings provide conclusive evidence for the role of OMVs in the transport of nutrients such as iron and show the presence of proteins with proven roles in pathogenicity and immune response. IMPORTANCE TonB-dependent transporters (TonRs) play a crucial role in transporting nutrients such as iron, nickel, copper, and complex carbohydrates across the energy-deprived outer membrane. Due to their unique structural features, TonRs capture nutrients in an energy-independent manner and transport them across the outer membrane by harvesting energy derived from the inner membrane-localized Ton-complex. In this study, we report the presence of TonRs capable of transporting various nutrients in OMVs and demonstrate their role in capturing and transporting ferric iron complexed with enterobactin into A. baumannii DS002 cells. The OMV-associated TonRs appear to play a critical role in the survival of A. baumannii, listed as a priority pathogen, under nutrient-deprived conditions.
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Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052870. [PMID: 35270562 PMCID: PMC8910769 DOI: 10.3390/ijerph19052870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023]
Abstract
In recent decades, Acinetobacter baumannii emerged as a major infective menace in healthcare settings due to scarce therapeutic options to treat infections. Therefore, undertaking genome comparison analyses of multi-resistant A. baumannii strains could aid the identification of key bacterial determinants to develop innovative anti-virulence approaches. Following genome sequencing, we performed a molecular characterization of key genes and genomic comparison of two A. baumannii strains, #36 and #150, with selected reference genomes. Despite a different antibiotic resistance gene content, the analyzed strains showed a very similar antibiogram profile. Interestingly, the lack of some important virulence determinants (i.e., bap, ata and omp33–36) did not abrogate their adhesive abilities to abiotic and biotic surfaces, as reported before; indeed, strains retained these capacities, although to a different extent, suggesting the presence of distinct vicarious genes. Conversely, secretion systems, lipopolysaccharide (LPS), capsule and iron acquisition systems were highly similar to A. baumannii reference strains. Overall, our analyses increased our knowledge on A. baumannii genomic content and organization as well as the genomic events occurring in nosocomial isolates to better fit into changing healthcare environments.
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Velázquez-Ríos IO, Rincón-Rosales R, Gutiérrez-Miceli FA, Alcántara-Hernández RJ, Ruíz-Valdiviezo VM. Prokaryotic diversity across a pH gradient in the “El Chichón” crater-lake: a naturally thermo-acidic environment. Extremophiles 2022; 26:8. [DOI: 10.1007/s00792-022-01257-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
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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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Urhan A, Abeel T. A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids. Microb Genom 2021; 7. [PMID: 34761737 PMCID: PMC8743560 DOI: 10.1099/mgen.0.000690] [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] [Indexed: 11/25/2022] Open
Abstract
Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many successful applications and a rapid increase in the number of methods available in the literature. Despite this enthusiasm, there has been no attempt at exploring these graph construction methods in depth, demonstrating their practical use. In this study, we aim to develop a general guide to help researchers who may want to incorporate pan-genomes in their analyses of microbial organisms. We evaluated the state-of-the art pan-genome construction tools to model a collection of 70 Acinetobacter baumannii strains. Our results suggest that all tools produced pan-genome graphs conforming to our expectations based on previous literature, and that their approach to homologue detection is likely to be the most influential in determining the final size and complexity of the pan-genome. The graphs overlapped most in the core pan-genome content while the cloud genes varied significantly among tools. We propose an alternative approach for pan-genome construction by combining two of the tools, Panaroo and Ptolemy, to further exploit them in downstream analyses, and demonstrate the effectiveness of our pipeline for structural variant calling in beta-lactam resistance genes in the same set of A. baumannii isolates, identifying various transposon structures for carbapenem resistance in chromosome, as well as plasmids. We identify a novel plasmid structure in two multidrug-resistant clinical isolates that had previously been studied, and which could be important for their resistance phenotypes.
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Affiliation(s)
- Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
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22
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Real-time PCR method for qualitative and quantitative detection of Lactobacillus sakei group species targeting novel markers based on bioinformatics analysis. Int J Food Microbiol 2021; 355:109335. [PMID: 34343716 DOI: 10.1016/j.ijfoodmicro.2021.109335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/06/2021] [Accepted: 07/17/2021] [Indexed: 11/21/2022]
Abstract
Latilactobacillus sakei group comprises four closely related species, making it difficult to accurately distinguish them with standard markers such as the 16S rRNA gene. The objective of our study was to mine novel markers for PCR detection and discrimination of L. sakei group species and L. sakei subspecies by comparative pan-genomic analysis. A total of 63 genome sequences of L. sakei group species consisted of 119,899 coding genes, yielding 5741 pan-genomes, 831 core-genomes, 3347 accessory-genomes, and 1563 unique-genomes. The accessory-genome was compared to extract unique candidate genes common only to genomes of the same species. The candidate genes were then aligned with the other bacterial genomes to select marker genes present in all genomes of a given species, but not in the genomes of other species. We identified the arginine/ornithine antiporter, putative cell surface protein precursor, sodium:solute symporter, PRD domain protein, PTS sugar transporter subunit IIC, and phosphoenolpyruvate-dependent sugar phosphotransferase system EIIC as marker genes for L. sakei, L. sakei subsp. sakei, L. sakei subsp. carnosus, L. curvatus, L. graminis, and L. fuchuensis, respectively. Primer pairs were designed for each marker and showed 100% specificity for 48 lactic acid bacterial reference strains. The PCR method developed in this study was used to evaluate 106 strains isolated from fermented foods to demonstrate that the marker genes provided a viable alternative to the 16S rRNA gene. We also applied the method to the monitoring of kimchi samples to quantify L. sakei group species or subspecies. Our PCR method based on novel markers can rapidly identify L. sakei group with high accuracy and high throughput.
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Nasim F, Dey A, Qureshi IA. Comparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential. INFECTION GENETICS AND EVOLUTION 2021; 93:104928. [PMID: 34022437 DOI: 10.1016/j.meegid.2021.104928] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
Non-diphtherial Corynebacterium species or diphtheroids were previously considered as the mere contaminants of clinical samples. Of late, they have been reckoned as the formidable infection causing agents of various diseases. While the scientific database is filled with articles that document whole genome analysis of individual isolates, a comprehensive comparative genomic analysis of diphtheroids alongside Corynebacterium diphtheriae is expected to enable us in understanding their genomic as well as evolutionary divergence. Here, we have analysed the whole genome sequences of forty strains that were selected from a range of eleven Corynebacterium species (pathogenic and non-pathogenic). A statistical analysis of the pan and core genomes revealed that even though the core genome is saturated, the pan genome is yet open rendering scope for newer gene families to be accumulated in the course of evolution that might further change the pathogenic behavior of these species. Every strain had bacteriophage components integrated in its genome and some of them were intact and consisted of toxins. The presence of diversified genomic islands was observed across the dataset and most of them consisted of genes for virulence and multidrug resistance. Moreover, the phylogenetic analysis showed that a diphtheroid is the last common ancestor of all the Corynebacterium species. The current study is a compilation of genomic features of pathogenic as well as non-pathogenic Corynebacterium species which provides insights into their virulence potential in the times to come.
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Affiliation(s)
- Fouzia Nasim
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Arijit Dey
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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Klebba PE, Newton SMC, Six DA, Kumar A, Yang T, Nairn BL, Munger C, Chakravorty S. Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics. Chem Rev 2021; 121:5193-5239. [PMID: 33724814 PMCID: PMC8687107 DOI: 10.1021/acs.chemrev.0c01005] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
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Affiliation(s)
- Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Salete M C Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - David A Six
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Brittany L Nairn
- Department of Biological Sciences, Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112, United States
| | - Colton Munger
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Somnath Chakravorty
- Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, New York 14203, United States
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Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen. Pathogens 2021; 10:pathogens10040387. [PMID: 33804894 PMCID: PMC8063835 DOI: 10.3390/pathogens10040387] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is regarded as a life-threatening pathogen associated with community-acquired and nosocomial infections, mainly pneumonia. The rise in the number of A. baumannii antibiotic-resistant strains reduces effective therapies and increases mortality. Bacterial comparative genomic studies have unraveled the innate and acquired virulence factors of A. baumannii. These virulence factors are involved in antibiotic resistance, environmental persistence, host-pathogen interactions, and immune evasion. Studies on host–pathogen interactions revealed that A. baumannii evolved different mechanisms to adhere to in order to invade host respiratory cells as well as evade the host immune system. In this review, we discuss current data on A. baumannii genetic features and virulence factors. An emphasis is given to the players in host–pathogen interaction in the respiratory tract. In addition, we report recent investigations into host defense systems using in vitro and in vivo models, providing new insights into the innate immune response to A. baumannii infections. Increasing our knowledge of A. baumannii pathogenesis may help the development of novel therapeutic strategies based on anti-adhesive, anti-virulence, and anti-cell to cell signaling pathways drugs.
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Ten KE, Md Zoqratt MZH, Ayub Q, Tan HS. Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing. BMC Res Notes 2021; 14:83. [PMID: 33663564 PMCID: PMC7934414 DOI: 10.1186/s13104-021-05493-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/16/2021] [Indexed: 01/21/2023] Open
Abstract
Objective The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. Results One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.
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Affiliation(s)
- Kah Ern Ten
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Muhammad Zarul Hanifah Md Zoqratt
- 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
| | - 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, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Tropical Medicine and Biology Multidisciplinary Platform, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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27
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Zhang X, Li F, Awan F, Jiang H, Zeng Z, Lv W. Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms. Front Cell Infect Microbiol 2021; 11:633817. [PMID: 33718283 PMCID: PMC7952536 DOI: 10.3389/fcimb.2021.633817] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried blaOXA-23, blaOXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.
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Affiliation(s)
- Xiufeng Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Fangping Li
- Department of Biomedical Engineering, College of Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Furqan Awan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, Guangzhou, China
| | - Hongye Jiang
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Zhenling Zeng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, Guangzhou, China
| | - Weibiao Lv
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
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Mayer C, Muras A, Parga A, Romero M, Rumbo-Feal S, Poza M, Ramos-Vivas J, Otero A. Quorum Sensing as a Target for Controlling Surface Associated Motility and Biofilm Formation in Acinetobacter baumannii ATCC ® 17978 TM. Front Microbiol 2020; 11:565548. [PMID: 33101239 PMCID: PMC7554515 DOI: 10.3389/fmicb.2020.565548] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
The important nosocomial pathogen Acinetobacter baumannii presents a quorum sensing (QS) system (abaI/abaR) mediated by acyl-homoserine-lactones (AHLs) and several quorum quenching (QQ) enzymes. However, the roles of this complex network in the control of the expression of important virulence-related phenotypes such as surface-associated motility and biofilm formation is not clear. Therefore, the effect of the mutation of the AHL synthase AbaI, and the exogenous addition of the QQ enzyme Aii20J on surface-associated motility and biofilm formation by A. baumannii ATCC® 17978TM was studied in detail. The effect of the enzyme on biofilm formation by several multidrug-resistant A. baumannii clinical isolates differing in their motility pattern was also tested. We provide evidence that a functional QS system is required for surface-associated motility and robust biofilm formation in A. baumannii ATCC® 17978TM. Important differences were found with the well-studied strain A. nosocomialis M2 regarding the relevance of the QS system depending on environmental conditions The in vitro biofilm-formation capacity of A. baumannii clinical strains was highly variable and was not related to the antibiotic resistance or surface-associated motility profiles. A high variability was also found in the sensitivity of the clinical strains to the action of the QQ enzyme, revealing important differences in virulence regulation between A. baumannii isolates and confirming that studies restricted to a single strain are not representative for the development of novel antimicrobial strategies. Extracellular DNA emerges as a key component of the extracellular matrix in A. baumannii biofilms since the combined action of the QQ enzyme Aii20J and DNase reduced biofilm formation in all tested strains. Results demonstrate that QQ strategies in combination with other enzymatic treatments such as DNase could represent an alternative approach for the prevention of A. baumannii colonization and survival on surfaces and the prevention and treatment of infections caused by this pathogen.
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Affiliation(s)
- Celia Mayer
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andrea Muras
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Parga
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Romero
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Soraya Rumbo-Feal
- Microbioloxía, Instituto de Investigación Biomédica da Coruña, Centro de Investigacións Científicas Avanzadas da Coruña, Universidade da Coruña, A Coruña, Spain
| | - Margarita Poza
- Microbioloxía, Instituto de Investigación Biomédica da Coruña, Centro de Investigacións Científicas Avanzadas da Coruña, Universidade da Coruña, A Coruña, Spain
| | - José Ramos-Vivas
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Valdecilla, Santander, Spain
| | - Ana Otero
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Samantarrai D, Yakkala H, Siddavattam D. Analysis of indigenous plasmid sequences of A. baumannii DS002 reveals the existence of lateral mobility and extensive genetic recombination among Acinetobacter plasmids. J Genet 2020. [DOI: 10.1007/s12041-020-01232-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Acinetobacter baumannii NCIMB8209: a Rare Environmental Strain Displaying Extensive Insertion Sequence-Mediated Genome Remodeling Resulting in the Loss of Exposed Cell Structures and Defensive Mechanisms. mSphere 2020; 5:5/4/e00404-20. [PMID: 32727858 PMCID: PMC7392541 DOI: 10.1128/msphere.00404-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. A. baumannii arose from the Acinetobacter calcoaceticus-A. baumannii complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus, the study of nonclinical (“environmental”) A. baumannii isolates is necessary. We conducted here comparative genomic and virulence studies on A. baumannii NCMBI8209 isolated in 1943 from the microbiota responsible for the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the multidrug-resistant strains that are predominant nowadays. Our work provides insights on the adaptive strategies used by A. baumannii to escape from host defenses and may help the adoption of measures aimed to limit its further dissemination. Acinetobacter baumannii represents nowadays an important nosocomial pathogen of poorly defined reservoirs outside the clinical setting. Here, we conducted whole-genome sequencing analysis of the Acinetobacter sp. NCIMB8209 collection strain, isolated in 1943 from the aerobic degradation (retting) of desert guayule shrubs. Strain NCIMB8209 contained a 3.75-Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes indicated NCIMB8209 affiliation to A. baumannii, a result supported by the identification of a chromosomal blaOXA-51-like gene. Seven genomic islands lacking antimicrobial resistance determinants, 5 regions encompassing phage-related genes, and notably, 93 insertion sequences (IS) were found in this genome. NCIMB8209 harbors most genes linked to persistence and virulence described in contemporary A. baumannii clinical strains, but many of the genes encoding components of surface structures are interrupted by IS. Moreover, defense genetic islands against biological aggressors such as type 6 secretion systems or CRISPR-cas are absent from this genome. These findings correlate with a low capacity of NCIMB8209 to form biofilm and pellicle, low motility on semisolid medium, and low virulence toward Galleria mellonella and Caenorhabditis elegans. Searching for catabolic genes and concomitant metabolic assays revealed the ability of NCIMB8209 to grow on a wide range of substances produced by plants, including aromatic acids and defense compounds against external aggressors. All the above features strongly suggest that NCIMB8209 has evolved specific adaptive features to a particular environmental niche. Moreover, they also revealed that the remarkable genetic plasticity identified in contemporary A. baumannii clinical strains represents an intrinsic characteristic of the species. IMPORTANCEAcinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. A. baumannii arose from the Acinetobacter calcoaceticus-A. baumannii complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus, the study of nonclinical (“environmental”) A. baumannii isolates is necessary. We conducted here comparative genomic and virulence studies on A. baumannii NCMBI8209 isolated in 1943 from the microbiota responsible for the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the multidrug-resistant strains that are predominant nowadays. Our work provides insights on the adaptive strategies used by A. baumannii to escape from host defenses and may help the adoption of measures aimed to limit its further dissemination.
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Fereshteh S, Abdoli S, Shahcheraghi F, Ajdary S, Nazari M, Badmasti F. New putative vaccine candidates against Acinetobacter baumannii using the reverse vaccinology method. Microb Pathog 2020; 143:104114. [DOI: 10.1016/j.micpath.2020.104114] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/15/2020] [Accepted: 03/01/2020] [Indexed: 01/15/2023]
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Colquhoun JM, Rather PN. Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis. Front Cell Infect Microbiol 2020; 10:253. [PMID: 32547965 PMCID: PMC7273844 DOI: 10.3389/fcimb.2020.00253] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/30/2020] [Indexed: 01/10/2023] Open
Abstract
Multidrug resistant Acinetobacter baumannii is a serious healthcare threat. In fact, the Center for Disease Control recently reported that carbapenem-resistant A. baumannii is responsible for more than 8,500 infections, 700 deaths, and $281 million in healthcare costs annually in the United States with few, if any, treatment options available, leading to its designation as a pathogen of urgent concern and a priority for novel antimicrobial development. It is hypothesized that biofilms are, at least in part, responsible for the high prevalence of A. baumannii nosocomial and recurrent infections because they frequently contaminate hospital surfaces and patient indwelling devices; therefore, there has been a recent push for mechanistic understanding of biofilm formation, maturation and dispersal. However, most research has focused on A. baumannii pneumonia and bloodstream infections, despite a recent retrospective study showing that 17.1% of A. baumannii isolates compiled from clinical studies over the last two decades were obtained from urinary samples. This highlights that A. baumannii is an underappreciated uropathogen. The following minireview will examine our current understanding of A. baumannii biofilm formation and how this influences urinary tract colonization and pathogenesis.
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Affiliation(s)
- Jennifer M Colquhoun
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Philip N Rather
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States.,Research Service, Atlanta VA Healthcare System, Decatur, GA, United States
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Cameranesi MM, Paganini J, Limansky AS, Moran-Barrio J, Salcedo SP, Viale AM, Repizo GD. Acquisition of plasmids conferring carbapenem and aminoglycoside resistance and loss of surface-exposed macromolecule structures as strategies for the adaptation of Acinetobacter baumannii CC104 O/CC15 P strains to the clinical setting. Microb Genom 2020; 6. [PMID: 32213259 PMCID: PMC7643966 DOI: 10.1099/mgen.0.000360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Acinetobacter baumannii (Aba) is an emerging opportunistic pathogen associated to nosocomial infections. The rapid increase in multidrug resistance (MDR) among Aba strains underscores the urgency of understanding how this pathogen evolves in the clinical environment. We conducted here a whole-genome sequence comparative analysis of three phylogenetically and epidemiologically related MDR Aba strains from Argentinean hospitals, assigned to the CC104O/CC15P clonal complex. While the Ab244 strain was carbapenem-susceptible, Ab242 and Ab825, isolated after the introduction of carbapenem therapy, displayed resistance to these last resource β-lactams. We found a high chromosomal synteny among the three strains, but significant differences at their accessory genomes. Most importantly, carbapenem resistance in Ab242 and Ab825 was attributed to the acquisition of a Rep_3 family plasmid carrying a blaOXA-58 gene. Other differences involved a genomic island carrying resistance to toxic compounds and a Tn10 element exclusive to Ab244 and Ab825, respectively. Also remarkably, 44 insertion sequences (ISs) were uncovered in Ab825, in contrast with the 14 and 11 detected in Ab242 and Ab244, respectively. Moreover, Ab825 showed a higher killing capacity as compared to the other two strains in the Galleria mellonella infection model. A search for virulence and persistence determinants indicated the loss or IS-mediated interruption of genes encoding many surface-exposed macromolecules in Ab825, suggesting that these events are responsible for its higher relative virulence. The comparative genomic analyses of the CC104O/CC15P strains conducted here revealed the contribution of acquired mobile genetic elements such as ISs and plasmids to the adaptation of A. baumannii to the clinical setting.
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Affiliation(s)
- María M Cameranesi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julian Paganini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Moran-Barrio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Suzana P Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR5086, University of Lyon, LyonF-69367, France
| | - Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.,Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR5086, University of Lyon, LyonF-69367, France
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Spatio-Temporal Distribution of Acinetobacter baumannii in Germany-A Comprehensive Systematic Review of Studies on Resistance Development in Humans (2000-2018). Microorganisms 2020; 8:microorganisms8030375. [PMID: 32155886 PMCID: PMC7143851 DOI: 10.3390/microorganisms8030375] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Acinetobacter (A.) baumannii has gained global notoriety as a significant nosocomial pathogen because it is frequently associated with multi-drug resistance and hospital-based outbreaks. There is a substantial difference in the incidence of A. baumannii infections between different countries and within Germany. However, its continuous spread within Germany is a matter of concern. A systematic literature search and analysis of the literature published between 2000 and 2018 on A. baumannii in humans was performed. Forty-four studies out of 216 articles met the criteria for inclusion, and were selected and reviewed. The number of published articles is increasing over time gradually. Case reports and outbreak investigations are representing the main body of publications. North Rhine-Westphalia, Hesse and Baden-Wuerttemberg were states with frequent reports. Hospitals in Cologne and Frankfurt were often mentioned as specialized institutions. Multiresistant strains carrying diverse resistance genes were isolated in 13 of the 16 German states. The oxacillinase blaOXA-23-like, intrinsic blaOXA-51-like, blaOXA-58 variant, blaNDM-1, blaGES-11, blaCTX-M and blaTEM are the most predominant resistance traits found in German A. baumannii isolates. Five clonal lineages IC-2, IC-7, IC-1, IC-4 and IC-6 and six sequence types ST22, ST53, ST195, ST218, ST944/ST78 and ST348/ST2 have been reported. Due to multidrug resistance, colistin, tigecycline, aminoglycosides, fosfomycin, ceftazidime/avibactam and ceftolozan/tazobactam were often reported to be the only effective antibiotics left to treat quadruple multi-resistant Gram-negative (4MRGN) A. baumannii. Dissemination and infection rates of A. baumannii are on the rise nationwide. Hence, several aspects of resistance development and pathogenesis are not fully understood yet. Increased awareness, extensive study of mechanisms of resistance and development of alternative strategies for treatment are required. One-Health genomic surveillance is needed to understand the dynamics of spread, to identify the main reservoirs and routes of transmission and to develop targeted intervention strategies.
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Samantarrai D, Lakshman Sagar A, Gudla R, Siddavattam D. TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation. Microorganisms 2020; 8:microorganisms8030359. [PMID: 32138166 PMCID: PMC7142613 DOI: 10.3390/microorganisms8030359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane.
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Abstract
Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.
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Affiliation(s)
- Steen Christensen
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Laura R Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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Hicks AL, Wheeler N, Sánchez-Busó L, Rakeman JL, Harris SR, Grad YH. Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. PLoS Comput Biol 2019; 15:e1007349. [PMID: 31479500 PMCID: PMC6743791 DOI: 10.1371/journal.pcbi.1007349] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/13/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Prediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics. However, there has been no systematic evaluation of factors that may influence performance of such models, how they might apply to and vary across clinical populations, and what the implications might be in the clinical setting. Here, we performed a meta-analysis of seven large Neisseria gonorrhoeae datasets, as well as Klebsiella pneumoniae and Acinetobacter baumannii datasets, with whole genome sequence data and antibiotic susceptibility phenotypes using set covering machine classification, random forest classification, and random forest regression models to predict resistance phenotypes from genotype. We demonstrate how model performance varies by drug, dataset, resistance metric, and species, reflecting the complexities of generating clinically relevant conclusions from machine learning-derived models. Our findings underscore the importance of incorporating relevant biological and epidemiological knowledge into model design and assessment and suggest that doing so can inform tailored modeling for individual drugs, pathogens, and clinical populations. We further suggest that continued comprehensive sampling and incorporation of up-to-date whole genome sequence data, resistance phenotypes, and treatment outcome data into model training will be crucial to the clinical utility and sustainability of machine learning-based molecular diagnostics.
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Affiliation(s)
- Allison L. Hicks
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
| | - Nicole Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer L. Rakeman
- Public Health Laboratory, Division of Disease Control, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Simon R. Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
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