1
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Wong Z, Ong EBB. Unravelling bacterial virulence factors in yeast: From identification to the elucidation of their mechanisms of action. Arch Microbiol 2024; 206:303. [PMID: 38878203 DOI: 10.1007/s00203-024-04023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Pathogenic bacteria employ virulence factors (VF) to establish infection and cause disease in their host. Yeasts, Saccharomyces cerevisiae and Saccharomyces pombe, are useful model organisms to study the functions of bacterial VFs and their interaction with targeted cellular processes because yeast processes and organelle structures are highly conserved and similar to higher eukaryotes. In this review, we describe the principles and applications of the yeast model for the identification and functional characterisation of bacterial VFs to investigate bacterial pathogenesis. The growth inhibition phenotype caused by the heterologous expression of bacterial VFs in yeast is commonly used to identify candidate VFs. Then, subcellular localisation patterns of bacterial VFs can provide further clues about their target molecules and functions during infection. Yeast knockout and overexpression libraries are also used to investigate VF interactions with conserved eukaryotic cell structures (e.g., cytoskeleton and plasma membrane), and cellular processes (e.g., vesicle trafficking, signalling pathways, and programmed cell death). In addition, the yeast growth inhibition phenotype is also useful for screening new drug leads that target and inhibit bacterial VFs. This review provides an updated overview of new tools, principles and applications to study bacterial VFs in yeast.
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Affiliation(s)
- ZhenPei Wong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800 USM, Malaysia
| | - Eugene Boon Beng Ong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800 USM, Malaysia.
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2
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Neil B, Cheney GL, Rosenzweig JA, Sha J, Chopra AK. Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing. Appl Microbiol Biotechnol 2024; 108:205. [PMID: 38349402 PMCID: PMC10864486 DOI: 10.1007/s00253-024-13055-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans.
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Affiliation(s)
- Blake Neil
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Gabrielle L Cheney
- John Sealy School of Medicine, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Jason A Rosenzweig
- Department of Biology, Texas Southern University, Houston, TX, 77004, USA
| | - Jian Sha
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Ashok K Chopra
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA.
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3
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Zhu Z, Wu S, Zhu J, Wang T, Wen Y, Yang C, Lv J, Zhang H, Chen L, Du H. Emergence of Aeromonas veronii strain co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b cluster from hospital sewage in China. Front Microbiol 2023; 14:1115740. [PMID: 37266015 PMCID: PMC10229833 DOI: 10.3389/fmicb.2023.1115740] [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: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction The raise of multi-drug resistant bacteria involving carbapenem, colistin, or tigecycline resistance constitutes a threat to public health, which partly results from the transmission of corresponding mobile resistance genes, such as blaKPC and blaNDM for carbapenem, mcr for colistin, and tmexCD-toprJ gene cluster for tigecycline. Herein, we described the emergence of an Aeromonas veronii strain HD6454 co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster from hospital sewage. Methods Whole genome sequencing (WGS) was used to determine the genome sequence of HD6454, and the detailed genomic analysis of genetic elements or regions carrying key antimicrobial resistance genes (ARGs) from HD6454 were performed. Cloning experiment was conducted to confirm the function of key ARGs in mediating antimicrobial resistance. Conjugation experiment was conducted to determine the mobility of the plasmid. Results The results showed that this strain belonged to a novel sequence type (ST) variant ST1016, and carried 18 important ARGs. Among them, the blaKPC-2 was carried by non-self-transmissible IncP-6 plasmid, while tmexC3.2-tmexD3.3-toprJ1b gene cluster and mcr-3.17 were carried by integrative and mobilizable element (IME) or IME-related region in chromosome. The mcr-3.17, mcr-3.6, and mcr-3-like3 genes were further inferred to originate from IMEs of Aeromonas species. Additionally, for the first time, the mcr-3.17 was confirmed to confer low-level resistance to colistin under inducible expression, while tmexC3.2-tmexD3.3-toprJ1b gene cluster was confirmed to confer low-level resistance to tigecycline. Discussion This is the first report of a strain co-harboring blaKPC-2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster. Although the resistance and/or mobility of these ARGs are limited in this strain, the emergence of this multiple important ARGs-carrying strain deserves further attention.
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Affiliation(s)
- Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Shuhua Wu
- Department of Geriatrics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of General Practice, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jie Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tao Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yicheng Wen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chengcheng Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jinnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Seton Hall University, Nutley, NJ, United States
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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4
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Matys J, Turska-Szewczuk A, Gieroba B, Kurzylewska M, Pękala-Safińska A, Sroka-Bartnicka A. Evaluation of Proteomic and Lipidomic Changes in Aeromonas-Infected Trout Kidney Tissue with the Use of FT-IR Spectroscopy and MALDI Mass Spectrometry Imaging. Int J Mol Sci 2022; 23:ijms232012551. [PMID: 36293421 PMCID: PMC9604335 DOI: 10.3390/ijms232012551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Aeromonas species are opportunistic bacteria causing a vast spectrum of human diseases, including skin and soft tissue infections, meningitis, endocarditis, peritonitis, gastroenteritis, and finally hemorrhagic septicemia. The aim of our research was to indicate the molecular alterations in proteins and lipids profiles resulting from Aeromonas sobria and A. salmonicida subsp. salmonicida infection in trout kidney tissue samples. We successfully applied FT-IR (Fourier transform infrared) spectroscopy and MALDI-MSI (matrix-assisted laser desorption/ionization mass spectrometry imaging) to monitor changes in the structure and compositions of lipids, secondary conformation of proteins, and provide useful information concerning disease progression. Our findings indicate that the following spectral bands’ absorbance ratios (spectral biomarkers) can be used to discriminate healthy tissue from pathologically altered tissue, for example, lipids (CH2/CH3), amide I/amide II, amide I/CH2 and amide I/CH3. Spectral data obtained from 10 single measurements of each specimen indicate numerous abnormalities concerning proteins, lipids, and phospholipids induced by Aeromonas infection, suggesting significant disruption of the cell membranes. Moreover, the increase in the content of lysolipids such as lysophosphosphatidylcholine was observed. The results of this study suggest the application of both methods MALDI-MSI and FT-IR as accurate methods for profiling biomolecules and identifying biochemical changes in kidney tissue during the progression of Aeromonas infection.
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Affiliation(s)
- Joanna Matys
- Department of Biopharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (J.M.); (A.S.-B.)
| | - Anna Turska-Szewczuk
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Barbara Gieroba
- Independent Unit of Spectroscopy and Chemical Imaging, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Maria Kurzylewska
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Agnieszka Pękala-Safińska
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland
| | - Anna Sroka-Bartnicka
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
- Independent Unit of Spectroscopy and Chemical Imaging, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (J.M.); (A.S.-B.)
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5
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Gosselin S, Fullmer MS, Feng Y, Gogarten JP. Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support. Syst Biol 2022; 71:396-409. [PMID: 34289044 PMCID: PMC8830074 DOI: 10.1093/sysbio/syab060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 11/13/2022] Open
Abstract
Whole-genome comparisons based on average nucleotide identities (ANI) and the genome-to-genome distance calculator have risen to prominence in rapidly classifying prokaryotic taxa using whole-genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole-genome divergence data to the delineation of higher taxonomic units and to phylogenetic inference have had difficulty matching those produced by more complex phylogenetic methods. We present a novel method for generating statistically supported phylogenies of archaeal and bacterial groups using a combined ANI and alignment fraction-based metric. For the test cases to which we applied the developed approach, we obtained results comparable with other methodologies up to at least the family level. The developed method uses nonparametric bootstrapping to gauge support for inferred groups. This method offers the opportunity to make use of whole-genome comparison data, that is already being generated, to quickly produce phylogenies including support for inferred groups. Additionally, the developed ANI methodology can assist the classification of higher taxonomic groups.[Average nucleotide identity (ANI); genome evolution; prokaryotic species delineation; taxonomy.].
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Affiliation(s)
- Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268-3125, USA
| | - Matthew S Fullmer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268-3125, USA.,Bioinformatics Institute, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268-3125, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268-3125, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06268-3125, USA
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6
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Chen YW, Su SL, Li CW, Tsai CS, Lo CL, Syue LS, Li MC, Lee CC, Lee NY, Ko WC, Chen PL. Pancreaticobiliary Cancers and Aeromonas Isolates Carrying Type Ⅲ Secretion System Genes ascF-ascG Are Associated With Increased Mortality: An Analysis of 164 Aeromonas Infection Episodes in Southern Taiwan. Front Cell Infect Microbiol 2021; 11:749269. [PMID: 34737976 PMCID: PMC8562565 DOI: 10.3389/fcimb.2021.749269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
This prospective study aimed to investigate the clinical and microbiological characteristics of different Aeromonas species. Clinical isolates of Aeromonas species between 2016 to 2018 were collected in a university hospital in southern Taiwan. The species was determined by rpoD or gyrB sequencing. A total of 222 Aeromonas isolates from 160 patients in 164 episodes were identified. The crude in-hospital mortality was 17.2%. The most frequently isolated species was Aeromonas veronii (30.6%), followed by A. caviae (24.8%), A. hydrophila (23%), and A. dhakensis (16.7%). The major clinical manifestations were primary bacteremia (31.1%), skin and soft tissue infection (22.6%), and biliary tract infection (18.3%). The most common underlying diseases were malignancy (45.1%), diabetes mellitus (27.4%), and liver cirrhosis or chronic hepatitis (26.2%). A. hydrophila and A. dhakensis predominated in the skin and soft tissue infection (p<0.0001), whereas A. vernoii and A. caviae prevailed in primary bacteremia and biliary tract infections (p=0.012). Pneumonia, malignancy, and ascF-ascG genotype were independent factors associated with mortality. Ertapenem susceptibility was decreased in A. sobria (42.9%), A. veronii (66.7%), A. dhakensis (73%), and A. hydrophila (84.3%). Cefotaxime resistance was found in 30.9% of A. caviae and 18.9% of A. dhakensis isolates, much more prevalent than the other species. The metallo-β-lactamase blaCphA was almost invariably present in A. dhakensis, A. hydrophila, and A. veronii (100%, 100% and 89.9%, respectively). Amp-C β-lactamases such as blaMOX and blaAQU-1 were identified in all A. caviae and 91.9% of A. dhakensis isolates. Cefepime, fluoroquinolones and tigecycline showed good in vitro activity against aeromonads.
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Affiliation(s)
- Ying-Wen Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Li Su
- Diagnostic Microbiology and Antimicrobial Resistance Laboratory, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Wen Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Shiang Tsai
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Lung Lo
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ling-Shan Syue
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Min-Chi Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chi Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Infection Control Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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7
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Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP. An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets. Genome Biol Evol 2021; 13:6352501. [PMID: 34390574 PMCID: PMC8483891 DOI: 10.1093/gbe/evab187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 11/25/2022] Open
Abstract
Assessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances. The utilization of pairwise distance matrices circumvents comparisons between gene tree topologies, which are inherently uncertain and sensitive to evolutionary model choice, phylogenetic reconstruction artifacts, and other sources of error. Furthermore, IES enables the many-to-many pairing of multiple copies between similarly evolving gene families. This is done by selecting non-overlapping pairs of copies, one from each assessed family, and yielding the least sum of squared residuals. Analyses of simulated gene family data sets show that IES’s accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model fitting. Applying IES to an empirical data set of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. The most cohesive cluster consisted of 62 genes with compatible evolutionary signal, which occur as both single-copy and multiple homologs per genome; phylogenetic analysis of concatenated alignments from this cluster produced a tree closely matching previously published species trees for Archaea. Four other clusters are mainly composed of accessory genes with limited distribution among Archaea and enriched toward specific metabolic functions. Pairwise evolutionary distances obtained from these accessory gene clusters suggest patterns of interphyla horizontal gene transfer. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.
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Affiliation(s)
- Luiz Thibério Rangel
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Corresponding author: E-mail:
| | - Shannon M Soucy
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brasil
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, USA
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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8
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Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS. Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes. Mol Biol Evol 2021; 38:2639-2659. [PMID: 33565580 PMCID: PMC8136488 DOI: 10.1093/molbev/msab043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.
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Affiliation(s)
- Lina Kloub
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matthew Fullmer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Bioinformatics Institute, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mukul S Bansal
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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9
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Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP. The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biol Evol 2021; 13:6320066. [PMID: 34255041 PMCID: PMC8350355 DOI: 10.1093/gbe/evab166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2021] [Indexed: 12/12/2022] Open
Abstract
Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; whereas the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (distantly related groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/noncatalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.
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Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Neri
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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10
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Talagrand-Reboul E, Colston SM, Graf J, Lamy B, Jumas-Bilak E. Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas. Genome Biol Evol 2021; 12:535-552. [PMID: 32196086 PMCID: PMC7250499 DOI: 10.1093/gbe/evaa055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, France
| | - Sophie M Colston
- US Naval Research Laboratory, National Academy of Sciences, National Research Council, Washington, District of Columbia
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département de Bactériologie, CHU de Nice and Université Côte d'Azur, INSERM, C3M, Nice, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département d'Hygiène Hospitalière, CHRU de Montpellier, France
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Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech. Appl Environ Microbiol 2021; 87:AEM.02082-20. [PMID: 33674439 DOI: 10.1128/aem.02082-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
Leeches are found in terrestrial, aquatic, and marine habitats on all continents. Sanguivorous leeches have been used in medicine for millennia. Modern scientific uses include studies of neurons, anticoagulants, and gut microbial symbioses. Hirudo verbana, the European medicinal leech, maintains a gut community dominated by two bacterial symbionts, Aeromonas veronii and Mucinivorans hirudinis, which sometimes account for as much as 97% of the total crop microbiota. The highly simplified gut anatomy and microbiome of H. verbana make it an excellent model organism for studying gut microbial dynamics. The North American medicinal leech, Macrobdella decora, is a hirudinid leech native to Canada and the northern United States. In this study, we show that M. decora symbiont communities are very similar to those in H. verbana. We performed an extensive study using field-caught M. decora and purchased H. verbana from two suppliers. Deep sequencing of the V4 region of the 16S rRNA gene allowed us to determine that the core microbiome of M. decora consists of Bacteroides, Aeromonas, Proteocatella, and Butyricicoccus. The analysis revealed that the compositions of the gut microbiomes of the two leech species were significantly different at all taxonomic levels. The R 2 value was highest at the genus and amplicon sequence variant (ASV) levels and much lower at the phylum, class, and order levels. The gut and bladder microbial communities were distinct. We propose that M. decora is an alternative to H. verbana for studies of wild-caught animals and provide evidence for the conservation of digestive-tract and bladder symbionts in annelid models.IMPORTANCE Building evidence implicates the gut microbiome in critical animal functions such as regulating digestion, nutrition, immune regulation, and development. Simplified, phylogenetically diverse models for hypothesis testing are necessary because of the difficulty of assigning causative relationships in complex gut microbiomes. Previous research used Hirudo verbana as a tractable animal model of digestive-tract symbioses. Our data show that Macrobdella decora may work just as well without the drawback of being an endangered organism and with the added advantage of easy access to field-caught specimens. The similarity of the microbial community structures of species from two different continents reveals the highly conserved nature of the microbial symbionts in sanguivorous leeches.
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Bruce TJ, Ma J, Oliver LP, Jones EM, LaFrentz BR, Cain KD. Isolation and experimental challenge of cultured burbot (Lota lota maculosa) with Flavobacterium columnare and Aeromonas sp. isolates. JOURNAL OF FISH DISEASES 2020; 43:839-851. [PMID: 32618015 DOI: 10.1111/jfd.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Burbot (Lota lota maculosa) are a potential new species for commercial aquaculture. As burbot culture expands, there is a need to further define pathogen susceptibility and characterize aspects of the burbot immune response in an effort to assess fish health. A recent clinical diagnostic case from juvenile burbot reared at a commercial production facility resulted in the isolation and identification of Flavobacterium columnare along with several Aeromonas spp. The F. columnare isolate was assigned to genetic group 1 via multiplex PCR, a genetic group commonly associated with columnaris disease cases in rainbow trout (Oncorhynchus mykiss). Virulence of the F. columnare isolate was assessed in vivo in both juvenile burbot and rainbow trout. Additionally, several of the Aeromonas sp. case isolates were identified via sequencing (16S rRNA, gyrB and rpoD) and a putative A. sobria isolate (BI-3) was used to challenge burbot, along with a known virulent Aeromonas sp. (A141), but BI-3 was not found to be virulent. Burbot were refractory to F. columnare when challenged by immersion, and it is likely that this is a secondary pathogen for burbot. Although refractory in burbot, the identified F. columnare isolate (BI-1) was found to be virulent in rainbow trout.
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Affiliation(s)
- Timothy J Bruce
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Jie Ma
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Luke P Oliver
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Evan M Jones
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | | | - Kenneth D Cain
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
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Fernández-Bravo A, Figueras MJ. An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity. Microorganisms 2020; 8:microorganisms8010129. [PMID: 31963469 PMCID: PMC7022790 DOI: 10.3390/microorganisms8010129] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.
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