1
|
Starodumova IP, Dorofeeva LV, Prisyazhnaya NV, Tarlachkov SV, Vasilenko OV, Avtukh AN, Ospennikov YV, Subbotin SA, Evtushenko LI. Rathayibacter tanaceti sp. nov., a Novel Actinobacterium from Tanacetum vulgare Infested by Foliar Nematode Aphelenchoides sp. Curr Microbiol 2024; 81:123. [PMID: 38538917 DOI: 10.1007/s00284-024-03643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/17/2024] [Indexed: 04/23/2024]
Abstract
Two novel yellow-pigmented, rod-shaped and non-motile coryneform actinobacteria, strains VKM Ac-2596T and VKM Ac-2761, were isolated from a plant Tanacetum vulgare (Asteraceae) infested by foliar nematode Aphelenchoides sp. The strains exhibited the highest 16S rRNA gene sequence similarities to Rathayibacter agropyri CA4T (99.71%), Rathayibacter rathayi DSM 7485T (99.65%) and Rathayibacter iranicus VKM Ac-1602T (99.65%). The pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between VKM Ac-2596T and VKM Ac-2671 towards the type strains of Rathayibacter species did not exceed 85.24% and 29.40%, respectively, that are well below the thresholds for species delineation. The target strains had key chemotaxonomic properties typical of the genus Rathayibacter, namely, the DAB-based peptidoglycan, rhamnose and mannose as the predominant sugars and a rhamnomannan in the cell, the major menaquinone MK-10 and fatty acids of iso-anteiso type, with a large proportion of anteiso-15:0. The strains showed clear differences from the recognized Rathayibacter species in several phenotypic characteristics, including the difference in the composition of cell wall glycopolymers. Based on the results obtained in this study and the data published previously, we provide a description of a new species, Rathayibacter tanaceti sp. nov., with DL-642T (= VKM Ac-2596T = LMG 33114T) as the type strain.
Collapse
Affiliation(s)
- Irina P Starodumova
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290.
| | - Lubov V Dorofeeva
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Natalia V Prisyazhnaya
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Sergey V Tarlachkov
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Oleg V Vasilenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Alexander N Avtukh
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Yury V Ospennikov
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Sergei A Subbotin
- Center of Parasitology, A.N. Severtsov Institute of Ecology and Evolution, Moscow, Russia, 119071
- California Department of Food and Agriculture, Sacramento, CA, 95832, USA
| | - Lyudmila I Evtushenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| |
Collapse
|
2
|
Prusokiene A, Boonham N, Fox A, Howard TP. Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent. PLoS One 2024; 19:e0298834. [PMID: 38512939 PMCID: PMC10956839 DOI: 10.1371/journal.pone.0298834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024] Open
Abstract
Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of new viral genomes. To tackle these problems, we propose an approach that uses short-read mappers to create whole-genome maps, and gradient descent to isolate the homologous fraction and calculate the final distance value. We implement this approach as Mottle. With the use of simulated and biological sequences, Mottle was able to remain stable to 0.66-0.96 substitutions per base pair and identify viral outgroup genomes with 95% accuracy at the family-order level. Our results indicate that Mottle performs as well as existing programs in identifying taxonomic relationships, with more accurate numerical estimation of genomic distance over greater divergences. By contrast, one limitation is a reduced numerical accuracy at low divergences, and on genomes where insertions and deletions are uncommon, when compared to alternative approaches. We propose that Mottle may therefore be of particular interest in the study of viruses, viral relationships, and notably for viral discovery platforms, helping in benchmarking of homology search tools and defining the limits of taxonomic classification methods. The code for Mottle is available at https://github.com/tphoward/Mottle_Repo.
Collapse
Affiliation(s)
- Alisa Prusokiene
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
| | - Neil Boonham
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
| | - Adrian Fox
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
- Fera Ltd., Biotech Campus, York, United Kingdom
| | - Thomas P. Howard
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
| |
Collapse
|
3
|
Kudryakova I, Afoshin A, Tarlachkov S, Leontyevskaya E, Suzina N, (Vasilyeva) NL. Lysobacter gummosus 10.1.1, a Producer of Antimicrobial Agents. Microorganisms 2023; 11:2853. [PMID: 38137997 PMCID: PMC10745450 DOI: 10.3390/microorganisms11122853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
This work investigated the antimicrobial potential of Lysobacter gummosus 10.1.1. The culture fluid of the strain was found to contain antimicrobial agents active against Staphylococcus aureus, Micrococcus luteus, and Bacillus cereus. L. gummosus was first shown to be capable of forming outer membrane vesicles, which have a bacteriolytic effect against not only Gram-positive bacteria but also against the Gram-negative pathogen Pseudomonas aeruginosa. Transcriptomic analysis revealed the genes of almost all known bacteriolytic enzymes of Lysobacter, as well as the genes of enzymes with putative bacteriolytic activity. Also identified were genes involved in the biosynthesis of a number of secondary metabolites for which antimicrobial activities are known. This research is indicative of the relevance of isolating and studying L. gummosus antimicrobial agents.
Collapse
Affiliation(s)
| | | | | | | | | | - Natalia Leontyevskaya (Vasilyeva)
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia; (I.K.); (A.A.); (S.T.); (E.L.); (N.S.)
| |
Collapse
|
4
|
Crestani C, Arcari G, Landier A, Passet V, Garnier D, Brémont S, Armatys N, Carmi-Leroy A, Toubiana J, Badell E, Brisse S. Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex. Res Microbiol 2023; 174:104113. [PMID: 37572824 DOI: 10.1016/j.resmic.2023.104113] [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: 04/12/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The Corynebacterium diphtheriae species complex comprises seven bacterial species, including Corynebacterium ulcerans, a zoonotic pathogen from multiple animal species. In this work, we characterise phenotypically and genotypically isolates belonging to two C. ulcerans lineages. Results from phylogenetic analyses, in silico DNA-DNA hybridization (DDH) and MALDI-TOF spectra differentiate lineage 2 from C. ulcerans lineage 1, which, together with their distinct transmission dynamics (probable human-to-human vs animal-to-human), indicates that lineage 2 is a separate Corynebacterium species, which we propose to name Corynebacterium ramonii. This species is of particular medical interest considering that its human-to-human transmission is likely, and that some C. ramonii isolates carry the diphtheria toxin gene.
Collapse
Affiliation(s)
- Chiara Crestani
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
| | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Dorian Garnier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvie Brémont
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Nathalie Armatys
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Annick Carmi-Leroy
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France; Necker-Enfants Malades University Hospital, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France.
| |
Collapse
|
5
|
Baker DN, Langmead B. Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2. Genome Res 2023; 33:1218-1227. [PMID: 37414575 PMCID: PMC10538361 DOI: 10.1101/gr.277655.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023]
Abstract
A genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing data set. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. Although existing tools can easily compare tens of thousands of genomes, data sets can reach millions of sequences and beyond. Popular tools also fail to consider k-mer multiplicities, making them less applicable in quantitative settings. Here, we describe a method called Dashing 2 that builds on the SetSketch data structure. SetSketch is related to HyperLogLog (HLL) but discards use of leading zero count in favor of a truncated logarithm of adjustable base. Unlike HLL, SetSketch can perform multiplicity-aware sketching when combined with the ProbMinHash method. Dashing 2 integrates locality-sensitive hashing to scale all-pairs comparisons to millions of sequences. It achieves superior similarity estimates for the Jaccard coefficient and average nucleotide identity compared with the original Dashing, but in much less time while using the same-sized sketch. Dashing 2 is a free, open source software.
Collapse
Affiliation(s)
- Daniel N Baker
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218-2683, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218-2683, USA
| |
Collapse
|
6
|
Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01852-x. [PMID: 37338631 PMCID: PMC10371898 DOI: 10.1007/s10482-023-01852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, IFB-Core, UMS 3601, Institut Français de Bioinformatique, Evry, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, CIP - Collection of Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| |
Collapse
|
7
|
Xu X, Yin Z, Yan L, Zhang H, Xu B, Wei Y, Niu B, Schmidt B, Liu W. RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches. Genome Biol 2023; 24:121. [PMID: 37198663 PMCID: PMC10190105 DOI: 10.1186/s13059-023-02961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with streaming and parallelization on modern multi-core platforms. 113,674 complete bacterial genome sequences from RefSeq, 455 GB in FASTA format, can be clustered within less than 6 min and 1,009,738 GenBank assembled bacterial genomes, 4.0 TB in FASTA format, within only 34 min on a 128-core workstation. Our results further identify 1269 redundant genomes, with identical nucleotide content, in the RefSeq bacterial genomes database.
Collapse
Affiliation(s)
- Xiaoming Xu
- School of Software, Shandong University, Jinan, China
| | - Zekun Yin
- School of Software, Shandong University, Jinan, China
- Shenzhen Research Institute of Shandong University, Shandong University, Shenzhen, China
| | - Lifeng Yan
- School of Software, Shandong University, Jinan, China
- Shenzhen Research Institute of Shandong University, Shandong University, Shenzhen, China
| | - Hao Zhang
- School of Software, Shandong University, Jinan, China
- Shenzhen Research Institute of Shandong University, Shandong University, Shenzhen, China
| | - Borui Xu
- School of Software, Shandong University, Jinan, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Bertil Schmidt
- Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany
| | - Weiguo Liu
- School of Software, Shandong University, Jinan, China
| |
Collapse
|
8
|
Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes. Int J Mol Sci 2023; 24:ijms24032905. [PMID: 36769231 PMCID: PMC9918034 DOI: 10.3390/ijms24032905] [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: 12/06/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.
Collapse
|
9
|
Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root. Arch Microbiol 2022; 204:630. [PMID: 36115912 PMCID: PMC9482572 DOI: 10.1007/s00203-022-03225-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022]
Abstract
A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA−DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, Institut Français de Bioinformatique, IFB-Core, UMS 3601, Evry, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP-Collection of Institut Pasteur, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| |
Collapse
|
10
|
Harimanana A, Rakotondrasoa A, Rivoarilala LO, Criscuolo A, Opatowski L, Rakotomanana EFN, Herindrainy P, Collard JM, Crucitti T, Huynh BT. Neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the community of a low-income country (NeoLIC): protocol for a household cohort study in Moramanga, Madagascar. BMJ Open 2022; 12:e061463. [PMID: 36153019 PMCID: PMC9511544 DOI: 10.1136/bmjopen-2022-061463] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
INTRODUCTION Data regarding the acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) in neonates at the community level are scarce in low-income and middle-income countries (LMICs), where the burden of neonatal sepsis is high.Our study aims at identifying and quantifying the role of the different routes of ESBL-PE transmission for neonates, which are still undefined in the community in LMICs. METHODS AND ANALYSIS In a semirural community in Madagascar, 60 mothers and their neonates will be recruited at delivery, during which a maternal stool sample and meconium of the newborn will be collected. Home visits will be planned the day of the delivery and next at days 3, 7, 14, 21 and 28. Stool samples from the newborn, the mother and every other household member will be collected at each visit, as well as samples from the environment in contact with the newborn (food, surfaces and objects). Sociodemographic data and factors which might drive ESBL-PE acquisition will also be collected.We will analyse the isolated ESBL-PE using DNA sequencing methods to characterise clones, resistance genes and plasmids of ESBL-PE. To analyse these data globally, we will develop novel analytical approaches combining mathematical modelling and statistics. Finally, mathematical simulations will be performed to test different strategies of control of ESBL-PE transmission to neonates.In complement, we will conduct an anthropological investigation to understand local environments and practices that would contribute to neonatal ESBL-PE acquisition. In-depth interviews with members of 16 households will be conducted and 4 mother-newborn pairs will be followed by a participants' observations methodology. ETHICS AND DISSEMINATION The study was approved by the ethical committee in Madagascar and by the institutional review board of Institut Pasteur, Paris, France.Findings will be reported to participating families, collaborators and local government; presented at national and international conferences and disseminated by peer-review publications.
Collapse
Affiliation(s)
| | | | | | - Alexis Criscuolo
- Institut Pasteur, Paris, Île-de-France, France
- Université de Paris, Paris, Île-de-France, France
| | - Lulla Opatowski
- Institut Pasteur, Paris, Île-de-France, France
- Institut National de la Santé et de la Recherche Médicale, Université de Versailles Saint-Quentin-en-Yvelines and Université Paris-Saclay, Montigny-Le-Bretonneux, Île-de-France, France
| | | | - Perlinot Herindrainy
- Infectious Disease Detection and Surveillance, ICF International, Antananarivo, Madagascar
| | - Jean-Marc Collard
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Tania Crucitti
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Bich-Tram Huynh
- Institut Pasteur, Paris, Île-de-France, France
- Institut National de la Santé et de la Recherche Médicale, Université de Versailles Saint-Quentin-en-Yvelines and Université Paris-Saclay, Montigny-Le-Bretonneux, Île-de-France, France
| |
Collapse
|
11
|
Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Mol Biol Evol 2022; 39:6608353. [PMID: 35700230 PMCID: PMC9254007 DOI: 10.1093/molbev/msac135] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.
Collapse
Affiliation(s)
- Melanie Hennart
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Julien Guglielmini
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Sébastien Bridel
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alexis Criscuolo
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | | |
Collapse
|
12
|
Kämpfer P, McInroy JA, Clermont D, Neumann-Schaal M, Criscuolo A, Busse HJ, Glaeser SP. Leucobacter soli sp. nov., from soil amended with humic acid. Int J Syst Evol Microbiol 2021; 71. [PMID: 34904944 DOI: 10.1099/ijsem.0.005156] [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] [Indexed: 01/31/2023] Open
Abstract
A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, AL 36849, USA
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP-Collection de l´Institut Pasteur, F-75015 Paris, France
| | - Meina Neumann-Schaal
- Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015 Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| |
Collapse
|
13
|
Kämpfer P, Busse HJ, Clermont D, Criscuolo A, Glaeser SP. Devosia equisanguinis sp. nov., isolated from horse blood. Int J Syst Evol Microbiol 2021; 71. [PMID: 34788212 DOI: 10.1099/ijsem.0.005090] [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] [Indexed: 12/29/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25-37 °C (range: 10-36 °C), at a pH range of pH 6.5-10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia. Major fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia, for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien, Austria
| | - Dominique Clermont
- CIP - Collection of Institut Pasteur, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| |
Collapse
|
14
|
Kämpfer P, Busse HJ, McInroy JA, Clermont D, Criscuolo A, Glaeser SP. Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672916 DOI: 10.1099/ijsem.0.005051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA-DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK-6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien A-1210, Austria
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| |
Collapse
|
15
|
Kämpfer P, Glaeser SP, McInroy JA, Clermont D, Criscuolo A, Busse HJ. Pseudomonas carbonaria sp. nov., isolated from charcoal. Int J Syst Evol Microbiol 2021; 71. [PMID: 33835910 DOI: 10.1099/ijsem.0.004750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| |
Collapse
|