Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties

Deredjian, Amélie; Alliot, Nolwenn; Blanchard, Laurine; Brothier, Elisabeth; Anane, Makram; Cambier, Philippe; Jolivet, Claudy; Khelil, Mohamed Naceur; Nazaret, Sylvie; Saby, Nicolas P.A.; Thioulouse, Jean; Favre-Bonté, Sabine

doi:10.1016/j.resmic.2016.01.001

Cited by 33 publications

(26 citation statements)

References 43 publications

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“…S. maltophilia-like organisms display high genetic, ecological and phenotypic diversity (Valdezate et al, 2004;Vasileuskaya-Schulz et al, 2011), forming the so-called S. maltophilia complex (Smc) (Berg and Martinez, 2015;Svensson-Stadler et al, 2012). Heterogeneous resistance and virulence phenotypes have been reported for environmental isolates of diverse ecological origin classified as S. maltophilia (Adamek et al, 2011;Deredjian et al, 2016). We have recently shown that this phenotypic heterogeneity largely results from problems in species delimitations within the Smc (Ochoa-Sánchez and Vinuesa, 2017).…”

Section: Introductionmentioning

confidence: 99%

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Vinuesa

Ochoa-Sánchez

Contreras‐Moreira

2018

Preprint

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The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 14 misclassified RefSeq genome sequences, 12 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

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Section: Introductionmentioning

confidence: 99%

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Vinuesa

Ochoa-Sánchez

Contreras‐Moreira

2018

Preprint

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“…Regarding S. maltophilia, no supplementary antibiotic resistance was detected compared to natural resistance. These strains displayed an antibiotic resistance phenotype close to S. maltophilia strains isolated from French soils and different to MDR S. maltophilia strains isolated from Tunisia and Burkina Faso soils (Deredjian et al 2016).…”

Section: Discussionmentioning

confidence: 82%

“…Those from Burkina Faso were collected in a field planted with sorghum at the periphery of Ouagadougou during summer (February after a rainy period) under sub-Sahelian climate. At each location, the samples were collected from the upper layer (0-10 or 0-20 cm) and sifted through 2-mm-mesh sieves before processing (Deredjian et al 2016). Soil characteristics are shown in Supplementary Table 1.…”

Section: Soil Origin and Samplingmentioning

confidence: 99%

Diversity of free-living amoebae in soils and their associated human opportunistic bacteria

et al. 2017

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Free-living amoebae (FLA) are ubiquitous protozoa found worldwide in the environment. They feed by phagocytosis on various microorganisms. However, some bacteria, i.e., amoebae-resistant bacteria (ARB) or bacterial endocytobionts, can resist phagocytosis and even multiply inside FLA. This study investigated the diversity of culturable FLA in various soils from agricultural and mining sites and their bacterial endocytobionts. FLA were cultured on non-nutrient agar with alive Escherichia coli and identified by PCR and sequencing. Amoebae were lysed and bacterial endocytobionts were cultured on TSA 1/10 and Drigalski medium. Bacterial isolates were identified by PCR and 16S rDNA sequencing and characterized for their antibiotic resistance properties. To measure bacterial virulence, the amoebal model Dictyostelium discoideum was used. The analysis of FLA diversity showed that Tetramitus was the most prevalent genus in agricultural soil from Burkina Faso (73%) and garden soil from Vietnam (42%) while Naegleria and Acanthamoeba were dominant genera in mining soil from Vietnam (55%) and French alpine soil (77%). Some genera were only present in one out of the four soils analyzed. The bacterial endocytobiont included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Human opportunistic pathogens identified as Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Burkholderia cepacia were found associated with amoebae including Micriamoeba, Tetramitus, Willaertia, or Acanthamoeba. Some of these bacteria showed various antibiotic resistance phenotypes and were virulent. Our study confirms that the occurrence of these opportunistic bacteria with FLA in soils may be important for the survival, multiplication, and spread of pathogens in the environment.

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“…The nif gene presence/absence profiles were found to be highly similar for all but four of the bacterial isolates characterized here, those which are not members of the Klebsiella genus, or closely related species, and do not encode any nif genes. The four non-nitrogen fixing isolates represent bacterial species that are commonly found in soil (20–23), but they are not predicted to be viable biofertilizers. The Kosakonia radicincitans genome encodes the largest number of nif genes ( n =17) observed for any of the Colombian sugarcane isolates.…”

Section: Resultsmentioning

confidence: 99%

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Medina-Cordoba

Chande

Rishishwar

et al. 2019

Preprint

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23 24 KEYWORDS: biofertilizer, nitrogen fixation, plant growth promoter, genome 25 sequencing, computational phenotyping 26 2ABSTRACT Previous studies have shown that the sugarcane microbiome harbors diverse 27 plant growth promoting (PGP) microorganisms, including nitrogen-fixing bacteria, and the 28 objective of this study was to design a genome-enabled approach to prioritize sugarcane 29 associated nitrogen-fixing bacteria according to their potential as biofertilizers. Using a 30 systematic high throughput approach, 22 pure cultures of nitrogen-fixing bacteria were isolated 31 and tested for diazotrophic potential by PCR amplification of nitrogenase (nifH) genes, common 32 molecular markers for nitrogen fixation capacity. Genome sequencing confirmed the presence 33 of intact nitrogenase nifH genes and operons in the genomes of 18 of the isolates. Isolate 34 genomes also encoded operons for phosphate solubilization, siderophore production operons, 35 and other PGP phenotypes. Klebsiella pneumoniae strains comprised 14 of the 22 nitrogen-36fixing isolates, and four others were members of closely related genera to Klebsiella. A 37 computational phenotyping approach was developed to rapidly screen for strains that have high 38 potential for nitrogen fixation and other PGP phenotypes while showing low risk for virulence 39 and antibiotic resistance. The majority of sugarcane isolates were below a genotypic and 40 phenotypic threshold, showing uniformly low predicted virulence and antibiotic resistance 41 compared to clinical isolates. Six prioritized strains were experimentally evaluated for PGP 42 phenotypes: nitrogen fixation, phosphate solubilization, and the production of siderophores, 43 gibberellic acid and indole acetic acid. Results from the biochemical assays were consistent 44 with the computational phenotype predictions for these isolates. Our results indicate that 45 computational phenotyping is a promising tool for the assessment of benefits and risks 46 associated with bacteria commonly detected in agricultural ecosystems. IMPORTANCE A genome-enabled approach was developed for the prioritization of 48 native bacterial isolates with the potential to serve as biofertilizers for sugarcane fields 49 in Colombia's Cauca Valley. The approach is based on computational phenotyping, 50 which entails predictions related to traits of interest based on bioinformatic analysis of 51 whole genome sequences. Bioinformatic predictions of the presence of plant growth 52 promoting traits were validated with experimental assays and more extensive genome 53 comparisons, thereby demonstrating the utility of computational phenotyping for 54 assessing the benefits and risks posed by bacterial isolates that can be used as 55 biofertilizers. The quantitative approach to computational phenotyping developed here 56 for the discovery of biofertilizers has the potential for use with a broad range of 57 applications in environmental and industrial microbiology, food safety, water quality, and 58 antibiotic resistance studies. 6...

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Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties

Cited by 33 publications

References 43 publications

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Diversity of free-living amoebae in soils and their associated human opportunistic bacteria

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

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