Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC 13637)

Davenport, Karen W.; Daligault, Hajnalka E.; Minogue, Timothy D.; Broomall, S. M.; Bruce, David; Chain, Patrick; Coyne, S. R.; Gibbons, Henry S.; Jaissle, J.; Li, P.-E.; Rosenzweig, C. Nicole; Scholz, Matthew; Johnson, Shannon L.

doi:10.1128/genomea.00974-14

Cited by 16 publications

(14 citation statements)

References 12 publications

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“…Bacterial study. Five collection strains and widely known biofilm producers, that is, S. aureus 15981 (77-80), S. epidermidis ATCC 35984 (81)(82)(83), E. coli ATCC 25922 (84)(85)(86), P. aeruginosa ATCC 27853 (87)(88)(89), and S. maltophilia ATCC 13637 (90,91), were used. All the strains were kept frozen at Ϫ80°C until the experiments were performed.…”

Section: Methodsmentioning

confidence: 99%

Microbiological and Cellular Evaluation of a Fluorine-Phosphorus-Doped Titanium Alloy, a Novel Antibacterial and Osteostimulatory Biomaterial with Potential Applications in Orthopedic Surgery

Aguilera-Correa

Mediero

Conesa-Buendía

et al. 2019

Appl Environ Microbiol

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Joint prosthesis failure is mainly related to aseptic loosening and prosthetic joint infections, both of which are associated with high morbidity and substantial costs for patients and health systems. The development of a biomaterial that is capable of stimulating bone growth while minimizing bacterial adhesion would reduce the incidence of prosthetic failure. We report antibacterial and osteostimulatory effects in a novel fluorine-phosphorus (F-P)-doped TiO2 oxide film grown on Ti-6Al-4V alloy with a nanostructure of bottle-shaped nanotubes (bNT) using five bacterial species (Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia) and MCT3T3-E1 osteoblastic cells. The interaction between the bacteria and bNT Ti-6Al-4V was complex, as the adhesion of four bacterial species decreased (two staphylococcus species, E. coli, and S. maltophilia), and the viability of staphylococci and S. maltophilia also decreased because of the aluminum (Al) released by bNT Ti-6Al-4V. This released Al can be recruited by the bacteria through siderophores and was retained only by the Gram-negative bacteria tested. P. aeruginosa showed higher adhesion on bNT Ti-6Al-4V than on chemically polished (CP) samples of Ti-6Al-4V alloy and an ability to mobilize Al from bNT Ti-6Al-4V. The cell adhesion and proliferation of MCT3T3-E1 osteoblastic cells significantly increased at 48 and 168 h, as did the matrix mineralization of these cells and the gene expression levels of three of the most important markers related to bone differentiation. According to our results, the bNT Ti-6Al-4V alloy could have clinical application, preventing infection and stimulating bone growth and thus preventing the two main causes of joint prosthesis failure. IMPORTANCE This work evaluates F-P-doped bNT Ti-6Al-4V from microbiological and cellular approaches. The bacterial results highlight that the antibacterial ability of bNT Ti-6Al-4V is the result of a combination of antiadhesive and bactericidal effects exerted by Al released from the alloy. The cell results highlight that F-P bNT Ti-6Al-4V alloy increases osseointegration due to modification of the chemical composition of the alloy resulting from P incorporation and not due to the nanostructure, as reported previously. A key finding was the detection of Al release from inside the bNT Ti-6Al-4V nanostructures, a result of the nanostructure growth during the anodizing process that is in part responsible for its bactericidal effect.

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Section: Methodsmentioning

confidence: 99%

Microbiological and Cellular Evaluation of a Fluorine-Phosphorus-Doped Titanium Alloy, a Novel Antibacterial and Osteostimulatory Biomaterial with Potential Applications in Orthopedic Surgery

Aguilera-Correa

Mediero

Conesa-Buendía

et al. 2019

Appl Environ Microbiol

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“…The main objectives of this study were: (i) to identify genetically cohesive and differentiated sequence clusters (genospecies) among a collection of environmental Stenotrophomonas isolates by using a combination of state-of-the-art phylogenetic and population genetic methods; (ii) to test whether such lineages exhibit distinct phenotypic and ecological attributes, as predicted by current models of bacterial speciation. We used the multilocus dataset for the genus available at pubmlst.org ( Kaiser et al, 2001 ; Vasileuskaya-Schulz et al, 2011 ), and extended it with sequences extracted from complete ( Crossman et al, 2008 ; Lira et al, 2012 ; Zhu et al, 2012 ; Davenport et al, 2014 ; Vinuesa and Ochoa-Sánchez, 2015 ) and draft ( Patil et al, 2016 ) genome sequences to assemble a comprehensive MLSA dataset with representative strains of 11 out of 12 validly described Stenotrophomonas species. We used this reference dataset to study our collection of environmental Stenotrophomonas isolates ( n = 108) recovered from the sediments and water column of several rivers with contrasting levels of contamination in the state of Morelos, Central Mexico.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

Ochoa-Sánchez

Vinuesa

2017

Front. Microbiol.

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The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.

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“…We analyzed the genetic diversity in a collection of 108 Stenotrophomonas isolates recovered from several water bodies in Morelos, Central Mexico, based on sequence data generated for the 7 loci used in the Multilocus Sequence Typing (MLST) scheme available for S. maltophilia at https://pubmlst.org. We assembled a large set of reference sequences retrieved from the MLST database (Kaiser et al, 2009;Vasileuskaya-Schulz et al, 2011) and from selected genome sequences (Crossman et al, 2008;Davenport et al, 2014;Lira et al, 2012;Patil et al, 2016;Vinuesa and Ochoa-Sánchez, 2015), encompassing 11 out of the 12 validly described species at the time. State-of-the-art phylogenetic and population genetics methods, including the multispecies coalescent model coupled with Bayes factor analysis and Bayesian clustering of the multilocus genotypes consistently resolved five conservativelydefined genospecies within the Smc clade, which were named S. maltophilia and Smc1-Smc4.…”

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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Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC 13637)

Cited by 16 publications

References 12 publications

Microbiological and Cellular Evaluation of a Fluorine-Phosphorus-Doped Titanium Alloy, a Novel Antibacterial and Osteostimulatory Biomaterial with Potential Applications in Orthopedic Surgery

Microbiological and Cellular Evaluation of a Fluorine-Phosphorus-Doped Titanium Alloy, a Novel Antibacterial and Osteostimulatory Biomaterial with Potential Applications in Orthopedic Surgery

Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

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

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