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1.
Rev Soc Bras Med Trop ; 53: e20190470, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32428175

RESUMEN

INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.


Asunto(s)
Genoma Bacteriano/genética , Modelos Genéticos , Mycobacterium tuberculosis/genética , Análisis de Ondículas , Humanos
2.
BMC Bioinformatics ; 21(1): 102, 2020 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-32164527

RESUMEN

BACKGROUND: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches. RESULTS: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark). CONCLUSIONS: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters).


Asunto(s)
Macrodatos , Análisis de los Alimentos/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenómica/métodos , Secuenciación Completa del Genoma/métodos , Biovigilancia , Genoma Bacteriano , Metagenoma , Microbiota/genética , Programas Informáticos
3.
Gene ; 741: 144566, 2020 May 30.
Artículo en Inglés | MEDLINE | ID: mdl-32171826

RESUMEN

Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals.


Asunto(s)
Absceso/genética , Adaptación Fisiológica/genética , Variación Genética , Micrococcaceae/genética , Absceso/microbiología , Absceso/veterinaria , Animales , Genoma Bacteriano , Islas Genómicas/genética , Genómica , Caballos/microbiología , Masculino , Micrococcaceae/patogenicidad , Filogenia , Virulencia/genética
4.
Microbiol Res ; 236: 126450, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32146295

RESUMEN

The industrial ethanol fermentation imposes several stresses to microorganisms. However, some bacterial species are well adapted and manage to endure these harmful conditions. Lactobacillus vini is one of the most found bacteria in these environments, indicating the existence of efficient tolerance mechanisms. In view of this premise, the present study aimed to describe the tolerance of L. vini to several stressing agents encounter in industrial environments and the genetic components of the stress response. In general, L. vini showed significant tolerance to stressors commonly found in fuel-ethanol fermentations, and only doses higher than normally reached in processes restrained its growth. The lag phase and the growth rate were the most responsive kinetic parameter affected. Gene expression analysis revealed that uspII gene positively responded to all conditions tested, a typical profile of a general stress response gene. In addition, the results also revealed aspects of regulatory modules of co-expressed genes responding to different stresses, and also the similarities of response mechanism with basis in common cellular damages. Altogether, these data contribute to uncover the factors that could favour L. vini in the industrial fermentation which could be shared with other well adapted species and reports the first stress response genes in this bacterium.


Asunto(s)
Adaptación Fisiológica/genética , Microbiología Industrial , Lactobacillus , Estrés Fisiológico/genética , Etanol , Fermentación , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Concentración de Iones de Hidrógeno , Lactobacillus/genética , Lactobacillus/crecimiento & desarrollo , Lactobacillus/metabolismo , Temperatura , Transcriptoma
5.
Int J Nanomedicine ; 15: 1387-1395, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32184593

RESUMEN

Introduction: A previous study demonstrated the virucidal effect of an electrically charged disinfectant (CAC-717), which contains meso-structure nanoparticles, on enveloped viruses (influenza viruses). However, the effect of CAC-717 on other microorganisms and the mechanisms by which CAC-717 inactivates the microorganisms remain unclear. In this study, CAC-717 was further evaluated in terms of its biocidal and virucidal activity as well as its effect on bacterial and viral nucleic acids. Methods: The inactivation effects of CAC-717 against various microorganisms [non-enveloped virus, feline calicivirus (FCV); bacteria, Salmonella enterica and Escherichia coli] were investigated by comparing the viral titer of the medium tissue culture infectious dose (TCID50) and the D value (estimated treatment time required to reduce the number of microorganisms by 90%). Furthermore, the effects of CAC-717 on viral and bacterial genomic RNA/DNA were examined using a polymerase chain reaction (PCR). Results: Treatment of an equal volume of CAC-717 with cell lysate infected with a non-enveloped virus, feline calicivirus (FCV), reduced the TCID50. Viral titer dropped below the detection limit after 2 min of treatment. The D value of FCV was 0.256 min (average of multiple endpoint D values) and endpoint D value was 0.341 min. The D value for E. coli and S. enterica was 0.290 min and 0.080 min (average of multiple endpoint D values), respectively and the endpoint D value was 0.545 min and 0.054 min, respectively. In addition, PCR showed the inhibition of nucleic acid amplification of the RNA and DNA genome of FCV and bacteria, respectively. Conclusion: Our findings suggest that CAC-717 inactivates viruses and bacteria by modifying the viral and bacterial nucleic acids.


Asunto(s)
Bacterias/efectos de los fármacos , Calicivirus Felino/efectos de los fármacos , Desinfectantes/farmacología , Genoma Bacteriano/efectos de los fármacos , Genoma Viral/efectos de los fármacos , Nanopartículas/administración & dosificación , Inactivación de Virus/efectos de los fármacos , Animales , Bacterias/genética , Calicivirus Felino/genética , Gatos , Desinfectantes/química , Desinfección/métodos , Electricidad , Nanopartículas/química , Carga Viral/efectos de los fármacos
6.
J Med Microbiol ; 69(3): 396-401, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32125266

RESUMEN

Introduction. Transmission of Enterobacterales in neonatal intensive care units (NICU) can cause outbreaks of colonization and invasive infections among neonates. Two clusters of nosocomial transmission of Klebsiella pneumoniae identified by MALDI-ToF mass-spectrometry were suspected at two NICUs in July and August 2016.Aim. To assess the potential transmission of K. pneumoniae among neonates.Methodology. Whole-genome sequencing (WGS) was performed of K. pneumoniae isolates obtained through targeted surveillance of patients and environmental sampling.Results. WGS data revealed that patient and environmental isolates represented two species, K. pneumoniae and K. variicola. Core-genome multi-locus sequence typing (cgMLST) of the isolates identified three separate transmission clusters, in Hospital A a cluster of K. pneumoniae isolates in 12 children and two environmental samples and a second cluster of K. variicola isolates in five children. In Hospital B a cluster of K. pneumoniae isolates from three children and five unrelated isolates of K. pneumoniae and two unrelated isolates of K. variicola were found.Conclusion. K. variicola can cause hospital outbreaks of colonization and infection similar to other Klebsiella spp.Preliminary results from this study were presented at the 27th European Congress of Clinical Microbiology and Infectious Diseases, April 22-25, 2018, Vienna, Austria.


Asunto(s)
Infección Hospitalaria , Brotes de Enfermedades , Genoma Bacteriano/genética , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/genética , Klebsiella/genética , Técnicas de Tipificación Bacteriana , Alemania/epidemiología , Humanos , Recién Nacido , Unidades de Cuidado Intensivo Neonatal , Klebsiella/efectos de los fármacos , Klebsiella/aislamiento & purificación , Infecciones por Klebsiella/microbiología , Infecciones por Klebsiella/transmisión , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/aislamiento & purificación , Tipificación de Secuencias Multilocus , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Secuenciación Completa del Genoma
7.
PLoS One ; 15(3): e0230006, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32163465

RESUMEN

The Caulobacter genus, including the widely-studied model organism Caulobacter crescentus, has been thought to be non-pathogenic and thus proposed as a bioengineering vector for various environmental remediation and medical purposes. However, Caulobacter species have been implicated as the causative agents of several hospital-acquired infections, raising the question of whether these clinical isolates represent an emerging pathogenic species or whether Caulobacters on whole possess previously-unappreciated virulence capability. Given the proposed environmental and medical applications for C. crescentus, understanding the potential pathogenicity of this bacterium is crucial. Consequently, we sequenced a clinical Caulobacter isolate to determine if it has acquired novel virulence determinants. We found that the clinical isolate represents a new species, Caulobacter mirare that, unlike C. crescentus, grows well in standard clinical culture conditions. C. mirare phylogenetically resembles both C. crescentus and the related C. segnis, which was also thought to be non-pathogenic. The similarity to other Caulobacters and lack of obvious pathogenesis markers suggested that C. mirare is not unique amongst Caulobacters and that consequently other Caulobacters may also have the potential to be virulent. We tested this hypothesis by characterizing the ability of Caulobacters to infect the model animal host Galleria mellonella. In this context, two different lab strains of C. crescentus proved to be as pathogenic as C. mirare, while lab strains of E. coli were non-pathogenic. Further characterization showed that Caulobacter pathogenesis in the Galleria model is mediated by lipopolysaccharide (LPS), and that differences in LPS chemical composition across species could explain their differential toxicity. Taken together, our findings suggest that many Caulobacter species can be virulent in specific contexts and highlight the importance of broadening our methods for identifying and characterizing potential pathogens.


Asunto(s)
Caulobacter/patogenicidad , Mariposas Nocturnas/microbiología , Animales , Caulobacter/clasificación , Caulobacter/genética , Caulobacter/aislamiento & purificación , Modelos Animales de Enfermedad , Agua Dulce/microbiología , Genoma Bacteriano , Lipopolisacáridos/toxicidad , Longevidad/efectos de los fármacos , Mariposas Nocturnas/fisiología , Filogenia , Microbiología del Suelo , Virulencia
8.
Can J Microbiol ; 66(6): 401-412, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32160477

RESUMEN

Fusarium wilt is a devastating soil-borne disease mainly caused by highly host-specific formae speciales of Fusarium spp. Antagonistic microorganisms play a very important role in Fusarium wilt control. Isolation of potential biocontrol strains has become increasingly important. Bacterial strain SEM-2 was isolated from the high-temperature stage of silkworm excrement composting. SEM-2 exhibited a considerable antagonistic effect against Fusarium graminearum mycelial growth and spore germination. The results of pot experiments suggested that SEM-2 has a better inhibitory effect on the early stage of disease occurrence. The green fluorescent protein labelled SEM-2 coated on the surface of tomato seeds colonised the roots of tomato plants in 15 days. Genome sequencing identified SEM-2 as a new strain of Bacillus subtilis, and genome annotation and analysis determined gene clusters related to the biosynthesis of antimicrobials, such as bacillaene, fengycin, bacillibactin, subtilosin A, surfactin, and bacilysin. Interestingly, liquid chromatography - quadrupole time-of-flight mass spectrometry revealed that metabolites in pathways associated with the synthesis of secondary metabolites and antibiotics were highly differentially expressed. These findings may help to explain the mode of action of B. subtilis SEM-2 against Fusarium spp.


Asunto(s)
Antibiosis , Bacillus subtilis/fisiología , Bombyx/microbiología , Fusarium/crecimiento & desarrollo , Genoma Bacteriano/genética , Lycopersicon esculentum/microbiología , Enfermedades de las Plantas/prevención & control , Animales , Antiinfecciosos/metabolismo , Bacillus subtilis/química , Bacillus subtilis/genética , Bacillus subtilis/aislamiento & purificación , Agentes de Control Biológico , Cromatografía Liquida , Heces/microbiología , Espectrometría de Masas , Familia de Multigenes/genética , Enfermedades de las Plantas/microbiología , Semillas/microbiología
9.
PLoS Pathog ; 16(3): e1008344, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32150575

RESUMEN

A recent genome-wide screen identified ~300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around the Cas9 nuclease (Cas9Smu) encoded in the S. mutans UA159 genome. Using a xylose-inducible dead Cas9Smu with a constitutively active single-guide RNA (sgRNA), we observed titratable repression of GFP fluorescence that compared favorably to that of Streptococcus pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity and proto-spacer adjacent motif (PAM) requirements. Interference by sgRNAs did not occur with double or triple base-pair mutations, or if single base-pair mutations were in the 3' end of the sgRNA. Bioinformatic analysis of >450 S. mutans genomes allied with in vivo assays revealed a similar PAM recognition sequence as Cas9Spy. Next, we created a comprehensive library of sgRNA plasmids that were directed at essential and growth-supporting genes. We discovered growth defects for 77% of the CRISPRi strains expressing sgRNAs. Phenotypes of CRISPRi strains, across several biological pathways, were assessed using fluorescence microscopy. A variety of cell structure anomalies were observed, including segregational instability of the chromosome, enlarged cells, and ovococci-to-rod shape transitions. CRISPRi was also employed to observe how silencing of cell wall glycopolysaccharide biosynthesis (rhamnose-glucose polysaccharide, RGP) affected both cell division and pathogenesis in a wax worm model. The CRISPRi tool and sgRNA library are valuable resources for characterizing essential genes in S. mutans, some of which could prove to be promising therapeutic targets.


Asunto(s)
Sistemas CRISPR-Cas/fisiología , Regulación Bacteriana de la Expresión Génica/fisiología , Genoma Bacteriano/fisiología , Streptococcus mutans , Estudio de Asociación del Genoma Completo , ARN Bacteriano/biosíntesis , ARN Bacteriano/genética , ARN Guia/biosíntesis , ARN Guia/genética , Streptococcus mutans/genética , Streptococcus mutans/metabolismo
10.
PLoS Pathog ; 16(3): e1008417, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32187228

RESUMEN

Streptococcus pneumoniae is well known for phase variation between opaque (O) and transparent (T) colonies within clonal populations. While the O variant is specialized in invasive infection (with a thicker capsule and higher resistance to host clearance), the T counterpart possesses a relatively thinner capsule and thereby higher airway adherence and colonization. Our previous study found that phase variation is caused by reversible switches of the "opaque ON-or-OFF" methylomes or methylation patterns of pneumococcal genome, which is dominantly driven by the PsrA-catalyzed inversions of the DNA methyltransferase hsdS genes. This study revealed that switch frequency between the O and T variants is regulated by five transcriptional response regulators (rr) of the two-component systems (TCSs). The mutants of rr06, rr08, rr09, rr11 and rr14 produced significantly fewer O and more T colonies. Further mutagenesis revealed that RR06, RR08, RR09 and RR11 enrich the O variant by modulating the directions of the PsrA-catalyzed inversion reactions. In contrast, the impact of RR14 (RitR) on phase variation is independent of PsrA. Consistently, SMRT sequencing uncovered significantly diminished "opaque ON" methylome in the mutants of rr06, rr08, rr09 and rr11 but not that of rr14. Lastly, the phosphorylated form of RR11 was shown to activate the transcription of comW and two sugar utilization systems that are necessary for maintenance of the "opaque ON" genotype and phenotype. This work has thus uncovered multiple novel mechanisms that balance pneumococcal epigenetic status and physiology.


Asunto(s)
Proteínas Bacterianas , Metilación de ADN , Enzimas de Restricción-Modificación del ADN , ADN Bacteriano , Epigénesis Genética , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Streptococcus pneumoniae , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Enzimas de Restricción-Modificación del ADN/genética , Enzimas de Restricción-Modificación del ADN/metabolismo , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/metabolismo
11.
Life Sci ; 250: 117541, 2020 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-32169520

RESUMEN

AIM: Nontuberculous mycobacterial (NTM) infection such as endophthalmitis, dacryocystitis, and canaliculitis are pervasive across the globe and are currently managed by antibiotics. However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale and develop a chimeric vaccine against Mycobacteroides. MAIN METHODS: We carried out a vivid genomic study on five recently sequenced strains of Mycobacteroides and explored their Pan-core genome/proteome in three different phases. The promiscuous antigenic proteins were identified via a subtractive proteomics approach that qualified for virulence causation, resistance and essentiality factors for this notorious bacterium. An integrated pipeline was developed for the identification of B-Cell, MHC (Major histocompatibility complex) class I and II epitopes. KEY FINDINGS: Phase I identified the shreds of evidence of reductive evolution and propensity of the Pan-genome of Mycobacteroides getting closed soon. Phase II and Phase III produced 8 vaccine constructs. Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. V6 contains ß-defensin as an adjuvant, linkers, Lysosomal-associated membrane protein 1 (LAMP1) signal peptide, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Besides, V6 also interacts with a maximum number of MHC molecules and the TLR4/MD2 (Toll-like receptor 4/Myeloid differentiation factor 2) complex confirmed by docking and molecular dynamics simulation studies. SIGNIFICANCE: The knowledge harnessed from the current study can help improve the current treatment regimens or in an event of an outbreak and propel further related studies.


Asunto(s)
Vacunas Bacterianas/química , Infecciones por Bacterias Grampositivas/prevención & control , Mycobacteriaceae/genética , Vacunología , Alelos , Linfocitos B/inmunología , Bacteriófagos , Sistemas CRISPR-Cas , Biología Computacional , Farmacorresistencia Bacteriana , Epítopos , Epítopos de Linfocito T/genética , Microbioma Gastrointestinal , Genoma Bacteriano , Genómica , Antígenos de Histocompatibilidad Clase I/metabolismo , Antígenos de Histocompatibilidad Clase II/metabolismo , Humanos , Inmunoterapia , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Mycobacteriaceae/patogenicidad , Proteoma , Virulencia
12.
BMC Infect Dis ; 20(1): 223, 2020 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-32171281

RESUMEN

BACKGROUND: Streptococcus suis is a zoonotic pathogen that causes serious systemic infections in pigs and occupation-related infections in humans who contact with pigs or pork products. In China, it has caused two outbreaks of human infection and surveillance for S.suis has been ongoing since last time. CASE PRESENTATION: Two cases of meningitis and sepsis caused by S. suis were reported in this study. Both patients work in relation to the pork trade, a risk factor for S. suis infection. The outcome was favorable after a prolonged ceftriaxone therapy but one patient was left with mild hearing loss. Two isolates were identified as sequencing type (ST) 7, S. suis serotype 2 (SS2), which is one the most prevalent and cause two outbreaks in China. Whole-genome sequencing (WGS) revealed that a high degree identity was noted in the genome organizations and sequences between two sporadic ST7 SS2 isolates in this study and representative epidemic virulent isolates. Major differences among them are two sporadic ST7 SS2 isolates lacked a virulence factor called agglutinin receptor and an 89 K pathogenicity island (PAI), which plays important role in the pathogenesis of streptococcal toxic shock syndrome (STSS). A summary about STs of human infection with S. suis in China was completed. The result showed ST1 and ST7 were still the major STs and several novel STs were successfully discovered in different provinces. CONCLUSIONS: Our results enhanced the understanding of the ability to cause life-threatening infections in humans and the distribution and evolution of the S. suis in China.


Asunto(s)
Epidemias , Enfermedades Profesionales/microbiología , Serogrupo , Infecciones Estreptocócicas/epidemiología , Infecciones Estreptocócicas/genética , Streptococcus suis/genética , Enfermedades de los Porcinos/epidemiología , Anciano , Animales , Antibacterianos/uso terapéutico , Ceftriaxona/uso terapéutico , China/epidemiología , Genoma Bacteriano/genética , Humanos , Masculino , Persona de Mediana Edad , Enfermedades Profesionales/tratamiento farmacológico , Choque Séptico/tratamiento farmacológico , Choque Séptico/microbiología , Infecciones Estreptocócicas/tratamiento farmacológico , Infecciones Estreptocócicas/microbiología , Streptococcus suis/aislamiento & purificación , Porcinos/microbiología , Enfermedades de los Porcinos/transmisión , Resultado del Tratamiento , Factores de Virulencia
13.
Gene ; 742: 144554, 2020 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-32173539

RESUMEN

The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.


Asunto(s)
Bacterias/genética , Uso de Codones/efectos de la radiación , Genoma Bacteriano/efectos de la radiación , Tolerancia a Radiación/genética , Selección Genética/efectos de la radiación , Bacterias/efectos de la radiación , Mutación/efectos de la radiación , ARN de Transferencia/genética
14.
PLoS Genet ; 16(3): e1008615, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32130223

RESUMEN

The relative linear order of most genes on bacterial chromosomes is not conserved over evolutionary timescales. One explanation is that selection is weak, allowing recombination to randomize gene order by genetic drift. However, most chromosomal rearrangements are deleterious to fitness. In contrast, we propose the hypothesis that rearrangements in gene order are more likely the result of selection during niche adaptation (SNAP). Partial chromosomal duplications occur very frequently by recombination between direct repeat sequences. Duplicated regions may contain tens to hundreds of genes and segregate quickly unless maintained by selection. Bacteria exposed to non-lethal selections (for example, a requirement to grow on a poor nutrient) can adapt by maintaining a duplication that includes a gene that improves relative fitness. Further improvements in fitness result from the loss or inactivation of non-selected genes within each copy of the duplication. When genes that are essential in single copy are lost from different copies of the duplication, segregation is prevented even if the original selection is lifted. Functional gene loss continues until a new genetic equilibrium is reached. The outcome is a rearranged gene order. Mathematical modelling shows that this process of positive selection to adapt to a new niche can rapidly drive rearrangements in gene order to fixation. Signature features (duplication formation and divergence) of the SNAP model were identified in natural isolates from multiple species showing that the initial two steps in the SNAP process can occur with a remarkably high frequency. Further bioinformatic and experimental analyses are required to test if and to which extend the SNAP process acts on bacterial genomes.


Asunto(s)
Aclimatación/genética , Cromosomas Bacterianos/genética , Duplicación de Gen/genética , Reordenamiento Génico/genética , Selección Genética/genética , Aberraciones Cromosómicas , Evolución Molecular , Frecuencia de los Genes/genética , Orden Génico/genética , Genoma Bacteriano/genética , Modelos Teóricos , Filogenia
15.
PLoS One ; 15(3): e0229863, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32150564

RESUMEN

Brucellosis is an important zoonotic disease that affects both humans and animals. To date, laboratory surveillance is still essentially based on the traditional MLVA-16 methodology and the associated epidemiological information is frequently scarce. Our goal was to contribute to the improvement of Brucella spp. surveillance through the implementation of a whole genome sequencing (WGS) approach. We created a curated ready-to-use species-specific wgMLST scheme enrolling a panel of 2656 targets (http://doi.org/10.5281/zenodo.3575026) and used this schema to perform a retrospective analysis of the genetic relatedness among B. melitensis strains causing human infection in Portugal (a country where brucellosis is an endemic disease) from 2010 to 2018. The strains showed a phylogenetic clustering within genotype II (25 out of 36) and IV (4 out of 36), and shared clades with strains isolated from countries with which Portugal has intense food trading, tourism and similar eating habits, such as Spain, Italy and Greece. In addition, our results point to the identification of strong associations between B. melitensis strains, likely underlying missed "outbreaks" as 22 out of the 36 strains showed genetic linkage with others. In fact, the applied gene-by-gene approach grouped these strains into six genetic clusters each one containing putative epidemiological links. Nevertheless, more studies will be needed in order to define the appropriate range of cut-offs (probable non-static cut-offs) that best illustrate the association between genetic linkage and epidemiological information and may serve as alerts for the health authorities. The release of this freely available and scalable schema contributes to the required technological transition for laboratorial surveillance of brucellosis and will facilitate the assessment of ongoing and future outbreaks in order to prevent the transmission spread.


Asunto(s)
Brucella melitensis/genética , Brucelosis/microbiología , Genoma Bacteriano , Brucelosis/epidemiología , Humanos , Filogenia , Portugal/epidemiología , Secuenciación Completa del Genoma
16.
Microbes Environ ; 35(1)2020.
Artículo en Inglés | MEDLINE | ID: mdl-32037377

RESUMEN

Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.


Asunto(s)
Genoma Bacteriano/genética , Elementos de la Serie de los Lantanoides/metabolismo , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , Oxidorreductasas de Alcohol/genética , Proteínas Bacterianas/genética , Medios de Cultivo/metabolismo , Sedimentos Geológicos/microbiología , Metales de Tierras Raras/metabolismo , Metano/metabolismo , Methylosinus/clasificación , Methylosinus/genética , Methylosinus/aislamiento & purificación , Methylosinus/metabolismo , Estanques/microbiología , Proteobacteria/clasificación , Proteobacteria/fisiología , ARN Ribosómico 16S/genética
17.
Gene ; 737: 144449, 2020 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-32032746

RESUMEN

Ureibacillus thermophilus strain LM102 is a facultative thermophile with growth in range 37 °C-60 °C. Upon identification using the 16S rRNA marker, it showed highest similarity of 99.8% with U. thermophilus strain HC148. A phylogenetic analysis revealed U. suwonensis strain 6 T19 to be the closest species to strain LM102. Our aim was to determine the unique thermotolerant properties of LM102 by identifying thermostablity of its proteins and the interactions existing in its heat shock response systems (HSRS). The strain was sequenced, assembled and the draft genome (3,017,325 bp) was analyzed. Post-annotation, we randomly selected a set of hundred proteins and computed the percentage distribution of 12 amino acids which have been substantially studied for their role in thermostability. The protein homologues were searched and the residues of LM102 were compared with Bacillus subtilis and Thermus thermophilus, a mesophile and hyperthermophile respectively. Within the 95% confidence limit, a Z-score of -0.61 was observed between LM102 and B. subtilis. However, a significantly lower value of -8.84 was observed for the pair LM102 and T. thermophilus. The amino acid distribution did not appear to influence the protein thermostability. Further, we investigated the role of Protein-Protein interactions by building networks for heat shock responses, namely DNA repair, transcriptional regulation, and activation of heat shock proteins. Interaction data retrieved from the STRING database for more than 50 species were used to build these networks. Highly clustered MCODE results notably revealed RNA 3'-5' exonuclease, CshA and HemW previously unreported, in association with other proteins. Additionally, these and other proteins estimated from the HSRS networks were found in both mesophiles and thermophiles, suggesting a crucial role of gene regulatory networks in the cellular viability of LM102 at high temperatures.


Asunto(s)
Proteínas Bacterianas/metabolismo , Genoma Bacteriano , Respuesta al Choque Térmico , Planococcaceae/genética , Mapas de Interacción de Proteínas , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Reparación del ADN , Regulación Bacteriana de la Expresión Génica , Filogenia , ARN Ribosómico 16S/genética , Transcripción Genética
18.
Plant Dis ; 104(4): 1011-1012, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32065568

RESUMEN

The bacterial plant pathogen Xanthomonas hyacinthi is the causal agent of yellow disease of Hyacinthus and other ornamental plant genera. There is no available complete genome for X. hyacinthi, limiting basic research for this pathogen. Here, we release a high-quality complete genome sequence for the X. hyacinthi type strain, CFBP 1156. Single-molecule real-time (SMRT) sequencing with a mean coverage of 306× revealed two contigs of 4,918,645 and 44,381 bp in size. This was the first characterized plant-disease-causing species of Xanthomonas and this genome provides a resource to better understand the biology of yellow disease of hyacinth.


Asunto(s)
Xanthomonas , Genoma Bacteriano , Enfermedades de las Plantas
19.
Biochim Biophys Acta Gene Regul Mech ; 1863(3): 194506, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32068131

RESUMEN

Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation to various perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated the identification and characterization of sRNAs (length, structure and expression conditions) and their RNA targets in several bacteria. Nevertheless, it could be very difficult for non-experts to understand the advantages and drawbacks related to each offered option and, consequently, to make an informed choice. Therefore, the main goal of this review is to provide a guide to navigate through the twists and turns of high-throughput RNA sequencing technologies, with a specific focus on those applied to the study of sRNAs. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.


Asunto(s)
ARN Bacteriano/química , ARN Bacteriano/metabolismo , ARN Pequeño no Traducido/química , ARN Pequeño no Traducido/metabolismo , Análisis de Secuencia de ARN , Genoma Bacteriano , Secuenciación de Nucleótidos de Alto Rendimiento , Conformación de Ácido Nucleico
20.
Exp Appl Acarol ; 80(3): 363-380, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32072355

RESUMEN

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.


Asunto(s)
Bacteroidetes/aislamiento & purificación , Dermatophagoides farinae/microbiología , Genoma Bacteriano , Animales , China , Dermatophagoides pteronyssinus/microbiología , Europa (Continente) , Femenino , Masculino , Microbiota , Simbiosis , Estados Unidos , Secuenciación Completa del Genoma
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