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1.
Microb Genom ; 10(7)2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38949867

RESUMO

Lactobacillus species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.


Assuntos
Lactobacillus , Microbiota , Polimorfismo de Nucleotídeo Único , Vagina , Humanos , Feminino , Vagina/microbiologia , Lactobacillus/genética , Lactobacillus/classificação , Genoma Bacteriano , Filogenia , Sistema Urinário/microbiologia , Sequenciamento Completo do Genoma , Urina/microbiologia
2.
Can Vet J ; 65(7): 698-702, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38952754

RESUMO

Objective: The present study reports the first isolation and whole-genome sequencing of a Trueperella abortisuis bacterium from a goat. Animals and sample: The T. abortisuis was isolated from the uterus of a goat following an abortion. Procedure: The T. abortisuis was identified by pure culture phenotype and MALDI-TOF analysis and further characterized by whole-genome sequencing. Results: This isolate was reliably identified as T. abortisuis and showed similar properties to type strain T. abortisuis DSM 19515T, which was recovered from a sow following an abortion. The assembled genome of this isolate was 2 564 866 bp long with a GC content of 63.9%. A total of 30 virulence-related genes were determined, suggesting the pathogenic potential of this organism. Conclusion and clinical relevance: This study details the first isolation of T. abortisuis from goats. The genotypic findings of this isolate will serve as a baseline description for any similar future studies.


Premier isolement et séquençage du génome entier de Trueperella abortisuis provenant d'une chèvre au Canada. Objectif: La présente étude rapporte le premier isolement et séquençage du génome entier d'un isolat de Trueperella abortisuis provenant d'une chèvre. Animaux et échantillon: Le T. abortisuis a été isolé de l'utérus d'une chèvre à la suite d'un avortement. Procédure: Le T. abortisuis a été identifié par un phénotype de culture pure et analyse par MALDI-TOF, puis caractérisé par séquençage du génome entier. Résultats: Cet isolat a été identifié de manière fiable comme étant T. abortisuis et a montré des propriétés similaires à la souche type T. abortisuis DSM 19515T, qui a été récupérée chez une truie après un avortement. Le génome assemblé de cet isolat mesurait 2 564 866 pb avec une teneur en GC de 63,9 %. Au total, 30 gènes liés à la virulence ont été déterminés, suggérant le potentiel pathogène de cet organisme. Conclusion et pertinence clinique: Cette étude détaille le premier isolement de T. abortisuis chez la chèvre. Les résultats génotypiques de cet isolat serviront de description de base pour toute étude future similaire.(Traduit par Dr Serge Messier).


Assuntos
Doenças das Cabras , Cabras , Sequenciamento Completo do Genoma , Animais , Doenças das Cabras/microbiologia , Feminino , Infecções por Actinomycetales/veterinária , Infecções por Actinomycetales/microbiologia , Actinomycetaceae/isolamento & purificação , Actinomycetaceae/genética , Genoma Bacteriano , Canadá , Aborto Animal/microbiologia , Gravidez
3.
Curr Microbiol ; 81(8): 254, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38955887

RESUMO

Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This multifaceted bacterium contributes substantially to plant growth promotion, stress resilience, and biocontrol but can also act as a pathogen to its host. The genetic determinants underlying these diverse functions remain largely unfathomed and to uncover this phenomenon, nineteen strains of Pantoea agglomerans were selected and analyzed. Genome-to-Genome Distance Calculator (GGDC) which uses the Genome Blast Distance Phylogeny (GBDP) technique to calculate digital DDH values. Phylogenetic analysis via Genome-to-Genome distance, Average Nucleotide Identity, and Amino Acid Identity calculation revealed that all strains belonged to the genus Pantoea. However, strain 33.1 had a lower value than the threshold for the same species delineation. Bacterial Pan Genome Analysis (BPGA) Pipeline and MinPath analysis revealed genetic traits associated with environmental resilience, such as oxidative stress, UV radiation, temperature extremes, and metabolism of distinct host-specific carbohydrates. Protein-protein interactome analysis illustrated osmotic stress proteins closely linked with core proteins, while heavy metal tolerance, nitrogen metabolism, and Type III and VI secretion systems proteins generally associated with pathogenicity formed a separate network, indicating strain-specific characteristics. These findings shed new light on the intricate genetic architecture of Pantoea agglomerans, revealing its adaptability to inhabit diverse niches and thrive in varied environments.


Assuntos
Genoma Bacteriano , Pantoea , Filogenia , Pantoea/genética , Pantoea/fisiologia , Pantoea/classificação , Genômica , Adaptação Fisiológica , Humanos , Animais , Plantas/microbiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo
4.
Artigo em Inglês | MEDLINE | ID: mdl-38963413

RESUMO

A Gram-stain-negative, yellow-pigmented, and facultatively aerobic bacterium, designated strain GPA1T, was isolated from plastic waste landfill soil in the Republic of Korea. The cells were non-motile short rods exhibiting oxidase-negative and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-2.5 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was the sole respiratory quinone, and iso-C15 : 0, C16 : 1 ω5c, and iso-C17 : 0 3-OH were the major cellular fatty acids (>10 % of the total fatty acids). Phosphatidylethanolamine was identified as a major polar lipid. Phylogenetic analyses based on 16S rRNA gene sequences and 120 concatenated marker protein sequences revealed that strain GPA1T formed a distinct lineage within the genus Chitinophaga. The genome of strain GPA1T was 6078 kb in size with 53.8 mol% G+C content. Strain GPA1T exhibited the highest similarity to Chitinophaga rhizosphaerae T16R-86T, with a 98.6 % 16S rRNA gene sequence similarity, but their average nucleotide identity and digital DNA-DNA hybridization values were 82.5 and 25.9 %, respectively. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain GPA1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga pollutisoli sp. nov. is proposed. The type strain is GPA1T (=KACC 23415T=JCM 36644T).


Assuntos
Técnicas de Tipagem Bacteriana , Bacteroidetes , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Sedimentos Geológicos , Fosfatidiletanolaminas , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2 , RNA Ribossômico 16S/genética , República da Coreia , Ácidos Graxos/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Vitamina K 2/análise , DNA Bacteriano/genética , Sedimentos Geológicos/microbiologia , Bacteroidetes/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Hibridização de Ácido Nucleico , Instalações de Eliminação de Resíduos , Genoma Bacteriano
5.
BMC Microbiol ; 24(1): 240, 2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38961341

RESUMO

OBJECTIVE: We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks. METHODS: 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems. RESULTS: We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity. CONCLUSIONS: Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.


Assuntos
Sistemas CRISPR-Cas , Conjugação Genética , Klebsiella pneumoniae , Plasmídeos , Klebsiella pneumoniae/genética , Plasmídeos/genética , beta-Lactamases/genética , Enzimas de Restrição-Modificação do DNA/genética , China , Infecções por Klebsiella/microbiologia , Transferência Genética Horizontal , Humanos , Genoma Bacteriano/genética
6.
Antimicrob Resist Infect Control ; 13(1): 70, 2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38961463

RESUMO

OBJECTIVES: Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence, drug-resistance monitoring, and outbreak containment. METHODS: Genomic analysis on 87 KPC-Kp strains isolated from 3 Northern Italy hospitals in 2019-2021 was performed by whole genome sequencing (WGS), to characterize resistome, virulome, and mobilome, and to assess potential associations with phenotype resistance and clinical presentation. Maximum Likelihood and Minimum Spanning Trees were used to determine strain correlations and identify potential transmission clusters. RESULTS: Overall, 15 different STs were found; the predominant ones included ST307 (35, 40.2%), ST512/1519 (15, 17.2%), ST20 (12, 13.8%), and ST101 (7, 8.1%). 33 (37.9%) KPC-Kp strains were noticed to be in five transmission clusters (median number of isolates in each cluster: 5 [3-10]), four of them characterized by intra-hospital transmission. All 87 strains harbored Tn4401a transposon, carrying blaKPC-3 (48, 55.2%), blaKPC-2 (38, 43.7%), and in one case (1.2%) blaKPC-33, the latter gene conferred resistance to ceftazidime/avibactam (CZA). Thirty strains (34.5%) harbored porin mutations; of them, 7 (8.1%) carried multiple Tn4401a copies. These strains were characterized by significantly higher CZA minimum inhibitory concentration compared with strains with no porin mutations or single Tn4401a copy, respectively, even if they did not overcome the resistance breakpoint of 8 ug/mL. Median 2 (IQR:1-2) virulence factors per strain were detected. The lowest number was observed in ST20 compared to the other STs (p<0.001). While ST307 was associated with infection events, a trend associated with colonization events could be observed for ST20. CONCLUSIONS: Integration of genomic, resistance score, and clinical data allowed us to define a relative diversification of KPC-Kp in Northern Italy between 2019 and 2021, characterized by few large transmission chains and rare inter-hospital transmission. Our results also provided initial evidence of correlation between KPC-Kp genomic signatures and higher MIC levels to some antimicrobial agents or colonization/infection status, once again underlining WGS's importance in bacterial surveillance.


Assuntos
Antibacterianos , Proteínas de Bactérias , Hospitais Universitários , Infecções por Klebsiella , Klebsiella pneumoniae , Testes de Sensibilidade Microbiana , Sequenciamento Completo do Genoma , beta-Lactamases , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/classificação , Klebsiella pneumoniae/enzimologia , Itália/epidemiologia , Humanos , beta-Lactamases/genética , Infecções por Klebsiella/microbiologia , Infecções por Klebsiella/epidemiologia , Proteínas de Bactérias/genética , Antibacterianos/farmacologia , Genoma Bacteriano , Farmacorresistência Bacteriana Múltipla/genética , Genômica , Infecção Hospitalar/microbiologia , Infecção Hospitalar/epidemiologia
7.
PLoS One ; 19(7): e0306442, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38980842

RESUMO

We aimed to determine the molecular characteristics of carbapenem-resistant Pseudomonas aeruginosa strains 18081308 and 18083286, which were isolated from the urine and the sputum of two Chinese patients, respectively. Additionally, we conducted a comparative analysis between Tn6411 carrying blaIMP-1 in strain 18083286 and transposons from the same family available in GenBank. Bacterial genome sequencing was carried out on strains 18081308 and 18083286 to obtain their whole genome sequence. Average nucleotide identity (ANI) was used for their precise species identification. Serotyping and multilocus sequence typing were performed. Furthermore, the acquired drug resistance genes of these strains were identified. The carbapenem-resistant P. aeruginosa strains isolated in the present study were of sequence type ST865 and serotype O6. They all carried the same resistance genes (aacC2, tmrB, and blaIMP-1). Tn6411, a Tn7-like transposon carrying blaIMP-1, was found in strain 18083286 by single molecule real time (SMRT) sequencing. We also identified the presence of this transposon sequence in other chromosomes of P. aeruginosa and plasmids carried by Acinetobacter spp. in GenBank, indicating the necessity for heightening attention to the potential transferability of this transposon.


Assuntos
Elementos de DNA Transponíveis , Genômica , Pseudomonas aeruginosa , beta-Lactamases , Pseudomonas aeruginosa/genética , Elementos de DNA Transponíveis/genética , beta-Lactamases/genética , Humanos , Genômica/métodos , Genoma Bacteriano , Infecções por Pseudomonas/microbiologia , Carbapenêmicos/farmacologia , Tipagem de Sequências Multilocus , Antibacterianos/farmacologia , Proteínas de Bactérias/genética
8.
Sci Rep ; 14(1): 15830, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38982145

RESUMO

Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05-80.63% for PMTSA13T and 74.02-80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13T ranged from 19 to 39%, and 19.1-38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to 'carbohydrate metabolism and transport (G)', according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant-microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13T (= KCTC 59028T = GDMCC 1.4451T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.


Assuntos
Capsicum , Filogenia , Rizosfera , Capsicum/microbiologia , Capsicum/crescimento & desenvolvimento , Microbiologia do Solo , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Actinobacteria/classificação , RNA Ribossômico 16S/genética , Genoma Bacteriano , Desenvolvimento Vegetal
9.
Sci Rep ; 14(1): 15779, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38982270

RESUMO

Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.


Assuntos
Lignina , Paenibacillus , Vitis , Madeira , Madeira/microbiologia , Vitis/microbiologia , Lignina/metabolismo , Paenibacillus/genética , Paenibacillus/metabolismo , Doenças das Plantas/microbiologia , Basidiomycota/genética , Basidiomycota/metabolismo , Polissacarídeos/metabolismo , Celulose/metabolismo , Genoma Bacteriano
10.
BMC Bioinformatics ; 25(1): 233, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38982375

RESUMO

BACKGROUND: Structural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The detection of structural variations in bacteria is challenging, and the recognition of even small rearrangements can be important. Even though most detection tools are aimed at and benchmarked on eukaryotic genomes, they can also be used on prokaryotic genomes. The key features of detection are the ability to detect small rearrangements and support haploid genomes. Because of the limiting performance of a single detection tool, combining the detection abilities of multiple tools can lead to more robust results. There are already available workflows for structural variation detection for long-reads technologies and for the detection of single-nucleotide variation and indels, both aimed at bacteria. Yet we are unaware of structural variations detection workflows for the short-reads sequencing platform. Motivated by this gap we created our workflow. Further, we were interested in increasing the detection performance and providing more robust results. RESULTS: We developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool. CONCLUSIONS: The ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV .


Assuntos
Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Software , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Bactérias/genética
11.
Curr Microbiol ; 81(9): 276, 2024 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-39023551

RESUMO

Klebsiella pneumoniae is an opportunistic pathogen mostly found in health care-associated infections but can also be associated with community-acquired infections and is in critical need of new antimicrobial agents for strains resistant to carbapenems. The prevalence of carbapenemase-encoding genes varies among studies. Multidrug-resistant K. pneumoniae strains can harbor several antimicrobial-resistant determinants and mobile genetic elements (MGEs), along with virulence genetic determinants in community settings. We aim to determine the genetic profile of a multidrug-resistant K. pneumoniae strain isolated from a patient with community-acquired UTI. We isolated a K. pneumoniae strain UABC-Str0120, from a urine sample of community-acquired urinary tract infection. Antimicrobial susceptibility tests and Whole-genome sequencing (WGS) were performed. The phylogenetic relationship was inferred by SNPs calling and filtering. UABC-Str0120 showed resistance toward ß-lactams, combinations with ß-lactamase inhibitors, and carbapenems. WGS revealed the presence of genes conferring resistance to aminoglycosides, ß-lactams, carbapenems, quinolones, sulfonamides, phosphonates, phenicols, and quaternary ammonium compounds, 77 subsystems of virulence genes were identified, and an uncommon sequence type ST5889 was also determined. The sequenced strain harbors several MGEs. The UABC-Str0120 recovered from a urine sample harbors several virulence and antimicrobial resistance determinants, which assembles an endangering combination for an immunocompromised or a seemly healthy host, given its presence in a community setting.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana Múltipla , Genoma Bacteriano , Infecções por Klebsiella , Klebsiella pneumoniae , Testes de Sensibilidade Microbiana , Filogenia , Infecções Urinárias , Sequenciamento Completo do Genoma , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Humanos , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Klebsiella/microbiologia , Infecções por Klebsiella/urina , Antibacterianos/farmacologia , Infecções Urinárias/microbiologia , Infecções Comunitárias Adquiridas/microbiologia , Urina/microbiologia
12.
Arch Microbiol ; 206(7): 332, 2024 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-38951206

RESUMO

A Gram-stain-negative, aerobic, rod-shaped and motile strain HL-JVS1T, was isolated from the gastric tract of a juvenile Pacific white shrimp. Molecular phylogenetic analysis based on 16S rRNA gene sequences of strain HL-JVS1T revealed its affiliation with the genus Pleionea, with close relatives including Pleionea mediterranea MOLA115T (97.5%) and Pleionea sediminis S1-5-21T (96.2%). The complete genome of strain HL-JVS1T consisted of a circular 4.4 Mb chromosome and two circular plasmids (6.6 and 35.0 kb) with a G + C content of 43.1%. The average nucleotide identity and digital DNA-DNA hybridization values between strain HL-JVS1T and the type strains of described Pleionea species were 69.7-70.4% and 18.3-18.6%, respectively. Strain HL-JVS1T grew at 10-40 °C (optimum, 30 °C) in the presence of 0.5 - 9.0% (w/v) sea salts (optimum, 2.0 - 2.5%), and at pH range of 5.5 - 10.0 (optimum, pH 6.5). The major fatty acids (> 10%) were summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl) (23.3%), iso-C16:0 (14.5%), iso-C11:0 3-OH (13.8%) and iso-C15:0 (11.0%). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, two unidentified aminolipids, and two unidentified lipids. The respiratory quinone was ubiquinone-8. The comprehensive phylogenetic, phylogenomic, phenotypic and chemotaxonomic results showed that strain HL-JVS1T is distinct from other Pleionea species. Hence, we propose strain HL-JVS1T as a novel species belonging to the genus Pleionea, for which the name Pleionea litopenaei sp. nov. is proposed with HL-JVS1T (= KCCM 90514T = JCM 36490T) as the type strain.


Assuntos
Composição de Bases , DNA Bacteriano , Ácidos Graxos , Penaeidae , Filogenia , RNA Ribossômico 16S , Animais , RNA Ribossômico 16S/genética , Ácidos Graxos/análise , Ácidos Graxos/metabolismo , DNA Bacteriano/genética , Técnicas de Tipagem Bacteriana , Hibridização de Ácido Nucleico , Análise de Sequência de DNA , Genoma Bacteriano , Planococáceas/genética , Planococáceas/isolamento & purificação , Planococáceas/classificação , Trato Gastrointestinal , Fosfolipídeos/análise
13.
Curr Microbiol ; 81(8): 247, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38951210

RESUMO

Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.


Assuntos
Genoma Bacteriano , Stenotrophomonas , Zea mays , Zea mays/microbiologia , Stenotrophomonas/genética , Stenotrophomonas/metabolismo , Biotecnologia , Composição de Bases , Raízes de Plantas/microbiologia , Microbiologia do Solo , Agricultura , Filogenia , Família Multigênica
14.
Methods Mol Biol ; 2833: 121-128, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949706

RESUMO

Going back in time through a phylogenetic tree makes it possible to evaluate ancestral genomes and assess their potential to acquire key polymorphisms of interest over evolutionary time. Knowledge of this kind may allow for the emergence of key traits to be predicted and pre-empted from currently circulating strains in the future. Here, we present a novel genome-wide survival analysis and use the emergence of drug resistance in Mycobacterium tuberculosis as an example to demonstrate the potential and utility of the technique.


Assuntos
Mycobacterium tuberculosis , Filogenia , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Genoma Bacteriano , Humanos , Evolução Molecular , Farmacorresistência Bacteriana/genética , Tuberculose/microbiologia , Tuberculose/genética
15.
Methods Mol Biol ; 2833: 161-183, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949710

RESUMO

Outbreaks are a risk to public health particularly when pathogenic, hypervirulent, and/or multidrug-resistant organisms (MDROs) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbreak detection is essential to implement effective interventions in clinical areas to control and stop further transmission. Advances in the field of whole genome sequencing (WGS) have resulted in lowered costs, increased capacity, and improved reproducibility of results. WGS now has the potential to revolutionize the investigation and management of outbreaks replacing conventional genotyping and other discrimination systems. Here, we outline specific procedures and protocols to implement WGS into investigation of outbreaks in healthcare settings.


Assuntos
Surtos de Doenças , Genômica , Sequenciamento Completo do Genoma , Humanos , Sequenciamento Completo do Genoma/métodos , Genômica/métodos , Genoma Bacteriano
16.
Methods Mol Biol ; 2833: 195-210, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949712

RESUMO

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and susceptibility for many first- and second-line anti-tuberculosis drugs. However, bioinformatic pipelines and mutation catalogs to predict antimicrobial resistances in MTBC isolates are often customized and detailed protocols are difficult to access. Here, we provide a step-by-step workflow for the processing and interpretation of short-read sequencing data and give an overview of available analysis pipelines.


Assuntos
Antituberculosos , Biologia Computacional , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis , Sequenciamento Completo do Genoma , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Sequenciamento Completo do Genoma/métodos , Testes de Sensibilidade Microbiana/métodos , Humanos , Antituberculosos/farmacologia , Biologia Computacional/métodos , Genoma Bacteriano , Farmacorresistência Bacteriana/genética , Mutação , Tuberculose/microbiologia , Tuberculose/tratamento farmacológico
17.
Methods Mol Biol ; 2833: 185-193, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949711

RESUMO

Whole genome sequencing (WGS) is becoming an important diagnostic tool for antimicrobial susceptibility testing of Mycobacterium tuberculosis complex (MTBC) isolates in many countries. WGS protocols usually start with the preparation of a DNA-library: the critical first step in the process. A DNA-library represents the genomic content of a DNA sample and consists of unique short DNA fragments. Although available DNA-library protocols come with manufacturer instructions, details of the entire process, including quality controls, instrument parameters, and run evaluations, often need to be developed and customized by each laboratory to implement WGS technology effectively. Here, we provide a detailed workflow for a DNA-library preparation based on an adapted Illumina protocol optimized for the reduction of reagent costs.


Assuntos
Genoma Bacteriano , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis , Sequenciamento Completo do Genoma , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Sequenciamento Completo do Genoma/métodos , Testes de Sensibilidade Microbiana/métodos , Humanos , Antituberculosos/farmacologia , Biblioteca Gênica , DNA Bacteriano/genética , Tuberculose/microbiologia , Tuberculose/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala/métodos
18.
Methods Mol Biol ; 2833: 211-223, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949713

RESUMO

Genomic sequencing has revolutionized microbial typing methods and transformed high-throughput methods in reference, clinical, and research laboratories. The detection of antimicrobial-resistant (AMR) determinants using genomic methods can provide valuable information on the emergence of resistance. Here we describe an approach to detecting AMR determinants using an open access and freely available platform which does not require bioinformatic expertise.


Assuntos
Biologia Computacional , Farmacorresistência Bacteriana , Genoma Bacteriano , Sequenciamento Completo do Genoma , Sequenciamento Completo do Genoma/métodos , Farmacorresistência Bacteriana/genética , Biologia Computacional/métodos , Humanos , Antibacterianos/farmacologia , Genômica/métodos , Software , Bactérias/genética , Bactérias/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala/métodos
19.
Database (Oxford) ; 20242024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38958433

RESUMO

Myxobacteria are predatory bacteria with antimicrobial activity, utilizing complex mechanisms to kill their prey and assimilate their macromolecules. Having large genomes encoding hundreds of secondary metabolites, hydrolytic enzymes and antimicrobial peptides, these organisms are widely studied for their antibiotic potential. MyxoPortal is a comprehensive genomic database hosting 262 genomes of myxobacterial strains. Datasets included provide genome annotations with gene locations, functions, amino acids and nucleotide sequences, allowing analysis of evolutionary and taxonomical relationships between strains and genes. Biosynthetic gene clusters are identified by AntiSMASH, and dbAMP-generated antimicrobial peptide sequences are included as a resource for novel antimicrobial discoveries, while curated datasets of CRISPR/Cas genes, regulatory protein sequences, and phage associated genes give useful insights into each strain's biological properties. MyxoPortal is an intuitive open-source database that brings together application-oriented genomic features that can be used in taxonomy, evolution, predation and antimicrobial research. MyxoPortal can be accessed at http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Database URL:  http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Graphical Abstract.


Assuntos
Bases de Dados Genéticas , Genoma Bacteriano , Myxococcales , Myxococcales/genética , Genômica/métodos
20.
Front Cell Infect Microbiol ; 14: 1407246, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38962322

RESUMO

Introduction: In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms. Methods: This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS). Results: Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids. Discussion: The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.


Assuntos
Antibacterianos , Compostos Azabicíclicos , Carbapenêmicos , Ceftazidima , Combinação de Medicamentos , Farmacorresistência Bacteriana Múltipla , Escherichia coli , Klebsiella pneumoniae , Sequenciamento Completo do Genoma , beta-Lactamases , Ceftazidima/farmacologia , Compostos Azabicíclicos/farmacologia , Humanos , Líbano , beta-Lactamases/genética , beta-Lactamases/metabolismo , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efeitos dos fármacos , Antibacterianos/farmacologia , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Carbapenêmicos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Plasmídeos/genética , Testes de Sensibilidade Microbiana , Transferência Genética Horizontal , Genoma Bacteriano , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Centros de Atenção Terciária
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