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1.
Mol Biol (Mosk) ; 53(4): 600-612, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397434

RESUMO

A new plasmid, pSM22, was isolated from Serratia marcescens and sequenced. Its 43 190-bp sequence with an average GC-content of 58% contains 31 open reading frames (ORFs) which form replication, conjugation, stability, and adaptive modules. The replication module includes a site of initiation of leading-strand synthesis in plasmid replication, a replication termination site (terC), the rep A (=repA1) and repA4 genes, and the copA sequence, which codes for an antisense RNA (asRNA). These structures are functionally integrated in an FII replicon (incompatibility group IncFII). Based on the significant differences between the FII replicon and the canonical sequences of the R plasmids R1 and NR1 (=R100=R222), pSM22 was assigned to a new subtype. The conjugation module includes 13 genes with a high identity to the genes responsible for conjugation of the F plasmid. A comparative genomic analysis showed that the conjugation modules of pSM22 and F are structurally similar. By the conjugation system and the presence of three conserved motifs in relaxase (TraI), pSM22 belongs to the F12 clade of the MOBF type. The stability module includes the resD and parA genes, which are responsible for the resolution of multimeric plasmid forms and their subsequent segregation between daughter cells. The adaptive module contains the microcin H47 (MccH47) secretion/processing and UV resistance genes. The mosaic structure of pSM22 and reductive evolution of its modules suggest high genomic plasticity for the genus Serratia. An analysis of the architecture of the pSM22 modules clarifies the evolutionary relationships among IncF/MOBF12 group plasmids in bacteria of the family Enterobacteriaceae and opens a novel avenue for further comparative genomic studies of Serratia plasmids.


Assuntos
Evolução Molecular , Genômica , Plasmídeos/classificação , Plasmídeos/genética , Replicação do DNA , Genes Bacterianos , Genoma Bacteriano/genética , Replicon/genética , Serratia marcescens/genética
2.
J Med Microbiol ; 68(8): 1173-1188, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31268417

RESUMO

PURPOSE: Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY: A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS: The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS: These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.


Assuntos
Cápsulas Bacterianas/genética , Tipagem Molecular/métodos , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/genética , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Genoma Bacteriano/genética , Humanos , Infecções Pneumocócicas/microbiologia , Proteínas Tirosina Fosfatases/genética , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA , Sorogrupo , Sorotipagem/normas , Streptococcus/classificação , Streptococcus/genética , Streptococcus/isolamento & purificação , Streptococcus pneumoniae/isolamento & purificação , Fluxo de Trabalho
3.
J Microbiol Biotechnol ; 29(7): 1144-1154, 2019 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-31288301

RESUMO

There have been several studies regarding lichen-associated bacteria obtained from diverse environments. Our screening process identified 49 bacterial species in two lichens from the Himalayas: 17 species of Actinobacteria, 19 species of Firmicutes, and 13 species of Proteobacteria. We discovered five types of strong antimicrobial agent-producing bacteria. Although some strains exhibited weak antimicrobial activity, NP088, NP131, NP132, NP134, and NP160 exhibited strong antimicrobial activity against all multidrug-resistant strains. Polyketide synthase (PKS) fingerprinting revealed results for 69 of 148 strains; these had similar genes, such as fatty acid-related PKS, adenylation domain genes, PfaA, and PksD. Although the association between antimicrobial activity and the PKS fingerprinting results is poorly resolved, NP160 had six types of PKS fingerprinting genes, as well as strong antimicrobial activity. Therefore, we sequenced the draft genome of strain NP160, and predicted its secondary metabolism using antiSMASH version 4.2. NP160 had 46 clusters and was predicted to produce similar secondary metabolites with similarities of 5-100%. Although NP160 had 100% similarity with the alkylresorcinol biosynthetic gene cluster, our results showed low similarity with existing members of this biosynthetic gene cluster, and most have not yet been revealed. In conclusion, we expect that lichen-associated bacteria from the Himalayas can produce new secondary metabolites, and we found several secondary metabolite-related biosynthetic gene clusters to support this hypothesis.


Assuntos
Anti-Infecciosos/metabolismo , Genoma Bacteriano/genética , Líquens/microbiologia , Streptomyces/genética , Streptomyces/metabolismo , Anti-Infecciosos/farmacologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Sequência de Bases , Impressões Digitais de DNA , DNA Bacteriano/genética , Testes de Sensibilidade Microbiana , Família Multigênica , Filogenia , Policetídeo Sintases/genética , RNA Ribossômico 16S/genética , Metabolismo Secundário/genética , Análise de Sequência de DNA
4.
Nat Commun ; 10(1): 3100, 2019 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-31308405

RESUMO

Of the 473 genes in the genome of the bacterium with the smallest genome generated to date, 149 genes have unknown function, emphasising a universal problem; less than 1% of proteins have experimentally determined annotations. Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins. Proteins that are still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins. Twenty-four likely transporter proteins are identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell in a nutrient-rich environment after removal of metabolic enzymes. Hence, the environment shapes the nature of a minimal genome. Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and identify crucial gaps for further development.


Assuntos
Adaptação Biológica/genética , Bactérias/genética , Genoma Bacteriano/genética , Biologia Computacional/métodos , Genes Essenciais/genética , Anotação de Sequência Molecular/métodos , Software
5.
J Med Microbiol ; 68(9): 1320-1323, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31329091

RESUMO

The recent increase in pertussis cases observed in some countries may have several causes, including the evolution of Bordetella pertussis populations towards escape of vaccine-induced immunity. Most genomic studies of B. pertussis isolates performed so far are from countries that use acellular vaccines. The objective was to analyse genomic sequences of isolates collected during the 2014 whooping cough epidemic in Tunisia, a country where whole-cell vaccines are used. Ten Tunisian isolates and four vaccine strains were sequenced and compared to 169 isolates from countries where acellular vaccines are used. Phylogenetic analysis showed that Tunisian isolates are diverse, demonstrating a multi-strain 2014 epidemic peak, and are intermixed with those circulating in other world regions, showing inter-country transmission. Consistently, Tunisian isolates have antigen variant composition observed in other world regions. No pertactin-deficient strain was observed. The Tunisian B. pertussis population appears to be largely connected with populations from other countries.


Assuntos
Bordetella pertussis/genética , Variação Genética , Genoma Bacteriano/genética , Filogenia , Coqueluche/microbiologia , Antígenos de Bactérias/genética , Proteínas da Membrana Bacteriana Externa/genética , Bordetella pertussis/classificação , Bordetella pertussis/imunologia , Bordetella pertussis/isolamento & purificação , DNA Bacteriano/genética , Humanos , Lactente , Recém-Nascido , Epidemiologia Molecular , Vacina contra Coqueluche/administração & dosagem , Vacina contra Coqueluche/genética , Análise de Sequência de DNA , Tunísia/epidemiologia , Virulência/genética , Fatores de Virulência de Bordetella/genética , Coqueluche/epidemiologia , Coqueluche/transmissão
6.
J Med Microbiol ; 68(9): 1367-1372, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31329093

RESUMO

Methicillin-resistant Staphylococcus lugdunensis (MRSL) is increasingly recognized in healthcare and community settings. To obtain a better understanding of the emergence of MRSL, this study characterized the structure and content of the SCCmec elements harboured by 36 MRSL isolates obtained from diverse sources in Hong Kong from 2008 to 2017. The isolates were investigated by whole-genome sequencing. SCCmec types and subtypes were assigned according to the guidelines from the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The sequence type (ST)-SCCmec combinations in the 36 MRSL isolates were as follows: ST3-SCCmec IV (n=2), ST3-SCCmec V (n=28), ST27-SCCmec V (n=5) and ST42-SCCmec V (n=1). The two SCCmec IV elements were highly similar to the SCCmec IV element harboured by the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain, JCSC6668. The J3-mec complex-J2 regions in the SCCmec V elements were highly similar to the corresponding regions in the CA-MRSA strains PM1 (n=13) or WIS (n=21). Based on the J1 to J3 sequences, the SCCmec V elements can be categorized into nine different subtypes. Our findings highlight the diversified structures of SCCmec elements among MRSL strains and their close relationship with SCCmec elements harboured by CA-MRSA.


Assuntos
Cromossomos Bacterianos/genética , Infecções Comunitárias Adquiridas/microbiologia , Genes Bacterianos/genética , Staphylococcus aureus Resistente à Meticilina/genética , Infecções Estafilocócicas/microbiologia , Staphylococcus lugdunensis/genética , Antibacterianos/farmacologia , Infecções Comunitárias Adquiridas/epidemiologia , DNA Bacteriano/genética , Genoma Bacteriano/genética , Hong Kong/epidemiologia , Humanos , Staphylococcus aureus Resistente à Meticilina/classificação , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Análise de Sequência de DNA , Infecções Estafilocócicas/epidemiologia , Estudantes de Medicina
7.
BMC Vet Res ; 15(1): 235, 2019 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-31286947

RESUMO

BACKGROUND: Enterococcus is an important component of normal flora in human and animals, but in recent years, the pathogenicity of Enterococcus has been confirmed in clinical medicine. More and more animal infections have been reported in veterinary clinics. For the last decades, outbreaks of encephalitis in lambs have become much more common in Northern Xinjiang, China. Consequent studies have confirmed that these affected lambs had been commonly infected with E. faecalis. More than 60 E. faecalis were isolated from the brain of infected lambs, A highly virulent strain entitled E. faecalis 2A (XJ05) were selected, sequenced and analyzed. RESULT: Using whole genome sequence and de novo assembly, 18 contigs with NGS and annotation were obtained. It is confirmed that the genome has a size of 2.9 Mb containing 2783 protein-coding genes, as well as 54 tRNA genes and 4 rRNA genes. Some key features of this strain were identified, which included 7 predicted antibiotic resistance genes and 18 candidate virulence factor genes. CONCLUSION: The E. faecalis 2A (XJ05) genome is conspicuous smaller than E.faecalis V583, but not significantly different from other non-pathogenic E. faecalis. It carried 7 resistance genes including 4 kind of antibiotics which were consistent with the results of extensive drug resistance phenotypic, including aminoglycoside, macrolide, phenicol, and tetracycline. 2A (XJ05) also carried 18 new virulence factor genes related to virulence, hemolysin genes (cylA, cylB, cylM, cylL) may play an important role in lamb encephalitis by E. faecalis 2A (XJ05).


Assuntos
Farmacorresistência Bacteriana/genética , Encefalite/veterinária , Enterococcus faecalis/genética , Enterococcus faecalis/patogenicidade , Genoma Bacteriano/genética , Doenças dos Ovinos/microbiologia , Virulência/genética , Animais , Resistência a Múltiplos Medicamentos/genética , Encefalite/microbiologia , Ovinos
8.
Nat Commun ; 10(1): 2449, 2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-31164644

RESUMO

DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. We sequence a human genome HX1 and a Chlamydomonas reinhardtii genome using Nanopore sequencing, and then evaluate DeepMod on three types of genomes (Escherichia coli, Chlamydomonas reinhardtii and human genomes). For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species.


Assuntos
Chlamydomonas reinhardtii/genética , Metilação de DNA , Escherichia coli/genética , Genoma Bacteriano/genética , Genoma Humano/genética , Genoma de Planta/genética , Redes Neurais (Computação) , Bases de Dados de Ácidos Nucleicos , Epigênese Genética , Humanos , Nanoporos
9.
Nature ; 571(7764): 219-225, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31189177

RESUMO

Conventional CRISPR-Cas systems maintain genomic integrity by leveraging guide RNAs for the nuclease-dependent degradation of mobile genetic elements, including plasmids and viruses. Here we describe a notable inversion of this paradigm, in which bacterial Tn7-like transposons have co-opted nuclease-deficient CRISPR-Cas systems to catalyse RNA-guided integration of mobile genetic elements into the genome. Programmable transposition of Vibrio cholerae Tn6677 in Escherichia coli requires CRISPR- and transposon-associated molecular machineries, including a co-complex between the DNA-targeting complex Cascade and the transposition protein TniQ. Integration of donor DNA occurs in one of two possible orientations at a fixed distance downstream of target DNA sequences, and can accommodate variable length genetic payloads. Deep-sequencing experiments reveal highly specific, genome-wide DNA insertion across dozens of unique target sites. This discovery of a fully programmable, RNA-guided integrase lays the foundation for genomic manipulations that obviate the requirements for double-strand breaks and homology-directed repair.


Assuntos
Sistemas CRISPR-Cas/genética , Elementos de DNA Transponíveis/genética , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Edição de Genes/métodos , Mutagênese Insercional/métodos , RNA Bacteriano/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Proteínas Associadas a CRISPR/genética , Proteínas Associadas a CRISPR/metabolismo , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/metabolismo , Escherichia coli/genética , Genoma Bacteriano/genética , Integrases/genética , Integrases/metabolismo , Mutagênese Sítio-Dirigida/métodos , RNA Guia/genética , Especificidade por Substrato , Vibrio cholerae/genética
10.
J Med Microbiol ; 68(8): 1148-1158, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31199220

RESUMO

PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.


Assuntos
Microbiota , Boca/microbiologia , Fumar , Adulto , Bactérias/classificação , Bactérias/genética , Feminino , Genoma Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Adulto Jovem
11.
J Med Microbiol ; 68(8): 1219-1226, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31237534

RESUMO

PURPOSE: The new third-generation sequencing platform MinION is an attractive maintenance-free and disposable portable tool that can perform long-read and real-time sequencing. In this study, we validated this technology for the identification of pathogens from positive blood culture (BC) bottles. METHODOLOGY: A total of 38 positive BC bottles were collected from patients with bloodstream infections, and 18 isolates of Gram-negative (GN) bacteria and 20 isolates of Gram-positive (GP) bacteria were identified from these using 16S rRNA sequencing and then used in this study. DNA was extracted from each aliquot using an extraction protocol that combined glass bead beating and chemical lysis. Up to 200 ng of each purified DNA sample was processed for library preparation and whole-genome sequencing was performed on up to 12 samples through a single MinION flow cell. RESULTS: All GN bacteria identifications made by MinION sequencing for 30 min using the What's In My Pot? (WIMP) workflow via EPI2ME on the basis of the most frequent classified reads were consistent with those made by 16S rRNA sequencing. On the other hand, for GP bacteria specimens, the identification results for 16S rRNA sequencing and MinION were only in agreement in 12 out of 20 (60.0 %) cases. ARMA analysis was able to detect extended-spectrum ß-lactamase (ESBL)-associated genes among various antimicrobial resistance-related genes. CONCLUSION: We demonstrated the potential of the MinION sequencer for the identification of GN bacteria from positive BC bottles and the confirmation of an ESBL phenotype. This innovative sequence technology and its application could lead to a breakthrough in the diagnosis of infectious diseases.


Assuntos
Bacteriemia/microbiologia , Bactérias Gram-Negativas/genética , Bactérias Gram-Negativas/isolamento & purificação , Técnicas de Diagnóstico Molecular/instrumentação , Técnicas de Diagnóstico Molecular/métodos , beta-Lactamases/genética , Antibacterianos/farmacologia , DNA Bacteriano/genética , Genoma Bacteriano/genética , Bactérias Gram-Negativas/classificação , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/classificação , Bactérias Gram-Positivas/genética , Bactérias Gram-Positivas/isolamento & purificação , Humanos , Testes de Sensibilidade Microbiana , Nanoporos , Reação em Cadeia da Polimerase/normas , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/normas , Análise de Sequência de DNA , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/normas , Fatores de Tempo
12.
Syst Appl Microbiol ; 42(4): 488-494, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31204142

RESUMO

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273T and Pantoea rwandensis LMG 26275T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596T was 5.1Mbp, comprising 4896 predicted genes with DNA G+C content of 57.8mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596T were C16:0, summed feature 2 (C12:0 aldehyde), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596T (=DSM 100,785T=CGMCC 1.15280T) as type strain.


Assuntos
Pantoea/classificação , Pantoea/fisiologia , Filogenia , Zea mays/microbiologia , China , DNA Bacteriano/genética , Endófitos , Ácidos Graxos/química , Genes Bacterianos/genética , Genes Essenciais/genética , Genoma Bacteriano/genética , Pantoea/química , Pantoea/genética , Fenótipo , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Ubiquinona/química
13.
J Microbiol Biotechnol ; 29(6): 962-972, 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31216839

RESUMO

Non-typhoidal Salmonella (NTS) is one of the most frequent causes of bacterial foodborne illnesses. Considering that the main reservoir of NTS is the intestinal tract of livestock, foods of animal origin are regarded as the main vehicles of Salmonella infection. In particular, poultry colonized with Salmonella Typhimurium (S. Typhimurium), a dominant serotype responsible for human infections, do not exhibit overt signs and symptoms, thereby posing a potential health risk to humans. In this study, comparative genomics approaches were applied to two S. Typhimurium strains, ST1539 and ST1120, isolated from a duck slaughterhouse and a pig farm, respectively, to characterize their virulence and antimicrobial resistance-associated genomic determinants. ST1539 containing a chromosome (4,905,039 bp; 4,403 CDSs) and a plasmid (93,876 bp; 96 CDSs) was phylogenetically distinct from other S. Typhimurium strains such as ST1120 and LT2. Compared to the ST1120 genome (previously deposited in GenBank; CP021909.1 and CP021910.1), ST1539 possesses more virulence determinants, including ST64B prophage, plasmid spv operon encoding virulence factors, genes encoding SseJ effector, Rck invasin, and biofilm-forming factors (bcf operon and pefAB). In accordance with the in silico prediction, ST1539 exhibited higher cytotoxicity against epithelial cells, better survival inside macrophage cells, and faster mice-killing activity than ST1120. However, ST1539 showed less resistance against antibiotics than ST1120, which may be attributed to the multiple resistanceassociated genes in the ST1120 chromosome. The accumulation of comparative genomics data on S. Typhimurium isolates from livestock would enrich our understanding of strategies Salmonella employs to adapt to diverse host animals.


Assuntos
Farmacorresistência Bacteriana , Genoma Bacteriano/genética , Aves Domésticas , Salmonelose Animal/microbiologia , Salmonella typhimurium/genética , Salmonella typhimurium/patogenicidade , Matadouros , Animais , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Sobrevivência Celular , Farmacorresistência Bacteriana/genética , Feminino , Células HeLa , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Filogenia , Plasmídeos/genética , Prófagos/genética , República da Coreia , Salmonella typhimurium/classificação , Salmonella typhimurium/isolamento & purificação , Sorogrupo , Suínos , Virulência/genética
14.
Nat Commun ; 10(1): 2595, 2019 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-31197163

RESUMO

Plasmid acquisition is an important mechanism of rapid adaptation and niche expansion in prokaryotes. Positive selection for plasmid-coded functions is a major driver of plasmid evolution, while plasmids that do not confer a selective advantage are considered costly and expected to go extinct. Yet, plasmids are ubiquitous in nature, and their persistence remains an evolutionary paradox. Here, we demonstrate that non-mobile plasmids persist over evolutionary timescales without selection for the plasmid function. Evolving a minimal plasmid encoding for antibiotics resistance in Escherichia coli, we discover that plasmid stability emerges in the absence of antibiotics and that plasmid loss is determined by transcription-replication conflicts. We further find that environmental conditions modulate these conflicts and plasmid persistence. Silencing the transcription of the resistance gene results in stable plasmids that become fixed in the population. Evolution of plasmid stability under non-selective conditions provides an evolutionary explanation for the ubiquity of plasmids in nature.


Assuntos
Adaptação Biológica/genética , Resistência Microbiana a Medicamentos/genética , Escherichia coli/genética , Plasmídeos/genética , Antibacterianos/farmacologia , Variações do Número de Cópias de DNA/genética , Evolução Molecular Direcionada/métodos , Genoma Bacteriano/genética , Plasmídeos/efeitos dos fármacos , Temperatura Ambiente
15.
Nat Commun ; 10(1): 2043, 2019 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-31053724

RESUMO

Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 1012 hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one.


Assuntos
Proteínas de Bactérias/genética , Bacteroidetes/genética , Enzimas/genética , Genoma Bacteriano/genética , Polissacarídeos/metabolismo , Proteínas de Bactérias/metabolismo , Bacteroidetes/metabolismo , Enzimas/metabolismo , Loci Gênicos , Isomerismo , Polissacarídeos/química
16.
Nat Commun ; 10(1): 2176, 2019 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-31092817

RESUMO

Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.


Assuntos
Predisposição Genética para Doença , Meningite Pneumocócica/genética , Streptococcus pneumoniae/genética , Adulto , Idoso , Proteínas de Bactérias/genética , Feminino , Variação Genética , Genoma Bacteriano/genética , Genoma Humano/genética , Estudo de Associação Genômica Ampla , Interações Hospedeiro-Patógeno/genética , Humanos , Masculino , Meningite Pneumocócica/microbiologia , Pessoa de Meia-Idade , Estudos Prospectivos , Proteínas/genética , Streptococcus pneumoniae/isolamento & purificação
17.
Nat Commun ; 10(1): 2128, 2019 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-31086182

RESUMO

Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.


Assuntos
Antituberculosos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Genoma Bacteriano/genética , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Análise Mutacional de DNA , Loci Gênicos/genética , Estudo de Associação Genômica Ampla , Humanos , Testes de Sensibilidade Microbiana , Mutação , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/isolamento & purificação , Regiões Promotoras Genéticas/genética , Escarro/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Sequenciamento Completo do Genoma
18.
J Basic Microbiol ; 59(7): 754-764, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31099101

RESUMO

To date, a small number of temperate phages are known to infect members of the genus Erwinia. In this study, the genomes of temperate phages vB_EhrS_49 and vB_EhrS_59 infecting Erwinia horticola, the causative agent of beech black bacteriosis in Ukraine, were sequenced and annotated. Their genomes reveal no significant similarity to that of any previously reported viruses of Enterobacteriaceae. At the same time, phages 49 and 59 share extensive nucleotide sequence identity across the regions encoding head assembly, DNA packaging, and lysis. Despite significant homology between structural modules, the organization of distal tail morphogenesis genes is different. Furthermore, a number of putative morons and DNA methylases have been found in both phage genomes. Due to the revealed synteny as well as the structure of lysogeny module, phages 49 and 59 are suggested to be novel members of the lambdoid phage group. Conservative structural genes together with varying homology across the nonstructural region of the genomes make phages 49 and 59 highly promising objects for studying the genetic recombination and evolution of microbial viruses. The obtained data may as well be helpful for better understanding of relationships among Erwinia species.


Assuntos
Bacteriófagos/genética , Erwinia/virologia , Genoma Bacteriano/genética , Genoma Viral/genética , Siphoviridae/genética , DNA Viral/genética , Genes Virais , Lisogenia , Filogenia , Doenças das Plantas/microbiologia , Análise de Sequência de DNA , Siphoviridae/classificação , Especificidade da Espécie , Sintenia
19.
Curr Microbiol ; 76(7): 835-841, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31053905

RESUMO

A novel facultative anaerobic and Gram-stain-positive coccus, designated strain ChDC F135T, was isolated from human subgingival dental plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene (16S rDNA) sequence of strain ChDC F135T was closest to that of Streptococcus sinensis HKU4T (98.2%), followed by Streptococcus intermedia SK54T (97.0%), Streptococcus constellatus NCTC11325T (96.0%), and Streptococcus anginosus NCTC 10713T (95.7%). In contrast, phylogenetic analysis based on the superoxide dismutase gene (sodA) and the RNA polymerase beta-subunit gene (rpoB) showed that the nucleotide sequence similarities of strain ChDC F135T were highly similar to the corresponding genes of S. anginosus NCTC 10713T (99.2% and 97.6%, respectively), S. constellatus NCTC11325T (87.8% and 91.4%, respectively), and S. intermedia SK54T (85.8% and 91.2%, respectively) rather than those of S. sinensis HKU4T (80.5% and 82.6%). The complete genome of strain ChDC F135T consisted of 1,901,251 bp and the G+C content was 38.9 mol %. Average nucleotide identity value between strain ChDC F135T and S. sinensis HKU4T or S. anginosus NCTC 10713T were 75.7% and 95.6%, respectively. The C14:0 composition of the cellular fatty acids of strain ChDC F135T (32.8%) was different from that of S. intermedia (6-8%), S. constellatus (6-13%), and S. anginosus (13-20%). Based on the results of phylogenetic and phenotypic analysis, strain ChDC F135T (= KCOM 2412T = JCM 33300T) was classified as a type strain of a novel species of the genus Streptococcus, for which we proposed the name Streptococcus periodonticum sp. nov.


Assuntos
Placa Dentária/microbiologia , Periodontite/microbiologia , Streptococcus/classificação , Streptococcus/fisiologia , Bactérias Anaeróbias , Proteínas de Bactérias/genética , Composição de Bases , DNA Bacteriano/genética , RNA Polimerases Dirigidas por DNA/genética , Ácidos Graxos/análise , Genoma Bacteriano/genética , Humanos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Streptococcus/genética , Superóxido Dismutase/genética
20.
Curr Microbiol ; 76(7): 872-878, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31079192

RESUMO

A rod-shaped, Gram-negative and aerobic bacterium, strain XWS2, was isolated from rhizosphere soil of a camphor tree in Hubei University of Chinese Medicine Huangjiahu Campus, Wuhan, China. Cells grew at 4-37 °C (optimum 28 °C), pH 5.0-9.0 (optimum 7.0) and with 0-5% NaCl (optimum 1%). Colonies growing on tryptone soybean agar are round, beige in color and approximately 2 mm in diameter after 24 h incubation at 28 °C. Pellicle formation during liquid culture and strong fluorescent pigment production on King's B medium are typical features of strain XWS2. The genome of XWS2 is 6,170,117 bp, containing 5682 predicted genes and 4770 genes are functionally annotated. Phylogenetic analysis based on 16S rRNA sequence showed that strain XWS2 formed an independent branch within the Pseudomonas putida group, with P. putida NBRC 14164T (99.86% similarity) and P. alkylphenolica KL28T (99.36% similarity) as the most closely related type strains. Genome sequence analysis based on average nucleotide identity and digital DNA-DNA hybridization are below the threshold values for species delineation. Phenotypic characteristics, physiological and biochemical tests also supported the strain represents a separate novel species within the Pseudomonas genus. The name Pseudomonas hutmensis sp. nov. is proposed, with type strain XWS2T (= CCTCC AB 2018189 T = KACC 19898T).


Assuntos
Pigmentos Biológicos/metabolismo , Pseudomonas putida/classificação , Pseudomonas putida/fisiologia , Microbiologia do Solo , Composição de Bases , China , Cinnamomum camphora/microbiologia , DNA Bacteriano/genética , Fluorescência , Genoma Bacteriano/genética , Hibridização de Ácido Nucleico , Filogenia , Pseudomonas putida/genética , RNA Ribossômico 16S/genética , Rizosfera , Análise de Sequência de DNA , Especificidade da Espécie
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