Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 3.951
Filtrar
1.
Nat Commun ; 11(1): 4915, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004811

RESUMO

A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the ß-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B. The TU re-inserts into the chromosome adjacent to IS26 and forms a tandem array of TUs, which increases the copy number of blaTEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in blaTEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of blaTEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/tratamento farmacológico , Proteínas de Escherichia coli/genética , Escherichia coli/genética , beta-Lactamases/genética , Antibacterianos/uso terapêutico , Cromossomos Bacterianos/genética , Elementos de DNA Transponíveis/genética , DNA Bacteriano/genética , Quimioterapia Combinada/métodos , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/microbiologia , Amplificação de Genes , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano/genética , Humanos , Testes de Sensibilidade Microbiana , Piperacilina/farmacologia , Piperacilina/uso terapêutico , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Tazobactam/farmacologia , Tazobactam/uso terapêutico , Sequenciamento Completo do Genoma
2.
Curr Biol ; 30(19): R1124-R1130, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33022254

RESUMO

Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these 'microbe hunters' have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.


Assuntos
Bactérias/genética , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/epidemiologia , Epidemiologia Molecular/métodos , Prevenção Primária/métodos , Bactérias/patogenicidade , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Infecções por Coronavirus/epidemiologia , Genoma Bacteriano/genética , Genoma Viral/genética , História do Século XIX , História do Século XX , Humanos , Microbiota/genética , Pandemias , Pneumonia Viral/epidemiologia
3.
Nat Commun ; 11(1): 4918, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004800

RESUMO

In order to control and eradicate epidemic cholera, we need to understand how epidemics begin, how they spread, and how they decline and eventually end. This requires extensive sampling of epidemic disease over time, alongside the background of endemic disease that may exist concurrently with the epidemic. The unique circumstances surrounding the Argentinian cholera epidemic of 1992-1998 presented an opportunity to do this. Here, we use 490 Argentinian V. cholerae genome sequences to characterise the variation within, and between, epidemic and endemic V. cholerae. We show that, during the 1992-1998 cholera epidemic, the invariant epidemic clone co-existed alongside highly diverse members of the Vibrio cholerae species in Argentina, and we contrast the clonality of epidemic V. cholerae with the background diversity of local endemic bacteria. Our findings refine and add nuance to our genomic definitions of epidemic and endemic cholera, and are of direct relevance to controlling current and future cholera epidemics.


Assuntos
Cólera/microbiologia , Doenças Endêmicas/prevenção & controle , Genoma Bacteriano/genética , Pandemias/prevenção & controle , Vibrio cholerae/genética , Argentina/epidemiologia , Cólera/epidemiologia , Cólera/prevenção & controle , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , História do Século XIX , História do Século XX , Humanos , Anotação de Sequência Molecular , Pandemias/história , Filogenia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Vibrio cholerae/isolamento & purificação , Vibrio cholerae/patogenicidade
4.
PLoS Comput Biol ; 16(9): e1007646, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32925899

RESUMO

In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide computational evidences supporting potential axenic growth of B. bacteriovorus's in a rich medium based on its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacteria's metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.


Assuntos
Bdellovibrio bacteriovorus/genética , Bdellovibrio bacteriovorus/metabolismo , Genoma Bacteriano/genética , Redes e Vias Metabólicas , Modelos Biológicos , Redes e Vias Metabólicas/genética , Redes e Vias Metabólicas/fisiologia , Biologia de Sistemas/métodos
5.
Antimicrob Resist Infect Control ; 9(1): 154, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32962759

RESUMO

BACKGROUND: Currently, hospitals have been forced to divert substantial resources to cope with the ongoing coronavirus disease 2019 (COVID-19) pandemic. It is unclear if this situation will affect long-standing infection prevention practices and impact on healthcare associated infections. Here, we report a nosocomial cluster of vancomycin-resistant enterococci (VRE) that occurred on a COVID-19 dedicated intensive care unit (ICU) despite intensified contact precautions during the current pandemic. Whole genome sequence-based typing (WGS) was used to investigate genetic relatedness of VRE isolates collected from COVID-19 and non-COVID-19 patients during the outbreak and to compare them to environmental VRE samples. METHODS: Five VRE isolated from patients (three clinical and two screening samples) as well as 11 VRE and six vancomycin susceptible Enterococcus faecium (E. faecium) samples from environmental sites underwent WGS during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing (cgMLST). RESULTS: WGS revealed two genotypic distinct VRE clusters with genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control bundle strategies. CONCLUSIONS: Our results illustrate the importance of continued adherence to infection prevention and control measures during the COVID-19 pandemic to prevent VRE transmission and healthcare associated infections.


Assuntos
Coinfecção/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Infecções por Bactérias Gram-Positivas/tratamento farmacológico , Infecções por Bactérias Gram-Positivas/epidemiologia , Enterococos Resistentes à Vancomicina/efeitos dos fármacos , Betacoronavirus , Coinfecção/microbiologia , Infecções por Coronavirus/patologia , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , Surtos de Doenças , Genoma Bacteriano/genética , Infecções por Bactérias Gram-Positivas/microbiologia , Humanos , Controle de Infecções , Unidades de Terapia Intensiva , Tipagem de Sequências Multilocus , Pandemias , Pneumonia Viral/patologia , Prevenção Primária , Enterococos Resistentes à Vancomicina/genética , Enterococos Resistentes à Vancomicina/isolamento & purificação , Sequenciamento Completo do Genoma
6.
PLoS One ; 15(8): e0238151, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32833990

RESUMO

Bacteria often possess relatively flexible genome structures and adaptive genetic variants that allow survival in unfavorable growth conditions. Bacterial survival tactics in disadvantageous microenvironments include mutations that are beneficial against threats in their niche. Here, we report that the aerobic rice bacterial pathogen Burkholderia glumae BGR1 changes a specific gene for improved survival in static culture conditions. Static culture triggered formation of colony variants with deletions or point mutations in the gene bspP (BGLU_RS28885), which putatively encodes a protein that contains PDC2, PAS-9, SpoIIE, and HATPase domains. The null mutant of bspP survived longer in static culture conditions and produced a higher level of bis-(3'-5')-cyclic dimeric guanosine monophosphate than the wild type. Expression of the bacterial cellulose synthase regulator (bcsB) gene was upregulated in the mutant, consistent with the observation that the mutant formed pellicles faster than the wild type. Mature pellicle formation was observed in the bspP mutant before pellicle formation in wild-type BGR1. However, the population density of the bspP null mutant decreased substantially when grown in Luria-Bertani medium with vigorous agitation due to failure of oxalate-mediated detoxification of the alkaline environment. The bspP null mutant was less virulent and exhibited less effective colonization of rice plants than the wild type. All phenotypes caused by mutations in bspP were recovered to those of the wild type by genetic complementation. Thus, although wild-type B. glumae BGR1 prolonged viability by spontaneous mutation under static culture conditions, such genetic changes negatively affected colonization in rice plants. These results suggest that adaptive gene sacrifice of B. glumae to survive unfavorable growth conditions is not always desirable as it can adversely affect adaptability in the host.


Assuntos
Adaptação Biológica/genética , Burkholderia/genética , Burkholderia/metabolismo , Burkholderia/patogenicidade , Regulação Bacteriana da Expressão Gênica/genética , Genoma Bacteriano/genética , Genômica/métodos , Mutação , Oryza/microbiologia , Doenças das Plantas/microbiologia , Percepção de Quorum/genética , Virulência/genética
7.
PLoS Genet ; 16(8): e1008987, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32853297

RESUMO

Replication-transcription conflicts promote mutagenesis and give rise to evolutionary signatures, with fundamental importance to genome stability ranging from bacteria to metastatic cancer cells. This review focuses on the interplay between replication-transcription conflicts and the evolution of gene directionality. In most bacteria, the majority of genes are encoded on the leading strand of replication such that their transcription is co-directional with the direction of DNA replication fork movement. This gene strand bias arises primarily due to negative selection against deleterious consequences of head-on replication-transcription conflict. However, many genes remain head-on. Can head-on orientation provide some benefit? We combine insights from both mechanistic and evolutionary studies, review published work, and analyze gene expression data to evaluate an emerging model that head-on genes are temporal targets for adaptive mutagenesis during stress. We highlight the alternative explanation that genes in the head-on orientation may simply be the result of genomic inversions and relaxed selection acting on nonessential genes. We seek to clarify how the mechanisms of replication-transcription conflict, in concert with other mutagenic mechanisms, balanced by natural selection, have shaped bacterial genome evolution.


Assuntos
Replicação do DNA/genética , Evolução Molecular , Seleção Genética/genética , Transcrição Genética , Bactérias/genética , Genoma Bacteriano/genética
8.
PLoS Comput Biol ; 16(8): e1008137, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32804944

RESUMO

Genome-scale metabolic models have been utilized extensively in the study and engineering of the organisms they describe. Here we present the analysis of a published dataset from pooled transposon mutant fitness experiments as an approach for improving the accuracy and gene-reaction associations of a metabolic model for Zymomonas mobilis ZM4, an industrially relevant ethanologenic organism with extremely high glycolytic flux and low biomass yield. Gene essentiality predictions made by the draft model were compared to data from individual pooled mutant experiments to identify areas of the model requiring deeper validation. Subsequent experiments showed that some of the discrepancies between the model and dataset were caused by polar effects, mis-mapped barcodes, or mutants carrying both wild-type and transposon disrupted gene copies-highlighting potential limitations inherent to data from individual mutants in these high-throughput datasets. Therefore, we analyzed correlations in fitness scores across all 492 experiments in the dataset in the context of functionally related metabolic reaction modules identified within the model via flux coupling analysis. These correlations were used to identify candidate genes for a reaction in histidine biosynthesis lacking an annotated gene and highlight metabolic modules with poorly correlated gene fitness scores. Additional genes for reactions involved in biotin, ubiquinone, and pyridoxine biosynthesis in Z. mobilis were identified and confirmed using mutant complementation experiments. These discovered genes, were incorporated into the final model, iZM4_478, which contains 747 metabolic and transport reactions (of which 612 have gene-protein-reaction associations), 478 genes, and 616 unique metabolites, making it one of the most complete models of Z. mobilis ZM4 to date. The methods of analysis that we applied here with the Z. mobilis transposon mutant dataset, could easily be utilized to improve future genome-scale metabolic reconstructions for organisms where these, or similar, high-throughput datasets are available.


Assuntos
Aptidão Genética/genética , Genoma Bacteriano/genética , Modelos Genéticos , Mutação/genética , Zymomonas , Anaerobiose , Engenharia Metabólica , Zymomonas/genética , Zymomonas/metabolismo
9.
Nat Commun ; 11(1): 3442, 2020 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-32651390

RESUMO

Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.


Assuntos
Infecções Pneumocócicas/genética , Streptococcus pneumoniae/genética , Evolução Molecular , Genética , Genoma Bacteriano/genética , Humanos , Sequenciamento Completo do Genoma
10.
Nat Commun ; 11(1): 3526, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32665571

RESUMO

Gene tandem amplifications are thought to drive bacterial evolution, but they are transient in the absence of selection, making their investigation challenging. Here, we analyze genomic sequences of Staphylococcus aureus USA300 isolates from the same geographical area to identify variations in gene copy number, which we confirm by long-read sequencing. We find several hotspots of variation, including the csa1 cluster encoding lipoproteins known to be immunogenic. We also show that the csa1 locus expands and contracts during bacterial growth in vitro and during systemic infection of mice, and recombination creates rapid heterogeneity in initially clonal cultures. Furthermore, csa1 copy number variants differ in their immunostimulatory capacity, revealing a mechanism by which gene copy number variation can modulate the host immune response.


Assuntos
Genoma Bacteriano/genética , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Animais , Evolução Biológica , Genótipo , Camundongos , Fenótipo , Staphylococcus aureus/patogenicidade
11.
PLoS Genet ; 16(7): e1008931, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32644999

RESUMO

Shigella species are specialised lineages of Escherichia coli that have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies of Shigella evolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individual Shigella species have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent in Shigella genomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations of Shigella dysenteriae Sd1, Shigella sonnei and Shigella flexneri. We find that five IS (IS1, IS2, IS4, IS600 and IS911) have undergone expansion in all Shigella species, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced in S. dysenteriae and least advanced in S. sonnei; and using genome-scale models of metabolism we show that Shigella species display convergent loss of core E. coli metabolic capabilities, with S. sonnei and S. flexneri following a similar trajectory of metabolic streamlining to that of S. dysenteriae. This study highlights the importance of IS to the evolution of Shigella and provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species.


Assuntos
Elementos de DNA Transponíveis/genética , Disenteria/genética , Evolução Molecular , Shigella dysenteriae/genética , DNA Bacteriano/genética , Disenteria/microbiologia , Escherichia coli/genética , Escherichia coli/patogenicidade , Genoma Bacteriano/genética , Humanos , Shigella dysenteriae/patogenicidade
12.
Arch Microbiol ; 202(9): 2591-2597, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32607725

RESUMO

To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content of 59.87%. From a total of 3,465 genes predicted, 96 of them are annotated as glycoside hydrolases (GHs). Within these GHs, 20 encoded genes are related to cellulosic biomass degradation, including 12 endoglucanases (5 GH10, 4 GH5, and 3 GH51), 2 exoglucanases (GH9) and 6 ß-glucosidases (GH3). In addition, highest relative enzyme activities (endoglucanase, exoglucanase, and ß-glucosidase) were observed at 27th hour when the strain was cultured in the carboxymethyl cellulose/Avicel®-containing medium for 45 h. The combination of genome analysis with experimental studies indicated the ability of strain NH6-79 T to produce extracellular endoglucanase, exoglucanase, and ß-glucosidase. These findings suggest the potential of Parvularcula flava strain NH6-79 T in cellulose-containing biomass degradation and that the strain could be used in cellulosic biorefining process.


Assuntos
Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Genoma Bacteriano/genética , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Composição de Bases , Biomassa , Celulase/genética , Celulase/metabolismo , Celulose/metabolismo , beta-Glucosidase/genética , beta-Glucosidase/metabolismo
13.
Arch Microbiol ; 202(9): 2517-2523, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32653934

RESUMO

Strain ZZJ9T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZZJ9T showed the highest 16S rRNA gene sequence similarities with Larkinella rosea 15J16-1T3AT (97.1%), Larkinella terrae 15J8-8T (97.0%), Larkinella knui 15J6-3T6T (96.8%), and Larkinella ripae 15J11-1T (95.3%). The genome size of strain ZZJ9T was 8.01 Mb and the DNA G+C content was 51.8 mol%. ANI values among strain ZZJ9T and Larkinella rosea 52004 T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 80.5%, 82.7%, and 80.5%, respectively. dDDH values among strain ZZJ9T and Larkinella rosea 52004T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 23.5%, 26.0%, and 23.6%, respectively. Furthermore, the genome of strain ZZJ9T contained 6302 predicted protein-coding genes and 3114 (49%) of them had classificatory functions. The major quinone of strain ZZJ9T was menaquinone-7 and the main cellular fatty acids were C16:1ω5c (39.5%), iso-C15:0 (25.6%), and iso-C17:0 3OH (11.5%). The polar lipids of strain ZZJ9T were phosphatidylethanolamine, unidentified lipid, and two unidentified aminolipids. Based on the results of phylogenetic, genome, phenotypic, and chemotaxonomic analytical, strain ZZJ9T represents a novel species of the genus Larkinella, for which the name Larkinella punicea sp. Nov. is proposed. The type strain is ZZJ9T (= KCTC 62876T = CCTCC AB 2018215T).


Assuntos
Cytophagaceae/classificação , Microbiologia do Solo , Composição de Bases , Cytophagaceae/genética , Cytophagaceae/isolamento & purificação , Ácidos Graxos/análise , Genoma Bacteriano/genética , Manganês , Filogenia , RNA Ribossômico 16S/genética , Solo/química , Especificidade da Espécie
14.
Nat Commun ; 11(1): 3551, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669542

RESUMO

Predicting effects of gene regulatory elements (GREs) is a longstanding challenge in biology. Machine learning may address this, but requires large datasets linking GREs to their quantitative function. However, experimental methods to generate such datasets are either application-specific or technically complex and error-prone. Here, we introduce DNA-based phenotypic recording as a widely applicable, practicable approach to generate large-scale sequence-function datasets. We use a site-specific recombinase to directly record a GRE's effect in DNA, enabling readout of both sequence and quantitative function for extremely large GRE-sets via next-generation sequencing. We record translation kinetics of over 300,000 bacterial ribosome binding sites (RBSs) in >2.7 million sequence-function pairs in a single experiment. Further, we introduce a deep learning approach employing ensembling and uncertainty modelling that predicts RBS function with high accuracy, outperforming state-of-the-art methods. DNA-based phenotypic recording combined with deep learning represents a major advance in our ability to predict function from genetic sequence.


Assuntos
Biologia Computacional/métodos , Aprendizado Profundo , Anotação de Sequência Molecular/métodos , Fenótipo , Análise de Sequência de DNA/métodos , Sítios de Ligação/genética , Conjuntos de Dados como Assunto , Escherichia coli/genética , Técnicas de Inativação de Genes , Genoma Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Sequências Reguladoras de Ácido Nucleico/genética , Ribossomos/metabolismo
15.
Nat Commun ; 11(1): 2719, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32483195

RESUMO

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Genoma Bacteriano/genética , Genômica/métodos , Sequenciamento Completo do Genoma/métodos , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Infecções Bacterianas/epidemiologia , Infecções Bacterianas/microbiologia , Infecções Bacterianas/prevenção & controle , Humanos , Testes de Sensibilidade Microbiana/métodos , Filipinas/epidemiologia , Inquéritos e Questionários
16.
Proc Natl Acad Sci U S A ; 117(27): 15740-15747, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32576688

RESUMO

Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.


Assuntos
Organismos Aquáticos/metabolismo , Cobalto/metabolismo , Prochlorococcus/metabolismo , Vitamina B 12/metabolismo , Biomassa , Genoma Bacteriano/genética , Ferro/metabolismo , Oceano Pacífico , Filogenia , Prochlorococcus/genética , Prochlorococcus/crescimento & desenvolvimento , Proteômica , Água do Mar/química , Vitamina B 12/genética
17.
PLoS Genet ; 16(6): e1008850, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32511244

RESUMO

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and ß) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade ß contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and ß was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade ß lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4).


Assuntos
Evolução Molecular , Gastroenterite/microbiologia , Intoxicação Alimentar por Salmonella/microbiologia , Salmonelose Animal/microbiologia , Salmonella typhimurium/genética , Animais , Aves/microbiologia , Genoma Bacteriano/genética , Interações Hospedeiro-Patógeno/genética , Humanos , Gado/microbiologia , Filogenia , Salmonelose Animal/transmissão , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/patogenicidade , Seleção Genética , Sorogrupo , Sequenciamento Completo do Genoma
18.
PLoS Genet ; 16(6): e1008866, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32530914

RESUMO

Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.


Assuntos
Escherichia coli/genética , Evolução Molecular , Transferência Genética Horizontal , Variação Genética , Genoma Bacteriano/genética , Animais , Animais Selvagens/microbiologia , Austrália , Galinhas/microbiologia , Farmacorresistência Bacteriana/genética , Escherichia coli/isolamento & purificação , Escherichia coli/patogenicidade , Fezes/microbiologia , Água Doce/microbiologia , Tamanho do Genoma , Humanos , Doenças Inflamatórias Intestinais/microbiologia , Sequências Repetitivas Dispersas/genética , Mucosa Intestinal/microbiologia , Carne/microbiologia , Anotação de Sequência Molecular , Filogenia , Microbiologia do Solo , Fatores de Virulência/genética , Sequenciamento Completo do Genoma
19.
Nat Commun ; 11(1): 3259, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32591509

RESUMO

Fusobacterium nucleatum is an oral anaerobe recently found to be prevalent in human colorectal cancer (CRC) where it is associated with poor treatment outcome. In mice, hematogenous F. nucleatum can colonize CRC tissue using its lectin Fap2, which attaches to tumor-displayed Gal-GalNAc. Here, we show that Gal-GalNAc levels increase as human breast cancer progresses, and that occurrence of F. nucleatum gDNA in breast cancer samples correlates with high Gal-GalNAc levels. We demonstrate Fap2-dependent binding of the bacterium to breast cancer samples, which is inhibited by GalNAc. Intravascularly inoculated Fap2-expressing F. nucleatum ATCC 23726 specifically colonize mice mammary tumors, whereas Fap2-deficient bacteria are impaired in tumor colonization. Inoculation with F. nucleatum suppresses accumulation of tumor infiltrating T cells and promotes tumor growth and metastatic progression, the latter two of which can be counteracted by antibiotic treatment. Thus, targeting F. nucleatum or Fap2 might be beneficial during treatment of breast cancer.


Assuntos
Neoplasias da Mama/microbiologia , Neoplasias da Mama/patologia , Progressão da Doença , Fusobacterium nucleatum/crescimento & desenvolvimento , Animais , Antibacterianos/farmacologia , Proteínas de Bactérias/metabolismo , Neoplasias da Mama/diagnóstico por imagem , Neoplasias da Mama/imunologia , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Contagem de Colônia Microbiana , DNA Bacteriano/genética , Modelos Animais de Doenças , Feminino , Fusobacterium nucleatum/efeitos dos fármacos , Fusobacterium nucleatum/genética , Galactosamina/metabolismo , Galactose/metabolismo , Genoma Bacteriano/genética , Humanos , Imunidade/efeitos dos fármacos , Neoplasias Pulmonares/secundário , Camundongos Endogâmicos BALB C , Metástase Neoplásica
20.
PLoS One ; 15(6): e0234440, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32530971

RESUMO

Research for biotechnological applications of cyanobacteria focuses on synthetic pathways and bioreactor design, while little effort is devoted to introduce new, promising organisms in the field. Applications are most often based on recombinant work, and the establishment of transformation can be a risky, time-consuming procedure. In this work we demonstrate the natural transformation of the filamentous cyanobacterium Phormidium lacuna and insertion of a selection marker into the genome by homologous recombination. This is the first example for natural transformation filamentous non-heterocystous cyanobacterium. We found that Phormidium lacuna is polyploid, each cell has about 20-90 chromosomes. Transformed filaments were resistant against up to 14 mg/ml of kanamycin. Formerly, natural transformation in cyanobacteria has been considered a rare and exclusive feature of a few unicellular species. Our finding suggests that natural competence is more distributed among cyanobacteria than previously thought. This is supported by bioinformatic analyses which show that all protein factors for natural transformation are present in the majority of the analyzed cyanobacteria.


Assuntos
Cianobactérias/genética , Farmacorresistência Bacteriana/genética , Genoma Bacteriano/genética , Recombinação Homóloga , Transformação Bacteriana , Cromossomos Bacterianos/genética , Biologia Computacional , Canamicina/farmacologia , Poliploidia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA