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1.
Nat Commun ; 12(1): 4188, 2021 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-34234121

RESUMO

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.


Assuntos
Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Tipagem Molecular/métodos , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Conjuntos de Dados como Assunto , Farmacorresistência Bacteriana Múltipla/genética , Monitoramento Epidemiológico , Microbioma Gastrointestinal/genética , Genoma Bacteriano , Humanos , Lactente , Recém-Nascido , Infecções por Klebsiella/diagnóstico , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/patogenicidade , Metagenoma/genética , Epidemiologia Molecular/métodos , Mutação , Filogenia , Software , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma , beta-Lactamases/genética
2.
BMC Genomics ; 22(1): 522, 2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34238216

RESUMO

BACKGROUND: Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank. RESULTS: We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an "open" pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB. CONCLUSIONS: Based on the virulence gene content of 27 S. intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.


Assuntos
Genômica , Streptococcus intermedius , Genoma Bacteriano , Humanos , Filogenia , Streptococcus intermedius/genética , Virulência/genética , Fatores de Virulência/genética
3.
Artigo em Inglês | MEDLINE | ID: mdl-34232855

RESUMO

A novel bacterial strain, named HC41T, was isolated from a cyanobacterial bloom sample and was characterized as Gram-stain-negative, rod-shaped and non-motile. According to 16S rRNA phylogenetic analyses, this strain HC41T belongs to the family Rhodocyclaceae and is most closely related to Niveibacterium umoris KACC 17062T (=MIC 2059T; 98.63 %) and Uliginosibacterium gangwonense 5YN10-9 T (=KACC 11603T; 93.64 %). The genome size and DNA G+C content of strain HC41T were 4.8 Mbp and 64.17 mol%, respectively. Moreover, the average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values between strain HC41T and N. umoris KACC 17062T were 81.8, 43.1 and 90.89 %, respectively. Additionally, strain HC41T exhibited weak catalase and oxidase activities and had no motility (swimming and swarming motilities). The cells grew at 11-40 °C (optimum, 30 °C), pH 5.5-8.0 (optimum, pH 7) and with 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl) in Reasoner's 2A medium. Its major respiratory quinone was ubiquinone-8 and its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Furthermore, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; C16 : 1 ω6c and/or C16 : 1 ω7c) were the predominant cellular fatty acids in strain HC41T according to fatty acid methyl ester analysis. Based on its genotypic and phenotypic characteristics, strain HC41T was identified as representing a novel Niveibacterium species, for which the name Niveibacterium microcysteis sp. nov. is proposed (=KACC 22091T=DSM 111425T).


Assuntos
Eutrofização , Filogenia , Rhodocyclaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Cianobactérias , DNA Bacteriano/genética , Ácidos Graxos/química , Genoma Bacteriano , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodocyclaceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/química
4.
J Med Microbiol ; 70(7)2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34236301

RESUMO

Introduction. Tigecycline is currently acknowledged to be one of the most effective antibiotics against infections caused by Mycobacteroides abscessus.Gap statement. The genetic determinants of tigecycline resistance in M. abscessus are not well understood.Aim. In this study, we characterized a tigecycline-resistant M. abscessus mutant, designated CL7, to identify the potential resistance mechanism.Methodology. CL7 was characterized using antimicrobial susceptibility testing, whole-genome sequencing, PCR and RT-qPCR. For biological verification, gene overexpression assays were carried out.Results. Whole-genome sequencing and the subsequent gene overexpression assays showed that CL7 harboured a stop-gain mutation in MAB_3543 c, which may be responsible for the tigecycline resistance phenotype. This gene encodes an orthologue of SigH, which is involved in the positive regulation of physiological stress response and is negatively regulated by the RshA anti-sigma factor in Mycobacterium tuberculosis. We hypothesized that the MAB_3543 c mutation may disrupt the interaction between SigH and RshA (MAB_3542 c). RT-qPCR analyses revealed the upregulation of MAB_3543 c and other key stress response genes, which has previously been shown to be a hallmark of SigH-RshA bond disruption and tigecycline resistance.Conclusion. The MAB_3543c mutation may represent a novel determinant of tigecycline resistance in M. abscessus. The findings of this study will hopefully contribute to our knowledge of potential tigecycline resistance mechanisms in M. abscessus, which may lead to better diagnostics and treatment modalities in the future.


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Mycobacterium abscessus/efeitos dos fármacos , Mycobacterium abscessus/genética , Fator sigma/genética , Tigeciclina/farmacologia , Genoma Bacteriano , Mutação , Sequenciamento Completo do Genoma
5.
Front Cell Infect Microbiol ; 11: 660007, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34268133

RESUMO

Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.


Assuntos
Afídeos , Simbiose , Animais , Afídeos/genética , Genoma Bacteriano , Genômica , Filogenia , Serratia
6.
J Med Microbiol ; 70(7)2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34269673

RESUMO

Introduction. Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations.Gap statement. BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking.Aim. Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting.Methodology. Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters.Results. From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential.Conclusion. WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.


Assuntos
Antibacterianos/farmacologia , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana , Oxacilina/farmacologia , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação , Infecção Hospitalar/transmissão , Genoma Bacteriano , Hospitais/estatística & dados numéricos , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Polimorfismo de Nucleotídeo Único , Infecções Estafilocócicas/transmissão , Staphylococcus aureus/classificação , Staphylococcus aureus/efeitos dos fármacos , Sequenciamento Completo do Genoma
7.
Front Cell Infect Microbiol ; 11: 663933, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34222039

RESUMO

Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to ß-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.


Assuntos
Antibacterianos , Integrons , Antibacterianos/farmacologia , China , Delftia , Farmacorresistência Bacteriana/genética , Feminino , Genoma Bacteriano , Genômica , Humanos , Filogenia
8.
Nat Commun ; 12(1): 3254, 2021 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-34059668

RESUMO

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth and butyrate production separately, providing key insights into ecological mechanisms driving butyrate production. We use our model to explore a vast community design space using a design-test-learn cycle to identify high butyrate-producing communities. Our model can accurately predict community assembly and butyrate production across a wide range of species richness. Guided by the model, we identify constraints on butyrate production by high species richness and key molecular factors driving butyrate production, including hydrogen sulfide, environmental pH, and resource competition. In sum, our model-guided approach provides a flexible and generalizable framework for understanding and accurately predicting community assembly and metabolic functions.


Assuntos
Bactérias/metabolismo , Técnicas Bacteriológicas/métodos , Butiratos/metabolismo , Microbioma Gastrointestinal/fisiologia , Anaerobiose , Bactérias/genética , Bactérias/isolamento & purificação , Biologia Computacional , DNA Bacteriano/isolamento & purificação , Genoma Bacteriano , Humanos , Sulfeto de Hidrogênio/metabolismo , Concentração de Íons de Hidrogênio , Microbiologia Industrial/métodos , Engenharia Metabólica , Análise de Sequência de DNA
9.
Science ; 372(6546): 1057-1062, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34083482

RESUMO

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)-making their cognate codons unreadable-might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.


Assuntos
Códon , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Escherichia coli/virologia , Compostos Macrocíclicos/metabolismo , Polímeros/metabolismo , Biossíntese de Proteínas , Fagos T/crescimento & desenvolvimento , Aminoácidos/metabolismo , Bacteriólise , Uso do Códon , Códon de Terminação , Evolução Molecular Direcionada , Escherichia coli/metabolismo , Proteínas de Escherichia coli/biossíntese , Deleção de Genes , Código Genético , Genoma Bacteriano , Compostos Macrocíclicos/química , Mutagênese , Fatores de Terminação de Peptídeos/genética , Polímeros/química , RNA Bacteriano/genética , RNA de Transferência/genética , RNA de Transferência de Serina/genética , Ubiquitina/biossíntese , Ubiquitina/genética
10.
Int J Mol Sci ; 22(11)2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-34073951

RESUMO

Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug target against pathogens. Understanding the evolution of P450s in a bacterial population is gaining momentum. In this study, we report comprehensive analysis of P450s in the ancient group of the bacterial class Alphaproteobacteria. Genome data mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs), compared other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. Our study identified that some of the P450 families found in alphaproteobacterial species were passed to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum.


Assuntos
Alphaproteobacteria/genética , Vias Biossintéticas/genética , Sistema Enzimático do Citocromo P-450/genética , Família Multigênica , Metabolismo Secundário/genética , Colesterol/metabolismo , Cianobactérias/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Mineração de Dados , Evolução Molecular , Firmicutes/genética , Genoma Bacteriano , Mycobacterium tuberculosis/genética , Filogenia , Streptomyces/genética
11.
BMC Genomics ; 22(1): 474, 2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34172000

RESUMO

BACKGROUND: Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. RESULTS: We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes. CONCLUSIONS: MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe .


Assuntos
Escherichia coli , Genoma Bacteriano , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , Fluxo de Trabalho
12.
BMC Bioinformatics ; 22(1): 349, 2021 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-34174810

RESUMO

BACKGROUND: Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance propagation. Bioinformatics methods have been developed to detect plasmids. However, they suffer from low sensitivity (i.e., most plasmids remain undetected) or low precision (i.e., these methods identify chromosomes as plasmids), and are overall not adapted to identify plasmids in whole genomes that are not fully assembled (contigs and scaffolds). RESULTS: We developed PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in partially assembled genomes. Without knowing the taxonomical origin of the samples, PlasForest identifies contigs as plasmids or chromosomes with a F1 score of 0.950. Notably, it can detect 77.4% of plasmid contigs below 1 kb with 2.8% of false positives and 99.9% of plasmid contigs over 50 kb with 2.2% of false positives. CONCLUSIONS: PlasForest outperforms other currently available tools on genomic datasets by being both sensitive and precise. The performance of PlasForest on metagenomic assemblies are currently well below those of other k-mer-based methods, and we discuss how homology-based approaches could improve plasmid detection in such datasets.


Assuntos
Genoma Bacteriano , Genômica , Biologia Computacional , Metagenômica , Plasmídeos
13.
Nat Commun ; 12(1): 3457, 2021 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-34103505

RESUMO

Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.


Assuntos
Bacillus subtilis/genética , Transferência Genética Horizontal , Adaptação Fisiológica , Membrana Celular/metabolismo , DNA Bacteriano/genética , Genoma Bacteriano , Mutação/genética , Nucleotídeos/genética , Recombinação Genética/genética , Estresse Fisiológico , Transformação Genética , Regulação para Cima
14.
Artigo em Inglês | MEDLINE | ID: mdl-34152267

RESUMO

A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).


Assuntos
Microbiologia do Ar , Bacteroidetes/isolamento & purificação , Ilhas , Regiões Antárticas , Bacteroidetes/classificação , Bacteroidetes/genética , Composição de Bases , DNA Bacteriano/genética , Genoma Bacteriano , Funções Verossimilhança , Filogenia , RNA Ribossômico 16S/genética
15.
BMC Ecol Evol ; 21(1): 108, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078265

RESUMO

BACKGROUND: Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect's diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse's diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect's diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. RESULTS: We sequenced the genome of a bacterial symbiont from a feather feeding louse (Columbicola wolffhuegeli) that parasitizes the Pied Imperial Pigeon (Ducula bicolor) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. CONCLUSIONS: Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of symbiotic bacteria in evolution of diverse avian parasites.


Assuntos
Iscnóceros , Parasitos , Animais , Bactérias/genética , Genoma Bacteriano/genética , Simbiose
16.
Euro Surveill ; 26(22)2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34085631

RESUMO

BackgroundCampylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied.AimTyping-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks.MethodsWe performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat.ResultsSeventy-two clusters were detected, 58 small clusters (2-4 cases) and 14 large clusters (5-91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak.ConclusionOur WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.


Assuntos
Infecções por Campylobacter , Campylobacter jejuni , Animais , Infecções por Campylobacter/diagnóstico , Infecções por Campylobacter/epidemiologia , Campylobacter jejuni/genética , Galinhas , Dinamarca/epidemiologia , Surtos de Doenças , Genoma Bacteriano , Humanos , Tipagem de Sequências Multilocus , Sequenciamento Completo do Genoma
17.
Int J Food Microbiol ; 351: 109269, 2021 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-34102570

RESUMO

Microbial population heterogeneity contributes to differences in stress response between individual cells in a population, and can lead to the selection of genetically stable variants with increased stress resistance. We previously provided evidence that the multiple-stress resistant Listeria monocytogenes LO28 variant 15, carries a point mutation in the rpsU gene, resulting in an arginine-proline substitution in ribosomal protein RpsU (RpsU17Arg-Pro). Here, we investigated the trade-off between general stress sigma factor SigB-mediated stress resistance and fitness in variant 15 using experimental evolution. By selecting for higher fitness in two parallel evolving cultures, we identified two evolved variants: 15EV1 and 15EV2. Whole genome sequencing and SNP analysis showed that both parallel lines mutated in the same codon in rpsU as the original mutation resulting in RpsU17Pro-His (15EV1) and RpsU17Pro-Thr (15EV2). Using a combined phenotyping and proteomics approach, we assessed the resistance of the evolved variants to both heat and acid stress, and found that in both lines reversion to WT-like fitness also resulted in WT-like stress sensitivity. Proteome analysis of L. monocytogenes LO28 WT, variant 15, 15EV1, and 15EV2 revealed high level expression of SigB regulon members only in variant 15, whereas protein profiles of both evolved variants were highly similar to that of the LO28 WT. Experiments with constructed RpsU17Arg-Pro mutants in L. monocytogenes LO28 and EGDe, and RpsU17Arg-His and RpsU17Arg-Thr in LO28, confirmed that single amino acid substitutions in RpsU enable switching between multiple-stress resistant and high fitness states in L. monocytogenes.


Assuntos
Adaptação Fisiológica/genética , Proteínas de Bactérias/genética , Listeria monocytogenes/fisiologia , Proteínas Ribossômicas/genética , Ácidos/metabolismo , Substituição de Aminoácidos , Proteínas de Bactérias/metabolismo , Evolução Molecular Direcionada , Genoma Bacteriano/genética , Temperatura Alta , Listeria monocytogenes/genética , Mutação , Proteoma/metabolismo , Proteínas Ribossômicas/metabolismo , Fator sigma/genética , Fator sigma/metabolismo
18.
Nat Commun ; 12(1): 3801, 2021 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-34155204

RESUMO

The recent emergence of strains of Neisseria gonorrhoeae associated with treatment failures to ceftriaxone, the foundation of current treatment options, has raised concerns over a future of untreatable gonorrhea. Current global data on gonococcal strains suggest that several lineages, predominately characterized by mosaic penA alleles, are associated with elevated minimum inhibitory concentrations (MICs) to extended spectrum cephalosporins (ESCs). Here we report on whole genome sequences of 813 N. gonorrhoeae isolates collected through the Gonococcal Isolate Surveillance Project in the United States. Phylogenomic analysis revealed that one persisting lineage (Clade A, multi-locus sequence type [MLST] ST1901) with mosaic penA-34 alleles, contained the majority of isolates with elevated MICs to ESCs. We provide evidence that an ancestor to the globally circulating MLST ST1901 clones potentially emerged around the early to mid-20th century (1944, credibility intervals [CI]: 1935-1953), predating the introduction of cephalosporins, but coinciding with the use of penicillin. Such results indicate that drugs with novel mechanisms of action are needed as these strains continue to persist and disseminate globally.


Assuntos
Antibacterianos/farmacologia , Cefalosporinas/farmacologia , Genes Bacterianos/genética , Neisseria gonorrhoeae/efeitos dos fármacos , Neisseria gonorrhoeae/genética , Alelos , Resistência às Cefalosporinas/efeitos dos fármacos , Resistência às Cefalosporinas/genética , Variação Genética , Genoma Bacteriano/genética , Gonorreia/epidemiologia , Gonorreia/microbiologia , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Neisseria gonorrhoeae/classificação , Neisseria gonorrhoeae/isolamento & purificação , Filogenia , Recombinação Genética , Análise de Sequência de DNA , Estados Unidos/epidemiologia
19.
Gene ; 795: 145780, 2021 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-34147570

RESUMO

The genome sequences of entomopathogenic nematode (EPN) bacteria and their functional analyses can lead to the genetic engineering of the bacteria for use as biocontrol agents. The bacterial symbiont Photorhabdus heterorhabditis strain ETL isolated from an insect pathogenic nematode, Heterorhabditis zealandica strain ETL, collected in the northernmost region of South Africa was studied to reveal information that can be useful in the design of improvement strategies for both effective and liquid production method of EPN-based pesticides. The strain ETL genome was found closely related to the type strain genome of P. australis DSM 17,609 (~60 to 99.9% CDSs similarity), but closely related to the not yet genome-sequenced type strain, P. heterorhabditis. It has a genome size of 4,866,148 bp and G + C content of 42.4% similar to other Photorhabdus. It contains 4,351 protein coding genes (CDSs) of which, at least 84% are shared with the de facto type strain P. luminescens subsp. laumondii TTO1, and has 318 unknown CDSs and the genome has a higher degree of plasticity allowing it to adapt to different environmental conditions, and to be virulent against various insects; observed through genes acquired through horizontal gene transfer mechanisms, clustered regularly interspaced short palindromic repeats, non-determined polyketide- and non-ribosomal peptide- synthase gene clusters, and many genes associated with uncharacterized proteins; which also justify the strain ETL's genes differences (quantity and quality) compared to P. luminescens subsp. laumondii TTO1. The protein coding sequences contained genes with both bio-engineering and EPNs mass production importance, of which numerous are uncharacterized.


Assuntos
Genes Bacterianos , Genoma Bacteriano , Photorhabdus/genética , Photorhabdus/patogenicidade , Strongyloidea/microbiologia , Animais , Sequência de Bases , Agentes de Controle Biológico , Interações Hospedeiro-Patógeno , Anotação de Sequência Molecular , Photorhabdus/classificação , Filogenia , Virulência/genética
20.
Nat Commun ; 12(1): 3864, 2021 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-34162873

RESUMO

Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes.


Assuntos
Biologia Computacional/métodos , Mineração de Dados/métodos , Genoma Bacteriano/genética , Genoma de Planta/genética , Genômica/métodos , Produtos Biológicos/química , Produtos Biológicos/metabolismo , Vias Biossintéticas/genética , Descoberta de Drogas/métodos , Estrutura Molecular , Metabolismo Secundário/genética
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