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1.
Proc Natl Acad Sci U S A ; 121(25): e2314262121, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38861609

RESUMO

The emergence of SARS-CoV-2 variants with increased fitness has had a strong impact on the epidemiology of COVID-19, with the higher effective reproduction number of the viral variants leading to new epidemic waves. Tracking such variants and their genetic signatures, using data collected through genomic surveillance, is therefore crucial for forecasting likely surges in incidence. Current methods of estimating fitness advantages of variants rely on tracking the changing proportion of a particular lineage over time, but describing successful lineages in a rapidly evolving viral population is a difficult task. We propose a method of estimating fitness gains directly from nucleotide information generated by genomic surveillance, without a priori assigning isolates to lineages from phylogenies, based solely on the abundance of single nucleotide polymorphisms (SNPs). The method is based on mapping changes in the genetic population structure over time. Changes in the abundance of SNPs associated with periods of increasing fitness allow for the unbiased discovery of new variants, thereby obviating a deliberate lineage assignment and phylogenetic inference. We conclude that the method provides a fast and reliable way to estimate fitness advantages of variants without the need for a priori assigning isolates to lineages.


Assuntos
COVID-19 , Genoma Viral , Filogenia , Polimorfismo de Nucleotídeo Único , SARS-CoV-2 , COVID-19/virologia , COVID-19/epidemiologia , COVID-19/genética , SARS-CoV-2/genética , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , Humanos , Aptidão Genética , Genômica/métodos
2.
ISME Commun ; 3(1): 116, 2023 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-37945978

RESUMO

Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.

3.
Biomedicines ; 11(8)2023 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-37626677

RESUMO

Canine parvovirus (CPV-2) is one of the most important pathogens of dogs of all ages, causing pandemic infections that are characterized by fatal hemorrhagic enteritis. The CPV-2 vaccine is recommended as a core vaccine for pet animals. Despite the intensive practice of active immunization, CPV-2 remains a global threat. In this study, a multi-epitope vaccine against CPV-2 was designed, targeting the highly conserved capsid protein (VP2) via in silico approaches. Several immunoinformatics methods, such as epitope screening, molecular docking, and simulation were used to design a potential vaccine construct. The partial protein sequences of the VP2 gene of CPV-2 and protein sequences retrieved from the NCBI were screened to predict highly antigenic proteins through antigenicity, trans-membrane-topology screening, an allergenicity assessment, and a toxicity analysis. Homologous VP2 protein sequences typically linked to the disease were identified using NCBI BLAST, in which four conserved regions were preferred. Overall, 10 epitopes, DPIGGKTGI, KEFDTDLKP, GTDPDDVQ, GGTNFGYIG, GTFYFDCKP, NRALGLPP, SGTPTN, LGLPPFLNSL, IGGKTG, and VPPVYPN, were selected from the conserved regions to design the vaccine construct. The molecular docking demonstrated the higher binding affinity of these epitopes with dog leukocyte antigen (DLA) molecules. The selected epitopes were linked with Salmonella enterica flagellin FliC adjuvants, along with the PADRE sequence, by GGS linkers to construct a vaccine candidate with 272 nucleotides. The codon adaptation and in silico cloning showed that the generated vaccine can be expressed by the E. coli strain, K12, and the sequence of the vaccine construct showed no similarities with dog protein. Our results suggest that the vaccine construct might be useful in preventing canine parvoviral enteritis (CPE) in dogs. Further in vitro and in vivo experiments are needed for the validation of the vaccine candidate.

4.
Ann Clin Microbiol Antimicrob ; 22(1): 52, 2023 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-37391819

RESUMO

BACKGROUND: NDM-producing Acinetobacter baumannii (NDMAb) were reported sporadically worldwide but little is known about the transmission, epidemiology and clinical features of NDMAb-infected patients. The goals of this study were to characterize (1) the epidemiology and clinical features of NDMAb-infected patients; (2) the microbiological and molecular features of NDMAb isolates and (3) the transmission networks of NDMAb within healthcare facilities. METHODS: The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical centers (TASMC, RMC and SZMC, respectively) in Israel. All cases detected between January 2018 and July 2019 were included. Phylogenetic analysis was based on core genome SNP distances. Clonal transmission was defined according to molecular (≤ 5 SNP) and epidemiological criteria (overlapping hospital stay). NDMAb cases were compared at a ratio of 1:2 with non-NDM carbapenem-resistant A. baumannii (CRAb) cases. RESULTS: The study included 54 NDMAb-positive out of 857 CRAb patients, including 6/179 (3.3%) in TASMC, 18/441 (4.0%) in SZMC and 30/237 (12.6%) in RMC. Patients infected by NDMAb had similar clinical features and risk factors as patients with non-NDM CRAb. The length-of-stay was higher in NDMAb cases (48.5 days vs. 36 days, respectively, p = 0.097) and the in-hospital mortality was similarly high in both groups. Most isolates (41/54, 76%) were first detected from surveillance culture. The majority of isolates harbored the blaNDM-2 gene allele (n = 33), followed by the blaNDM-1 (n = 20) allele and the blaNDM-4 allele (n = 1). The majority of isolates were related within the ST level to other isolates in SZMC and RMC: 17/18 and 27/30 isolates, respectfully. The common ST's were the blaNDM-1 harboring ST-2 (n = 3) and ST-107 (n = 8) in SZMC and the blaNDM-2 harboring ST-103 in SZMC (n = 6) and in RMC (n = 27). All blaNDM alleles were located within a conserved mobile genetic environment flanked by the ISAb125 and IS91 family transposon. Clonal transmission was identified in most hospital-acquired cases in RMC and SZMC. CONCLUSION: NDMAb constitutes a minor part of CRAb cases and are clinically similar to non-NDM CRAb. Transmission of NDMAb occurs mostly by clonal spread.


Assuntos
Acinetobacter baumannii , Humanos , Israel/epidemiologia , Acinetobacter baumannii/genética , Filogenia , Alelos , Carbapenêmicos/farmacologia
5.
J Antimicrob Chemother ; 78(3): 719-723, 2023 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-36640136

RESUMO

OBJECTIVES: NDM-producing Enterobacterales (NDME) account for 34.9% of new carbapenemase-producing Enterobacterales cases in Israeli hospitals. The goals of this study were to characterize the genomic composition of NDME isolates and mobile genetic elements (MGEs) and to identify NDME transmission events (TEs). METHODS: The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical Centers (TASMC, RMC and SZMC, respectively). All NDME isolates detected between January 2018 and July 2019 were included.Phylogenetic analysis was based on core-genome SNP distances. Core-genome distance of ≤5 SNPs between isolates from patients with overlapping hospitalization periods was suggestive of a potential TE. MGEs were classified by comparison of the blaNDM gene flanking regions. RESULTS: The study included 212 NDME isolates from 203 patients, including 104 isolates from TASMC, 30 isolates from RMC and 78 isolates from SZMC. The majority of isolates (n = 157; 74%) harboured the blaNDM-1 gene, followed by the blaNDM-5 (n = 48) and blaNDM-15 genes (n = 7). The most common NDME species were Klebsiella pneumoniae (n = 67), Escherichia coli (n = 65) and Enterobacter cloacae (n = 45), all showing a highly diverse clonal structure. Most blaNDM-1-harbouring isolates (134/157; 85%) were divided into nine different MGE modules, variably distributed across species and hospitals.The numbers of post-admission acquisition cases (n = 118) that could be linked to other cases by both molecular and epidemiological criteria were 13/58 (24.2%), 3/48 (6.3%) and 4/12 (33.3%) in TASMC, SZMC and RMC, respectively. CONCLUSIONS: The study depicted a complex and diverse population structure, suggesting that NDME had not spread via clonal expansion.


Assuntos
Antibacterianos , beta-Lactamases , Humanos , Filogenia , Israel/epidemiologia , beta-Lactamases/genética , Proteínas de Bactérias/genética , Hospitais , Klebsiella pneumoniae/genética , Escherichia coli/genética , Testes de Sensibilidade Microbiana , Plasmídeos
6.
Gastroenterology ; 160(6): 1970-1985, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33476671

RESUMO

BACKGROUND & AIMS: It is currently unclear whether reported changes in the gut microbiome are cause or consequence of inflammatory bowel disease (IBD). Therefore, we studied the gut microbiome of IBD-discordant and -concordant twin pairs, which offers the unique opportunity to assess individuals at increased risk of developing IBD, namely healthy cotwins from IBD-discordant twin pairs. METHODS: Fecal samples were obtained from 99 twins (belonging to 51 twin pairs), 495 healthy age-, sex-, and body mass index-matched controls, and 99 unrelated patients with IBD. Whole-genome metagenomic shotgun sequencing was performed. Taxonomic and functional (pathways) composition was compared among healthy cotwins, IBD-twins, unrelated patients with IBD, and healthy controls with multivariable (ie, adjusted for potential confounding) generalized linear models. RESULTS: No significant differences were observed in the relative abundance of species and pathways between healthy cotwins and their IBD-twins (false discovery rate <0.10). Compared with healthy controls, 13, 19, and 18 species, and 78, 105, and 153 pathways were found to be differentially abundant in healthy cotwins, IBD-twins, and unrelated patients with IBD, respectively (false discovery rate <0.10). Of these, 8 (42.1%) of 19 and 1 (5.6%) of 18 species, and 37 (35.2%) of 105 and 30 (19.6%) of 153 pathways overlapped between healthy cotwins and IBD-twins, and healthy cotwins and unrelated patients with IBD, respectively. Many of the shared species and pathways have previously been associated with IBD. The shared pathways include potentially inflammation-related pathways, for example, an increase in propionate degradation and L-arginine degradation pathways. CONCLUSIONS: The gut microbiome of healthy cotwins from IBD-discordant twin pairs displays IBD-like signatures. These IBD-like microbiome signatures might precede the onset of IBD. However, longitudinal follow-up studies are needed to infer a causal relationship.


Assuntos
Microbioma Gastrointestinal , Neoplasias Inflamatórias Mamárias/epidemiologia , Neoplasias Inflamatórias Mamárias/microbiologia , Adulto , Antígenos de Bactérias/biossíntese , Estudos de Casos e Controles , Estudos Transversais , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal/fisiologia , Humanos , Masculino , Metagenômica , Pessoa de Meia-Idade , Países Baixos/epidemiologia , Fenótipo , Fatores de Risco , Sideróforos/biossíntese , Gêmeos Dizigóticos , Gêmeos Monozigóticos , Adulto Jovem
7.
Microbiol Resour Announc ; 9(43)2020 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-33093052

RESUMO

Here, we report the high-quality complete genome sequence of Staphylococcus aureus EDCC 5398, which was isolated from a patient with implant-associated bone infection. The assembled genome consists of 2,843,534 bp, with a G+C content of 33%; it has 2,739 coding sequences, belongs to sequence type 22, and contains mecA and balz genes, which contribute to methicillin resistance.

8.
Microbiol Resour Announc ; 9(17)2020 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327513

RESUMO

Over the past decades, drug-resistant Mycobacterium tuberculosis strains have presented a significant challenge, with inadequate diagnosis of tuberculosis (TB) cases. Here, we report the draft whole-genome sequence of drug-resistant M. tuberculosis strain S7, which was isolated from a patient from Tripura, India, who was diagnosed with pulmonary TB.

9.
Front Microbiol ; 8: 2318, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29209306

RESUMO

Extended-spectrum beta-lactamases (ESBL) mediating resistance to 3rd generation cephalosporins are a major public health issue. As food may be a vehicle in the spread of ESLB-producing bacteria, a study on the occurrence of cephalosporin-resistantu Escherichia coli in food was initiated. A total of 404 ESBL-producing isolates were obtained from animal-derived food samples (e.g., poultry products, pork, beef and raw milk) between 2011 and 2013. As CTX-M-15 is the most abundant enzyme in ESBL-producing E. coli causing human infections, this study focusses on E. coli isolates from food samples harboring the blaCTX-M-15 gene. The blaCTX-M-15 gene was detected in 5.2% (n = 21) of all isolates. Molecular analyses revealed a phylogenetic group A ST167 clone that was repeatedly isolated from raw milk and beef samples over a period of 6 months. The analyses indicate that spread of CTX-M-15-producing E. coli in German food samples were associated with a multireplicon IncF (FIA FIB FII) plasmid and additional antimicrobial resistance genes such as aac(6)-Ib-cr, blaOXA-1, catB3, different tet-variants as well as a class 1 integron with an aadA5/dfrA17 gene cassette. In addition, four phylogenetic group A ST410 isolates were detected. Three of them carried a chromosomal copy of the blaCTX-M-15 gene and a single isolate with the gene on a 90 kb IncF plasmid. The blaCTX-M-15 gene was always associated with the ISEcp1 element. In conclusion, CTX-M-15-producing E. coli were detected in German food samples. Among isolates of different matrices, two prominent clonal lineages, namely A-ST167 and A-ST410, were identified. These lineages may be important for the foodborne dissemination of CTX-M-15-producing E. coli in Germany. Interestingly, these clonal lineages were reported to be widely distributed and especially prevalent in isolates from humans and livestock. Transmission of CTX-M-15-harboring isolates from food-producing animals to food appears probable, as isolates obtained from livestock and food samples within the same time period exhibit comparable characteristics as compared to isolates detected from human. However, the routes and direction of transmission need further investigation.

11.
Genome Announc ; 5(31)2017 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-28774984

RESUMO

Escherichia coli sequence type 131 (ST131) is the most frequent antimicrobial-resistant lineage of E. coli, propagating extended-spectrum ß-lactamases (ESBL) worldwide. Recently, an alarming rate of increase in isolates of the sublineage C1/H30R-blaCTX-M-27 of ST131 in geographically distant countries was reported. Here, we present the complete genome sequence of the ST131 sublineage C1/H30R E. coli isolate harboring blaCTX-M-27 from Germany.

13.
Vet Microbiol ; 200: 114-117, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26411323

RESUMO

Carbapenem-resistant Enterobacteriaceae are not any more isolated only from human settings, but also from livestock. We reported for the first time the presence of VIM-1 carbapenemases in a livestock farm in Germany. The VIM-1 resistance gene found in these farms was located on IncHI2 plasmids. In order to be able to analyse these plasmids in more detail, two different plasmids from a single farm (pRH-R27 from Salmonella enterica and pRH-R178 from Escherichia coli) were completely sequenced and analysed for the presence of antibiotic and heavy metal resistances. The plasmids showed to harbour blaVIM-1, aacA4, aadA1, sul1, qacEΔ (encoded in an In110 class 1 integron), as well as blaACC-1, strA/strB, and catA1 genes together with resistance to heavy metals (ter-, mer-, sil-, ars-, rcn-, and pco). Comparison with other IncHI2 plasmid revealed that while pRH-R27 is a mosaic IncHI2 plasmid with both high homology to the plasmid pSTm-A54650 and R478, both isolated from humans, pRH-R178 is a deletion derivative of pRH-R27, presumably caused by several IS-mediated deletions indicating genetic evolution of plasmids in this environment.


Assuntos
Proteínas de Bactérias/genética , Escherichia coli/genética , Genoma Bacteriano/genética , Plasmídeos/genética , Salmonella enterica/genética , beta-Lactamases/genética , Animais , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Escherichia coli/enzimologia , Fazendas , Genômica , Alemanha/epidemiologia , Humanos , Integrons/genética , Gado/microbiologia , Metais Pesados/toxicidade , Salmonella enterica/enzimologia , Análise de Sequência de DNA/veterinária , Deleção de Sequência
14.
Front Microbiol ; 7: 1862, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27990135

RESUMO

Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria are a common cause of healthcare and community-associated infections worldwide. The distribution of such isolates in the environment and their presence in fish as a result of sewage contamination is not well-studied. Here we examined fish and environmental samples from Mwanza city for the presence of ESBL-producing bacteria. From 196 fish sampled from local markets, 26 (13.3%) contained lactose-fermenting ESBL-producing bacteria, while 39/73 (53.4%) environmental samples from the same area were ESBL producers. Antibiotic resistance genes, multi locus sequence types (MLST) and plasmid replicon types in 24 selected isolates from both populations were identified with whole genome sequencing using Illumina MiSeq. Nine of eleven sequenced fish isolates had the blaCTX-M-15 gene whereas 12/13 from environment carried blaCTX-M-15. Antibiotic resistance genes encoding resistance to sulfonamides (sul1/sul2), tetracyclines [tet(A)/tet(B)] fluoroquinolones [e.g., aac(6')-Ib-cr, qnrS1], aminoglycosides [e.g., aac(3)-lld, strB, strA,] and trimethoprim (e.g., dfrA14) were detected. E. coli sequence type ST-38 (2) and ST-5173 (2) were detected in isolates both from the environment and fish. IncY plasmids carrying blaCTX-M-15, qnrS1, strA, and strB were detected in five environmental E. coli isolates and in one E. coli isolate from fish. Our data indicate spillage of resistant environmental isolates into Lake Victoria through the sewage system. Persistence of blaCTX-M-15 in the Mwanza city environment is complex, and involves both clonal spread of resistant strains as well as dissemination by commonly occurring IncY plasmids circulating in isolates present in humans, the environment as well as in the food chain.

15.
Int J Syst Evol Microbiol ; 66(11): 4555-4559, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27498788

RESUMO

The taxonomic status of all species of the genus Elizabethkingia was re-evaluated by comparative genomics based on whole-genome sequencing. From these results it is clear that Elizabethkingia endophytica is a later subjective synonym of Elizabethkingia anophelis. In addition, genome-based analysis revealed the misidentification of isolates previously identified by traditional approaches and indicates the presence of two more species. We propose a more rapid identification scheme on the basis of an in silico PCR assay derived from comparative genomics of whole-genome sequences (WGS) from 29 well-curated strains.


Assuntos
Flavobacteriaceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Hibridização Genômica Comparativa , DNA Bacteriano/genética , Análise de Sequência de DNA
18.
Int J Antimicrob Agents ; 47(6): 457-65, 2016 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-27208899

RESUMO

Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum ß-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A-E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of blaCTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations.


Assuntos
Antibacterianos/farmacologia , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/veterinária , Escherichia coli/classificação , Escherichia coli/enzimologia , Fluoroquinolonas/farmacologia , beta-Lactamases/metabolismo , Animais , Cães , Farmacorresistência Bacteriana Múltipla , Microbiologia Ambiental , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/epidemiologia , Variação Genética , Genoma Bacteriano , Genótipo , Alemanha/epidemiologia , Humanos , Gado , Epidemiologia Molecular , Tipagem de Sequências Multilocus , Análise de Sequência de DNA
20.
Berl Munch Tierarztl Wochenschr ; 127(11-12): 458-63, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25872255

RESUMO

We characterized ESBL-producing Escherichia coli isolates from diseased dog, cat and human sources for their plasmid content. Plasmids with different Inc groups and combinations of resistance genes were detected in these isolates. The pan-genome of the plasmid-associated genes was found to be large, indicating diversity of the gene pool among the plasmids. No commonly occurring plasmids with similar gene content in isolates from dog, cats and humans were detected.


Assuntos
Doenças do Gato/microbiologia , Doenças do Cão/microbiologia , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/veterinária , Escherichia coli/genética , Plasmídeos/genética , beta-Lactamases/genética , Animais , Antibacterianos/farmacologia , Gatos , Cães , Escherichia coli/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Plasmídeos/isolamento & purificação
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