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1.
J Hum Genet ; 2022 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-35606503

RESUMO

Epigenetics play an essential role in colorectal neoplasia process. There is a need to determine the appropriateness of epigenetic biomarkers for early detection as well as expand our understanding of the carcinogenic process. Therefore, the aim of the study was to assess how DNA methylation pattern of GALR1 gene evolves in a sample set representing colorectal neoplastic progression. The study was designed into three phases. Firstly, Methylation status of GALR1 was assessed with genome-wide DNA methylation beadchip and pyrosequencing assays in colorectal lesions and paired normal tissues. Then, linear mixed-effects modeling analyses were applied to describe the trend of DNA methylation during the progression of colorectal neoplasia. In the third phase, quantitative RT-PCR was used to examine GALR1 expression in patients with precursor lesion and colorectal cancer. We found that significant hypermethylation of GALR1 promoter was a widely existent modification in CRCs (P < 0.001). When further examined methylation pattern of GALR1 during neoplastic progression of CRC, we found that DNA methylation level of GALR1 showed a significant stepwise increase from normal to hyperplastic polyps, to adenomas and to carcinoma samples (P < 0.001). Besides, loss of mRNA expression is a common accompaniment to adenomas and carcinomas. Public omics data analyses showed an inverse correlation between gene expression and DNA methylation (P < 0.001). Our findings indicate that epigenetic alteration of GALR1 promoter is gradually accumulated during the colorectal neoplastic progression. It can potentially be a promising biomarker used for screening and surveillance of colorectal cancer.

3.
mSystems ; : e0140621, 2022 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-35430877

RESUMO

Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in immunocompromised individuals. However, the evolution, diversity, and pathogenesis of N. cyriacigeorgica have remained unclear. Here, we performed a comparative genomic analysis using 91 N. cyriacigeorgica strains, 45 of which were newly sequenced in this study. Phylogenetic and average nucleotide identity (ANI) analyses revealed that N. cyriacigeorgica contained five species-level clades (8.6 to 14.6% interclade genetic divergence), namely, the N. cyriacigeorgica complex (NCC). Further pan-genome analysis revealed extensive differences among the five clades in nine functional categories, such as energy production, lipid metabolism, secondary metabolites, and signal transduction mechanisms. All 2,935 single-copy core genes undergoing purifying selection were highly conserved across NCC. However, clades D and E exhibited reduced selective constraints, compared to clades A to C. Horizontal gene transfer (HGT) and mobile genetic elements contributed to genomic plasticity, and clades A and B had experienced a higher level of HGT events than other clades. A total of 129 virulence factors were ubiquitous across NCC, such as the mce operon, hemolysin, and type VII secretion system (T7SS). However, different distributions of three toxin-coding genes and two new types of mce operons were detected, which might contribute to pathogenicity differences among the members of the NCC. Overall, our study provides comprehensive insights into the evolution, genetic diversity, and pathogenicity of NCC, facilitating the prevention of infections. IMPORTANCE Nocardia species are opportunistic bacterial pathogens that can affect all organ systems, primarily the skin, lungs, and brain. N. cyriacigeorgica is the most prevalent species within the genus, exhibits clinical significance, and can cause severe infections when disseminated throughout the body. However, the evolution, diversity, and pathogenicity of N. cyriacigeorgica remain unclear. Here, we have conducted a comparative genomic analysis of 91 N. cyriacigeorgica strains and revealed that N. cyriacigeorgica is not a single species but is composed of five closely related species. In addition, we discovered that these five species differ in many ways, involving selection pressure, horizontal gene transfer, functional capacity, pathogenicity, and antibiotic resistance. Overall, our work provides important clues in dissecting the evolution, genetic diversity, and pathogenicity of NCC, thereby advancing prevention measures against these infections.

4.
Infect Dis Model ; 7(2): 117-126, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35475256

RESUMO

Numerous studies have proposed search engine-based estimation of COVID-19 prevalence during the COVID-19 pandemic; however, their estimation models do not consider the impact of various urban socioeconomic indicators (USIs). This study quantitatively analysed the impact of various USIs on search engine-based estimation of COVID-19 prevalence using 15 USIs (including total population, gross regional product (GRP), and population density) from 369 cities in China. The results suggested that 13 USIs affected either the correlation (SC-corr) or time lag (SC-lag) between search engine query volume and new COVID-19 cases ( p <0.05). Total population and GRP impacted SC-corr considerably, with their correlation coefficients r for SC-corr being 0.65 and 0.59, respectively. Total population, GRP per capita, and proportion of the population with a high school diploma or higher had simultaneous positive impacts on SC-corr and SC-lag ( p <0.05); these three indicators explained 37-50% of the total variation in SC-corr and SC-lag. Estimations for different urban agglomerations revealed that the goodness of fit, R 2 , for search engine-based estimation was more than 0.6 only when total urban population, GRP per capita, and proportion of the population with a high school diploma or higher exceeded 11.08 million, 120,700, and 38.13%, respectively. A greater urban size indicated higher accuracy of search engine-based estimation of COVID-19 prevalence. Therefore, the accuracy and time lag for search engine-based estimation of infectious disease prevalence can be improved only when the total urban population, GRP per capita, and proportion of the population with a high school diploma or higher are greater than the aforementioned thresholds.

5.
Sci Total Environ ; : 155028, 2022 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-35390371

RESUMO

BACKGROUND: High atmospheric temperature has been associated with the occurrence of bacillary dysentery (BD). Recent studies have suggested that hot extremes may influence health outcomes, however, none have examined the association between hot extremes and BD risk, especially at the national level. OBJECTIVES: To assess the effect and attributable burden of hot extremes on bacillary dysentery (BD) cases and to identify populations at high risk of BD. METHODS: Daily incident BD data of 31 capital cities from 2010 to 2018 were collected from the Chinese Center for Disease Control and Prevention, weather data was obtained from the fifth generation of the European Re-Analysis Dataset. Three types of hot extremes, including hot day, hot night, and hot day and night, were defined according to single or sequential occurrence of daytime hot and nighttime hot within 24 h. A two-stage analytical strategy combined with distributed lag non-linear models (DLNM) was used to evaluate city-specific associations and national pooled estimates. RESULTS: Hot extremes were significantly associated with the risk of BD on lagged 1-6 days. The overall cumulative relative risk (RR) was 1.136 [95% confidence interval (CI): 1.022, 1.263] for hot day, 1.181 (95% CI: 1.019, 1.369) for hot night, and 1.154 (95% CI: 1.038, 1.283) for hot day and night. Northern residents, females, and children younger than or equal to 14 years old were vulnerable under hot night, southern residents were vulnerable under hot day, and males were vulnerable under hot day and night. 1.854% (95% CI: 1.294%, 2.205%) of BD cases can be attributable to hot extremes, among which, hot night accounted for a large proportion. CONCLUSIONS: Hot extremes may significantly increase the incidence risk and disease burden of BD. Type-specific protective measures should be taken to reduce the risk of BD, especially in those we found to be particularly vulnerable.

6.
Front Immunol ; 13: 858609, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35309304

RESUMO

Males are generally more susceptible to Nocardia infection than females, with a male-to-female ratio of 2 and higher clinical disease. 17ß-Estradiol has been implicated in affecting the sex-based gap by inhibiting the growth of N. brasiliensis in experiments, but the underlying mechanisms have not yet been fully clarified. In the present study, however, we report increased severity in N. farcinica IFM 10152-infected female mice compared with male mice with increased mortality, elevated lung bacterial loads and an exaggerated pulmonary inflammatory response, which was mimicked in ovariectomized female mice supplemented with E2. Similarly, the overwhelming increase in bacterial loads was also evident in E2-treated host cells, which were associated with downregulating the phosphorylation level of the MAPK pathway by binding the estrogen receptor. We conclude that although there are more clinical cases of Nocardia infection in males, estrogen promotes the survival of the bacteria, which leads to aggravated inflammation in females. Our data emphasize the need to include and separately analyze both sexes in future studies of Nocardia to understand the sex differences in immune responses and disease pathogenesis.


Assuntos
Nocardiose , Nocardia , Animais , Estradiol/farmacologia , Estrogênios , Feminino , Masculino , Camundongos , Nocardiose/microbiologia
7.
Microbiol Spectr ; 10(2): e0216221, 2022 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-35293804

RESUMO

In human medicine, antibiotics have been widely used to treat microbial infections. The extensive use of antibiotics is a leading cause of antibiotic resistance. Currently, the influence of the use of antibiotics on the ocular surface microbiome in the course of keratitis treatment remains to be explored in depth. We performed metagenomic analyses in a cohort of 26 healthy controls (HCs), 28 keratitis patients (KPs) who received antibiotics [KP (abx+) group], and 12 KPs who were antibiotic naive [KP (abx-) group]. We identified that the dissimilarities in microbial community structure (Bray-Curtis and Jaccard analyses) between the KP (abx+) group and the HC group were greater than those between the KP (abx-) group and the HC group. Pseudomonas lactis, P. aeruginosa, Pseudomonas sp. FDAARGOS_380, Pseudomonas sp. J380, Corynebacterium simulans, Streptococcus pyogenes, Finegoldia magna, and Aspergillus oryzae had no statistically significant differences between the KP (abx+) and KP (abx-) groups but did have statistically significant differences between the KP (abx+) and HC groups and between the KP (abx-) and HC groups. Among them, Pseudomonas lactis, P. aeruginosa, Pseudomonas sp. FDAARGOS_380, and Pseudomonas sp. J380 were identified as possible hosts carrying multidrug-resistant genes. The total abundance and number of antibiotic resistance genes (ARGs) were greater in the KP (abx+) group than in the HC and KP (abx-) groups. The functional profile analysis of ocular surface microbiota revealed that pathogenesis-related functional pathways and virulence functions were enriched in KPs. In conclusion, our results show that empirical antibiotic treatment in KPs leads to increases in the antibiotic resistance of ocular surface microbiota. IMPORTANCE Treatment for keratitis is based on appropriate antimicrobial therapy. A direct correlation between antibiotic use and the extent of antibiotic resistance has been reported. Therefore, knowledge of the antibiotic resistance patterns of ocular surface microbial flora in KPs is important for clinical treatment. To the best of our knowledge, this is the first study to use metagenomic approaches to investigate the associations between ophthalmic antibiotic use and the ocular surface microbiome of KPs. Monitoring the microbiota and antibiotic resistome profiles for the ocular surface has huge potential to help ophthalmologists choose the appropriate antibiotics and will thereby improve the efficacy of treatment regimens, which has important implications for reducing the development of antibiotic resistance of the ocular surface to a certain extent.


Assuntos
Ceratite , Microbiota , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Resistência Microbiana a Medicamentos , Humanos , Ceratite/tratamento farmacológico , Ceratite/microbiologia , Pseudomonas , Pseudomonas aeruginosa
8.
Artigo em Inglês | MEDLINE | ID: mdl-35283335

RESUMO

OBJECTIVES: The objective of this study is to explore the molecular basis of trimethoprim-sulfamethoxazole (SXT) resistance in Nocardia, an SXT-resistant N. farcinica strain, named SZ 1509, by whole-genome sequencing. METHODS: Antimicrobial susceptibility testing of SZ 1509 was performed by broth microdilution, E-test, and disk diffusion arrays. Genome sequencing and analysis were performed to discover the SXT resistance determinant and its genetic context. Inverse PCR was conducted to confirm the circular form of the composite transposon. PCR for the sul1 gene was performed among SXT-susceptible isolates. RESULTS: SZ 1509 is resistant to many drugs, especially SXT, with a minimum inhibitory concentration (MIC) of up to 32/608 µg/mL (ratio of 1:19 for trimethoprim: sulfamethoxazole). Its assembled genome consists of one chromosome and four plasmids with a total size of 6,613,629 bp and 71.1% of GC content. The plasmid 2 was found to carry one IS6-composite transposon containing IS6100 carrying the sul1 gene, one tellurite resistance gene TerC and several transcriptional regulators. Inverse PCR analyses showed its circular form. All ten SXT-susceptible isolates do not contain sul1. In addition, mutations with strong associations to SXT resistance were not conclusive. CONCLUSION: This is the first study to elucidate the transposon-mediated sulfamethoxazole resistance in N. farcinica. Our results provide insights on acquired drug resistance of N. farcinica and further suggest that the prevalence and correlation of this resistance's determinants in clinical isolates should be continuously monitored to provide effective clinical management of its resultant diseases.

9.
J Plant Physiol ; 271: 153665, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35279561

RESUMO

Selenium (Se) is a micronutrient essential for human and animal health. However, Se is toxic at high levels because the nonspecific substitution of cysteine by selenocysteine could lead to protein malfunction. In an attempt to prevent nonspecific selenocysteine incorporation into proteins, we simultaneously overexpressed the gene encoding selenocysteine lyase from Homo sapiens (HsSL), which specifically catalyzes the decomposition of selenocysteine into elemental Se0 and alanine, and the gene encoding selenocysteine methyltransferase from Astragalus bisulcatus (AbSMT), which methylates selenocysteine into methylselenocysteine in rice. The transgenic plants showed normal growth under standard conditions. Se treatment resulted in higher levels of alanine and methylselenocysteine in transgenic plants than in wild-type plants, which indicated that this approach might have successfully redirected Se flow in the plant. Overexpression of HsSL and AbSMT in rice also endows transgenic plants with hyposensitivity to Se stress at the seed germination stage. The transgenic plants showed enhanced selenate and selenite tolerance, which was simultaneously supported by fresh weight values. Moreover, our phytoremediation assay revealed that the transgenic plants exhibited greatly improved Se elimination capabilities and accumulated about 38.5% and 128.6% more Se than wild-type plants when treated with selenate and selenite, respectively. This study offers hope that genetically modified plants could play a role in the restoration of Se-contaminated environment.


Assuntos
Oryza , Selênio , Animais , Biodegradação Ambiental , Oryza/genética , Oryza/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Ácido Selênico/metabolismo , Selênio/metabolismo
10.
Front Microbiol ; 13: 780651, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35250920

RESUMO

Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai-Tibet Plateau.

11.
Front Cell Infect Microbiol ; 12: 835213, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35310854

RESUMO

Nocardia cyriacigeorgica has gradually become a common pathogen in clinical microbial infections. Identification of Nocardia at the species level is essential to assess the susceptibility and pathogenicity of antimicrobials. However, there is no suitable method for rapid and accurate laboratory detection of N. cyriacigeorgica. In this study, we combined PCR amplification with the CRISPR-Cas12a system to establish a novel detection platform, named CRISPR-PCR, and applied it to the detection of N. cyriacigeorgica in clinical samples. The Cas12a protein exhibited collateral cleavage activity following CRISPR RNA binding to specific targets, then indiscriminately cleaved nearby single-stranded DNA, and this was evaluated for diagnostic nucleic acid detection by measuring the fluorescence signal using a fluorescence reader. The assay takes only 2 h, including DNA extraction for 20 min, nucleic acid pre-amplification for 70 min, and fluorescence detection for 20 min. The limit of detection for N. cyriacigeorgica was 10-3 ng and the specificity was 100%. Thus, the N. cyriacigeorgica CRISPR-PCR assay is a rapid and specific method for detecting N. cyriacigeorgica, and the CRISPR-PCR fluorescence detection platform has great potential for detection of other pathogens.


Assuntos
Sistemas CRISPR-Cas , Nocardia , DNA de Cadeia Simples , Nocardia/genética , Técnicas de Amplificação de Ácido Nucleico/métodos
12.
Virol Sin ; 2022 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-35234631

RESUMO

Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth's vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus.

13.
Nat Commun ; 13(1): 1465, 2022 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-35304465

RESUMO

Due to the two-dimensional character of graphene, the plasmons sustained by this material have been invariably studied in supported samples so far. The substrate provides stability for graphene but often causes undesired interactions (such as dielectric losses, phonon hybridization, and impurity scattering) that compromise the quality and limit the intrinsic flexibility of graphene plasmons. Here, we demonstrate the visualization of plasmons in suspended graphene at room temperature, exhibiting high-quality factor Q~33 and long propagation length > 3 µm. We introduce the graphene suspension height as an effective plasmonic tuning knob that enables in situ change of the dielectric environment and substantially modulates the plasmon wavelength, propagation length, and group velocity. Such active control of micrometer plasmon propagation facilitates near-unity-order modulation of nanoscale energy flow that serves as a plasmonic switch with an on-off ratio above 14. The suspended graphene plasmons possess long propagation length, high tunability, and controllable energy transmission simultaneously, opening up broad horizons for application in nano-photonic devices.

14.
Front Microbiol ; 13: 679126, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35222319

RESUMO

Organophosphate compounds are widely used in pesticides to control weeds, crop diseases, and insect pests. Unfortunately, these synthetic compounds are hazardous and toxic to all types of living organisms. In the present work, Escherichia coli was bioengineered to achieve methyl parathion (MP) degradation via the introduction of six synthetic genes, namely, opdS, pnpAS, pnpBS, pnpCS, pnpDS, and pnpES, to obtain a new transformant, BL-MP. MP and its subsequent decomposition intermediates were completely degraded by this transformant to enter the metabolites of multiple anabolic pathways. The MP-degraded strain created in this study may be a promising candidate for the bioremediation of MP and potential toxic intermediates.

15.
Sci Total Environ ; 820: 153283, 2022 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-35066037

RESUMO

Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have caused serious environmental pollution worldwide. Phytoremediation is an efficient technology in treating hazardous wastes from the environment. However, the phytoremediation efficiency of thiocyanate is very low due to the fact that plants lack thiocyanate degradation enzymes. In this study, the thiocyanate hydrolase module was assembled correctly in rice seedlings and showed thiocyanate hydrolase activity. Rice seedlings engineered to express thiocyanate degrading activity were able to completely remove thiocyanate from coking wastewater. Our findings suggest that transforming the thiocyanate hydrolase module into plants is an efficient strategy for rapid phytoremediation of thiocyanate in the environment. Moreover, the rice seedlings expressing apoplastic or cytoplasmic targeted thiocyanate hydrolase module were constructed to compare the phytoremediation efficiency of secretory/intracellular recombinant thiocyanate hydrolase. The most obvious finding from this study is that the apoplastic expression system is more efficient than the cytoplasm expression system in the phytoremediation of thiocyanate. At last, this research also shows that the secreted thiocyanate hydrolase from engineered rice plants does not influence rhizosphere bacterial community composition.


Assuntos
Oryza , Biodegradação Ambiental , Engenharia Metabólica , Oryza/metabolismo , Plântula/metabolismo , Tiocianatos
16.
Emerg Microbes Infect ; 11(1): 593-605, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-35094669

RESUMO

Although previous studies have reported the use of metabolomics for infectious diseases, little is known about the potential function of plasma metabolites in children infected with Mycoplasma pneumoniae (MP). Here, a combination of liquid chromatography-quadrupole time-of-flight mass spectrometry and random forest-based classification model was used to provide a broader range of applications in MP diagnosis. In the training cohort, plasma from 63 MP pneumonia children (MPPs), 37 healthy controls (HC) and 29 infectious disease controls (IDC) was collected. After multivariate analyses, 357 metabolites were identified to be differentially expressed among MPP, HC and IDC groups, and 3 metabolites (568.5661, 459.3493 and 411.3208) had high diagnostic values. In an independent cohort with 57 blinded subjects, samples were successfully classified into different groups, demonstrating the reliability of these biomarkers for distinguishing MPPs from controls. A metabolomic signature analysis identified major classes of glycerophospholipids, sphingolipids and fatty acyls were increased in MPPs. These markedly altered metabolites are mainly involved in glycerophospholipid and sphingolipid metabolism. As the ubiquitous building blocks of eukaryotic cell membranes, dysregulated lipid metabolism indicates damage of the cellular membrane and the activation of immunity in MPPs. Moreover, lipid metabolites, differentially expressed between severe and mild MPPs, were correlated with the markers of extrapulmonary complications, suggesting that they may be involved in MPP disease severity. These findings may offer new insights into biomarker selection and the pathogenesis of MPP in children.


Assuntos
Mycoplasma pneumoniae , Pneumonia por Mycoplasma , Biomarcadores , Humanos , Metabolômica , Pneumonia por Mycoplasma/diagnóstico , Reprodutibilidade dos Testes
17.
J Microbiol ; 60(2): 137-146, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34826100

RESUMO

Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546T and 573) and respiratory tracts of marmots (strains 1318T and 1311). The 16S rRNA gene sequencing revealed that strains 546T and 573 were 97.8% identical to Roseomonas wenyumeiae Z23T, whereas strains 1311 and 1318T were 98.3% identical to Roseomonas ludipueritiae DSM 14915T. In addition, a 98.0% identity was observed between strains 546T and 1318T. Phylogenetic and phylogenomic analyses revealed that strains 546T and 573 clustered with R. wenyumeiae Z23T, whereas strains 1311 and 1318T grouped with R. ludipueritiae DSM 14915T. The average nucleotide identity between our isolates and members of the genus Roseomonas was below 95%. The genomic G+C content of strains 546T and 1318T was 70.9% and 69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the major polar lipids, with Q-10 as the predominant respiratory quinone. According to all genotypic, phenotypic, phylogenetic, and phylogenomic analyses, the four strains represent two novel species of the genus Roseomonas, for which the names Roseomonas haemaphysalidis sp. nov. and Roseomonas marmotae sp. nov. are proposed, with 546T (= GDMCC 1.1780T = JCM 34187T) and 1318T (= GDMCC 1.1781T = JCM 34188T) as type strains, respectively.


Assuntos
Marmota/microbiologia , Methylobacteriaceae/citologia , Methylobacteriaceae/isolamento & purificação , Carrapatos/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Cardiolipinas/análise , DNA Bacteriano , Methylobacteriaceae/genética , Fosfatidiletanolaminas/análise , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA
18.
J Appl Microbiol ; 132(5): 3685-3693, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-34936163

RESUMO

AIMS: To establish a CRISPR-based nucleic acid detection platform and apply it to the detection of Nocardia farcinica. METHODS AND RESULTS: A CRISPR-based nucleic acid detection platform, termed CRISPR-CPA (CRISPR/Cas12a combined with PCR amplification), which employed PCR for pre-amplification of target sequences and CRISPR-Cas12a-based detection for decoding of the PCR amplicons, was developed. To demonstrate its feasibility, CRISPR-CPA was applied to the detection of N. farcinica. A pair of PCR primers and a crRNA, which targeting the conservative and specific part of gyrA of N. farcinica reference strain IFM 10152, were designed according to the principle of CRISPR-CPA. The whole detection process of N. farcinica CRISPR-CPA assay, including sample pre-treatment and DNA extraction (~20 min), PCR pre-amplification (60 min), CRISPR-based detection (10 min), can be completed within 90 min. A total of 62 isolates were used to evaluate the specificity of N. farcinica CRISPR-CPA assay. Clinical specimens were employed to determine the feasibility of the method in practical application. The limit of detection of the N. farcinica CRISPR-CPA assay is 1 pg DNA per reaction in pure cultures and 105  CFU/ml in sputum specimens, which is similar with culture but significantly more timesaving. CONCLUSIONS: The N. farcinica CRISPR-CPA assay is an economic and specific method to detect N. farcinica and provides a high-efficiency tool for screening of pathogens especially of some hard-to-culture and slow-growth infectious agents. SIGNIFICANCE AND IMPACT OF THE STUDY: In CRISPR-CPA system, the PCR primers are engineered with a protospacer adjacent motif (PAM) site of Cas12a effector and an additional base A was added at the 5' end of the engineered PCR primer for protecting PAM site, thus the CRISPR-CPA can detect any sequence. Also, we applied CRISPR-CPA to rapidly detect N. farcinica, which is slow-growing bacteria and is firstly detected by a CRISPR-based method.


Assuntos
Sistemas CRISPR-Cas , Nocardia , DNA , Nocardia/genética , Técnicas de Amplificação de Ácido Nucleico/métodos
19.
20.
Int J Hyg Environ Health ; 240: 113882, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-34915282

RESUMO

As the COVID-19 pandemic spread globally, the consumption of antibiotics increased. However, no studies exist evaluating the effect of antibiotics use on the antibiotic resistance of intestinal flora in COVID-19 patients during the pandemic. To explore this issue, we collected 15 metagenomic data of fecal samples from healthy controls (HCs) with no use history of antibiotics, 23 metagenomic data of fecal samples from COVID-19 patients who received empirical antibiotics [COVID-19 (abx+)], 18 metagenomic data of fecal samples from antibiotics-naïve COVID-19 patients [COVID-19 (abx-)], and six metagenomic data of fecal samples from patients with community-acquired pneumonia [PC (abx+)] from the Sequence Read Archive database. A total of 513 antibiotic-resistant gene (ARG) subtypes of 18 ARG types were found. Antibiotic treatment resulted in a significant increase in the abundance of ARGs in intestinal flora of COVID-19 patients and markedly altered the composition of ARG profiles. Grouped comparisons of pairs of Bray-Curtis dissimilarity values demonstrated that the dissimilarity of the HC versus the COVID-19 (abx+) group was significantly higher than the dissimilarity of the HC versus the COVID-19 (abx-) group. The mexF, mexD, OXA_209, major facilitator superfamily transporter, and EmrB_QacA family major facilitator transporter genes were the discriminative ARG subtypes for the COVID-19 (abx+) group. IS621, qacEdelta, transposase, and ISCR were significantly increased in COVID-19 (abx+) group; they greatly contributed toward explaining variation in the relative abundance of ARG types. Overall, our data provide important insights into the effect of antibiotics use on the antibiotic resistance of COVID-19 patients during the COVID-19 epidemic.


Assuntos
COVID-19 , Antibacterianos , Genes Bacterianos , Humanos , Pandemias , SARS-CoV-2
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