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3.
Environ Pollut ; 291: 118155, 2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34530239

RESUMO

Composting is an effective technology to recycle organic solid waste as a green resource. However, pharmaceutical fermentation residue (PFR) contains a variety of pollutants, such as residual drug and antibiotic resistance genes (ARGs), which limits the green cycle of using PFR as a resource. To promote the green recycling of PFR, this study evaluated the characteristics of abundance and the response relationship of ARGs during the process of rapid composting. Different rapid composting samples were collected, and DNA was extracted from each sample. The absolute abundance of ARGs was quantified using quantitative PCR, and the microbial community structure was identified using high-throughput sequencing. The results showed that ermB, ermF, tetM and tetQ were reduced by 89.55%, 15.10%, 89.55%, and 82.30% respectively, and only sul2 increased by approximately 5-fold. Mobile genetic elements (MGEs) directly affected the changes in abundance of ARGs. As typical MGEs, intl1 and intl2 decreased by 3.40% and 54.32%, respectively. Potential host microorganisms important factors that affected ARGs and MGEs. A network analysis indicated that the potential host microorganisms were primarily distributed in Firmicutes and Proteobacteria at the phylum level. The pH and content of water-extractable sulfur were physicochemical parameters that substantially affected the abundance of potential host microorganisms through redundancy analysis. Industrial-scale rapid composting could reduce the number of ARGs and shorten the composting cycle, which merits its popularization and application.


Assuntos
Compostagem , Microbiota , Preparações Farmacêuticas , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos/genética , Fermentação , Genes Bacterianos , Sequências Repetitivas Dispersas , Esterco
4.
PLoS One ; 16(8): e0254836, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34432793

RESUMO

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins-Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.


Assuntos
Indústria de Laticínios , Resistência Microbiana a Medicamentos/genética , Sequências Repetitivas Dispersas/genética , Esterco/microbiologia , Anaerobiose , Reatores Biológicos/microbiologia , Genes Bacterianos , Análise dos Mínimos Quadrados , Dinâmica não Linear , RNA Ribossômico 16S/genética
5.
Sci Rep ; 11(1): 16145, 2021 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-34373516

RESUMO

The genetic element s2m has been acquired through horizontal transfer by many distantly related viruses, including the SARS-related coronaviruses. Here we show that s2m is evolutionarily conserved in these viruses. Though several lineages of severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) devoid of the element can be found, these variants seem to have been short lived, indicating that they were less evolutionary fit than their s2m-containing counterparts. On a species-level, however, there do not appear to be any losses and this pattern strongly suggests that the s2m element is essential to virus replication in SARS-CoV-2 and related viruses. Further experiments are needed to elucidate the function of s2m.


Assuntos
Coronaviridae/genética , Sequências Repetitivas Dispersas/genética , RNA Viral/genética , SARS-CoV-2/genética , Replicação Viral/genética , Animais , Sequência de Bases , COVID-19/virologia , Coronaviridae/classificação , Evolução Molecular , Transferência Genética Horizontal , Humanos , Filogenia , SARS-CoV-2/fisiologia , Homologia de Sequência do Ácido Nucleico , Especificidade da Espécie
7.
Nucleic Acids Res ; 49(14): 8135-8144, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34232995

RESUMO

Mobile genetic elements have been harnessed for gene transfer for a wide variety of applications including generation of stable cell lines, recombinant protein production, creation of transgenic animals, and engineering cell and gene therapy products. The piggyBac transposon family includes transposase or transposase-like proteins from a variety of species including insect, bat and human. Recently, human piggyBac transposable element derived 5 (PGBD5) protein was reported to be able to transpose piggyBac transposons in human cells raising possible safety concerns for piggyBac-mediated gene transfer applications. We evaluated three piggyBac-like proteins across species including piggyBac (insect), piggyBat (bat) and PGBD5 (human) for their ability to mobilize piggyBac transposons in human cells. We observed a lack of cross-species transposition activity. piggyBac and piggyBat activity was restricted to their cognate transposons. PGBD5 was unable to mobilize piggyBac transposons based on excision, colony count and plasmid rescue analysis, and it was unable to bind piggyBac terminal repeats. Within the piggyBac family, we observed a lack of cross-species activity and found that PGBD5 was unable to bind, excise or integrate piggyBac transposons in human cells. Transposition activity appears restricted within species within the piggyBac family of mobile genetic elements.


Assuntos
Elementos de DNA Transponíveis/genética , Sequências Repetitivas Dispersas/genética , Transposases/genética , Animais , Linhagem Celular , Vetores Genéticos/genética , Humanos , Mutagênese Insercional/genética , Plasmídeos/genética , Fatores de Transcrição/genética
8.
Mar Genomics ; 58: 100848, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34217484

RESUMO

The monogenean Benedenia humboldti is a pathogen of the yellowtail Seriola lalandi in the South-Eastern Pacific ocean. Using low-coverage short Illumina 150bp pair-end reads sequencing, this study examines, for the first time, the 'repeatome' (= repetitive genomic elements), including the 45S ribosomal RNA DNA operon and microsatellites, in B. humboldti. Repetitive elements comprised a large fraction of the nuclear genome and a considerable proportion of them could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to the 45S ribosomal RNA operon or were classified as satellite DNA and Class I - Long Interspersed Nuclear Elements (LINEs) which were considerably more abundant than Class I - LTR elements. The ribosomal RNA gene operon in B. humboldti is comprised of, in the following order, a 5' ETS (length = 233 bp), ssrDNA (2082 bp), ITS1 (346 bp), 5.8S rDNA (150 bp), ITS2 (572 bp), lsrDNA (3887 bp), and a 3' ETS (1097 bp). A total of 15 SSRs were identified. These newly developed genomic resources will contribute to the better understanding of meta-population connectivity in this species, cryptic species in the genus, and will advance pest management strategies.


Assuntos
Genoma Helmíntico , Sequências Repetitivas Dispersas , Repetições de Microssatélites , Óperon , Trematódeos/genética , Animais , Núcleo Celular/genética
9.
Int J Mol Sci ; 22(14)2021 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-34299116

RESUMO

Corynebacterium striatum, a bacterium that is part of the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and in-hospital and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. However, there are no studies about the genomic determinants related to antimicrobial resistance in C. striatum. This review updates global information related to antimicrobial resistance found in C. striatum and highlights the essential genomic aspects in its persistence and dissemination. The resistome of C. striatum comprises chromosomal and acquired elements. Resistance to fluoroquinolones and daptomycin are due to mutations in chromosomal genes. Conversely, resistance to macrolides, tetracyclines, phenicols, beta-lactams, and aminoglycosides are associated with mobile genomic elements such as plasmids and transposons. The presence and diversity of insertion sequences suggest an essential role in the expression of antimicrobial resistance genes (ARGs) in genomic rearrangements and their potential to transfer these elements to other pathogens. The present study underlines that the resistome of C. striatum is dynamic; it is in evident expansion and could be acting as a reservoir for ARGs.


Assuntos
Antibacterianos/farmacologia , Infecções por Corynebacterium/tratamento farmacológico , Corynebacterium/efeitos dos fármacos , Corynebacterium/genética , Farmacorresistência Bacteriana Múltipla/genética , Sequências Repetitivas Dispersas , Infecções por Corynebacterium/genética , Infecções por Corynebacterium/microbiologia , Humanos
10.
Science ; 373(6554)2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34326207

RESUMO

Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.


Assuntos
Farmacorresistência Bacteriana/genética , Sequências Repetitivas Dispersas , Myoviridae/fisiologia , Vibrio cholerae/efeitos dos fármacos , Vibrio cholerae/virologia , Bacteriólise , Cólera/microbiologia , Conjugação Genética , Epigênese Genética , Fezes/microbiologia , Fezes/virologia , Gammaproteobacteria/genética , Gammaproteobacteria/virologia , Genes Bacterianos , Genes Virais , Genoma Bacteriano , Genoma Viral , Especificidade de Hospedeiro , Humanos , Interações Microbianas , Myoviridae/genética , Myoviridae/isolamento & purificação , Vibrio cholerae/genética , Vibrio cholerae/isolamento & purificação , Proteínas Virais/genética , Proteínas Virais/metabolismo
11.
J Environ Manage ; 296: 113270, 2021 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-34271348

RESUMO

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.


Assuntos
Águas Residuárias , Purificação da Água , Antibacterianos/farmacologia , Bactérias/genética , Bacteroidetes , Resistência Microbiana a Medicamentos/genética , Flavobacteriaceae , Genes Bacterianos , Hospitais , Humanos , Sequências Repetitivas Dispersas , Metagenoma , Prevalência , RNA Ribossômico 16S , Esgotos
12.
PLoS Biol ; 19(7): e3001276, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34228700

RESUMO

Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the high-priority multidrug-resistant nosocomial pathogens (ESKAPE), the first point of contact between the cell and virions or conjugative pili is the capsule. While the capsule can be a barrier to MGEs, it also evolves rapidly by horizontal gene transfer (HGT). Here, we aim at understanding this apparent contradiction by studying the covariation between the repertoire of capsule genes and MGEs in approximately 4,000 genomes of Klebsiella pneumoniae (Kpn). We show that capsules drive phage-mediated gene flow between closely related serotypes. Such serotype-specific phage predation also explains the frequent inactivation of capsule genes, observed in more than 3% of the genomes. Inactivation is strongly epistatic, recapitulating the capsule biosynthetic pathway. We show that conjugative plasmids are acquired at higher rates in natural isolates lacking a functional capsular locus and confirmed experimentally this result in capsule mutants. This suggests that capsule inactivation by phage pressure facilitates its subsequent reacquisition by conjugation. Accordingly, capsule reacquisition leaves long recombination tracts around the capsular locus. The loss and regain process rewires gene flow toward other lineages whenever it leads to serotype swaps. Such changes happen preferentially between chemically related serotypes, hinting that the fitness of serotype-swapped strains depends on the host genetic background. These results enlighten the bases of trade-offs between the evolution of virulence and multidrug resistance and caution that some alternatives to antibiotics by selecting for capsule inactivation may facilitate the acquisition of antibiotic resistance genes (ARGs).


Assuntos
Cápsulas Bacterianas/metabolismo , Sequências Repetitivas Dispersas , Klebsiella pneumoniae/metabolismo , Vias Biossintéticas , Conjugação Genética , Fluxo Gênico , Genoma Bacteriano , Klebsiella pneumoniae/genética , Recombinação Genética
13.
Nat Commun ; 12(1): 3586, 2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34117247

RESUMO

Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.


Assuntos
Sistemas CRISPR-Cas , Genômica , Sequências Repetitivas Dispersas , Sequenciamento por Nanoporos/métodos , Linhagem Celular , Proteínas de Ligação a DNA , Genoma Humano , Humanos , Sequências Repetitivas de Ácido Nucleico , Ribonucleoproteínas/metabolismo , Análise de Sequência de DNA
14.
Malar J ; 20(1): 288, 2021 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-34183015

RESUMO

BACKGROUND: Plasmodium vivax proteins with variant interspersed repeats (VIR) are the key proteins used by the parasite to escape from the host immune system through the creation of antigenic variations. However, few studies have been done to elucidate their role as targets of immunity. Thus, this study evaluated the naturally-acquired immune response against VIR proteins in vivax malaria-infected individuals in the Republic of Korea (ROK). METHODS: Seven recombinant VIR proteins and two synthetic peptides previously studied in other countries that elicited a robust immune response were used to investigate the antibody and cellular immune response in 681 P. vivax-infected people in ROK. The expression of IgM, IgG, and IgG subclasses against each VIR antigen or against PvMSP1-19 was analysed by ELISA. PvMSP1-19, known as a promising vaccine candidate of P. vivax, was used as the positive control for immune response assessment. Furthermore, the cellular immune response to VIR antigens was evaluated by in vitro proliferative assay, cellular activation assay, and cytokine detection in mononuclear cells of the P. vivax-infected population. RESULTS: IgM or IgG were detected in 52.4% of the population. Among all the VIR antigens, VIR25 elicited the highest humoral immune response in the whole population with IgG and IgM prevalence of 27.8% and 29.2%, respectively, while PvMSP1-19 elicited even higher prevalence (92%) of IgG in the population. As for the cellular immune response, VIR-C2, PvLP2, and PvMSP1-19 induced high cell activation and secretion of IL-2, IL-6, IL-10, and G-CSF in mononuclear cells from the P. vivax-infected population, comparable with results from PvMSP1-19. However, no significant proliferation response to these antigens was observed between the malaria-infected and healthy groups. CONCLUSION: Moderate natural acquisition of antibody and cellular responses in P. vivax-infected Korean malaria patients presented here are similar to that in other countries. It is interesting that the immune response to VIR antigens is conserved among malaria parasites in different countries, considering that VIR genes are highly polymorphic. This thus warrants further studies to elucidate molecular mechanisms by which human elicit immune response to the malaria parasite VIR antigens.


Assuntos
Antígenos de Protozoários/imunologia , Imunidade Celular , Imunidade Humoral , Vacinas Antimaláricas/imunologia , Plasmodium vivax/imunologia , Adolescente , Adulto , Feminino , Humanos , Sequências Repetitivas Dispersas , Malária Vivax , Masculino , Pessoa de Meia-Idade , República da Coreia , Vacinas Sintéticas/imunologia , Adulto Jovem
15.
Nucleic Acids Res ; 49(13): 7571-7587, 2021 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-34165564

RESUMO

In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.


Assuntos
Chlamydomonas reinhardtii/genética , Evolução Molecular , Telômero , Clorófitas/genética , Cromatina/metabolismo , Cromossomos de Plantas , DNA Ribossômico , Sequências Repetitivas Dispersas , Repetições de Microssatélites , Sequências de Repetição em Tandem , Transcrição Genética
16.
Appl Environ Microbiol ; 87(16): e0037321, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34085858

RESUMO

Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids, which are byproducts of sewage treatment processes, and biosolids-amended soil. Quantitative reverse transcription-PCR (RT-qPCR) was employed to assess responses of select antibiotic resistance genes (ARGs) and mobile elements to environmentally relevant concentrations of two biosolids-borne antibiotics, azithromycin (AZ) and ciprofloxacin (CIP). Additionally, we examined sequence distribution of gyrA (encoding DNA gyrase; site of action of CIP) to assess potential shifts in genotype. Increasing antibiotic concentrations generally increased the transcriptional activities of qnrS (encoding CIP resistance) and ermB and mefE (encoding AZ resistance). The transcriptional activity of intl1, a marker of class 1 integrons, was unaffected by CIP or AZ concentrations, but biosolids amendment increased intl1 activity in the soil by 4 to 5 times, which persisted throughout incubation. While the dominant gyrA sequences found herein were unrelated to known CIP-resistant genotypes, the increasing CIP concentrations significantly decreased the diversity of genes encoding the DNA gyrase A subunit, suggesting changes in microbial community structures. This study suggests that biosolids harbor transcriptionally active ARGs and mobile elements that could survive and spread in biosolids-amended soils. However, more research is warranted to investigate these trends under field conditions. IMPORTANCE Although previous studies have indicated that biosolids may be important spreaders of antibiotics and antibiotic resistance genes (ARGs) in environments, the potential activities of ARGs or their responses to environmental parameters have been understudied. This study highlights that certain biosolids-borne antibiotics can induce transcriptional activities of ARGs and mobile genetic elements in biosolids and biosolids-amended soil, even when present at environmentally relevant concentrations. Furthermore, these antibiotics can alter the structure of microbial populations expressing ARGs. Our findings indicate the bioavailability of the antibiotics in biosolids and provide evidence that biosolids can promote the activities and dissemination of ARGs and mobile genes in biosolids and soils that receive contaminated biosolids, thus, underscoring the importance of investigating anthropogenically induced antibiotic resistance in the environment under real-world scenarios.


Assuntos
Antibacterianos/farmacologia , Azitromicina/farmacologia , Bactérias/efeitos dos fármacos , Biossólidos/microbiologia , Ciprofloxacina/farmacologia , Farmacorresistência Bacteriana , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequências Repetitivas Dispersas/efeitos dos fármacos , Solo/química , Microbiologia do Solo , Poluentes do Solo/farmacologia
17.
Sci Rep ; 11(1): 13381, 2021 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-34183725

RESUMO

Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232-0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.


Assuntos
Elementos de DNA Transponíveis/genética , Éxons/genética , Sequências Repetitivas Dispersas/genética , Proteínas Associadas aos Microtúbulos/genética , Adolescente , Adulto , Estudos de Coortes , Simulação por Computador , Oftalmopatias Hereditárias/genética , Oftalmopatias Hereditárias/metabolismo , Proteínas do Olho/genética , Feminino , Frequência do Gene/genética , Genótipo , Heterozigoto , Humanos , Degeneração Macular/genética , Masculino , Mutação/genética , Linhagem , Fenótipo , Retina/metabolismo , Adulto Jovem
18.
J Antibiot (Tokyo) ; 74(8): 508-518, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34103703

RESUMO

Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, ß-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.


Assuntos
Bovinos/microbiologia , Farmacorresistência Bacteriana/genética , Metagenômica/métodos , Microbiota/genética , Ração Animal , Animais , Laticínios , Fezes/microbiologia , Humanos , Integrons/genética , Sequências Repetitivas Dispersas/genética , Carne , Microbiologia do Solo , Especificidade da Espécie
19.
J Antimicrob Chemother ; 76(8): 1991-2003, 2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34015100

RESUMO

OBJECTIVES: To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. METHODS: Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. RESULTS: Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm(B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm11/ST403 clone persisted throughout the period. Two lineages, emm9/ST75 with erm(B) and emm77/ST63 with erm(TR), emerged in 2016-18. The erm(B) was predominantly encoded on the Tn916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn6263, ICESpHKU372 and one harbouring an MDR cluster called ICESp1070HUB). The erm(TR) was found in ICESp2905 (8/17), ICESp1108-like (4/17), ICESpHKU165 (3/17) and two structures described in this study (IMESp316HUB and ICESp3729HUB). The M phenotype [mef(A)-msr(D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. CONCLUSIONS: We detected several different MGEs harbouring erm(B) or erm(TR). This is the first known description of Tn6263 in GAS and three MGEs [IMESp316HUB, ICESp3729HUB and ICESp1070HUB] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.


Assuntos
Infecções Estreptocócicas , Streptococcus pyogenes , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Humanos , Sequências Repetitivas Dispersas , Macrolídeos/farmacologia , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Espanha/epidemiologia , Infecções Estreptocócicas/epidemiologia , Streptococcus pyogenes/genética
20.
Food Chem Toxicol ; 153: 112277, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34004226

RESUMO

Streptococcus salivarius DB-B5 was previously isolated from the supragingival plaque of a healthy female adult and selected for development as a probiotic candidate for oral health. Probiotics are an important emerging therapeutic method for preventing, treating, and maintaining oral health. Although S. salivarius is a predominant member of the commensal oral microbiota and generally regarded as a safe species, it is recognized that each strain needs to be comprehensively assessed for safety. This study describes the in silico, in vitro, and clinical testing that were conducted to evaluate the safety of S. salivarius DB-B5. Both 16S rRNA and multi-gene phylogenetic reconstruction was used to confirm the taxonomic identity of this strain. Bioinformatic analysis of the genome demonstrated the absence of transmissible antibiotic resistance genes or virulence factors. Phenotypic testing further showed S. salivarius DB-B5 to be susceptible to clinically relevant antibiotics. S. salivarius DB-B5 displayed weak alpha-hemolysis, and does not produce biogenic amines. In a randomized, double-blind, placebo-controlled clinical study, consumption of S. salivarius DB-B5 at 10 billion CFU/day for 4 weeks by healthy adults was safe and well-tolerated (ClinicalTrials.gov registry number NCT04492631). This work has indicated that S. salivarius DB-B5 is a safe probiotic candidate.


Assuntos
Probióticos/toxicidade , Streptococcus salivarius/patogenicidade , Adolescente , Adulto , Idoso , Método Duplo-Cego , Farmacorresistência Bacteriana/genética , Feminino , Genes Bacterianos , Hemólise/fisiologia , Humanos , Sequências Repetitivas Dispersas , Masculino , Metaboloma , Pessoa de Meia-Idade , Saúde Bucal , Filogenia , Medição de Risco , Streptococcus salivarius/genética , Streptococcus salivarius/metabolismo , Fatores de Virulência/genética , Adulto Jovem
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