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1.
J Med Virol ; 94(1): 327-334, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34524690

RESUMO

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in COVID-19 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays that target SARS-CoV-2 followed by either massively parallel or nanopore sequencing is a widely-used strategy to obtain genome sequences from primary samples. However, multiplex PCR-based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. Here we developed a two-pool, long-amplicon 36-plex PCR primer panel with ~1000-bp amplicon lengths for full-genome sequencing of SARS-CoV-2. We validated the panel by assessing nasopharyngeal swab samples with a <30 quantitative reverse transcription PCR cycle threshold value and found that ≥90% of viral genomes could be covered with high sequencing depths (≥20% mean depth). In comparison, the widely-used ARTIC panel yielded 79%-88% high-depth genome regions. We estimated that ~5 Mbp nanopore sequencing data may ensure a >95% viral genome coverage with a ≥10-fold depth and may generate reliable genomes at consensus sequence levels. Nanopore sequencing yielded false-positive variations with frequencies of supporting reads <0.8, and the sequencing errors mostly occurred on the 5' or 3' ends of reads. Thus, nanopore sequencing could not elucidate intra-host viral diversity.


Assuntos
Genoma Viral/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Sequenciamento por Nanoporos/métodos , SARS-CoV-2/genética , Sequenciamento Completo do Genoma/métodos , COVID-19 , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Nasofaringe/virologia , RNA Viral/genética , Análise de Sequência de RNA/métodos
2.
Zootaxa ; 5060(1): 137-145, 2021 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-34811179

RESUMO

A new species of the soft-shelled turtle genus Pelodiscus is described based on seven specimens from Huangshan, southern Anhui Province, China. The new species, Pelodiscus huangshanensis sp. nov., is distinguished from other species in the genus Pelodiscus by the following characteristics: (1) Small size (maximum carapace length of 101.16 mm and maximum body length of 190 mm); (2) keel high; (3) tiny yellowish-white spots on the throat; (4) no black pinstripes around the eyes; (5) white longitudinal bands on both sides of the neck in juveniles, absent in adults; (6) plastron yellowish-white, and only a dark patch on each side of the armpit; (7) many tubercles on the dorsal surface, but indistinct in the center; and (8) entoplastron ⌒ shaped. The phylogenetic relationships of the species in Pelodiscus were reconstructed using the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) genes. The new species formed a monophyletic clade with strong support. The uncorrected pairwise distances between the new species and other representatives of Pelodiscus ranged from 5.4% to 9.2% for cyt b and 4.1% to 7.6% for ND4. The new species brings the number of species of the genus Pelodiscus to six; five species are distributed in China, with three species endemic to China.


Assuntos
Tartarugas , Animais , China , Filogenia
3.
Ann Palliat Med ; 10(10): 10600-10606, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34763507

RESUMO

BACKGROUND: Malnutrition is common and detrimental in cancer patients undergoing chemotherapy. There are close associations between olfactory dysfunction, depression, and malnutrition, but how they correlate in cancer patients undergoing chemotherapy remains unclear. METHODS: Two hundred and one cancer patients undergoing chemotherapy were recruited to this study. Their risk of malnutrition was assessed using the Simplified Nutritional Appetite Questionnaire (SNAQ); odor identification was assessed by Sniffin' Sticks test; self-measurement of olfaction was assessed by Self-reported Mini Olfactory Questionnaire (Self-MOQ); and depressive symptoms were assessed using the Beck Depression Inventory (BDI). Correlation analyses and mediation analyses were used to explore the relationships between olfaction, depression, and risk of malnutrition. RESULTS: The SNAQ score was negatively correlated with the Self-MOQ score and BDI score, and positively correlated with body mass index (BMI) scores and odor identification. The Self-MOQ score was negatively correlated with odor identification and positively correlated with BDI scores, and the duration of chemotherapy was negatively correlated with odor identification. Mediation analyses suggested that BDI scores exhibited a partial mediation effect on the relationship between Self-MOQ score and SNAQ scores. CONCLUSIONS: The influence of olfactory dysfunction on risk of malnutrition is mediated by depressive symptoms in cancer patients undergoing chemotherapy. Early intervention of olfactory dysfunction and depressive symptoms may be helpful in reducing the risk malnutrition in cancer patients undergoing chemotherapy.


Assuntos
Desnutrição , Neoplasias , Transtornos do Olfato , Depressão , Humanos , Desnutrição/etiologia , Neoplasias/complicações , Neoplasias/tratamento farmacológico , Transtornos do Olfato/induzido quimicamente , Olfato
4.
Risk Manag Healthc Policy ; 14: 4545-4552, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34785963

RESUMO

Objective: The purpose of this study was to establish and verify a risk-scoring system for colorectal adenoma recurrence. Methods: A total of 359 patients with colorectal adenoma who underwent polypectomy from October 2017 to December 2018 were included in this retrospective study. Information including taking traditional Chinese medicine, demographic characteristics, adenoma characteristics were collected. The patients will review the colonoscopy one year after surgery. The patients were divided into a modeling cohort (216 cases) and a model validation cohort (143 cases) according to the ratio of 6:4. Modeling and model verification were performed by logistic regression, ROC curve, nomogram (calibration chart) and other methods. Results: After adjusting for confounding factors by logistic regression, it was found that taking Chinese medicine, the number, size, site, pathological type and morphology of adenoma were independent influencing factors for the recurrence of colorectal adenoma. The area under the ROC curve (AUC) in the model validation cohort of established risk scoring system was 0.771 (95% CI: 0.694-0.847), indicating that there was good consistency. Conclusion: The established risk prediction model of colorectal adenoma recurrence and its risk scoring system performed well and had high predictive value.

5.
BMC Genomics ; 22(1): 406, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078288

RESUMO

BACKGROUND: Chlamydia psittaci is an avian pathogen that can cause lethal human infections. Diagnosis of C. psittaci pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic techniques. RESULTS: The MinION platform established the diagnosis in the shortest time, while BGISEQ-500 generated additional in-depth sequence data that included the rapid characterization of antibiotic susceptibility. Cytopathy appeared only in cell cultures of BALF. BALF yielded a higher bacterial load than sputum or blood, and may be the most suitable clinical specimen for the genomic diagnosis of severe pneumonia. CONCLUSIONS: This study indicated that the benefits of metagenomic sequencing include rapid etiologic diagnosis of unknown infections and the provision of additional relevant information regarding antibiotic susceptibility. The continued optimization and standardization of sampling and metagenomic analysis promise to enhance the clinical utility of genomic diagnosis.


Assuntos
Chlamydophila psittaci , Pneumonia , Psitacose , Animais , Chlamydophila psittaci/genética , Humanos , Metagenoma , Metagenômica , Psitacose/diagnóstico
6.
Int J Gen Med ; 14: 2079-2086, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34079348

RESUMO

Objective: We aimed to establish and evaluate a time series model for predicting the seasonality of acute upper gastrointestinal bleeding (UGIB). Methods: Patients with acute UGIB who were admitted to the Emergency Department and Gastrointestinal Endoscopy Center of Guangdong Provincial Hospital of Traditional Chinese Medicine from January 2013 to December 2019 were enrolled in the present study. The incidence trend of UGIB was analyzed by seasonal decomposition method. Then, exponential smoothing model and autoregressive integrated moving average model (ARIMA) were used to establish the model and forecast, respectively. Results: Finally, the exponential smoothing model with better fitting and prediction effect was selected. The smooth R2 was 0.586, and the Ljung-Box Q (18) statistic value was 22.272 (P = 0.135). The incidence of UGIB had an obvious seasonal trend, with a peak in annual January and a seasonal factor of 140%. After that, the volatility had gradually declined, with a trough in August and a seasonal factor of 67.8%. Since then, it had gradually increased. Conclusion: The prediction effect of exponential smoothing model is better, which can provide prevention and treatment strategies for UGIB, and provide objective guidance for more medical staff in Emergency Department and Gastrointestinal Endoscopy Center during the peak period of UGIB.

7.
Infect Genet Evol ; 93: 104939, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34029726

RESUMO

The rise in human adenovirus (HAdV) infections poses a serious challenge to public health in China. Real-time (RT) sequencing provides solutions for achieving rapid pathogen identification during outbreaks, whereas high-throughput sequencing yields higher sequence accuracy. In the present study, we report the outcomes of applying nanopore and BGI platforms in the identification and genomic analysis of an HAdV outbreak in Hubei province, China in May of 2019. A mixed sample of nine nasopharyngeal swabs and one single sample were submitted to direct nanopore sequencing (MinION device), generating their first HAdV-55 reads within 13 and 20 min, respectively. The sequences were confirmed by RT-polymerase chain reaction (PCR). Ten HAdV-positive samples were further sequenced using next-generation high-throughput sequencing (BGISEQ-500 device). Phylogenetic analysis revealed that the outbreak strain had a close genetic relation to strains isolated in Sichuan province. Metagenomic analysis showed that HAdV-55 was not a dominant species in samples from which the whole HAdV-55 genome could not be assembled. The present results highlight the value of combining sequencing platforms and using mixed samples for nucleic acid enrichment in pathogen detection of infectious disease outbreaks.

8.
Int J Legal Med ; 135(5): 1685-1693, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33950286

RESUMO

The MinION nanopore sequencing device (Oxford Nanopore Technologies, Oxford, UK) is the smallest commercially available sequencer and can be used outside of conventional laboratories. The use of the MinION for forensic applications, however, is hindered by the high error rate of nanopore sequencing. One approach to solving this problem is to identify forensic genetic markers that can consistently be typed correctly based on nanopore sequencing. In this pilot study, we explored the use of nanopore sequencing for single nucleotide polymorphism (SNP) and short tandem repeat (STR) profiling using Verogen's (San Diego, CA, USA) ForenSeq DNA Signature Prep Kit. Thirty single-contributor samples and DNA standard material 2800 M were genotyped using the Illumina (San Diego, CA, USA) MiSeq FGx and MinION (with R9.4.1 flow cells) devices. With an optimized cutoff for allelic imbalance, all 94 identity-informative SNP loci could be genotyped reliably using the MinION device, with an overall accuracy of 99.958% (1 error among 2926 genotypes). STR typing was notably error prone, and its accuracy was locus dependent. We developed a custom-made bioinformatics workflow, and finally selected 13 autosomal STRs, 14 Y-STRs, and 4 X-STRs showing high consistency between nanopore and Illumina sequencing among the tested samples. These SNP and STR loci could be candidates for panel design for forensic analysis based on nanopore sequencing.


Assuntos
Técnicas de Genotipagem , Repetições de Microssatélites , Sequenciamento por Nanoporos/métodos , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA/métodos , Marcadores Genéticos , Humanos , Projetos Piloto
9.
mSphere ; 6(2)2021 04 14.
Artigo em Inglês | MEDLINE | ID: mdl-33853876

RESUMO

Antimicrobial resistance associated with colistin has emerged as a significant concern worldwide, threatening the use of one of the most important antimicrobials for treating human disease. This study aimed to investigate the prevalence of colistin-resistant avian-pathogenic Escherichia coli (APEC) and shed light on the possibility of transmission of mcr-1 (mobilized colistin resistance)-positive APEC. A total of 72 APEC isolates from Anhui Province in China were collected between March 2017 and December 2018 and screened for the mcr-1 gene. Antimicrobial susceptibility testing was performed using the broth dilution method. Pulsed-field gel electrophoresis, Southern blot analysis, and conjugation assay were performed to determine the location and conjugative ability of the mcr-1 gene. Whole-genome sequencing and analysis were performed using Illumina MiSeq and Nanopore MinION platforms. Three APEC isolates (AH25, AH62, and AH65) were found to be positive for the mcr-1 gene and showed multidrug resistance. The mcr-1 genes were located on IncI2 plasmids, and conjugation assays revealed that these plasmids were transferrable. Notably, strains AH62 and AH65, both belonging to ST1788, were collected from different places but carried the same drug resistance genes and shared highly similar plasmids. This study highlights the potential for a possible epidemic of mcr-1-positive APEC and the urgent need for continuous active monitoring.IMPORTANCE In this study, three plasmids carrying mcr-1 were isolated and characterized from APEC isolates from Anhui Province in China. The mcr-1 genes were located on IncI2 plasmids, and these plasmids were transferrable. These three IncI2 plasmids had high homology with the plasmids harbored by pathogenic bacteria isolated from other species. This finding showed that IncI2 plasmids poses a risk for the exchange of genetic material between different niches. Although colistin has been banned for use in food-producing animals in China, the coexistence of the broad-spectrum ß-lactamase and mcr-1 genes on a plasmid can also lead to the stable existence of mcr-1 genes. The findings illustrated the need to improve the monitoring of drug resistance in poultry systems so as to curb the transmission or persistence of multidrug-resistant bacteria.


Assuntos
Galinhas/microbiologia , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/veterinária , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Escherichia coli/patogenicidade , Animais , Antibacterianos/farmacologia , China , Escherichia coli/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Plasmídeos/genética , Sequenciamento Completo do Genoma
10.
Infect Drug Resist ; 14: 947-952, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33727835

RESUMO

Background: The emergence of multidrug-resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the bla NDM-1 and bla SHV-12 genes. Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of bla NDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the bla NDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain. Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of bla NDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that bla NDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10-3. Both the bla NDM-1 and bla SHV-12 genes were located on the self-transferable IncX3 plasmid. Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

11.
Microb Drug Resist ; 27(5): 706-709, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33090069

RESUMO

New Delhi-Metallo-1-producing (NDM-1-producing) Enterobacter cloacae is one of the highly resistant pathogens affecting the intensive care unit. A previous study reported that ST418 was the main epidemic type of NDM-1-producing E. cloacae in Shenzhen, China. However, few NDM-1-producing carbapenem-resistant Enterobacter cloacae ST418 strains have been described. In this study, we collected and characterized an NDM-1-producing carbapenem-resistant E. cloacae strain, E70, from a patient in Guangzhou. E70 was resistant to multiple antibiotics, including imipenem and meropenem. S1-Pulsed field gel electrophoresis and southern blotting showed that E70 harbored four plasmids and that the blaNDM-1 gene was located on an ∼50 kb plasmid. Conjugation experiments revealed that the two smaller plasmids were transferable and that transconjugants obtaining one or both plasmids acquired different antimicrobial resistances. Whole-genome sequencing and analysis revealed that E70 belonged to ST418. The blaNDM-1 and blaSHV-12 genes coexisted on the 53.7 kb IncX3 plasmid pE70-NDM1, whereas the blaCTX-M-3 and blaTEM-1 genes were located on another untyped 26.0 kb plasmid, pE70-TEM1. The blaNDM-1 plasmids in Enterobacter cloacae ST418 may serve as an important vehicle in the dissemination of NDM, and the coexistence of transferable plasmids increases the possibility of rapid horizontal spread of multidrug resistance genes. Long-term monitoring and detailed study are necessary for the prevention of blaNDM-1-carrying E. cloacae infection.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Enterobacter cloacae/efeitos dos fármacos , Enterobacter cloacae/genética , beta-Lactamases/genética , China , Eletroforese em Gel de Campo Pulsado , Enterobacter cloacae/enzimologia , Genes Bacterianos/genética , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus
12.
Infect Drug Resist ; 13: 3929-3935, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33173318

RESUMO

Background: A carbapenem-resistant Escherichia coli (sequence type 5415) strain was isolated from a male patient through routine surveillance in 2018 in Guangzhou, China. Materials and Methods: Bacteria were isolated from a sputum culture and identified by using the Vitek 2 compact system. The blaNDM-5 gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was determined by a Vitek 2 compact system. The blaNDM-5 gene was located by Southern blotting. Whole-genome sequencing was carried out using both Illumina MiSeq and Oxford Nanopore MinION. Results: S1-PFGE and Southern blotting showed that the bla NDM-5 gene was located on a novel 66-kb IncFII [F2:A-:B-] plasmid. Conjugation assays revealed that the bla NDM-5-bearing plasmid was self-transferrable. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the bla NDM-5 flanking genetic elements. Conclusion: This is the first report of an ST5414 E. coli strain expressing an NDM-5 ß-lactamase. This study highlights the genetic complexity of bla NDM-5 carrying plasmids and the urgent need for continuous active monitoring.

13.
Front Microbiol ; 11: 525479, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33042048

RESUMO

Background: Enterobacter cloacae is an opportunistic pathogen which is responsible for serious nosocomial infections. A gene which plays an important role in resistance to carbapenems is the New Delhi metallo-ß-lactamase 1 (NDM-1). Currently, the spread of NDM-1-producing E. cloacae strains is a serious public threat. Methods: A multidrug-resistant E. cloacae ssp. dissolvens strain CBG15936 was recovered in 2017 in Guangzhou, China. PCR, S1-pulsed-field gel electrophoresis, and Southern blotting were performed to locate the bla NDM - 1 gene. Susceptibility testing and conjugation experiments were also performed. Illumina HiSeq and Nanopore sequencers were used to perform whole-genome sequencing. Results: Strain CBG15936 belongs to ST932 and is resistant to carbapenems. The bla NDM- 1 gene was found on a ∼62-kb plasmid, which has a conjugation frequency of 1.68 × 10-3 events per donor cell. Genome sequencing and analysis revealed that the NDM-1-carrying IncN1 plasmid contained a new transposon Tn6696, which consists of an intact qnrS1-carrying Tn6292 element, an inverted 8.3-kb Tn3000 remnant, ISkpn19, ΔtnpA, and IS26. Conclusion: A new transposon, Tn6696, has been detected on a bla NDM- 1-carrying plasmid recovered from multidrug-resistant E. cloacae ssp. dissolvens CBG15936 from China. This finding provides a new perspective regarding the potential for bla NDM- 1 to undergo horizontal transfer among drug-resistant bacteria.

14.
J Glob Antimicrob Resist ; 23: 64-66, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32818668

RESUMO

OBJECTIVES: The aim of this study was to characterise a multidrug-resistant (MDR) Citrobacter freundii strain carrying a blaNDM-1-harbouring conjugative IncA/C2-type plasmid in China. METHODS: The whole genome of C. freundii strain L75 was sequenced both on HiSeq® (Novogene Corp., China) and GridION X5 (GrandOmics Biosciences Co., Ltd.) platforms. De novo genome assembly, genome annotation, multilocus sequence typing (MLST) and plasmid replicon typing were performed. RESULTS: Citrobacter freundii L75 was assigned to ST396 and contains a 5.1-Mb chromosome and two plasmids (∼146 kb and ∼73 kb) designated pCf75 and pCf76, respectively. The antibiotic resistance determinants blaNDM-1, sul1, sul2, arr-3, mph(A), aadA16, aph(3")-Ib, aac(3)-IId, aph(6)-Id, aac(6')-Ib-cr and dfrA27 were located on plasmid pCf75, whilst blaCMY-78 was chromosomally encoded. A 22.1-kb MDR-encoding region (MDRR) in a complex class 1 integron contained all of the resistance genes of plasmid pCf75. CONCLUSIONS: We detected and characterised a plasmid carrying a novel MDRR in which a complex class 1 integron plays an essential role. In addition, this study provides fresh genomic insights into the diversity of C. freundii ST396 prevalent in Guangzhou Province, China, and underscores the increasing clinical relevance of the IncA/C2 plasmid family.


Assuntos
Citrobacter freundii , Infecções por Enterobacteriaceae , China , Citrobacter freundii/genética , Humanos , Integrons , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , beta-Lactamases
15.
Infect Genet Evol ; 85: 104499, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32791239

RESUMO

The emergence of Escherichia coli strains coharboring the blaNDM and mcr genes has become a new challenge in clinical therapy because of their resistance to most antibiotics. This study reports the emergence of an E. coli strain GZEC065 isolated from blood sample of a patient in China with both chromosome-located mcr-1 and plasmid-mediated blaNDM-5 genes. Antimicrobial susceptibility testing showed that GZEC065 was resistant to most tested antimicrobials, including imipenem and polymyxin B. S1-nuclease-pulsed-field gel electrophoresis, Southern blotting analysis and conjugation assay was performed to determine the location and conjugative ability of mcr-1 and blaNDM-5 genes. Whole genome sequencing and analysis showed that GZEC065 belonged to sequence type ST156 and contained three different plasmids (46 kb, 88 kb and 142 kb) with multiple resistance genes, such as mcr-1, blaNDM-5 and blaTEM-1. The blaNDM-5 gene was carried by the 46 kb conjugative IncX3 plasmid, which has been reported frequently in China. The mcr-1 gene was located on the chromosome mediated by the Tn6330 mobile element and showed genetic complexity among different strains. The emergence of E. coli strains coharboring both chromosome-located mcr-1 and plasmid-mediated blaNDM-5 genes highlights the urgent need for alternative antibiotic treatment and continuous active surveillance.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Genes Bacterianos , Plasmídeos/genética , China/epidemiologia , Infecções por Escherichia coli/epidemiologia , Variação Genética , Genômica , Genótipo , Humanos , Análise de Sequência
16.
mSphere ; 5(4)2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669464

RESUMO

Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission.IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.


Assuntos
Disenteria Bacilar/epidemiologia , Genoma Bacteriano , Filogenia , Shigella flexneri/classificação , Antibacterianos/farmacologia , Pequim/epidemiologia , DNA Bacteriano/genética , Farmacorresistência Bacteriana Múltipla/genética , Disenteria Bacilar/microbiologia , Epidemias , Evolução Molecular , Humanos , Testes de Sensibilidade Microbiana , Sorogrupo , Shigella flexneri/efeitos dos fármacos , Sequenciamento Completo do Genoma
17.
Artigo em Inglês | MEDLINE | ID: mdl-32432051

RESUMO

Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified Klebsiella pneumoniae by an 823 bp specific sequence within 1 min. Genomic analysis further identified bla SHV-12, bla KPC-2, bla TEM-1, bla CTX-M-65, and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.


Assuntos
Nanoporos , Pneumonia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Klebsiella pneumoniae/genética , Metagenoma , Metagenômica , Pneumonia/diagnóstico , beta-Lactamases/genética
18.
Infect Drug Resist ; 13: 1105-1110, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32368101

RESUMO

Background: The New Delhi metallo-ß-lactamase-1 (NDM-1)-positive plasmid and its variants pose daunting threats to public health. Hospital sewage was considered as an important reservoir of antibiotic genes. Numerous and diverse taxa of multidrug-resistant (MDR) bacteria carrying NDM-1-positive plasmids have been identified during routine surveillance of hospital sewage. We herein report a carbapenem-resistant Acinetobacter towneri strain AeBJ009 with an NDM-1-positive plasmid isolated from hospital sewage. Materials and Methods: Bacteria were isolated from cultures of hospital sewage and identified by using the Vitek 2 compact system and 16S rRNA sequencing. The bla NDM-1 gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was performed using AST-GN14 on the Vitek2 compact system. In addition, the bla NDM-1 gene was located by Southern blotting. Conjugation experiment and whole-genome sequencing were performed for further analysis. Results: Strain AeBJ009 was isolated from hospital sewage and identified as A. towneri. Antimicrobial susceptibility testing revealed an MDR phenotype. Pulsed-field gel electrophoresis and Southern blotting showed that strain AeBJ009 carries three plasmids and that bla NDM-1 is located on the 47kb plasmid pNDM-AeBJ009. However, the conjugation experiment to transfer pNDM-AeBJ009 to Escherichia coli strain J53 was unsuccessful. Whole-genome sequencing found that pNDM-AeBJ009 contains a Tn125 element carrying bla NDM-1 . The ble gene downstream of bla NDM-1 displayed a single-nucleotide polymorphism compared to its homologue on plasmid pM131_NDM1. BLAST analysis using the Comprehensive Antibiotic Resistance Database identified no gene polymorphisms with 100% identity to our ble variant. Conclusion: The A. towneri strain AeBJ009 exhibiting an extended spectrum of antibiotic resistance was isolated from hospital sewage and may potentially exacerbate the risk of MDR bacterial infections. The prevention of nosocomial infections due to drug-resistant bacteria will require enhanced monitoring and control of MDR pathogens in environmental reservoirs.

19.
Ann Clin Lab Sci ; 50(2): 219-227, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32366560

RESUMO

OBJECTIVE: MicroRNAs (miRNAs) are associated with hepatocellular carcinoma (HCC) progression and metastasis. However, it is unclear whether they could act as biomarkers for HCC diagnosis and prognosis. METHODS: In this study, the miR-122 and miR-199a expression levels were determined by quantitative real-time PCR (qRT-PCR). The function and molecular mechanism of miR-122 and miR-199a target genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Correlation between miRNA expression levels and the overall survival (OS) of HCC patients was assessed by Kaplan-Meier analysis. RESULTS: Serum miR-122 expression had no significant difference between patients with HCC (HCC patients) and healthy controls (HCs), whereas serum miR-199a expression was significantly lower in HCC patients than the HCs (p<0.05). Receiver-operator characteristic (ROC) curve analysis revealed that miR-199a could be an effective diagnostic biomarker for HCC, which was confirmed by obvious expression polarization patterns of miR-199a target genes. Kaplan-Meier analysis revealed that miR-122 expression level was associated with the OS of HCC patients (p<0.001), suggesting that miR-122 could be a prognostic biomarker for HCC. CONCLUSIONS: Collectively, our results showed that circulating miR-199a and miR-122 levels could serve as novel, non-invasive biomarkers for HCC diagnosis and prognosis, respectively.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma Hepatocelular/patologia , MicroRNA Circulante/sangue , Regulação Neoplásica da Expressão Gênica , Neoplasias Hepáticas/patologia , MicroRNAs/genética , Biomarcadores Tumorais/sangue , Carcinoma Hepatocelular/sangue , Carcinoma Hepatocelular/genética , Estudos de Casos e Controles , MicroRNA Circulante/genética , Feminino , Seguimentos , Humanos , Neoplasias Hepáticas/sangue , Neoplasias Hepáticas/genética , Masculino , MicroRNAs/sangue , Pessoa de Meia-Idade , Prognóstico , Taxa de Sobrevida
20.
Front Genet ; 11: 285, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32318094

RESUMO

Human adenoviruses (HAdVs) have been demonstrated to cause a diversity of diseases among children and adults. The circulation of human adenovirus type 21 (HAdV21) has been mainly documented within closed environments in several countries. Nonetheless, respiratory infections or outbreaks due to HAdV21 have never been reported in China. MinION and Illumina platforms were employed to identify the potential pathogen from a throat swab. Discrepancies between MinION and Illumina sequencing were validated and corrected via polymerase chain reaction (PCR). Genomic characterization and recombinant event detection were then performed. Among the 35,466 high-quality MinION reads, a total of 5,999 reads (16.91%) could be aligned to HAdV21 reference genomes (genome sizes ≈35.3 kb), among which 20 had a length of >30 kb. A genome sequence assembled from MinION reads was further classified as HAdV subtype 21a. Random downsampling revealed as few as 500 nanopore reads could cover ≥96.49% of current genome. Illumina sequencing displayed good consistency (pairwise nucleotide identity = 99.91%) with MinION sequencing but with 31 discrepancies that were further validated and confirmed by PCR coupled with Sanger sequencing. Restriction enzymes such as BamHI and KpnI were able to distinguish the present genome from HAdV21 prototype and HAdV21b. Phylogenetic analysis employing whole-genome sequences placed our genome with members only from subtype 21a. Common features among HAdV21a strains were identified, including polymorphisms discovered in penton and 100 kDa hexon assembly-associated proteins and a recombinant event in the E4 gene. Using MinION and Illumina sequencers, we identified the first HAdV21a strain from China, which could provide key genomic data for disease control and epidemiological investigations.

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