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1.
J Vet Med Sci ; 83(10): 1545-1548, 2021 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-34526416

RESUMO

Rhodotorula mucilaginosa are saprophytic yeast, and opportunistic infections known as human rhodotorulosis are increasing in immunocompromised patients. In this study, we isolated R. mucilaginosa from pet dogs in Japan and determined the minimum inhibitory concentrations (MICs) of antifungal drugs on these isolates to investigate the drug susceptibility pattern. All 10 isolates according to the broth microdilution (BM) assay of the Clinical and Laboratory Standards Institute (CLSI) M27-A2 were resistance to azoles and genetically close to fluconazole (FLZ)-resistant human isolates of R. mucilaginosa. Due to resistance, it is expected that treatment will be difficult if they infect humans.


Assuntos
Antifúngicos , Preparações Farmacêuticas , Animais , Antifúngicos/farmacologia , Cães , Meato Acústico Externo , Tipagem Molecular/veterinária , Rhodotorula
2.
Fungal Biol ; 125(9): 733-747, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34420700

RESUMO

Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.


Assuntos
Ascomicetos , Oryza , Ascomicetos/genética , Ascomicetos/patogenicidade , Genoma Fúngico/genética , Tipagem Molecular , Oryza/microbiologia , Doenças das Plantas/microbiologia , Virulência/genética
3.
BMC Infect Dis ; 21(1): 748, 2021 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-34344310

RESUMO

BACKGROUND: Human Adenoviruses (HAdVs) cause a wide array of illnesses in all age groups. They particularly cause frequent morbidity among children. In China, human adenovirus types 3, 4, 7, 11, 14, 21, and 55 have caused at least seven outbreaks since 2000. However, limited studies are available regarding the epidemiological patterns and diversity of HAdVs types among hospitalized patients with respiratory tract infections (RTIs). METHODS: To understand the epidemiology and subtype distribution of HAdV infections associated with RTIs in China, nasal swab (NS) clinical samples were collected from 4129 patients in a Guangzhou hospital between August 2017 and October 2019. PCR, sequencing, and phylogenetic analysis were performed on these specimens to identify HAdV subtypes. RESULTS: HAdV was successfully sequenced in 99 (2.4%) of the 4129 NS specimens, with the highest HAdV prevalence (6.3%) found in children between the ages of 5 and 10 years. Among HAdV-positive specimens, the most prevalent genotypes identified were HAdV-B3 (55.6%) and HAdV-B7 (25.3%). The most common symptoms in the HAdV-infected patients were fever (100%), cough (80.8%), and rhinorrhea (71.8%). HAdV infections were detected throughout the year with a relatively higher prevalence in summer. CONCLUSION: All ages suffer adenovirus infections, but young children are at the greatest risk. This study data demonstrates that at least three species of HAdVs (species B, C, and E) are circulating in Guangzhou City, China. As antiviral therapies and type-specific vaccines become available, such epidemiological data will be useful in guiding therapy and public health interventions.


Assuntos
Infecções por Adenovirus Humanos , Adenovírus Humanos , Infecções Respiratórias , Infecções por Adenovirus Humanos/epidemiologia , Adenovírus Humanos/genética , Criança , Pré-Escolar , China/epidemiologia , Humanos , Lactente , Tipagem Molecular , Filogenia , Infecções Respiratórias/epidemiologia , Análise de Sequência de DNA , Centros de Atenção Terciária
4.
Trop Anim Health Prod ; 53(4): 412, 2021 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-34308515

RESUMO

Recently, inclusion body hepatitis (IBH) outbreaks have been increasingly reported in different regions of India, particularly in broiler flocks. The present study was undertaken to characterize fowl adenovirus associated with IBH in chicken and assessment of its pathogenicity. Liver samples were collected from fowl adenovirus (FAdV) suspected 100 commercial broiler and six broiler breeder flocks from eleven different States of India from 2016 to 2019. All the samples were subjected to 897-bp FAdV hexon gene-specific PCR for confirmation and primary chicken liver cells were used to isolate the field FAdVs. Sequencing and phylogenetic analysis of 897-bp FAdV hexon gene revealed that all the isolates have showed close evolutionary relationship with fowl adenovirus serotype 11 of species D. For pathogenicity assessment, 0.5 ml of 106.5 TCID50/ml of field FAdV serotype 11 isolate was orally inoculated in 1-day-old SPF chicks and observed for 21 days. This experimental study revealed that there was no mortality in infected chicks and showed clinical signs of dullness, depression and diarrhoea between third and fifth day of oral inoculation. The FAdV was reisolated and confirmed by PCR from experimentally infected chicken. Based on this study, among all serotypes, FAdV serotype 11 is involved in pathogenesis of inclusion body hepatitis in broiler-type chickens in India.


Assuntos
Infecções por Adenoviridae , Aviadenovirus , Hepatite , Doenças das Aves Domésticas , Infecções por Adenoviridae/epidemiologia , Infecções por Adenoviridae/veterinária , Animais , Aviadenovirus/genética , Galinhas , Corpos de Inclusão , Índia/epidemiologia , Tipagem Molecular/veterinária , Filogenia , Doenças das Aves Domésticas/epidemiologia , Virulência
5.
Nat Commun ; 12(1): 4188, 2021 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-34234121

RESUMO

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


Assuntos
Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Tipagem Molecular/métodos , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Conjuntos de Dados como Assunto , Farmacorresistência Bacteriana Múltipla/genética , Monitoramento Epidemiológico , Microbioma Gastrointestinal/genética , Genoma Bacteriano , Humanos , Lactente , Recém-Nascido , Infecções por Klebsiella/diagnóstico , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/patogenicidade , Metagenoma/genética , Epidemiologia Molecular/métodos , Mutação , Filogenia , Software , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma , beta-Lactamases/genética
6.
Arch Virol ; 166(8): 2225-2234, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34091782

RESUMO

In order to discover the causes of a coxsackievirus B4 (CV-B4)-associated hand, foot, and mouth disease (HFMD) outbreak and to study the evolutionary characteristics of the virus, we sequenced isolates obtained during an outbreak for comparative analysis with previously sequenced strains. Phylogenetic and evolutionary dynamics analysis was performed to examine the genetic characteristics of CV-B4 in China and worldwide. Phylogenetic analysis showed that CV-B4 originated from a common ancestor in Shandong. CV-B4 strains isolated worldwide could be classified into genotypes A-E based on the sequence of the VP1 region. All CV-B4 strains in China belonged to genotype E. The global population diversity of CV-B4 fluctuated substantially over time, and CV-B4 isolated in China accounted for a significant increase in the diversity of CV-B4. The average nucleotide substitution rate in VP1 of Chinese CV-B4 (5.20 × 10-3 substitutions/site/year) was slightly higher than that of global CV-B4 (4.82 × 10-3 substitutions/site/year). This study is the first to investigate the evolutionary dynamics of CV-B4 and its association with an HFMD outbreak. These findings explain both the 2011 outbreak and the global increase in CV-B4 diversity. In addition to improving our understanding of a major outbreak, these findings provide a basis for the development of surveillance strategies.


Assuntos
Proteínas do Capsídeo/genética , Enterovirus Humano B/classificação , Doença de Mão, Pé e Boca/virologia , Polimorfismo de Nucleotídeo Único , China , Enterovirus Humano B/genética , Enterovirus Humano B/isolamento & purificação , Evolução Molecular , Humanos , Tipagem Molecular , Taxa de Mutação , Filogenia , Análise de Sequência de RNA
7.
BMC Infect Dis ; 21(1): 559, 2021 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-34118893

RESUMO

BACKGROUND: Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are significant public health concerns globally. Nearly no gonococcal AMR data are available from Central Asia, and no data from Kyrgyzstan has been published. We examined, for the first time, AMR and molecular epidemiology of N. gonorrhoeae isolates cultured in Kyrgyzstan in 2012 and 2017, in order to inform refinements of the Kyrgyz national gonorrhoea management guidelines. METHODS: N. gonorrhoeae isolates cultured in 2012 (n = 84) and 2017 (n = 72) in Kyrgyzstan were examined. MICs of nine antimicrobials were determined using Etest and, where available, clinical breakpoints from the EUCAST were applied. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was also performed. RESULTS: The overall resistance levels were high to ciprofloxacin (88.5%), tetracycline (56.9%), benzylpenicillin (39.1%), and kanamycin (4.7%). Resistance to cefixime (0.6%, n = 1 isolate), azithromycin (0.6%, n = 1), and gentamicin (0.6%, n = 1) was rare. No resistance to ceftriaxone or spectinomycin was found. However, the proportion of isolates with decreased susceptibility (MIC = 0.125 mg/L) to ceftriaxone and cefixime was 12.8 and 11.5%, respectively. Gonococcal isolates were assigned 69 sequence types, of which 52 (75.4%) were new. CONCLUSIONS: The gonococcal population in Kyrgyzstan in 2012 and 2017 showed a high genetic diversity. Ceftriaxone, 500-1000 mg, in combination with azithromycin 2 g or doxycycline, particularly when chlamydial infection has not been excluded, should be recommended as empiric first-line treatment. Spectinomycin 2 g could be an alternative treatment, and given with azithromycin 2 g if pharyngeal gonorrhoea has not been excluded. Fluoroquinolones, aminoglycosides, benzylpenicillin, or tetracyclines should not be used for empiric treatment of gonorrhoea in Kyrgyzstan. Timely updating and high compliance to national gonorrhoea treatment guidelines based on quality-assured AMR data is imperative. Expanded and improved gonococcal AMR surveillance in Kyrgyzstan is crucial.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Gonorreia/microbiologia , Neisseria gonorrhoeae , Humanos , Quirguistão , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem Molecular , Neisseria gonorrhoeae/classificação , Neisseria gonorrhoeae/efeitos dos fármacos , Neisseria gonorrhoeae/genética
8.
World J Microbiol Biotechnol ; 37(6): 95, 2021 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-33963452

RESUMO

Huanglongbing (HLB), also known as 'citrus greening', is an extremely destructive disease of citrus worldwide. HLB is associated with three species of the fastidious proteobacterium, Candidatus Liberibacter asiaticus (CaLas), Ca. L. africanus and Ca. L. americanus with CaLas being the most widely distributed around the world and the only species detected and described so far in India, one of the major global citrus fruit producers. Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. Three types of prophages, Type 1, Type 2 and Type 3 have been identified and described in CaLas so far. In the present study, 441 CaLas isolates sampled across 18 Indian states were used for prophage typing. Based on detection of three prophage types by PCR, all the eight probable combinations of CaLas prophages were identified, including single Type 1 (26.5%), single Type 2 (18.8%), single Type 3 (1.4%), Type 1 + Type 2 (20.4%), Type 1 + Type 3 (12.5%), Type 2 + Type 3 (4.8%), Type 1 + Type 2 + Type 3 (11.3%) and None type (4.3%). Prophage types were confirmed by PCR amplicon sequencing and subsequent phylogenetic analysis. By discovery of all 3 prophages and based on genetic identity and genetic distance, CaLas populations from eighteen citrus growing states were separated into two major Prophage Typing Groups (PTGs): PTG1 and PTG2. The PTG1 comprised of CaLas from North-West India and PTG2 from rest of the country (North-East, Central and South India), and both major groups were further divided into two (PTG1-A, PTG1-B) and three (PTG2-A, PTG2-B and PTG2-C) subgroups respectively. The findings of CaLas population patterns provide evidence for independent origins of HLB-associated CaLas. CRISPR (clustered regularly interspaced short palindromic repeats) array was also detected in CaLas isolates. This is the first report evaluating the genetic variation of a large population of CaLas bacterium in India using the PCR markers from the prophage regions which would certainly assist the ongoing HLB management efforts in India.


Assuntos
Citrus/microbiologia , Liberibacter/classificação , Prófagos/genética , Análise de Sequência de DNA/métodos , Sistemas CRISPR-Cas , DNA Viral/genética , Variação Genética , Índia , Liberibacter/isolamento & purificação , Liberibacter/virologia , Tipagem Molecular , Filogenia , Doenças das Plantas/microbiologia , Prófagos/classificação
9.
Emerg Infect Dis ; 27(6): 1745-1748, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34013856

RESUMO

We collected 10 Burkholderia mallei isolates from equids in 9 districts in India during glanders outbreaks in 2013-2016. Multilocus variable-number tandem-repeat analysis showed 7 outbreak area-related genotypes. The study highlights the utility of this analysis for epidemiologically tracing of specific B. mallei isolates during outbreaks.


Assuntos
Burkholderia mallei , Mormo , Animais , Burkholderia mallei/genética , Cavalos , Índia , Repetições Minissatélites , Tipagem Molecular
10.
Nat Commun ; 12(1): 2619, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33976183

RESUMO

After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017-2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate dengue dynamics in recent years in Brazil. First, we estimate dengue virus force of infection (FOI) and model mosquito-borne transmission suitability since the early 2000s. Our estimates reveal that DENV transmission was low in 2017-2018, despite conditions being suitable for viral spread. Our study also shows a marked decline in dengue susceptibility between 2002 and 2019, which could explain the synchronous decline of dengue in the country, partially as a result of protective immunity from prior ZIKV and/or DENV infections. Furthermore, we performed phylogeographic analyses using 69 newly sequenced genomes of dengue virus serotype 1 and 2 from Brazil, and found that the outbreaks in 2018-2019 were caused by local DENV lineages that persisted for 5-10 years, circulating cryptically before and after the Zika epidemic. We hypothesize that DENV lineages may circulate at low transmission levels for many years, until local conditions are suitable for higher transmission, when they cause major outbreaks.


Assuntos
Vírus da Dengue/imunologia , Dengue/epidemiologia , Suscetibilidade a Doenças/imunologia , Epidemias/estatística & dados numéricos , Infecção por Zika virus/imunologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Anticorpos Antivirais/imunologia , Brasil/epidemiologia , Criança , Pré-Escolar , Dengue/imunologia , Dengue/transmissão , Dengue/virologia , Vírus da Dengue/genética , Vírus da Dengue/isolamento & purificação , Epidemias/prevenção & controle , Monitoramento Epidemiológico , Feminino , Genoma Viral/genética , Humanos , Imunidade Heteróloga , Incidência , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Tipagem Molecular , Mosquitos Vetores/virologia , Filogeografia , Sorotipagem , Adulto Jovem , Zika virus/imunologia , Infecção por Zika virus/epidemiologia
11.
J Med Microbiol ; 70(5)2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33999798

RESUMO

Introduction. New Delhi metallo-ß-lactamase (NDM)-producing Klebsiella pneumoniae has become a serious global health concern.Hypothesis/Gap Statement. Due to the high genetic diversity among NDM-positive K. pneumoniae, we need further surveillance and studies to better understand the relationships between them. In addition, the coexistence of several plasmid replicon types in NDM-positive K. pneumoniae may affect the copy number of bla NDM, the MIC level to antibiotics, as well as increasing the chance of horizontal gene transfer.Aim. The aim of this study was to determine incompatible plasmid groups and copy numbers of bla NDM, and to investigate the genetic relationship of 37 NDM-positive K. pneumoniae in Kerman, Iran.Methodology. The bla NDM-1 gene was detected and confirmed by PCR-sequencing. The plasmid replicon types were determined by PCR-based replicon typing (PBRT) and the copy number of bla NDM-1 was determined by quantitaive real time-PCR (qPCR). Random amplified polymorphic DNA (RAPD)-PCR typing was used to detect genetic relationships between the strains.Results. In this study, 10 different replicon types, including Frep [n=25 (67.5 %)], FIIAs [n=11 (29.7 %)], FIA [n=5 (13.5 %)], FIB [n=3 (8.1 %)], I1-Iγ [n=2 (5.4 %)], L/M [n=7 (18.9 %)], A/C [n=7 (18.9 %)], Y [n=3 (8.1 %)], P [n=1 (2.7 %)] and FIC [n=1 (2.7 %)] were reported. The copy numbers of the bla NDM-1 gene varied from 30.00 to 5.0×106 and no statistically significant correlation was observed between a rise of the MIC to imipenem and the copy numbers of bla NDM-1 (P>0.05). According to RAPD typing results, 35 strains were divided into five clusters, while two strains were non-typeable.Conclusion. The spread of NDM-1-producing K. pneumoniae strains that carry several plasmid replicon types increases the chance of horizontal transfer of antibiotic resistance genes in hospital settings. In this study, 10 different replicon types were identified. We could not find any relationship between the increase of MIC levels to imipenem and the copy numbers of bla NDM-1. Therefore, due to the identification of different replicon types in this study, the type and genetic characteristics of bla NDM-1-carrying plasmids, and other factors such as antibiotic selective pressure, probably affect the copy number of bla NDM-1 and change the MIC level to imipenem.


Assuntos
Antibacterianos/farmacologia , Carbapenêmicos/farmacologia , Dosagem de Genes , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Plasmídeos , beta-Lactamases/genética , Humanos , Irã (Geográfico) , Klebsiella pneumoniae/classificação , Tipagem Molecular , Técnica de Amplificação ao Acaso de DNA Polimórfico , Replicon , Resistência beta-Lactâmica
12.
Medicine (Baltimore) ; 100(20): e25930, 2021 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-34011066

RESUMO

BACKGROUND: To study the epidemic features of hand-foot-mouth disease (HFMD) in mainland China through systematic review and meta-analysis so as to provide evidence for the future prevention and control of HFMD. METHODS: Articles on the epidemic features of HFMD in mainland China, written in English or Chinese and released between January 1, 2015 and January 1, 2020, were searched from English literature databases including Embase, Web of Science, PubMed, Cochrane library, Google academic, and Chinese literature databases including China national knowledge infrastructure (CNKI), Wanfang, and China Biology Medicine (CBM). Papers were selected according to the inclusion and exclusion criteria, and quality scoring was performed. Meta-analysis, sensitivity analysis, and identification of publication bias were finished through STATA version 12.0 software. RESULTS: A total of 23 articles were included in this study, the total number of cases was 377,083, of which the total number of male cases was 231,798 and the total number of female cases was 145,285, the sex ratio was about 1.6:1, and the incidence of HFMD in China was 1.61‰ (95% confidence interval [CI]: 1.21‰-1.94‰). The results of the subgroup analysis showed that the incidence of HFMD in mainland China was the highest in South China, in 2014, in 1-year-old group and in other types of enteroviruses, respectively, with the rate of 3.48‰ (95% CI: 1.22‰-5.73‰), 1.81‰ (95% CI: 1.06‰-2.57‰), 15.20‰ (95% CI: 5.00‰-25.30‰), and 1.83‰ (95% CI: 1.32‰-2.33‰), respectively. The differences among the above 4 subgroups were statistically significant (P < .05). There were no publication bias in this study, and the sensitivity analysis results suggested that the meta-analysis results were robust. CONCLUSION: There were differences in the distribution of region, time, population, and etiology of HFMD in mainland China. Health departments should adopt key strategies and measures for key populations in key areas to prevent and control the development of HFMD, and improve the ability of pathogen detection and typing in laboratories.


Assuntos
Enterovirus/isolamento & purificação , Doença de Mão, Pé e Boca/epidemiologia , Distribuição por Idade , Pré-Escolar , China/epidemiologia , Enterovirus/genética , Feminino , Geografia , Doença de Mão, Pé e Boca/virologia , Humanos , Incidência , Lactente , Recém-Nascido , Masculino , Epidemiologia Molecular , Tipagem Molecular/estatística & dados numéricos , Distribuição por Sexo
13.
Int J Food Microbiol ; 350: 109246, 2021 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-34034079

RESUMO

Salmonella enterica is a major cause of foodborne diseases, and is also an important pathogenic bacterium in poultry industry. Whole genome sequencing (WGS) has become a crucial molecular typing technology used for the surveillance of the pathogenic bacteria. In the present study, we adopted WGS for tracking transmission of S. enterica in the production chain of broiler chickens. A total of 74 S. enterica strains were isolated from the different steps of breeding and slaughtering in a large production enterprise in Sichuan Province, China. The isolation rate of Salmonella was the highest in procedure of defeathering (50.0%) and evisceration (36.7%). Serotype identification showed that 74 Salmonella isolates included 7 serotypes, among which Mbandaka accounted for the highest proportions (35.1%). WGS revealed that 74 strains belonged to 7 different sequence types (STs), as well as 7 different ribosomal STs and 35 core genome STs. cgMLST-based Minimum Spanning Trees and phylogenetic tree based on the SNPs indicated that three serotypes, Mbandaka, Indiana and Kentucky, could be clonally transmitted between broiler farm and slaughterhouse. Heterogeneous resistant phenotypes and genotypes were found in two serotypes, Indiana and Kentucky. Our study indicated WGS in an accurate tool for molecular typing of S. enterica. Routine surveillance of S. enterica in the production chain of broiler chickens is needed.


Assuntos
Galinhas/microbiologia , Genoma Bacteriano/genética , Tipagem Molecular/métodos , Aves Domésticas/microbiologia , Salmonelose Animal/transmissão , Salmonella enterica/genética , Animais , Antibacterianos/farmacologia , China/epidemiologia , Filogenia , Doenças das Aves Domésticas/microbiologia , Doenças das Aves Domésticas/transmissão , Produtos Avícolas , Salmonelose Animal/microbiologia , Salmonella enterica/isolamento & purificação , Sorogrupo , Sequenciamento Completo do Genoma
14.
Eur J Protistol ; 79: 125796, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33975057

RESUMO

Blastocystis is a common enteric protist that inhabits the gastrointestinal tract of approximately 1 billion people worldwide. In this study, a total of 1,070 patients from two hospitals in Zhengzhou, Central China were enrolled to know molecular characteristics of Blastocystis sp. The microorganism was identified and subtyped with a PCR amplification and sequencing of the small subunit ribosomal deoxyribonucleic acid (SSU-rDNA). The overall minimum prevalence of Blastocystis sp. in participants was 3.1% (33/1070). Although there were no significant differences on Blastocystis sp. infections among study sites, age groups, and gender, the higher infection was observed in the patients with gastrointestinal diseases (8.8%, 15/170). Sequence analysis of the 33 isolates revealed three known subtypes, such as ST1 (n = 7), ST3 (n = 23), and ST7 (n = 3). Among them, ST3 was the dominant subtype being detected in 23 isolates (69.7%), followed by ST1 (21.2%, 7/33) and ST7 (9.1%, 3/33). The phylogenetic analysis demonstrated that three subtypes (ST1, ST3 and ST7) were clustered with their reference sequences with good bootstrap support. The subtype determination of Blastocystis sp. isolates by the phylogenetic analysis was well supported by online platform. The present study provides the first molecular report of Blastocystis sp. infections in hospital patients in Central China.


Assuntos
Infecções por Blastocystis/parasitologia , Blastocystis/classificação , Blastocystis/genética , Blastocystis/isolamento & purificação , Infecções por Blastocystis/epidemiologia , China/epidemiologia , DNA de Protozoário/genética , DNA Ribossômico/genética , Feminino , Humanos , Masculino , Tipagem Molecular , Filogenia , Prevalência , Especificidade da Espécie
15.
Ann Clin Microbiol Antimicrob ; 20(1): 24, 2021 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-33858427

RESUMO

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) are among common foodborne bacterial pathogens and healthy livestock are the main source of this bacterium. Severe diseases attribute to two types of cytotoxin Stx1 and Stx2, which are also called Shiga toxin (Stx). Infection of humans with STEC may result in Acute diarrhea with or without bleeding, hemorrhagic colitis (HC) and the hemolytic uremic syndrome (HUS). As antibiotic resistance is increasingly being reported among STEC isolates obtained from livestock and patients worldwide, in this study the pattern of antibiotic resistance in clinical isolates was determined. METHODS: Stool samples were collected from patients with diarrhea. All samples were cultured and identified by biochemical and molecular tests. Antimicrobial susceptibility test and assessment of extended-spectrum ß-lactamase (ESBL)-related genes were conducted. Moreover, phylogenetic groups were analyzed using quadruplex PCR, and DNA analysis assessed multi-locus sequence types (MLST). RESULTS: Out of 340 E. coli samples, 174 were identified as STEC by PCR. Antimicrobial susceptibility test results showed that, 99.4%, 96% and 93.1% of isolates were susceptible to imipenem/ertapenem, piperacillin-tazobactam and amikacin, respectively. The highest resistance was towards ampicillin (68.4%), followed by trimethoprim-sulfamethoxazole (59.8%), and tetracycline (57.5%). A total of 106 (60.9%) isolates were multidrug resistance (MDR) and 40.8% of isolates were determined to be extended spectrum ß-lactamase producers. In 94.4% of isolates, genes responsible for ESBL production could be detected, and blaTEM was the most prevalent, followed by blaCTX-M9. Furthermore, phylogenetic grouping revealed that majority of STEC strains belonged to Group C, followed by Groups E, B2 and A. MLST unveiled diverse ST types. CONCLUSION: A periodical surveillance studies and thorough understanding of antibiotic resistant profiles in STEC isolates could help select effective antibiotic treatment for patients and develop strategies to effectively manage food contamination and human infections.


Assuntos
Diarreia/microbiologia , Filogenia , Toxina Shiga/genética , Escherichia coli Shiga Toxigênica/classificação , Escherichia coli Shiga Toxigênica/genética , beta-Lactamases/genética , Adolescente , Adulto , Antibacterianos/farmacologia , Criança , Pré-Escolar , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/genética , Fezes/microbiologia , Feminino , Humanos , Irã (Geográfico) , Masculino , Testes de Sensibilidade Microbiana , Tipagem Molecular , Tipagem de Sequências Multilocus , Análise de Sequência de DNA , Sorogrupo , Escherichia coli Shiga Toxigênica/efeitos dos fármacos , Escherichia coli Shiga Toxigênica/isolamento & purificação , Adulto Jovem
16.
Nat Commun ; 12(1): 2296, 2021 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-33863880

RESUMO

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.


Assuntos
Vírus da Dengue/genética , Dengue/epidemiologia , Epidemias/prevenção & controle , Monitoramento Epidemiológico , Brasil/epidemiologia , Dengue/prevenção & controle , Dengue/transmissão , Dengue/virologia , Vírus da Dengue/isolamento & purificação , Estudos de Viabilidade , Variação Genética , Genoma Viral/genética , Humanos , Unidades Móveis de Saúde , Epidemiologia Molecular , Tipagem Molecular , Filogenia , Estudo de Prova de Conceito , RNA Viral/genética , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Estudos Retrospectivos , Sequenciamento Completo do Genoma
17.
Mol Biol Rep ; 48(4): 3629-3635, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33893925

RESUMO

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.


Assuntos
Reação em Cadeia da Polimerase/métodos , Polimorfismo Conformacional de Fita Simples , Animais , Coronavirus/classificação , Coronavirus/genética , Coronavirus/isolamento & purificação , Humanos , Tipagem Molecular/métodos , Patologia Molecular/métodos , Polimorfismo de Fragmento de Restrição , Análise de Sequência/métodos
18.
Int J Food Microbiol ; 347: 109188, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-33839439

RESUMO

Vibrio parahaemolyticus, which is commonly found in marine and estuarine environments worldwide and isolated from aquatic products, is one of the most important food-borne pathogens. Among the various typing methods, serotyping is widely accepted and utilized by infectious disease specialists and infection control agencies for the detection and epidemiological investigation of this pathogen. Thus far, 13 O serotypes and 71 K serotypes have been defined; however, untypeable strains are frequently isolated during routine detection, and some new O and/or K antigens have been identified and characterized. During a serotyping survey in Shandong province, China from 2016 to 2018, we collected 411 clinical V. parahaemolyticus strains and found that nine of them are untypeable K antigen strains. In this study, we identified three K serotypes of V. parahaemolyticus through in-depth genetic analysis of the K antigen gene cluster, serological tests, and the production of antisera. Among the nine strains, seven possess K untypeable 2 (KUT2) antigens, which have been reported recently by another group. However, two new O and K combinations (O3:KUT2 and O11:KUT2) were first characterized by us, with the remaining two each representing a novel K serotype. Moreover, through comparative genomic analysis, we showed that the Shandong KUT2 strains exhibit different virulence profiles compared to their identical K serotype partners from Zhejiang province, another Chinese coastal province; however, strains from these two regions are clustered into the same linage and may have evolved from a recent common ancestor. Additionally, one isolate, SD2016062, was phylogenetically similar to the strains associated with several local gastroenteritis outbreaks, with similar toxin patterns, suggesting its potential to cause sporadic occurrences of disease or even local pandemics. Finally, we developed a sero-specific PCR assay targeting the three novel K serotypes, which can monitor the V. parahaemolyticus spectrum for clinical and epidemiological purposes. Thus, we identified and characterized novel strains of V. parahaemolyticus and proposed a new technique for tracking the diversity of strains, which can help manage this food-borne pathogen.


Assuntos
Antígenos de Bactérias/genética , Antígenos de Superfície/genética , Vibrioses/epidemiologia , Vibrioses/microbiologia , Vibrio parahaemolyticus/genética , China/epidemiologia , Gastroenterite/epidemiologia , Gastroenterite/microbiologia , Humanos , Tipagem Molecular , Antígenos O/genética , Filogenia , Reação em Cadeia da Polimerase , Sorogrupo , Vibrio parahaemolyticus/classificação , Vibrio parahaemolyticus/patogenicidade , Virulência/genética
19.
Gene ; 787: 145639, 2021 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-33848576

RESUMO

Anomopoda is the widespread planktonic microcrustacean, which plays a crucial role in aquatic ecosystem. There are few studies about the evolutionary relationships among various Anomopoda basing on molecular data. In the present study, phylogenetic analysis of eight Anomopoda was carried out. Firstly, the culture system was developed to breed cladocerans. By using this system, eight species (Daphnia magna, D. pulex, D. sinensis, Ceriodaphnia reticulata, Moina micrura, Scapholeberis kingi, Simocephalus vetulus and Eurycercus lamellatus) were purified and cultured stably in the laboratory. Then, transcriptomic sequences and partial mitochondrial DNA sequences were both used to reconstruct the phylogenetic tree among 8 species. Transcriptomic sequences were sequenced on Illumina Hiseq 2500 platform. After assembly and annotation, transcriptomic sequences were spliced together and aligned for phylogenetic analysis. Basing on the orthologous genes derived from transcriptomic sequences, the phylogenetic analysis showed that 4 genera of Daphniidae were clustered into one group, and among the 4 genera, Ceriodaphnia was closer to Daphnia than Simocephalus, while Scapholeberis was farthest from other species. In addition, Eurycercidae was closer to Daphniidae than Moinidae. The phylogenetic trees based on both 12S rRNA and 16S rRNA sequences were similar with that based on transcriptomic sequences. Meanwhile, the phylogenetic tree based on 16S rRNA sequences was more suitable than that based on 12S rRNA sequences. These results suggested that the phylogenetic analysis basing on the transcriptomic sequences was available in cladocerans, which will help us to effectively understand the phylogenetic relationships among various cladocerans.


Assuntos
Cladóceros/classificação , Cladóceros/genética , DNA Mitocondrial , Animais , Anotação de Sequência Molecular , Tipagem Molecular , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie , Transcriptoma
20.
PLoS Negl Trop Dis ; 15(4): e0009288, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33872307

RESUMO

BACKGROUND: Visceral leishmaniasis (VL) is re-emerging in Armenia since 1999 with 167 cases recorded until 2019. The objectives of this study were (i) to determine for the first time the genetic diversity and population structure of the causative agent of VL in Armenia; (ii) to compare these genotypes with those from most endemic regions worldwide; (iii) to monitor the diversity of vectors in Armenia; (iv) to predict the distribution of the vectors and VL in time and space by ecological niche modeling. METHODOLOGY/PRINCIPAL FINDINGS: Human samples from different parts of Armenia previously identified by ITS-1-RFLP as L. infantum were studied by Multilocus Microsatellite Typing (MLMT). These data were combined with previously typed L. infantum strains from the main global endemic regions for population structure analysis. Within the 23 Armenian L. infantum strains 22 different genotypes were identified. The combined analysis revealed that all strains belong to the worldwide predominating MON1-population, however most closely related to a subpopulation from Southeastern Europe, Maghreb, Middle East and Central Asia. The three observed Armenian clusters grouped within this subpopulation with strains from Greece/Turkey, and from Central Asia, respectively. Ecological niche modeling based on VL cases and collected proven vectors (P. balcanicus, P. kandelakii) identified Yerevan and districts Lori, Tavush, Syunik, Armavir, Ararat bordering Georgia, Turkey, Iran and Azerbaijan as most suitable for the vectors and with the highest risk for VL transmission. Due to climate change the suitable habitat for VL transmission will expand in future all over Armenia. CONCLUSIONS: Genetic diversity and population structure of the causative agent of VL in Armenia were addressed for the first time. Further genotyping studies should be performed with samples from infected humans, animals and sand flies from all active foci including the neighboring countries to understand transmission cycles, re-emergence, spread, and epidemiology of VL in Armenia and the entire Transcaucasus enabling epidemiological monitoring.


Assuntos
Doenças Transmissíveis Emergentes/diagnóstico , Leishmania infantum/genética , Leishmaniose Visceral/diagnóstico , Leishmaniose Visceral/epidemiologia , Repetições de Microssatélites , Armênia/epidemiologia , Pré-Escolar , Doenças Transmissíveis Emergentes/epidemiologia , Doenças Transmissíveis Emergentes/parasitologia , Ecossistema , Feminino , Genótipo , Humanos , Lactente , Leishmaniose Visceral/parasitologia , Masculino , Epidemiologia Molecular , Tipagem Molecular , Projetos Piloto , Polimorfismo de Fragmento de Restrição , Medição de Risco
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