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1.
BMC Infect Dis ; 20(1): 750, 2020 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-33050903

RESUMO

BACKGROUND: Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS: MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS: The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION: The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.


Assuntos
Variação Genética , Mycobacterium bovis/genética , Mycobacterium tuberculosis/genética , Tuberculose Pulmonar/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Etiópia/epidemiologia , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Epidemiologia Molecular , Reação em Cadeia da Polimerase Multiplex , Mycobacterium bovis/isolamento & purificação , Mycobacterium tuberculosis/isolamento & purificação , Escarro/microbiologia , Tuberculose Pulmonar/microbiologia , Adulto Jovem
2.
Curr Biol ; 30(19): R1124-R1130, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33022254

RESUMO

Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these 'microbe hunters' have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.


Assuntos
Bactérias/genética , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/epidemiologia , Epidemiologia Molecular/métodos , Prevenção Primária/métodos , Bactérias/patogenicidade , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Infecções por Coronavirus/epidemiologia , Genoma Bacteriano/genética , Genoma Viral/genética , História do Século XIX , História do Século XX , Humanos , Microbiota/genética , Pandemias , Pneumonia Viral/epidemiologia
3.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(8): 1341-1344, 2020 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-32867447

RESUMO

Objective: To understand the molecular characteristics and correlation among isolated strains of Brucella melitensis (BM) so as to improve the strategies on prevention and control of the disease in Jiangxi province. Methods: A total of 25 strains of BM isolated from human in 17 counties of Jiangxi province were analyzed by multiple locus variable-number tandem repeat analysis (MLVA) method. Results: A total of 25 strains of BM were classified into 24 independent genotypes with similarities between 67.00% and 100.00% and Simpson index between 0.000 and 0.773. There were 3 genotypes in MLVA8, including 60.00% (15/25) as 42 genotype, 32.00% (8/25) as 43 genotype, and 8.00% (2/25) as 63 genotype, respectively. There were 7 genotypes in MLVA11 identified, with 116 genotype and 125 genotype the main genotypes, accounting for 56.00% (14/25) of all the identified strains. Conclusions: Genes from all the 25 strains of BM that isolated from human being were with high genetic diversities, and various, genotypes. However, no obvious epidemiological correlation was noticed among these strains, indicating the complexity of the source of infection on Brucella in Jiangxi province.


Assuntos
Brucella melitensis/genética , Brucelose/microbiologia , Brucella melitensis/isolamento & purificação , Brucelose/epidemiologia , China/epidemiologia , Genótipo , Humanos , Repetições Minissatélites/genética , Epidemiologia Molecular
4.
Nat Commun ; 11(1): 4376, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873808

RESUMO

Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integrate epidemiological, genomic and phylodynamic data to identify clusters and impact of interventions. The global diversity of SARS-CoV-2 is represented, consistent with multiple importations. Seventy-six distinct genomic clusters were identified, including large clusters associated with social venues, healthcare and cruise ships. Sequencing sequential samples from 98 patients reveals minimal intra-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicates a significant reduction in the effective viral reproductive number (Re) from 1.63 to 0.48 after implementing travel restrictions and physical distancing. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARS-CoV-2 transmission chains, increasingly important as social restrictions ease globally.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Adulto , Austrália/epidemiologia , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/transmissão , Feminino , Genoma Viral , Genômica/métodos , Pessoal de Saúde , Humanos , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Pandemias , Filogenia , Pneumonia Viral/transmissão , Saúde Pública , Estudos Retrospectivos , Viagem
5.
PLoS Negl Trop Dis ; 14(9): e0008018, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32991594

RESUMO

By combining a reference-independent SNP analysis and average nucleotide identity (ANI) with affinity propagation clustering (APC), we developed a significantly improved methodology allowing resolving phylogenetic relationships, based on objective criteria. These bioinformatics tools can be used as a general ruler to determine phylogenetic relationships and clustering of bacteria, exemplary done with Francisella (F.) tularensis. Molecular epidemiology of F. tularensis is currently assessed mostly based on laboratory methods and molecular analysis. The high evolutionary stability and the clonal nature makes Francisella ideal for subtyping with single nucleotide polymorphisms (SNPs). Sequencing and real-time PCR can be used to validate the SNP analysis. We investigate whole-genome sequences of 155 F. tularensis subsp. holarctica isolates. Phylogenetic testing was based on SNPs and average nucleotide identity (ANI) as reference independent, alignment-free methods taking small-scale and large-scale differences within the genomes into account. Especially the whole genome SNP analysis with kSNP3.0 allowed deciphering quite subtle signals of systematic differences in molecular variation. Affinity propagation clustering (APC) resulted in three clusters showing the known clades B.4, B.6, and B.12. These data correlated with the results of real-time PCR assays targeting canSNPs loci. Additionally, we detected two subtle sub-clusters. SplitsTree was used with standard-setting using the aligned SNPs from Parsnps. Together APC, HierBAPS, and SplitsTree enabled us to generate hypotheses about epidemiologic relationships between bacterial clusters and describing the distribution of isolates. Our data indicate that the choice of the typing technique can increase our understanding of the pathogenesis and transmission of diseases with the eventual for prevention. This is opening perspectives to be applied to other bacterial species. The data provide evidence that Germany might be the collision zone where the clade B.12, also known as the East European clade, overlaps with the clade B.6, also known as the Iberian clade. Described methods allow generating a new, more detailed perspective for F. tularensis subsp. holarctica phylogeny. These results may encourage to determine phylogenetic relationships and clustering of other bacteria the same way.


Assuntos
Francisella tularensis/classificação , Francisella tularensis/genética , Polimorfismo de Nucleotídeo Único , Genoma Bacteriano , Epidemiologia Molecular , Família Multigênica , Nucleotídeos/genética , Filogenia , Reação em Cadeia da Polimerase em Tempo Real , Sequenciamento Completo do Genoma
6.
Viruses ; 12(9)2020 08 27.
Artigo em Inglês | MEDLINE | ID: mdl-32867108

RESUMO

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compromises the ability of military forces to fulfill missions. At the beginning of May 2020, 22 out of 70 Belgian soldiers deployed to a military education and training center in Maradi, Niger, developed mild COVID-19 compatible symptoms. Immediately upon their return to Belgium, and two weeks later, all seventy soldiers were tested for SARS-CoV-2 RNA (RT-qPCR) and antibodies (two immunoassays). Nine soldiers had at least one positive COVID-19 diagnostic test result. Five of them exhibited COVID-19 symptoms (mainly anosmia, ageusia, and fever), while four were asymptomatic. In four soldiers, SARS-CoV-2 viral load was detected and the genomes were sequenced. Conventional and genomic epidemiological data suggest that these genomes have an African most recent common ancestor and that the Belgian military service men were infected through contact with locals. The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. Some military operational settings (e.g., training camps in austere environments and ships) were also equipped with mobile infectious disease (COVID-19) testing capacity.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/epidemiologia , Militares/estatística & dados numéricos , Pneumonia Viral/epidemiologia , Adulto , Bélgica/epidemiologia , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Surtos de Doenças , Humanos , Masculino , Epidemiologia Molecular , Níger/epidemiologia , Pandemias , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/métodos , Testes Sorológicos , Carga Viral , Adulto Jovem
7.
Viruses ; 12(8)2020 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-32824272

RESUMO

Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Pneumonia Viral/virologia , RNA Viral/genética , Sequência de Bases , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , DNA Complementar/genética , Genoma Viral , Humanos , Epidemiologia Molecular , Reação em Cadeia da Polimerase Multiplex/métodos , Pandemias , Sequenciamento Completo do Genoma/métodos
8.
PLoS Negl Trop Dis ; 14(8): e0008574, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32853274

RESUMO

BACKGROUND: Shifts have occurred in the epidemiological characteristics of Japanese encephalitis (JE), extending from the molecular level to the population level. The aim of this study was to investigate the seroprevalence of JE neutralizing antibodies in healthy populations from different age groups in Zhejiang Province, and to conduct mosquito monitoring to evaluate the infection rate of Japanese encephalitis virus (JEV) among vectors, as well as the molecular characteristics of the E gene of isolated JEV strains. METHODOLOGY/PRINCIPAL FINDINGS: A total of 1190 sera samples were screened by a microseroneutralization test, including 429 infants (28d-11m) and 761 participants (2y-82y). For those under 1 year old, the geometric mean titers (GMTs) of the JE neutralizing antibody was 9.49 at birth and significantly declined as the age of month increased (r = -0.225, P<0.001). For those above 1-year old, seropositive proportions were higher in subjects aged 1-3 years old as well as ≥25 years old (65%-75%), and relatively lower in subjects aged between 4-25 years old (22%-55%). Four or more years after the 2nd dose of JEV-L (first dose administered at 8 months and the second at 2 years of age), the seropositive proportion decreased to 32.5%, and GMTs decreased to 8.08. A total of 87,201 mosquitoes were collected from livestock sheds in 6 surveillance sites during 2015-2018, from which 139 E gene sequences were successfully amplified. The annual infection rate according to bias-corrected maximum likelihood estimation of JEV in Culex tritaeniorhynchus was 1.56, 2.36, 5.65 and 1.77 per 1000, respectively. JEV strains isolated during 2015-2018 all belonged to Genotype I. The E gene of amplified 139 samples differed from the JEV-L vaccine strain at fourteen amino acid residues, including the eight key residues related to virulence and virus attenuation. No divergence was observed at the sites related to antigenicity. CONCLUSIONS/SIGNIFICANCE: Zhejiang Province was at a high risk of JE exposure due to relatively lower neutralizing antibody levels among the younger-aged population and higher infection rates of JEV in mosquitoes. Continuous, timely and full coverage of JE vaccination are essential, as well as the separation of human living areas and livestock shed areas. In addition, annual mosquito surveillance and periodic antibody level monitoring are important for providing evidence for improvement in JE vaccines and immunization schedules.


Assuntos
Vírus da Encefalite Japonesa (Espécie)/genética , Encefalite Japonesa/epidemiologia , Encefalite Japonesa/virologia , Epidemiologia Molecular , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Anticorpos Neutralizantes , Criança , Pré-Escolar , China/epidemiologia , Estudos Transversais , Culex/virologia , Culicidae/virologia , Vírus da Encefalite Japonesa (Espécie)/classificação , Vírus da Encefalite Japonesa (Espécie)/imunologia , Vírus da Encefalite Japonesa (Espécie)/isolamento & purificação , Genes Virais/genética , Humanos , Lactente , Recém-Nascido , Pessoa de Meia-Idade , Mosquitos Vetores/virologia , Estudos Soroepidemiológicos , Adulto Jovem
9.
J Med Microbiol ; 69(9): 1203-1212, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32755531

RESUMO

Introduction. Respiratory syncytial virus (RSV) is the most frequently identified viral agent in children with lower respiratory tract infection (LRTI). No data are available to date regarding RSV genotypes circulating in Tunisia.Aim. The aim of the present study was to investigate the genetic variability of the glycoprotein G gene in Tunisian RSV strains.Methodology. Nasopharyngeal aspirates were collected from infants hospitalized for LRTI in five Tunisian hospitals. All specimens were screened for RSV by a direct immunofluorescence assay (DIFA). To molecularly characterize Tunisian RSV strains, a phylogenetic analysis was conducted. Randomly selected positive samples were subjected to reverse transcription PCR amplifying the second hyper-variable region (HVR2) of the G gene.Results. Among a total of 1417 samples collected between 2015 and 2018, 394 (27.8 %) were positive for RSV by DIFA. Analysis of 61 randomly selected RSV strains revealed that group A RSV (78.7 %) predominated during the period of study as compared to group B RSV (21.3 %). The phylogenetic analysis showed that two genotypes of RSV-A were co-circulating: the ON1 genotype with a 72-nt duplication in HVR2 of the G gene was predominant (98.0 % of RSV-A strains), while one RSV-A strain clustered with the NA1 genotype (2.0 %). Concerning Tunisian group B RSV strains, all sequences contained a 60-nt insertion in HVR2 and a clustered BA10 genotype.Conclusion. These data suggest that RSV-A genotype ON1 and RSV-B genotype BA10, both with duplications in the G gene, were widely circulating in the Central coastal region of Tunisia between 2015 and 2018.


Assuntos
Filogenia , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/genética , Pré-Escolar , Feminino , Genótipo , Humanos , Lactente , Masculino , Epidemiologia Molecular , Infecções por Vírus Respiratório Sincicial/epidemiologia , Vírus Sincicial Respiratório Humano/classificação , Vírus Sincicial Respiratório Humano/isolamento & purificação , Estações do Ano , Tunísia/epidemiologia
10.
Lancet Infect Dis ; 20(10): e251-e260, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32768390

RESUMO

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.


Assuntos
Metagenômica/métodos , Metagenômica/estatística & dados numéricos , Biologia Computacional , Humanos , Epidemiologia Molecular , Projetos de Pesquisa/normas
11.
Zhonghua Yu Fang Yi Xue Za Zhi ; 54(6): 696-701, 2020 Jun 06.
Artigo em Chinês | MEDLINE | ID: mdl-32842289

RESUMO

Objective: To understand the genotype distribution and molecular epidemiological characteristics of hepatitis E virus (HEV) isolated in Shandong Province, 2017. Methods: The cases of hepatitis E who were reported to the National Notifiable Disease Reporting System (NNDRS) from January to December 2017 in Shandong Province were chosen as the subjects in the study. Epidemiological information and blood samples were collected from 1 045 participants. Both anti-HEV IgM and anti-HEV IgG were detected using ELISA method. Viral nucleic acids were extracted only from those of anti-HEV IgM positive samples. Nested reverse transcription-polymerase chain reaction was carried out to amplify 644 bp nucleotide sequences within HEV open reading frame (ORF) 2 region. The sample sequences together with reference sequences from GenBank were subjected to phylogenetic analysis. Results: In total, 638 (61.1%) cases were detected positive for anti-HEV IgM. The average age of male was (57.9±12.2) years, and the anti-HEV IgM positive rate was 61.5% (496/807). The average age of female was (58.1±15.0) years, and the anti-HEV IgM positive rate was 59.7% (142/238). A total of 163 HEV strains were detected, and the positive rate was 25.6% (163/638). The positive rate of the eastern, central and western region was 23.0% (71/309), 33.6% (72/214) and 17.4% (20/115), respectively. Phylogenetic tree and homology analysis indicated that all isolates belonged to genotype Ⅳ, clustering into four different subgenotype (4a, 4b, 4d and 4h). Subgenotype 4d was predominant, accounting for 85.9% (140 strains), followed by 4b (7.4%, 12 strains), 4a (3.7%, 6 strains) and 4h (3.1%, 5 strains). The 4a, 4b, and 4h subgenotype were mainly detected in the eastern region, accounting for 3/5, 11/12, and 4/6, respectively. The 4d subgenotype was mainly in the middle region, accounting for 50.0% (70/140). The homology analysis showed that the 163 sequences shared 82.7% to 100.0% nucleotide sequence identity with each other. The 140 sequences of HEV 4d strains showed high similarity with swine-origin HEV(KF176351), cattle-origin HEV(KU904278)and sheep-origin HEV(KU904267)isolated in Shandong Province, and the nucleotide homology was 93.1%-98.3%, 92.7%-97.9% and 92.7%-97.9%, respectively. Conclusion: HEV genotype Ⅳ(4d subgenotype) was dominant in Shandong province. A complicated interspecies transmission might be the main source of human HEV infection in Shandong Province, China.


Assuntos
Vírus da Hepatite E , Hepatite E/epidemiologia , Adulto , Idoso , Animais , Bovinos , China/epidemiologia , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Filogenia , RNA Viral/genética , Ovinos , Suínos
12.
Zhonghua Yu Fang Yi Xue Za Zhi ; 54(8): 849-853, 2020 Aug 06.
Artigo em Chinês | MEDLINE | ID: mdl-32842314

RESUMO

Objective: To identify the epidemic clones of MRSA isolates at a hospital in shanghai. Methods: A total of 72 MRSA isolates have been isolated from a second grade hospital between 2017 and 2018, including 32 CA-MRSA isolates, 13 HA-MRSA isolates and 26 MRSA isolates from environment. In this study, MLST and PFGE typing methods were used to analyze the molecular epidemiology of the MRSA isolates. Results: A total of 72 MRSA isolates have been obtained including 46 isolates from clinical specimens, 26 isolates from environments. The 46 MRSA isolates from clinical specimens consisted of 33 CA-MRSA (community-acquired MRSA) and 13 HA-MRSA (hospital-acquired MRSA). Furthermore, these patients infected with MRSA isolates were mostly distributed in the department of geriatrics (34.8%, 16/46), internal medicine (26.1%, 12/46) and surgery (26.1%, 12/46). MLST typing results showed that ST764 was predominant in isolates from both clinical specimens and hospital environments. Furthermore, PFGE typing results showed that most ST764 MRSA had high homolog (>90%). Conclusion: ST764 MRSA isolates might spread in community, hospital and environments. Therefore, continuous monitoring of MRSA and its variation may be useful in understanding the involvement of epidemic clone, and in searching new strategies to control MRSA infection.


Assuntos
Infecções Comunitárias Adquiridas , Infecção Hospitalar/epidemiologia , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas/epidemiologia , Antibacterianos , China/epidemiologia , Eletroforese em Gel de Campo Pulsado , Humanos , Meticilina , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem de Sequências Multilocus
13.
Arch Virol ; 165(10): 2367-2372, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32757058

RESUMO

Mammalian orthoreoviruses (MRVs) infect almost all mammals, and there are some reports on MRVs in China. In this study, a novel strain was identified, which was designated as HLJYC2017. The results of genetic analysis showed that MRV HLJYC2017 is a reassortant strain. According to biological information analysis, different serotypes of MRV contain specific amino acid insertions and deletions in the σ1 protein. Neutralizing antibody epitope analysis revealed partial cross-protection among MRV1, MRV2, and MRV3 isolates from China. L3 gene recombination in MRV was identified for the first time in this study. The results of this study provide valuable information on MRV reassortment and evolution.


Assuntos
Antígenos Virais/genética , Proteínas do Capsídeo/genética , Orthoreovirus de Mamíferos/genética , Vírus Reordenados/genética , Infecções por Reoviridae/epidemiologia , Infecções por Reoviridae/veterinária , Animais , Anticorpos Neutralizantes/sangue , Anticorpos Antivirais/sangue , Antígenos Virais/imunologia , Proteínas do Capsídeo/imunologia , China/epidemiologia , Quirópteros , Cervos , Fezes/virologia , Expressão Gênica , Mutação INDEL , Camundongos , Epidemiologia Molecular , Orthoreovirus de Mamíferos/classificação , Orthoreovirus de Mamíferos/imunologia , Orthoreovirus de Mamíferos/isolamento & purificação , Filogenia , RNA Viral/genética , Vírus Reordenados/classificação , Vírus Reordenados/imunologia , Vírus Reordenados/isolamento & purificação , Infecções por Reoviridae/imunologia , Infecções por Reoviridae/virologia , Sorogrupo , Suínos
14.
Viruses ; 12(8)2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32722343

RESUMO

The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.


Assuntos
Betacoronavirus/classificação , Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Teorema de Bayes , Betacoronavirus/isolamento & purificação , Monitoramento Epidemiológico , Genoma Viral , Humanos , Itália/epidemiologia , Funções Verossimilhança , Epidemiologia Molecular , Tipagem Molecular , Mutação , Filogenia , Fatores de Tempo , Sequenciamento Completo do Genoma
15.
Int J Mol Sci ; 21(12)2020 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-32604724

RESUMO

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Genoma Viral , Pandemias/prevenção & controle , Pneumonia Viral/virologia , Animais , Betacoronavirus/imunologia , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/tratamento farmacológico , Desenho de Fármacos , Genes Virais , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , Epidemiologia Molecular , Filogenia , Pneumonia Viral/diagnóstico , Pneumonia Viral/tratamento farmacológico , Vírus da SARS/genética , Síndrome Respiratória Aguda Grave/virologia , Vacinas Virais/genética , Vacinas Virais/imunologia
16.
Parasitol Res ; 119(9): 2983-2990, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32705376

RESUMO

Entamoeba suis and E. polecki subtype (ST) 1 and ST3 recently have been inferred to be virulent in pigs. However, because relevant molecular epidemiological surveys have been limited, the prevalences of these species remain unknown and their pathogenicities are still controversial. We surveyed 196 fecal samples of pigs (118 of adults, 78 of piglets) at Tangerang in West Java, Indonesia, in 2017, employing PCR using porcine Entamoeba-specific primers. E. suis was the more frequently detected species, observed in 81.1% of samples, while E. polecki ST1 and ST3 were detected in 18.4% and 17.3% of samples, respectively; mixed infections (harboring 2-3 species or subtypes of Entamoeba) were confirmed in 29.3% of positive samples. Statistically significant differences in the positive rates were not seen between adult pigs and piglets, except for those of E. polecki ST3. The prevalences of Eimeria spp. and/or Cystoisospora suis (79.1%), strongyles (55.6%), and Strongyloides spp. (6.1%) were also observed morphologically in the samples. Further chronological or seasonal investigations of pigs and humans in these high-prevalence areas are needed to assess the virulence of the Entamoeba parasites, including the effects on pig productivity, and to evaluate the zoonotic impacts of these organisms.


Assuntos
Entamoeba/genética , Entamoeba/isolamento & purificação , Entamebíase/veterinária , Doenças dos Suínos/parasitologia , Animais , Entamoeba/classificação , Entamoeba/patogenicidade , Entamebíase/epidemiologia , Entamebíase/parasitologia , Fezes/parasitologia , Feminino , Indonésia/epidemiologia , Masculino , Epidemiologia Molecular , Filogenia , Reação em Cadeia da Polimerase , Prevalência , Suínos , Doenças dos Suínos/epidemiologia , Virulência
17.
Parasitol Res ; 119(8): 2733-2740, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32617726

RESUMO

Amebiasis is a worldwide parasitic zoonosis, with symptoms of abdominal discomfort, indigestion, diarrhea, and even death. However, limited information about the prevalence of Entamoeba spp. in experimental nonhuman primates (NHPs) in southwestern China is available. The objective of the current study was to investigate the frequency and species identity of Entamoeba to evaluate potential zoonotic risk factors for Entamoeba spp. infection in experimental NHPs. A total of 505 fecal samples were collected from NHPs (macaques) and analyzed by PCR analysis the small subunit rRNA (SSU rRNA) gene of Entamoeba spp. Forty-seven specimens were positive for Entamoeba spp., and the prevalence of Entamoeba spp. was 9.31% (47/505). Significant differences in the prevalence rates among the three breeds (P = 0.002 < 0.01, df = 2, χ2 = 12.33) and feed types (P = 0.001 < 0.01, df = 1, χ2 = 10.12) were observed. Altogether, four Entamoeba species, including E. dispar (57.44%), E. chattoni (29.78%), E. histolytica (6.38%), and E. coli (6.38%), were identified by DNA sequence analysis. The results suggested a low prevalence but high diversity of Entamoeba species in experimental NHPs in Yunnan Province, southwestern China. Results of this study contribute to the knowledge of the genetic characteristics of Entamoeba spp. in NHPs.


Assuntos
Entamoeba/genética , Entamebíase/veterinária , Macaca/parasitologia , Infecções Protozoárias em Animais/epidemiologia , Infecções Protozoárias em Animais/parasitologia , Animais , Animais de Laboratório , China/epidemiologia , DNA de Protozoário/genética , Entamoeba/classificação , Entamoeba/isolamento & purificação , Entamebíase/epidemiologia , Entamebíase/parasitologia , Entamebíase/transmissão , Fezes/parasitologia , Epidemiologia Molecular , Prevalência , Infecções Protozoárias em Animais/transmissão , RNA Ribossômico/genética , Subunidades Ribossômicas Menores/genética , Análise de Sequência de DNA
18.
PLoS One ; 15(7): e0234684, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702006

RESUMO

OBJECTIVE: To describe the clinical features, outcomes, and molecular epidemiology of an outbreak of multidrug resistant (MDR) A. baumannii. METHODS: We performed a retrospective analysis of all MDR A. baumannii isolates recovered during an outbreak from 2011 to 2015 in a tertiary care cancer hospital. Cases were classified as colonized or infected. We determined sequence types following the Bartual scheme and plasmid profiles. RESULTS: There were 106 strains of A. baumannii isolated during the study period. Sixty-six (62.3%) were considered as infection and 40 (37.7%) as colonization. The index case, identified by molecular epidemiology, was a patient with a drain transferred from a hospital outside Mexico City. Ninety-eight additional cases had the same MultiLocus Sequence Typing (MLST) 758, of which 94 also had the same plasmid profile, two had an extra plasmid, and two had a different plasmid. The remaining seven isolates belonged to different MLSTs. Fifty-three patients (50%) died within 30 days of A. baumanniii isolation: 28 (20%) in colonized and 45 (68.2%) in those classified as infection (p<0.001). In multivariate regression analysis, clinical infection and patients with hematologic neoplasm, predicted 30-day mortality. The molecular epidemiology of this outbreak showed the threat posed by the introduction of MDR strains from other institutions in a hospital of immunosuppressed patients and highlights the importance of adhering to preventive measures, including contact isolation, when admitting patients with draining wounds who have been hospitalized in other institutions.


Assuntos
Infecções por Acinetobacter/tratamento farmacológico , Infecções por Acinetobacter/mortalidade , Infecção Hospitalar/epidemiologia , Acinetobacter baumannii/genética , Acinetobacter baumannii/isolamento & purificação , Acinetobacter baumannii/patogenicidade , Adulto , Idoso , Estudos de Casos e Controles , Surtos de Doenças , Resistência a Múltiplos Medicamentos/fisiologia , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/genética , Feminino , Hospitais Gerais , Humanos , Masculino , México , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Epidemiologia Molecular/métodos , Tipagem de Sequências Multilocus/métodos , Plasmídeos/efeitos dos fármacos , Plasmídeos/genética , Estudos Retrospectivos , Análise de Sequência de DNA/métodos , beta-Lactamases/genética
19.
Arch Virol ; 165(10): 2317-2322, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32643035

RESUMO

Canine kobuviruses (CaKoV) have been found in healthy and diarrheic dogs as well as asymptomatic wild carnivores in various countries. In order to investigate the prevalence and evolution of CaKoV in Tangshan, China, 82 dog fecal samples from pet hospitals in Tangshan were subjected to RT-PCR targeting a segment of the 3D gene of CaKoV. Using this method, we identified CaKoV in 14 samples (17.07%, 14/82). Of the CaKoV-positive samples, 78.57% (11/14) and 50% (7/14) were positive for canine parvovirus and canine coronavirus, respectively. The nucleotide sequences of the 14 strains 96.6%-100% identical to each other and 77.6%-99.2% identical to representative sequences from the NCBI GenBank database. We also amplified the 14 VP1 gene sequences and found that they were 93.3%-99.6% identical to each other and 73.3%-97.8% identical to representative sequences from the NCBI GenBank database. Phylogenetic analysis revealed that the 14 CaKoV strains from Tangshan are closely related to those identified in China and Thailand and display less similarity to those found in Africa, the United States, and Europe. Our data suggest that CaKoV circulated in young pet dogs in Tangshan and displays a high co-infection rate with CCoV and CPV. However, the relationship between the three viruses and their roles in the host requires further investigation.


Assuntos
Doenças do Cão/epidemiologia , Kobuvirus/classificação , Kobuvirus/genética , Infecções por Picornaviridae/veterinária , Animais , China/epidemiologia , Coinfecção/epidemiologia , Coinfecção/veterinária , Coinfecção/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/veterinária , Infecções por Coronavirus/virologia , Coronavirus Canino/genética , Doenças do Cão/virologia , Cães/virologia , Feminino , Genes Virais , Masculino , Epidemiologia Molecular , Infecções por Parvoviridae/epidemiologia , Infecções por Parvoviridae/veterinária , Infecções por Parvoviridae/virologia , Parvovirus Canino/genética , Animais de Estimação/virologia , Filogenia , Infecções por Picornaviridae/epidemiologia , Infecções por Picornaviridae/virologia , Prevalência , Proteínas Estruturais Virais/genética
20.
Arch Virol ; 165(10): 2147-2163, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32653984

RESUMO

Small ruminants (e.g., sheep and goats) contribute considerably to the cash income and nutrition of small farmers in most countries in Africa and Asia. Their husbandry is threatened by the highly infectious transboundary viral disease peste des petits ruminants (PPR) caused by peste-des-petits-ruminants virus (PPRV). Given its social and economic impact, PPR is presently being targeted by international organizations for global eradication by 2030. Since its first description in Côte d'Ivoire in 1942, and particularly over the last 10 years, a large amount of molecular epidemiological data on the virus have been generated in Africa. This review aims to consolidate these data in order to have a clearer picture of the current PPR situation in Africa, which will, in turn, assist authorities in global eradication attempts.


Assuntos
Surtos de Doenças , Doenças das Cabras/epidemiologia , Proteínas do Nucleocapsídeo/genética , Peste dos Pequenos Ruminantes/epidemiologia , Vírus da Peste dos Pequenos Ruminantes/genética , Doenças dos Ovinos/epidemiologia , África/epidemiologia , Animais , Doenças das Cabras/transmissão , Doenças das Cabras/virologia , Cabras/virologia , Epidemiologia Molecular , Peste dos Pequenos Ruminantes/transmissão , Peste dos Pequenos Ruminantes/virologia , Vírus da Peste dos Pequenos Ruminantes/classificação , Vírus da Peste dos Pequenos Ruminantes/isolamento & purificação , Filogenia , Ovinos/virologia , Doenças dos Ovinos/transmissão , Doenças dos Ovinos/virologia
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