RESUMO
Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.
Assuntos
Disenteria Bacilar/epidemiologia , Doenças Endêmicas , Variação Genética , Shigella sonnei/genética , Antibacterianos/uso terapêutico , Criança , Pré-Escolar , Cromossomos Bacterianos/genética , Ciprofloxacina/uso terapêutico , Disenteria Bacilar/tratamento farmacológico , Disenteria Bacilar/microbiologia , Evolução Molecular , Fluoroquinolonas/uso terapêutico , Gatifloxacina , Genoma Bacteriano/genética , Genômica/métodos , Geografia , Humanos , Lactente , Dados de Sequência Molecular , Taxa de Mutação , Filogenia , Análise de Sequência de DNA , Shigella sonnei/classificação , Shigella sonnei/fisiologia , Vietnã/epidemiologiaRESUMO
We performed a case-control investigation to identify risk factors for norovirus infections among children in Vietnam. Of samples from 1,419 children who had diarrhea and 609 who were asymptomatic, 20.6% and 2.8%, respectively, were norovirus positive. Risk factors included residential crowding and symptomatic contacts, indicating person-to-person transmission of norovirus.
Assuntos
Infecções por Caliciviridae/epidemiologia , Diarreia/epidemiologia , Gastroenterite/epidemiologia , Norovirus , Infecções por Caliciviridae/história , Infecções por Caliciviridae/transmissão , Estudos de Casos e Controles , Criança , Diarreia/história , Diarreia/virologia , Gastroenterite/história , Gastroenterite/virologia , História do Século XXI , Humanos , Norovirus/classificação , Norovirus/genética , Norovirus/isolamento & purificação , Prevalência , Estudos Prospectivos , Fatores de Risco , Estações do Ano , Vietnã/epidemiologiaRESUMO
We performed a prospective multicenter study to address the lack of data on the etiology, clinical and demographic features of hospitalized pediatric diarrhea in Ho Chi Minh City (HCMC), Vietnam. Over 2,000 (1,419 symptomatic and 609 non-diarrheal control) children were enrolled in three hospitals over a 1-year period in 2009-2010. Aiming to detect a panel of pathogens, we identified a known diarrheal pathogen in stool samples from 1,067/1,419 (75.2%) children with diarrhea and from 81/609 (13.3%) children without diarrhea. Rotavirus predominated in the symptomatic children (664/1,419; 46.8%), followed by norovirus (293/1,419; 20.6%). The bacterial pathogens Salmonella, Campylobacter, and Shigella were cumulatively isolated from 204/1,419 (14.4%) diarrheal children and exhibited extensive antimicrobial resistance, most notably to fluoroquinolones and third-generation cephalosporins. We suggest renewed efforts in generation and implementation of policies to control the sale and prescription of antimicrobials to curb bacterial resistance and advise consideration of a subsidized rotavirus vaccination policy to limit the morbidity due to diarrheal disease in Vietnam.
Assuntos
Infecções Bacterianas/epidemiologia , Infecções por Caliciviridae/epidemiologia , Diarreia/complicações , Norovirus/isolamento & purificação , Infecções por Rotavirus/epidemiologia , Anti-Infecciosos/farmacologia , Bactérias/efeitos dos fármacos , Infecções Bacterianas/complicações , Infecções Bacterianas/microbiologia , Infecções por Caliciviridae/complicações , Infecções por Caliciviridae/microbiologia , Pré-Escolar , Estudos Transversais , Demografia , Diarreia/epidemiologia , Diarreia/microbiologia , Feminino , Hospitalização , Humanos , Lactente , Masculino , Testes de Sensibilidade Microbiana , Norovirus/efeitos dos fármacos , Estudos Prospectivos , Rotavirus/efeitos dos fármacos , Rotavirus/isolamento & purificação , Infecções por Rotavirus/complicações , Infecções por Rotavirus/microbiologia , Estações do Ano , Vietnã/epidemiologiaRESUMO
Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23% more NoV genogroup II positive samples from individuals with diarrhea and 9% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits.
Assuntos
Infecções por Caliciviridae/diagnóstico , Reação em Cadeia da Polimerase Multiplex , Norovirus/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Infecções por Rotavirus/diagnóstico , Rotavirus/isolamento & purificação , Infecções por Caliciviridae/virologia , Pré-Escolar , Diarreia/diagnóstico , Diarreia/virologia , Fezes/virologia , Gastroenterite/diagnóstico , Gastroenterite/genética , Genótipo , Humanos , Lactente , Recém-Nascido , Norovirus/genética , RNA Viral/análise , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Rotavirus/genética , Infecções por Rotavirus/virologiaRESUMO
Norovirus (NoV) is a major cause of epidemic gastroenteritis in industrialized countries, yet the epidemiological significance of NoV in industrializing countries remains poorly understood. The spatiotemporal distribution of NoV genotypes identified in 2054 enrolled children was investigated between May 2009 and December 2010, in Ho Chi Minh City (HCMC), Vietnam. A total of 315 NoV extracted from stool samples were genotyped and GPS mapped to their source. Genogroup II NoV, particularly GII.4, were predominant, and the GII.4 strains could be subgrouped into GII.4-2006b (Minerva) and GII.4-2010 (New Orleans) variants. There was no spatiotemporal structure among the endemic GII strains; yet a significant spatiotemporal signal corresponding with the novel introduction of GII.4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010.