Principais enteropatógenos causadores de diarréia em crianças, na região de Ribeirão Preto-SP, Brasil

Com o objetivo de caracterizar os principais enteropatógenos causadores de diarréia na região de Ribeirão Preto, quanto aos sorogrupos e sorotipos, por um período de 4 anos foram estudadas fezes de 1836 crianças, menores de 10 anos de idade, de ambos os sexos, portadoras de gastrenterite aguda no IAL de Ribeirão Preto, SP. Foram pesquisados os seguintes enteropatógenos: Escherichia coli, Salmonella sp., Shigella sp., Campylobacter sp., Yersinia sp., e Cryptosporidium sp., identificados através de metodologia tradicional. Foram positivas 419 (22,8%) amostras, com 1,7% de associação entre enteropatógenos. Houve predomínio na faixa etária de 0 a 11 meses. Destacou-se a E.coli enteropatogênica (EPEC) (8,7%), sendo mais frequente o sorogrupo O119 (40,2%), seguida do gênero Shigella (6,2%), dos quais 63,2% corresponderam à S. sonnei.To study the main enteropathogens causing diarrhea in the region of Ribeirão Preto regarding serogroups and serotypes, the feces of 1836 children under 10 years old, from both sexes, attack of acute gastroenteritis, were analysed during a period of 4 years in Adolfo Lutz Institute - Ribeirão Preto, SP. The pathogens identified by standard methods were the following: Escherichia coli, Salmonella spp., Shigella spp., Campylobacter spp., Yersinia spp., and Cryptosporidium spp. Positive samples were 22.8% (419) with 1.7% association of pathogens. Larger isolates were mainly from children 0 to 11 months old. Enteropathogenic E. coli (EPEC) was most frequent (8.7%) with predominance of serogroup O119 (40.2%), followed by Shigella (6.2%), 63.6% of which S. sonnei

Serotypes and antimicrobial resistance profile of Streptococcus pneumoniae: clinical implications in invasive disease and in national immunization program (1998-2013)

As infecções por Streptococcus pneumoniae (pneumococo) ainda desafiam os sistemas de saúde em todo mundo. Este é um estudo observacional, de seguimento retrospectivo, que avaliou aspectos microbiológicos e clínicos das cepas de pneumococo isoladas de pacientes com doença invasiva pneumocócica (DIP) isolados nos Departamentos Regionais de Saúde (DRS) de Araraquara, Barretos, Franca e Ribeirão Preto, em um período de 16 anos (1998-2013). As informações foram obtidas junto ao Instituto Adolfo Lutz e, no banco de dados do Hospital das Clínicas de Ribeirão Preto (HCRP). Analisou-se 796 linhagens, com predominio do gênero masculino (58,9%), da faixa etária de 20 a menores de 60 anos de idade (32,2%) e do período de 2003 a 2010 (60,2%). As DIPs mais comuns foram a meningite (45,7%) e a pneumonia (45,0%). Quanto aos sorotipos mais frequentes, observou-se em 83,3%: 14, 3, 19F, 1, 6A, 6B, 23F, 9V, 18C, 19A, 12F, 4, 7F, 5, 22F, 11A, 8, 9N, 10A e 15C, sendo o 14 o mais comum nos quatro DRS estudados. Os sorotipos 14, 3 e 19F foram mais frequentes na meningite, enquanto os sorotipos 14, 3 e 1 na pneumonia. Após 2010, verificou-se diminuição dos sorotipos 14, 1, 23F e 5 e aumento de 12F, 11A e 8, não contidos na vacina. A resistência à penicilina foi de 14,8%, sendo 3,0% resistência intermediária e 11,8% de resistência plena. Para ceftriaxona, 5,3% foram não sensíveis. A sensibilidade ao cloranfenicol, eritromicina e ceftriaxona manteve-se acima dos 90%, no período estudado. O maior nível de resistência foi observado para Sulfametoxazol/trimetoprim (49,4%). Destaca-se o aumento dos sorotipos 12F, 11A e 8 após a vacinação, considerando que nenhum deles compõe as vacinas conjugadas disponíveis. Observou-se variabilidade de resistência entre os diferentes sorotipos de pneumococo. A DIP mais frequente nos pacientes cadastrados no HCRP foi a pneumonia (67,8%), seguida da meningite (22,9%) tendo como sorotipos mais frequentes 14, 6A, 23F, 1, 3, 18C, 19F, 12F, 4,9V, 6B e 19A. Destes pacientes 67,5% apresentaram cura sem sequelas, 6,9% tiveram algum tipo de sequela e 25,6% evoluíram para óbito. A pneumonia causou 18,2% dos óbitos, principalmente na faixa etária de 20 a menores de 60 anos de idade. Os sorotipos 12F, 14, 18C, 9V, 18A, 19A e 23F foram responsáveis por 64,9% dos óbitos por meningite, enquanto os sorotipos 3, 14, 9V, 6B, 23F e 19F estiveram envolvidos em 63,4% das mortes por pneumonia. Entre os pacientes que morreram 68,2% tinham algum tipo de comorbidade, sendo HIV/AIDS, alcoolismo e câncer as mais comuns. A faixa etária com 60 anos ou mais foi a mais significativa (OR=4,2) para o insucesso, independente da presença de comorbidade. A presença do sorotipo 18C foi fator de risco significativo tanto na análise bruta (OR=3,8), quanto ao ajustar por comorbidade (OR=5,0) ou ajustada por idade (OR=5,4). O mesmo ocorreu para o sorotipo 12F (respectivamente, OR=5,1, OR=5,0 e OR=4,7). Observou-se alterações na circulação de alguns sorotipos de pneumococo no período pós VPC10. Ressalta-se a importância da continuidade da vigilância das DIPs, afim de determinar oscilações clínicas e microbiológicas da doença. Além disto, na era das vacinas conjugadas, o contínuo monitoramento sobre a distribuição de sorotipos na população é necessário para a avaliação do impacto e adequação da imunizaçãoInfections by Streptococcus pneumoniae (pneumococcus) are still a challenge to health systems worldwide. An observational retrospective study was developed to assess microbiological and clinical aspects of pneumococcus strains isolated from patients with invasive pneumococcal diseases (IPD) which were isolated in the Regional Health Departments (DRS) of Araraquara, Barretos, Franca and Ribeirão Preto, in a period of 16 years (1998-2013). Data were obtained at the Adolfo Lutz Institute and in databases of the Clinics Hospital of Ribeirão Preto (HCRP). A total of 796 strains were analyzed, with prevalence of male individuals (58.9%), aged between 20 and 60 years (32.2%), and in the period between 2003 and 2010 (60.2%). The most common IPD were meningitis (45.7%) and pneumonia (45.0%). Regarding the most frequent serotypes, in 83.3% they were: 14, 3, 19F, 1, 6A, 6B, 23F, 9V, 18C, 19A, 12F, 4, 7F, 5, 22F, 11A, 8, 9N, 10A and 15C, with 14 being the most common in the four DRS studied. Serotypes 14, 3 and 19F were more frequent in meningitis, whereas serotypes 14, 3 and 1 were more frequent in pneumonia. After 2010, there was a decrease in serotypes 14, 1, 23F and 5, and an increase in 12F, 11A and 8, which are not included in the vaccine. Resistance to penicillin was 14.8%, with 3.0% being intermediate, and 11.8% full resistance. For ceftriaxone, 5.3% were not sensitive. Sensitivity to chloramphenicol, erythromycin and ceftriaxone remained over 90% in the studied period. The highest level of resistance was observed for Sulfamethoxazole/trimethoprim (49.4%). It is noteworthy that there was an increase in the s serotypes 12F, 11A and 8 after vaccination, considering that none of them make up the combined vaccines available. Resistance varied among the different serotypes of pneumococcus. The most frequent IPD in the patients registered in the HCRP was pneumonia (67.8%), followed by meningitis (22.9%), with the most frequent serotypes being 14, 6A, 23F, 1, 3, 18C, 19F, 12F, 4, 9V, 6B and 19A. Of these patients, 67.5% were cured without sequela, 6.9% had some sort of sequela and 25.6% evolved to death. Pneumonia caused 18.2% of the deaths, mainly in the age range between 20 and 60 years. Serotypes 12F, 14, 18C, 9V, 18A, 19A and 23F were responsible for 64.9% of the deaths by meningitis, whereas serotypes 3, 14, 9V, 6B, 23F and 19F were involved in 63.4% of the deaths by pneumonia. Among the patients who died, 68.2% had some sort of comorbidity, with HIV/AIDS, alcoholism and cancer being the most common. The age range over 60 years was the most significant (OR=4.2) for failure, regardless of the presence of a comorbidity. The presence of serotype 18C was a significant risk factor both in the gross analysis (OR=3.8), and in the adjustment as for comorbidity (OR=5.0) or age (OR=5.4). This was also true for the serotype 12F (respectively, OR=5.1, OR=5.0 and OR=4.7). There were alterations in the circulation of some pneumococcus serotypes in the period after VPC10. it is emphasized the importance of continued monitoring of DIPs, in order to determine clinical and microbiological fluctuations of the disease. In addition, in the era of combined vaccines, it is necessary to keep monitoring the distribution of serotypes in the population to assess the impact and adequacy of immunizatio

Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans, Animals, Food, and the Environment in Brazil

Submitted by Sandra Infurna ([email protected]) on 2018-09-13T13:23:20Z No. of bitstreams: 1 sheila_duque_etal_IOC_2018.pdf: 174501 bytes, checksum: 1e185a82bdff86ebcaf2ef34bc9056f7 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2018-09-13T13:32:26Z (GMT) No. of bitstreams: 1 sheila_duque_etal_IOC_2018.pdf: 174501 bytes, checksum: 1e185a82bdff86ebcaf2ef34bc9056f7 (MD5)Made available in DSpace on 2018-09-13T13:32:26Z (GMT). No. of bitstreams: 1 sheila_duque_etal_IOC_2018.pdf: 174501 bytes, checksum: 1e185a82bdff86ebcaf2ef34bc9056f7 (MD5) Previous issue date: 2018Universidade de São Paulo. Faculdade de Ciências Farmacêuticas de Ribeirão Preto. Departamento Análises Clínicas, Toxicológicas e Bromatológicas. Ribeirão Preto, SP, Brasil.U.S. Food and Drug Administration. Center for Food Safety and Applied Nutrition. Division of Microbiology. Office of Regular Science. College Park, Maryland, USA.Instituto Adolfo Lutz de Ribeirão Preto. Ribeirão Preto, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Coleção de Campylobacter. Rio de Janeiro, RJ. Brasil.U.S. Food and Drug Administration. Center for Food Safety and Applied Nutrition. Division of Microbiology. Office of Regular Science. College Park, Maryland, USA.U.S. Food and Drug Administration. Center for Food Safety and Applied Nutrition. Division of Microbiology. Office of Regular Science. College Park, Maryland, USA.Universidade de São Paulo. Faculdade de Ciências Farmacêuticas de Ribeirão Preto. Departamento Análises Clínicas, Toxicológicas e Bromatológicas. Ribeirão Preto, SP, Brasil.Campylobacter jejuni is a major zoonotic pathogen that causes foodborne gastroenteritis worldwide. However, clinical cases of campylobacteriosis have been underreported and underdiagnosed in Brazil. Herein, we describe the draft genome sequences of 116 C. jejuni strains isolated from diverse sources in Brazi

Distribution of Streptococcus pneumoniae serotypes in the northeast macro-region of São Paulo state/Brazil after the introduction of conjugate vaccine

Abstract Background Infections caused by Streptococcus pneumoniae (Spn) still challenge health systems around the world, even with advances in vaccination programs. The present study evaluated the frequency of various Spn serotypes isolated in Regional Health Care Network 13 (RRAS 13), which includes the regional health departments (RHDs) of Araraquara, Barretos, Franca and Ribeirão Preto, especially after the introduction of 10-valent pneumococcal conjugate vaccine (PCV10) in 2010. Methods The analyzed Spn strains were isolated from patients with invasive pneumococcal diseases (IPDs) and then sent to Adolfo Lutz Institute (ALI) for further confirmative identification tests during the period from 1998 to 2013. The samples were from the cities in RRAS13, which is located in the Northeast region of São Paulo State, and totals 90 municipalities. Results We analyzed strains isolated from 796 patients. They were predominantly: men (58.9%); 20 to 60 years old (32.2%); evaluated from 2003 to 2010 (60.2%); and diagnosed with meningitis (45.7%) and pneumonia (45.0%), the most common invasive pneumococcal diseases. In 2010, serotypes 3, 19F, 1, 23F, 6A and 6B were among the most frequent, while serotypes 3, 12F, 14, 6A, 18C, 8 and 6B were more common after the introduction of PCV10. Serotypes 14, 19F and 3 were more frequent in meningitis, while serotypes 14, 3 and 1 prevailed in pneumonia. After 2010, there was a decrease in serotypes 14, 1, 23F and 5 and an increase in serotypes 3, 12F, 11A and 8, which were not present in the vaccine. Conclusions The present study noted the increase in serotypes 3, 12F, 11A and 8 after vaccination. None of those serotypes are included in the available conjugate vaccines, which highlights the importance of continued monitoring of IPDs in order to measure the disease burden in the population in the long term and provide new epidemiological information to determine the impact of PCV10 in Brazil

Clinical and microbiological implications of invasive pneumococcal disease in hospitalized patients (1998–2013)

Introduction: Infections caused by Streptococcus pneumoniae (pneumococcus) still represent a challenge for health systems around the world. Objective: The objective of this study was to assess microbiological and clinical aspects in hospitalized patients with invasive pneumococcus disease between 1998 and 2013. Materials and methods: This was a retrospective study that analyzed the results of pneumococcus identification, serotyping, and susceptibility testing found in the Adolfo Lutz Institute databank. Personal variables, medical history and clinical outcome of patients admitted with invasive pneumococcal disease were analyzed. These were obtained from records of a public teaching hospital – Hospital das Clínicas Faculdade de Medicina Ribeirão Preto. Results: The sample comprised 332 patients. Patient age ranged from less than one month to 89 years old (mean 20.3 years) and the sample was predominately male. Pneumonia (67.8%) was the most common disease, accounting for 18.2% of deaths. Serotypes 14, 1, 3, 9V, 6B, 6A, 23F, 19A, 18C, 19F, 12F, and 4 were the most common (75.3%). Most patients, or 67.5%, were cured without any complication (success), 6.9% had some type of sequela (failure), and 25.6% died (failure). In the case of deaths due to meningitis, strains of fully penicillin resistant pneumococcus were isolated. Furthermore, 68.2% of patients who died presented some type of comorbidity. The 60 and older age group presented the most significant association (Odds Ratio = 4.2), with outcome failure regardless of the presence of comorbidity. Serotype 18C was the most significant risk factor both in raw analysis (Odds Ratio = 3.8) and when adjusted for comorbidity (Odds Ratio = 5.0) or age (Odds Ratio = 5.4). The same occurred with serotype 12F (respectively, Odds Ratio = 5.1, Odds Ratio = 5.0, and Odds Ratio = 4.7) Conclusion: The present findings highlight the importance of IPD among young adults and older adults. In the era of conjugate vaccines, monitoring serotypes in different age groups is essential to assess the impact and adequacy of immunization. Keywords: Streptococcus pneumoniae, Serotypes, Death, Comorbidit

Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing.

Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil

Etiology of acute diarrhea among children in Ribeirão Preto-SP, Brazil

Com o objetivo de caracterizar os principais enteropatógenos causadores de diarréia na região de Ribeirão Preto, quanto aos sorogrupos e sorotipos, por um período de 4 anos foram estudadas fezes de 1836 crianças, menores de 10 anos de idade, de ambos os sexos, portadoras de gastrenterite aguda no IAL de Ribeirão Preto, SP. Foram pesquisados os seguintes enteropatógenos: Escherichia coli, Salmonella sp., Shigella sp., Campylobacter sp., Yersinia sp., e Cryptosporidium sp., identificados através de metodologia tradicional. Foram positivas 419 (22,8%) amostras, com 1,7% de associação entre enteropatógenos. Houve predomínio na faixa etária de 0 a 11 meses. Destacou-se a E.coli enteropatogênica (EPEC) (8,7%), sendo mais frequente o sorogrupo O119 (40,2%), seguida do gênero Shigella (6,2%), dos quais 63,2% corresponderam à S. sonnei.To study the main enteropathogens causing diarrhea in the region of Ribeirão Preto regarding serogroups and serotypes, the feces of 1836 children under 10 years old, from both sexes, attack of acute gastroenteritis, were analysed during a period of 4 years in Adolfo Lutz Institute - Ribeirão Preto, SP. The pathogens identified by standard methods were the following: Escherichia coli, Salmonella spp., Shigella spp., Campylobacter spp., Yersinia spp., and Cryptosporidium spp. Positive samples were 22.8% (419) with 1.7% association of pathogens. Larger isolates were mainly from children 0 to 11 months old. Enteropathogenic E. coli (EPEC) was most frequent (8.7%) with predominance of serogroup O119 (40.2%), followed by Shigella (6.2%), 63.6% of which S. sonnei

Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil.

Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) causes gastroenteritis in many countries. However, in Brazil there are few studies that have conducted a virulence characterization of this serovar. The aim of this study was to evaluate the virulence potential of S. Typhimurium strains isolated in Brazil. Forty S. Typhimurium strains isolated from humans (n = 20) and food (n = 20) from Brazil were studied regarding their invasion and survival in human epithelial cells (Caco-2) and macrophages (U937). Their virulence potential was determined using the Galleria mellonella larvae model combined with the analysis of virulence genes by whole genome sequencing (WGS). A total of 67.5% of the S. Typhimurium studied (32.5% isolated from humans and 35% isolated from food) invaded Caco-2 epithelial cells at levels similar to or greater than the S. Typhimurium SL1344 prototype strain. In addition, 37.5% of the studied strains (25% isolated from humans and 12.5% isolated from food) survived in U937 human macrophages at levels similar to or greater than SL1344. S. Typhimurium strains isolated from humans (40%) and food (25%) showed high or intermediate virulence in G. mellonella larvae after seven days exposure. Approximately, 153 virulence genes of chromosomal and plasmidial origin were detected in the strains studied. In conclusion, the ability of the S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages, and presented higher proportion of isolates with a virulent profile in G. mellonella in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmid genes, such as spvABCDR operon, pefABCD operon, rck and mig-5

Correction: Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil.

[This corrects the article DOI: 10.1371/journal.pone.0237886.]