Comparative metagenome of a stream impacted by the urbanization phenomenon

Abstract Rivers and streams are important reservoirs of freshwater for human consumption. These ecosystems are threatened by increasing urbanization, because raw sewage discharged into them alters their nutrient content and may affect the composition of their microbial community. In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream preserved and non-urbanized area, and a polluted urbanized area with discharged sewage. The metagenomic DNA was sequenced by pyrosequencing. Differences were observed in the community composition at the two sites. The non-urbanized area was overrepresented by genera of ubiquitous microbes that act in the maintenance of environments. In contrast, the urbanized metagenome was rich in genera pathogenic to humans. The functional profile indicated that the microbes act on the metabolism of methane, nitrogen and sulfur, especially in the urbanized area. It was also found that virulence/defense (antibiotic resistance and metal resistance) and stress response-related genes were disseminated in the urbanized environment. The structure of the microbial community was altered by uncontrolled anthropic interference, highlighting the selective pressure imposed by high loads of urban sewage discharged into freshwater environments.

O papel da microbiota na modulação da homeostase dos hospedeiros: correlação entre micobioma intestinal e obesidade / The role of microbiota in the modulation hosts homeostasis: correlation between obesity and intestinal mycobiome

Os fungos apresentam papel importante na saúde humana, sendo componentes da microbiota humana de diversos sítios anatômicos como, por exemplo, pele, cavidade bucal, trato gastrintestinal e trato geniturinário. São também agentes etiológicos de várias infecções, desde micoses superficiais até sistêmicas. Os fungos participam na regulação do sistema imunológico, podendo promover o surgimento de alergias das vias aéreas superiores. Estão presentes na composição da microbiota intestinal, formando o micobioma. Portanto, seu papel no desenvolvimento da obesidade deve ser considerado, atuando tanto na modulação da resposta imune local quanto através de sua interação com os demais microrganismos da microbiota intestinal. Este trabalho tem como objetivo revisar aspectos da participação microbiana na etiopatogenia da obesidade e discutir a participação dos fungos no microbioma intestinal, sua relação com a obesidade e as perspectivas futuras, com a utilização de metodologias moleculares, para um melhor entendimento do papel dos fungos na microbiota intestinal na saúde e na doença.

Associação entre cultura de secreção vaginal, características sociodemográficas e manifestações clínicas de pacientes com diagnóstico de candidíase vulvovaginal / Association between vaginal secretion culture, socio-demographic characteristics and clinical manifestations of patients with vulvovaginal candidiasis

OBJETIVO: Investigar a etiologia, o perfil epidemiológico de pacientes com candidíase vulvovaginal (CVV) e possíveis fatores predisponentes. MÉTODOS: Secreção vaginal das pacientes foi semeada em ágar Sabouraud e amostras de leveduras foram isoladas e identificadas por Polymerase Chain Reaction (PCR). Dados demográficos, clínicos e fatores predisponentes foram obtidos por meio de questionário. Para análise estatística, foram utilizados os testes t de Student, Fischer e do χ², com auxílio do software Statistical Package for the Social Sciences (SPSS), com nível de significância de 5%. RESULTADOS: Foram avaliadas 69 pacientes, com idade entre 15 e 52 anos, predominando mulheres brancas (79,7%), com escolaridade de nível superior completo (58%), casadas (56,5%) e com vida sexual ativa (97,1%). Dentre elas, 34,8% eram gestantes, 7,2% diabéticas, 1,4% soropositivas para AIDS e 36,2% usavam anticoncepcional oral. Antibioticoterapia recente foi citada por 13% das pacientes, uso de antifúngico por 5,8% e de antitricomonas por 1,4%. Uso de corticosteroides foi relatado por 2,9% das participantes e de antineoplásicos, por 1,4%. Fluxo vaginal e prurido foram as principais queixas apresentadas, respectivamente, por 97,1 e 73,9% das pacientes, seguido de ardência (63,8%) e hiperemia (63,8%). Quando presente, o fluxo foi majoritariamente branco (88,1%) ou grumoso (86,6%). O diagnóstico foi confirmado pela cultura em 55 (79,7%) pacientes, sendo 4 casos de infecção mista. A espécie prevalente foi C. albicans, seguida por um caso de C. glabrata, que foi encontrada em mais duas pacientes em associação com C. albicans. Nas outras duas infecções polimicrobianas, C. lusitaniae foi isolada com C. albicans. CONCLUSÕES: Embora a positividade da cultura tenha sido alta e os dados clínicos de CVV sejam característicos, a sintomatologia não é patognomônica. C. albicans é a espécie prevalente, mas deve-se atentar para a ocorrência de outras espécies na etiologia de CVV, como a emergência de C. lusitaniae.

PURPOSE: To investigate the etiology and the epidemiological profile of patients with vulvovaginal candidiasis (VVC) and predisposing factors. METHODS: Vaginal secretions were streaked in Sabouraud agar and yeast samples were isolated and identified by Polymerase Chain Reaction (PCR). Demographic and clinical data were obtained with a questionnaire. For statistical analysis, the Student's t-test, the χ² and Fischer tests were applied as needed using the Statistical Package for Social Sciences (SPSS) software, with the level of significance set at 5%. RESULTS: Sixty-nine patients aged from 15 to 52 years were evaluated. They were predominantly white (79.7%), with higher education (58%), married (56.5%) and sexually active (97.1%). Among them, 34.8% were pregnant, 7.2% diabetic, 1.4% seropositive for AIDS, and 36.2% were using oral contraceptives. Recent antibiotic therapy was mentioned by 13% of the patients, and antifungal or anti-trichomonas therapy was mentioned by 5.8 and 1.4% of the patients, respectively. Corticosteroid use was reported by 2.9% and antineoplastic by 1.4%. Vaginal discharge and itching were the main complaints (97.1 and 73.9%), followed by burning (63.8%) and erythema (63.8%). When present, the vaginal flow was predominantly white (88.1%) or lumpy (86.6%). The diagnosis was confirmed by culture in 55 (79.7%) patients, with mixed infections in 4 patients. The most prevalent species was C. albicans, followed by C. glabrata (one monoinfection and two mixed infections with C. albicans). C. lusitaniae and C. albicans were also identified in mixed infections (two patients). CONCLUSION: Despite the high culture positivity and clinical data characteristic of VVC, the symptoms were not pathognomonic. C. albicans is the most prevalent species, but other species are also involved in VVC etiology, such as the emergence of C. lusitaniae.

Detection of Group B Streptococcus in Brazilian pregnant women and antimicrobial susceptibility patterns

Group B Streptococcus (GBS) is still not routinely screened during pregnancy in Brazil, being prophylaxis and empirical treatment based on identification of risk groups. This study aimed to investigate GBS prevalence in Brazilian pregnant women by culture or polymerase chain reaction (PCR) associated to the enrichment culture, and to determine the antimicrobial susceptibility patterns of isolated bacteria, so as to support public health policies and empirical prophylaxis. After an epidemiological survey, vaginal and anorectal specimens were collected from 221 consenting laboring women. Each sample was submitted to enrichment culture and sheep blood agar was used to isolate suggestive GBS. Alternatively, specific PCR was performed from enrichment cultures. Antimicrobial susceptibility patterns were determined for isolated bacteria by agar diffusion method. No risk groups were identified. Considering the culture-based methodology, GBS was detected in 9.5 percent of the donors. Twenty five bacterial strains were isolated and identified. Through the culture-PCR methodology, GBS was detected in 32.6 percent specimens. Bacterial resistance was not detected against ampicillin, cephazolin, vancomycin and ciprofloxacin, whereas 22.7 percent were resistant to erythromycin and 50 percent were resistant to clindamycin. GBS detection may be improved by the association of PCR and enrichment culture. Considering that colony selection in agar plates may be laboring and technician-dependent, it may not reflect the real prevalence of streptococci. As in Brazil prevention strategies to reduce the GBS associated diseases have not been adopted, prospective studies are needed to anchor public health policies especially considering the regional GBS antimicrobial susceptibility patterns.

Distribution, detection of enterotoxigenic strains and antimicrobial drug susceptibility patterns of Bacteroides fragilis group in diarrheic and non-diarrheic feces from Brazilian infants

Despite the importance of gastrointestinal diseases and their global distribution, affecting millions of individuals around the world, the role and antimicrobial susceptibility patterns of anaerobic bacteria such as those in the Bacteroides fragilis group (BFG) are still unclear in young children. This study investigated the occurrence and distribution of species in the BFG and enterotoxigenic strains in the fecal microbiota of children and their antimicrobial susceptibility patterns. Diarrheic (n=110) and non-diarrheic (n=65) fecal samples from children aged 0-5 years old were evaluated. BFG strains were isolated and identified by conventional biochemical, physiological and molecular approaches. Alternatively, bacteria and enterotoxigenic strains were detected directly from feces by molecular biology. Antimicrobial drug susceptibility patterns were determined by the agar dilution method according to the guidelines for isolated bacteria. BFG was detected in 64.3 percent of the fecal samples (55 percent diarrheic and 80.4 percent non-diarrheic), and 4.6 percent were enterotoxigenic. Antimicrobial resistance was observed against ampicillin, ampicillin/sulbactam, piperacillin/tazobactam, meropenem, ceftriaxone, clindamycin and chloramphenicol. The data show that these bacteria are prevalent in fecal microbiota at higher levels in healthy children. The molecular methodology was more effective in identifying the B. fragilis group when compared to the biochemical and physiological techniques. The observation of high resistance levels stimulates thoughts about the indiscriminate use of antimicrobial drugs in early infancy. Further quantitative studies are needed to gain a better understanding of the role of these bacteria in acute diarrhea in children.

Bacterial vaginosis: clinical, epidemiologic and microbiological features / Bacterial vaginosis: clinical, epidemiologic and microbiological features

Bacterial Vaginosis (BV) is a polymicrobial clinical syndrome, whose etiology has not been fully understood. It occurs in approximately 30% of the women in childbearing age and is the result of the shift of protective resident microorganisms as Lactobacillus spp. by opportunistic pathogenic bacteria such as Gardnerella vaginalis. Patients with BV generally present copious, thin, homogeneous, milky, foul-smelling flow. Vaginal pH is > 4.5 and microscopy reveals bacteria-covered epithelial cells, termed “clue cells”. Around 50% of the patients are asymptomatic and the disease is associated with gynecologic complications, such as cervicitis, salpingitis, endometritis, post-operative infections and pelvic inflammatory disease; and obstetric complications, such as premature rupture of the membranes, preterm deliveries, chorioamniotitis and postpartum endometritis. Although the Nugent´s method is accepted as the “gold standard” for diagnosing BV, Amsel criteria are generally used for diagnosis in clinical practice. The Papanicolaou method is a valid diagnostic option, chiefly when it yields a positive result (mean specificity 95% when compared to gold standard). G. vaginalis has been almost universally recovered from women with BV, plays an important role in the pathogenesis of the disease, besides it may be detected in about 50% of healthy women. According to the literature, first-line drugs for BV treatment worldwide are metronidazole and clindamycin. However, regional studies on G. vaginalis drug susceptibility patterns are needed faced the so fast growing antimicrobial resistance phenomenon.

Ocorrência de bactérias clinicamente relevantes nos resíduos de serviços de saúde em um aterro sanitário brasileiro e perfil de susceptibilidade a antimicrobianos / Occurrence of clinically relevant bacteria in health service waste in a Brazilian sanitary landfill and antimicrobial susceptibility profile

Os resíduos de serviços de saúde suscitam polêmica quanto a importância para a saúde humana, animal e ambiental. Avaliou-se a ocorrência de bactérias clinicamente relevantes na pilha de resíduos de serviços de saúde em um aterro sanitário e seu perfil de susceptibilidade aos antimicrobianos. Alíquotas de chorume foram processadas para isolamento seletivo de Staphylococcus sp, bastonetes Gram negativos da família Enterobacteriaceae e não fermentadores. Resistência bacteriana a todos os antimicrobianos testados foi observada em todos os grupos microbianos, além de resistência a mais de uma droga. Os resultados permitem sugerir que bactérias viáveis nos resíduos de serviços de saúde representam riscos à saúde humana e animal. Além disso, a ocorrência de linhagens multirresistentes sustenta a hipótese dos resíduos de serviços de saúde atuarem como reservatórios de marcadores de resistência, com impacto ambiental. A falta de legislação regional de segregação, tratamento e destino de resíduos podem expor diferentes populações a riscos de transmissão de doenças infecciosas associadas a microrganismos multirresistentes.

Health service waste gives rise to controversy regarding its importance for human, animal and environmental health. Occurrences of clinically relevant bacteria in piles of health service waste in a sanitary landfill and their antimicrobial susceptibility profile were evaluated. Aliquots of leachate were processed for selective isolation of Staphylococcus sp, Gram-negative rods of the Enterobacteriaceae family and non-fermenters. Bacterial resistance to all the antimicrobials tested was observed in all microbial groups, including resistance to more than one drug. The results make it possible to suggest that viable bacteria in health service waste represent risks to human and animal health. Furthermore, occurrences of multiresistant strains support the hypothesis that health service waste acts as a reservoir for resistance markers, with an environmental impact. The lack of regional legislation concerning segregation, treatment and final disposal of waste may expose different populations to risks of transmission of infectious diseases associated with multiresistant microorganisms

Estudo piloto sobre a avaliação da periodontite crônica em pacientes com doença renal crônica / Pilot study on the association of chronic periodontitis in patients with chronic kidney disease

Introdução: Periodontite crônica (PC) é uma infecção bacteriana dos tecidos de suporte, encontrada na placa dental subgengival, e pode determinar uma resposta inflamatória sistêmica. Objetivo: Avaliar a ocorrência de PC em pacientes com doença renal crônica (DRC) pré-dialítica. Material e Métodos: O estagiamento da DRC baseou-se no Kidney Disease Outcome Quality Initiative da National Kidney Foundation. A filtração glomerular (FG) foi estimada pela equação da Modification of Diet in Renal Disease a partir da creatinina plasmática. A resposta inflamatória foi determinada pela proteína C-reativa (PCR) em 30 pacientes, divididos em três grupos: o grupo 1 (G1), composto de seis pacientes com PC e sem DRC, grupo 2 (G2), composto de 19 pacientes com PC localizada e DRC, e o grupo 3 (G3), composto de cinco pacientes com PC generalizada e DRC. A gravidade da PC baseou-se na profundidade de sondagem (PS). A identificação das bactérias foi realizada pela técnica de reação em cadeia da polimerase. Resultados: A PCR do G1 (2,4 ± 2,5 mg/L) não foi diferente do G2 (4,6 + 4,5 mg/L, p = 0,1), mas observou-se uma tendência de diferença relativamente ao G3 (7,6 ± 3,8 mg/L, p = 0,05). Comparativamente à PS do grupo G1 (PS = 2,1 ± 0,6 mm), as do G2 (PS = 2,9 ± 1,2 mm, p = 0,05) e do G3 (G3 de 4,3 ± 0,8 mm, p = 0,04) foram mais graves. Não foram observadas diferenças estatísticas entre as frequências das bactérias isoladas nos três grupos. Conclusão: Apesar do número limitado de pacientes, nossos resultados sugerem que a PC generalizada é mais frequente nos pacientes com DRC.

Introduction: Chronic periodontitis (CP) is a bacterial infection of the supporting soft tissue in the subgingival dental plaque that can trigger systemic inflammation. Objective: The objective of this study was to evaluate the incidence of CP in patients with predialytic and chronic kidney disease. Material and Methods: The definition of ESRD was based on the Kidney Disease Outcome Quality Initiative proposed by the National Kidney Foundation. The Modification of Diet in Renal Disease equation [P2] was used to estimate the glomerular filtration rate (GFR) from the plasma creatinine level. C-reactive protein (CRP) was used to determine the inflammatory response in 30 patients divided in three groups: group 1 (G1) was composed of six patients without CKD and with CP; group 2 (G2) comprised 19 patients with CKD and localized CP; and group 3 (G3) was composed of five patients with CKD and generalized CP. The severity of CP was based on the probing depth (PD). Bacteria were identified by polymerase chain reaction. Results: C-reactive protein in G1 (2.4 ± 2.5 mg/L) did not differ from that in G2 (4.6 ± 4.5 mg/L, p = 0.1), but a tendency to differ compared to G3 (7.6 ± 3.8 mg/L, p = 0.05) was observed. Probing depth in G1 (2.1 ± 0.6 mm) was less severe than in G2 (PD = 2.9 ± 1.2 mm, p = 0.05) and G3 (PD = 4.3 ± 0.8 mm, p = 0.04). Statistical differences in the frequency of the bacteria isolated in all three groups were not observed. Conclusion: Despite the limited number of patients, our results suggest that generalized CP is more frequent in patients with ESRD.