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OBJECTIVE: To compare the diagnosis of bacterial vaginosis (BV) by Nugent scoring criteria (Nugent-BV) and the diagnosis of BV and/or aerobic vaginitis (AV) using Donders criteria (Donders-BV/AV) for identifying Molecular-BV detected by bacterial 16s rRNA profiling. METHODS: We enrolled 512 women of reproductive age in Brazil with data available on Nugent and Donders microscopic analysis and 16S rRNA sequencing. We constructed receiver operating characteristic (ROC) curves of Nugent-BV and Donders-BV/AV and calculated their area under the curves (AUCs) and 95% confidence interval (CI) for matching Molecular-BV. RESULTS: A total of 155 (28.7%) participants were positive for Nugent-BV. Donders-BV and -AV were detected in 90 (17.6%) and 75 (14.6%) participants, respectively, while 28 (5.5%) had concurrent Donders-BV and -AV. Molecular-BV was identified in 139 (27.1%) participants. Analysis of ROC curves showed that diagnosis of Nugent-BV more accurately aligned with presence of Molecular-BV (AUC: 0.88, 95% CI: 0.84-0.91) when compared to Donders-AV/BV (AUC: 0.84; CI: 0.80-0.87) (P = 0.005). CONCLUSION: The use of Nugent-BV is more representative of Molecular-BV than Donders-AV/BV.
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Microbiota , Vaginite , Vaginose Bacteriana , Feminino , Humanos , Microbiota/genética , RNA Ribossômico 16S/genética , Vagina/microbiologia , Vaginite/diagnóstico , Vaginose Bacteriana/diagnóstico , Vaginose Bacteriana/microbiologiaRESUMO
OBJECTIVE: The protective role of Lactobacillus iners in the vaginal microbiota has been questioned. Recent studies have shown that L.â¯iners is the dominating taxon in a large subset of women worldwide. The aim of this study was to identify sociodemographic, behavioural and clinical variables associated with L.â¯iners-dominated community state type (CST) III in Brazilian women of reproductive age. PARTICIPANTS AND METHODS: This study leveraged microbiota compositional data generated by sequencing of the V3-V4 16S rRNA gene from vaginal samples collected from 442 participants enrolled in a previous cross-sectional study that included 609 women in five geographical regions of Brazil. A total of 167 (27.4%) participants were excluded from the current study as they did not present a Lactobacillus-dominated vaginal microbiota. Data on sociodemographic and behavioural characteristics of the study population were obtained through face-to-face interviews. Participants were assigned to two study groups: those with L.â¯iners-dominated CST III (n=222) and those with three distinct CSTs (I, II or V) dominated by another Lactobacillus spp. (n=220). Logistic regression analysis using a stepwise method was performed to test association between CST III and participants' characteristics, considering their OR and 95% CIs. RESULTS: Among the population characteristics assessed, L.â¯iners-dominated CST III was independently associated with having two or more sexual partners (OR 3.27; 95% CI 1.50 to 7.11) and microscopic detection of Candida sp. on vaginal smears (OR 2.24; 95% CI 1.02 to 4.89). Other characteristics were inversely associated with CST III, including condom use (OR 0.59; 95% CI 0.38 to 0.91), higher educational level (OR 0.61; 95% CI 0.41 to 0.91) and diet containing milk/dairy intake (OR 0.43; 95% CI 0.20 to 0.90). CONCLUSION: Unprotected sex practices, number of sexual partners and lower educational levels may be useful for identifying women with L.â¯iners-dominated microbiota and its suboptimal protective properties. L.â¯iners microbiota does not seem to provide optimal protection against Candida sp. colonisation, warranting further investigation.
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Microbiota , Vagina , Feminino , Humanos , Lactobacillus/genética , Microbiota/genética , RNA Ribossômico 16S/genéticaRESUMO
BACKGROUND: Interplay between vaginal microbiome and human papillomavirus (HPV) remains unclear, partly due to heterogeneity of microbiota. METHODS: We used data from 546 women enrolled in a cross-sectional study in 5 Brazil. We genotyped vaginal samples for HPV and sequenced V3-V4 region of 16S rRNA gene for vaginal microbiome analysis. We used stepwise logistic regression to construct 2 linear scores to predict high-risk HPV (hrHPV) positivity: one based exclusively on presence of individual bacterial taxa (microbiome-based [MB] score) and the other exclusively on participants' sociodemographic, behavioral, and clinical (SBC) characteristics. MB score combined coefficients of 30 (of 116) species. SBC score retained 6 of 25 candidate variables. We constructed receiver operating characteristic curves for scores as hrHPV correlates and compared areas under the curve (AUC) and 95% confidence intervals (CI). RESULTS: Overall, prevalence of hrHPV was 15.8%, and 26.2% had a Lactobacillus-depleted microbiome. AUCs were 0.8022 (95% CI, .7517-.8527) for MB score and 0.7027 (95% CI, .6419-.7636) for SBC score (Pâ =â .0163). CONCLUSIONS: The proposed MB score is strongly correlated with hrHPV positivity-exceeding the predictive value of behavioral variables-suggesting its potential as an indicator of infection and possible value for clinical risk stratification.
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Alphapapillomavirus , Microbiota , Infecções por Papillomavirus , Neoplasias do Colo do Útero , Alphapapillomavirus/genética , Estudos Transversais , Feminino , Humanos , Microbiota/genética , Papillomaviridae/genética , Infecções por Papillomavirus/epidemiologia , RNA Ribossômico 16S/genética , Vagina/microbiologiaRESUMO
INTRODUCTION: Sialidase activity in the cervicovaginal fluid (CVF) is associated with microscopic findings of bacterial vaginosis (BV). Sequencing of bacterial 16S rRNA gene in vaginal samples has revealed that the majority of microscopic BV cases fit into vaginal community-state type IV (CST IV), which was recently named "molecular-BV." Bacterial vaginosis-associated bacterial species, such as Gardnerella spp., may act as sources of CVF sialidases. These hydrolases lead to impairment of local immunity and enable bacterial adhesion to epithelial and biofilm formation. However, the impact of CVL sialidase on microbiota components and diversity remains unknown. OBJECTIVE: To assess if CVF sialidase activity is associated with changes in bacterial components of CST IV. METHODS: One hundred forty women were cross-sectionally enrolled. The presence of molecular-BV (CST IV) was assessed by V3-V4 16S rRNA sequencing (Illumina). Fluorometric assays were performed using 2-(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUAN) for measuring sialidase activity in CVF samples. Linear discriminant analysis effect size (LEfSe) was performed to identify the differently enriched bacterial taxa in molecular-BV according to the status of CVF sialidase activity. RESULTS: Forty-four participants (31.4%) had molecular-BV, of which 30 (68.2%) had sialidase activity at detectable levels. A total of 24 bacterial taxa were enriched in the presence of sialidase activity, while just two taxa were enriched in sialidase-negative samples. CONCLUSION: Sialidase activity in molecular-BV is associated with changes in bacterial components of the local microbiome. This association should be further investigated, since it may result in diminished local defenses against pathogens.
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Microbiota , Vaginose Bacteriana , Feminino , Humanos , Lactobacillus/genética , Neuraminidase/genética , RNA Ribossômico 16S/genética , Vagina/microbiologia , Vaginose Bacteriana/microbiologiaRESUMO
The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually active Amerindians (N = 82) spanning urbanization, and in urban mestizos (N = 29), in the Venezuelan Amazonas. HPV status was also considered. Sampling was performed in an urban gradient from remote villages to a town, and women were individually classified by the degree of urbanization (low, medium, and high). Amerindian cervicovaginal and introital microbiota diversity were not associated with major changes in urbanization or ethnicity. There was a non-significant trend of increased diversity with urbanization, with a few taxa found overrepresented in urban Amerindians (Brevibacterium linens and Peptoniphilus lacrimalis) or mestizos (Mobiluncus mulieris and Prevotella sp.). Among all women, cervicovaginal and introital samples clustered, respectively, in four and two community state types (CSTs), where most profiles were dominated by Lactobacillus iners, Gardnerella vaginalis or were highly diverse profiles. HPV status did not associate with microbial diversity. In conclusion, no association was found between urban level and the vaginal microbiome in Amerindian women, and little difference was found between ethnicities. L. iners and high diversity profiles, associated with vaginal health outcomes, prevail in these populations.
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Microbiota , Urbanização , Vagina/microbiologia , Biodiversidade , Colo do Útero/microbiologia , Análise por Conglomerados , Feminino , Geografia , Humanos , Infecções por Papillomavirus/microbiologia , Venezuela , Indígena Americano ou Nativo do AlascaRESUMO
BACKGROUND: Composition of the vaginal microbiome is strongly related to a woman's reproductive health and risk of sexually transmitted infections. Ethnoracial, behavioral, and environmental factors can influence microbiome. The Brazilian population is unique in terms of miscegenation of ethnic groups and behavioral characteristics across different regions. We aimed to characterize the vaginal microbiome of women from 5 geographical regions of Brazil. METHODS: We sequenced V3-V4 regions of 16S rRNA gene in vaginal samples of 609 reproductive-aged women. We performed logistic regression analyses to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between sociodemographic and behavioral factors with Lactobacillus-depleted microbiome (community state type [CST] IV). RESULTS: Vaginal samples were grouped into 5 CST: CST I (L. crispatus predominant, 30.5%), CST II (L. gasseri predominant, 4.4%), CST III (Lactobacillus iners predominant, 36.5%), CST IV (Lactobacillus-depleted, 27.4%), and CST V (L. jensenii predominant, 1.2%). Several factors were independently associated with CST IV, such as smoking (OR, 1.80; 95% CI, 1.02-3.18), number of partners (OR, 2.11; 95% CI, 1.20-3.70), and vaginal douching (OR, 2.24; 95% CI, 1.34-3.74). A protective effect was observed for milk/dairy intake (OR, 0.47; 95% CI, 0.27-0.82) and sitz bathing (OR, 0.43; 95% CI, 0.19-0.98). CONCLUSIONS: Nearly two thirds of Brazilian women may be at an increased risk for adverse outcomes associated with a vaginal microbiota characterized by the depletion of Lactobacillus or dominance by L. iners, whose protective role has been widely questioned. Several factors related to sexual behavior and intimate hygiene were associated with CST IV.
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Lactobacillus , Microbiota , Adulto , Brasil , Feminino , Humanos , Lactobacillus/genética , Microbiota/genética , RNA Ribossômico 16S/genética , VaginaRESUMO
Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico. The 16S rRNA gene V3-V4 region was sequenced using MiSeq platform for taxonomic profiles. PICRUSt was used to predict functional profiles. Human Microbiome Project was used for comparison. We showed that Hp is the most abundant member of gastric microbiota in both Chinese and Mexican samples (51 and 24%, respectively), followed by oral-associated bacteria. Taxonomic (phylum-level) profiles of stomach microbiota resembled oral microbiota, especially when the Helicobacter reads were removed. The functional profiles of stomach microbiota, however, were distinct from those found in other body sites and had higher inter-subject dissimilarity. Gastric microbiota composition did not differ by Hp colonization status or stomach anatomic sites, but did differ between paired non-malignant and tumor tissues in either Chinese or Mexican samples. Our study showed that Hp is the dominant member of the non-malignant gastric tissue microbiota in many gastric cancer patients. Our results provide insights on the gastric microbiota composition and function in gastric cancer patients, which may have important clinical implications.
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Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Neoplasias Gástricas/microbiologia , Estômago/microbiologia , Adulto , Idoso , Bactérias/classificação , Bactérias/genética , China , Feminino , Helicobacter pylori/classificação , Helicobacter pylori/genética , Helicobacter pylori/isolamento & purificação , Humanos , Masculino , México , Pessoa de Meia-Idade , Adulto JovemRESUMO
OBJECTIVE: To test the hypothesis that feeding and antibiotic exposures affect intestinal barrier maturation in preterm infants, we serially measured intestinal permeability (IP) biomarkers in infants <33 weeks gestation (gestational age [GA]) during the first 2 weeks of life. STUDY DESIGN: Eligible infants <33 weeks GA were enrolled within 4 days of birth in a prospective study of IP biomarkers (NCT01756040). Study participants received the nonmetabolized sugars lactulose/rhamnose enterally on study days 1, 8, and 15 and lactulose/rhamnose were measured in urine by high-performance liquid chromatography. Serum zonulin and fecal alpha-1-anti-trypsin, 2 other IP markers, were measured by semiquantitative Western blot and ELISA, respectively. RESULTS: In a cohort of 43 subjects, the lactulose/rhamnose ratio was increased on day 1 and decreased over 2 weeks, but remained higher in infants born at ≤28 weeks of gestation compared with IP in infants born at >28 weeks of gestation. Exclusive breastmilk feeding was associated with more rapid maturation in intestinal barrier function. A cluster analysis of 35 subjects who had urine samples from all time points revealed 3 IP patterns (cluster 1, normal maturation: n = 20 [57%]); cluster 2, decreased IP during the first week and subsequent substantial increase: n = 5 [14%]); and cluster 3, delayed maturation: n = 10 [29%]). There were trends toward more prolonged antibiotic exposure (P = .092) and delayed initiation of feeding ≥4 days (P = .064) in infants with abnormal IP patterns. CONCLUSIONS: Intestinal barrier maturation in preterm infants is GA and postnatal age dependent, and is influenced by feeding with a maturational effect of breastmilk feeding and possibly by antibiotic exposures. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01756040.
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Antibacterianos/administração & dosagem , Recém-Nascido de muito Baixo Peso/metabolismo , Absorção Intestinal/fisiologia , Leite Humano/metabolismo , Análise de Variância , Antibacterianos/farmacocinética , Biomarcadores/análise , Estudos de Casos e Controles , Desenvolvimento Infantil/fisiologia , Métodos de Alimentação , Feminino , Seguimentos , Idade Gestacional , Humanos , Lactente , Fórmulas Infantis , Fenômenos Fisiológicos da Nutrição do Lactente , Recém-Nascido , Mucosa Intestinal/metabolismo , Intestinos/efeitos dos fármacos , Lactose/administração & dosagem , Lactose/farmacocinética , Masculino , Permeabilidade/efeitos dos fármacos , Estudos Prospectivos , Ramnose/administração & dosagem , Ramnose/farmacocinéticaRESUMO
UNLABELLED: An outbreak of cholera occurred in 1991 in Mexico, where it had not been reported for more than a century and is now endemic. Vibrio cholerae O1 prototype El Tor and classical strains coexist with altered El Tor strains (1991 to 1997). Nontoxigenic (CTX(-)) V. cholerae El Tor dominated toxigenic (CTX(+)) strains (2001 to 2003), but V. cholerae CTX(+) variant El Tor was isolated during 2004 to 2008, outcompeting CTX(-) V. cholerae. Genomes of six Mexican V. cholerae O1 strains isolated during 1991 to 2008 were sequenced and compared with both contemporary and archived strains of V. cholerae. Three were CTX(+) El Tor, two were CTX(-) El Tor, and the remaining strain was a CTX(+) classical isolate. Whole-genome sequence analysis showed the six isolates belonged to five distinct phylogenetic clades. One CTX(-) isolate is ancestral to the 6th and 7th pandemic CTX(+) V. cholerae isolates. The other CTX(-) isolate joined with CTX(-) non-O1/O139 isolates from Haiti and seroconverted O1 isolates from Brazil and Amazonia. One CTX(+) isolate was phylogenetically placed with the sixth pandemic classical clade and the V. cholerae O395 classical reference strain. Two CTX(+) El Tor isolates possessing intact Vibrio seventh pandemic island II (VSP-II) are related to hybrid El Tor isolates from Mozambique and Bangladesh. The third CTX(+) El Tor isolate contained West African-South American (WASA) recombination in VSP-II and showed relatedness to isolates from Peru and Brazil. Except for one isolate, all Mexican isolates lack SXT/R391 integrative conjugative elements (ICEs) and sensitivity to selected antibiotics, with one isolate resistant to streptomycin. No isolates were related to contemporary isolates from Asia, Africa, or Haiti, indicating phylogenetic diversity. IMPORTANCE: Sequencing of genomes of V. cholerae is critical if genetic changes occurring over time in the circulating population of an area of endemicity are to be understood. Although cholera outbreaks occurred rarely in Mexico prior to the 1990s, genetically diverse V. cholerae O1 strains were isolated between 1991 and 2008. Despite the lack of strong evidence, the notion that cholera was transmitted from Africa to Latin America has been proposed in the literature. In this study, we have applied whole-genome sequence analysis to a set of 124 V. cholerae strains, including six Mexican isolates, to determine their phylogenetic relationships. Phylogenetic analysis indicated the six V. cholerae O1 isolates belong to five phylogenetic clades: i.e., basal, nontoxigenic, classical, El Tor, and hybrid El Tor. Thus, the results of phylogenetic analysis, coupled with CTXÏ array and antibiotic susceptibility, do not support single-source transmission of cholera to Mexico from African countries. The association of indigenous populations of V. cholerae that has been observed in this study suggests it plays a significant role in the dynamics of cholera in Mexico.
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Cólera/epidemiologia , Doenças Endêmicas , Variação Genética , Filogenia , Vibrio cholerae O1/classificação , Vibrio cholerae O1/genética , Toxina da Cólera/metabolismo , Genoma Bacteriano , Humanos , México/epidemiologia , Epidemiologia Molecular , Análise de Sequência de DNA , Vibrio cholerae O1/isolamento & purificaçãoRESUMO
UNLABELLED: For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. IMPORTANCE: In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.