RESUMEN
We report a 23% asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) Omicron carriage rate in participants being enrolled into a clinical trial in South Africa, 15-fold higher than in trials before Omicron. We also found lower CD4â +â T-cell counts in persons with human immunodeficiency virus (HIV) strongly correlated with increased odds of being SARS-CoV-2 polymerase chain reaction (PCR) positive.
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COVID-19 , SARS-CoV-2 , Humanos , Reacción en Cadena de la Polimerasa , Sudáfrica/epidemiologíaRESUMEN
BACKGROUND: Clostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood. METHODS: We identified asymptomatic C. difficile carriage among 1897 ICU patients using rectal swabs from an existing ICU vancomycin-resistant enterococci (VRE) surveillance program. C. difficile isolates from VRE swabs, and from C. difficile-positive stool samples, were genome sequenced. Spatial-temporal data from hospital records assessed genomically identified clusters for potential transmission events. RESULTS: Genomic analyses identified a diverse set of strains in infected patients and asymptomatic carriers. A total of 7.4% of ICU patients asymptomatically carried C. difficile; 69% of isolates carried an intact toxin locus. In contrast, 96% of C. difficile stool isolates were toxin encoding. CDI rates in asymptomatic carriers of toxin-encoding strains were 5.3% versus 0.57% in noncarriers. The relative risk for CDI with asymptomatic carriage of a toxin-encoding strain was 9.32 (95% confidence interval, 3.25-26.7). Genomic identification of clonal clusters supported analyses for asymptomatic transmission events, with spatial-temporal overlaps identified in 13 of 28 cases. CONCLUSIONS: Our studies provide the first genomically confirmed assessments of CDI relative risk from asymptomatic carriage of toxin-encoding strains and highlight the complex dynamics of asymptomatic transmission in ICUs. Asymptomatic carriers are an active reservoir of C. difficile in the nosocomial environment. C. difficile screening can be implemented within existing HAI surveillance programs and has the potential to support infection-control efforts against this pathogen.
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Clostridioides difficile , Infecciones por Clostridium , Clostridioides , Clostridioides difficile/genética , Infecciones por Clostridium/epidemiología , Genómica , Humanos , Unidades de Cuidados Intensivos , RiesgoRESUMEN
BACKGROUND: Prolonged enteropathogen shedding after diarrhea complicates the identification of etiology in subsequent episodes and is an important driver of pathogen transmission. A standardized approach has not been applied to estimate the duration of shedding for a wide range of pathogens. METHODS: We used a multisite birth cohort of children 0-24 months of age from whom diarrheal and monthly nondiarrheal stools were previously tested by quantitative polymerase chain reaction for 29 enteropathogens. We modeled the probability of detection of the etiologic pathogen before and after diarrhea using a log-normal accelerated failure time survival model and estimated the median duration of pathogen carriage as well as differences in subclinical pathogen carriage 60 days after diarrhea onset in comparison to a prediarrhea baseline. RESULTS: We analyzed 3247 etiologic episodes of diarrhea for the 9 pathogens with the highest attributable burdens of diarrhea. The median duration of postdiarrheal carriage varied widely by pathogen, from about 1 week for rotavirus (median, 8.1 days [95% confidence interval {CI}, 6.2-9.6]) to >1 month for Cryptosporidium (39.5 days [95% CI, 30.6-49.0]). The largest increases in subclinical pathogen carriage before and after diarrhea were seen for Cryptosporidium (prevalence difference between 30 days prior and 60 days after diarrhea onset, 0.30 [95% CI, .23-.39]) and Shigella (prevalence difference, 0.21 [95% CI, .16-.27]). CONCLUSIONS: Postdiarrheal shedding was widely variable between pathogens, with strikingly prolonged shedding seen for Cryptosporidium and Shigella. Targeted antimicrobial therapy and vaccination for these pathogens may have a relatively large impact on transmission.
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Criptosporidiosis , Cryptosporidium , Infecciones por Rotavirus , Rotavirus , Niño , Preescolar , Diarrea , Heces , Humanos , LactanteRESUMEN
BACKGROUND: Malaria in endemic countries is often asymptomatic during pregnancy, but it has substantial consequences for both the mother and her unborn baby. During pregnancy, anaemia is an important consequence of malaria infection. In Burkina Faso, the intensity of malaria varies according to the season, albeit the prevalence of malaria and anaemia as well as their risk factors, during high and low malaria transmission seasons is underexplored at the household level. METHODS: Data of 1751 pregnant women from October 2013 to March 2014 and 1931 pregnant women from April 2017 to June 2017 were drawn from two cross-sectional household surveys conducted in 24 health districts of Burkina Faso. Pregnant women were tested for malaria in their household after consenting. Asymptomatic carriage was defined as a positive result from malaria rapid diagnostic tests in the absence of clinical symptoms of malaria. Anaemia was defined as haemoglobin level less than 11 g/dL in the first and third trimester and less than 10.5 g/dL in the second trimester of pregnancy. RESULTS: Prevalence of asymptomatic malaria in pregnancy was estimated at 23.9% (95% CI 20.2-28.0) during the high transmission season (October-November) in 2013. During the low transmission season, it was 12.7% (95% CI 10.9-14.7) between December and March in 2013-2014 and halved (6.4%; 95% CI 5.3-7.6) between April and June 2017. Anaemia prevalence was estimated at 59.4% (95% CI 54.8-63.8) during the high transmission season in 2013. During the low transmission season, it was 50.6% (95% CI 47.7-53.4) between December and March 2013-2014 and 65.0% (95% CI 62.8-67.2) between April and June, 2017. CONCLUSION: This study revealed that the prevalence of malaria asymptomatic carriage and anaemia among pregnant women at the community level remain high throughout the year. Thus, more efforts are needed to increase prevention measures such as IPTp-SP coverage in order to reduce anaemia and contribute to preventing low birth weight and poor pregnancy outcomes.
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Anemia/epidemiología , Infecciones Asintomáticas/epidemiología , Malaria/epidemiología , Complicaciones Parasitarias del Embarazo/epidemiología , Adulto , Anemia/parasitología , Burkina Faso/epidemiología , Estudios Transversales , Femenino , Humanos , Malaria/parasitología , Embarazo , Complicaciones Parasitarias del Embarazo/parasitología , Mujeres Embarazadas , Prevalencia , Adulto JovenRESUMEN
Multidrug resistance due to the production of extended-spectrum beta-lactamases (ESBLs) is a major problem in human as well as in veterinary medicine. These strains appear in animal and human microbiomes and can be the source of infection both in animal and in human healthcare, in accordance with the One Health theorem. In this study we examined the prevalence of ESBL-producing bacteria in food-producing animals. We collected 100 porcine and 114 poultry samples to examine the prevalence of ESBL producers. Isolates were identified using the MALDI-TOF system and their antibiotic susceptibility was tested using the disk diffusion method. ESBL gene families and phylogroups were detected by polymerase chain reactions. The prevalence of ESBL producers was relatively high in both sample groups: 72 (72.0%) porcine and 39 (34.2%) poultry isolates were ESBL producers. Escherichia coli isolates were chosen for further investigations. The most common ESBL gene was CTX-M-1 (79.3%). Most of the isolates belong to the commensal E. coli phylogroups. The porcine isolates could be divided into three phylogroups, while the distribution of the poultry isolates was more varied. In summary, ESBL-producing bacteria are prevalent in the faecal samples of the examined food-producing animals, with a dominance of the CTX-M-1 group enzymes and commensal E. coli phylogroups.
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Infecciones por Escherichia coli , Enfermedades de los Porcinos , Animales , Antibacterianos , Escherichia coli/genética , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/veterinaria , Heces , Aves de Corral , Porcinos , Enfermedades de los Porcinos/epidemiología , beta-Lactamasas/genéticaRESUMEN
BACKGROUND: Asymptomatic patients colonized with Clostridioides difficile are at risk of developing C. difficile infection (CDI), but the factors associated with disease onset are poorly understood. Our aims were to identify predictors of hospital-onset CDI (HO-CDI) among colonized patients and to explore the potential benefits of primary prophylaxis to prevent CDI. METHODS: We conducted a retrospective cohort study in a tertiary academic institution. Colonized patients were identified by detecting the tcdB gene by polymerase chain reaction on a rectal swab. Univariate and multivariate logistic regression analyses were used to identify predictors of HO-CDI. RESULTS: There were 19 112 patients screened, from which 960 (5%) colonized patients were identified: 513 met the inclusion criteria. Overall, 39 (7.6%) developed a HO-CDI, with a 30-day attributable mortality of 15%. An increasing length of stay (adjusted odds ratio [aOR] per day, 1.03; P = .006), exposure to multiple classes of antibiotics (aOR per class, 1.45; P = .02), use of opioids (aOR, 2.78; P = .007), and cirrhosis (aOR 5.49; P = .008) were independently associated with increased risks of HO-CDI, whereas the use of laxatives was associated with a lower risk of CDI (aOR 0.36; P = .01). Among the antimicrobials, B-lactam with B-lactamase inhibitors (OR 3.65; P < .001), first-generation cephalosporins (OR 2.38; P = .03), and carbapenems (OR 2.44; P = .03) correlated with the greatest risk of HO-CDI. By contrast, patient age, the use of proton pump inhibitors, and the use of primary prophylaxis were not significant predictors of HO-CDI. CONCLUSIONS: This study identifies several factors that are associated with CDI among colonized patients. Whether modifying these variables could decrease the risk of CDI should be investigated.
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Toxinas Bacterianas , Clostridioides difficile , Infecciones por Clostridium , Clostridioides , Infecciones por Clostridium/diagnóstico , Infecciones por Clostridium/epidemiología , Humanos , Estudios Retrospectivos , Factores de RiesgoRESUMEN
BACKGROUND: Ongoing efforts to fight Plasmodium falciparum malaria has reduced malaria in many areas, but new tools are needed to monitor further progress, including indicators of decreasing exposure to parasite infection. Sero-surveillance is considered promising to monitor exposure, transmission and immunity. METHODS: IgG responses to three antigen biomarkers were evaluated in a retrospective study involving: (i) surveys of 798 asymptomatic villagers from 2 Senegalese endemic settings conducted before 2002 and after the 2013 intensification of control measures, and (ii) in 105 symptomatic individuals from different settings in Côte d'Ivoire. Response to up to eight P. falciparum antigens, including recombinant MSP1p9 antigen and LSA141 peptide, were analysed using multiplex technology and responses to whole P. falciparum schizont extract (SE, local strain adapted to culture) were measured by ELISA. RESULTS: MSP1p9 and LSA141 IgG responses were shown to be relevant indicators monitoring immune status in the different study sites both from Côte d'Ivoire and Senegal. Between 2002 and 2013, individuals participating in both studies showed higher decline of sero-positivity in young (< 15 years: range 12% to 50%) than older (> 15 years: no decline to 15%) individuals from Dielmo and Ndiop. A mathematical sero-catalytic model from the complete Dielmo/Ndiop survey was used to reconstruct declining levels of sero-positivity in more detail, demonstrating that anti-SE seroprevalence levels most accurately reflected malaria exposure in the two villages. CONCLUSION: For standard screening of population immune status at sites envisaging elimination, the use of ELISA-based assays targeting selected antigens can contribute to provide important epidemiologic surveillance data to aid malaria control programmes.
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Anticuerpos Antiprotozoarios/sangre , Antígenos de Protozoos/inmunología , Malaria Falciparum/diagnóstico , Malaria Falciparum/prevención & control , Adolescente , Adulto , Anciano , Anticuerpos Antiprotozoarios/inmunología , Antígenos de Protozoos/clasificación , Infecciones Asintomáticas/epidemiología , Biomarcadores/sangre , Niño , Preescolar , Côte d'Ivoire/epidemiología , Ensayo de Inmunoadsorción Enzimática , Humanos , Inmunoglobulina G/sangre , Inmunoglobulina G/inmunología , Lactante , Estudios Longitudinales , Malaria Falciparum/epidemiología , Tamizaje Masivo/estadística & datos numéricos , Persona de Mediana Edad , Estudios Retrospectivos , Estudios Seroepidemiológicos , Adulto JovenRESUMEN
BACKGROUND: KwaZulu-Natal, one of South Africa's three malaria endemic provinces, is nearing malaria elimination, reporting fewer than 100 locally-acquired cases annually since 2010. Despite sustained implementation of essential interventions, including annual indoor residual spraying, prompt case detection using malaria rapid diagnostics tests and treatment with effective artemisinin-based combination therapy, low-level focal transmission persists in the province. This malaria prevalence and entomological survey was therefore undertaken to identify the drivers of this residual transmission. METHODS: Malaria prevalence as well as malaria knowledge, attitudes and practices among community members and mobile migrant populations within uMkhanyakude district, KwaZulu-Natal were assessed during a community-based malaria prevalence survey. All consenting participants were tested for malaria by both conventional and highly-sensitive falciparum-specific rapid diagnostic tests. Finger-prick filter-paper blood spots were also collected from all participants for downstream parasite genotyping analysis. Entomological investigations were conducted around the surveyed households, with potential breeding sites geolocated and larvae collected for species identification and insecticide susceptibility testing. A random selection of households were assessed for indoor residual spray quality by cone bioassay. RESULTS: A low malaria prevalence was confirmed in the study area, with only 2% (67/2979) of the participants found to be malaria positive by both conventional and highly-sensitive falciparum-specific rapid diagnostic tests. Malaria prevalence however differed markedly between the border market and community (p < 0001), with the majority of the detected malaria carriers (65/67) identified as asymptomatic Mozambican nationals transiting through the informal border market from Mozambique to economic hubs within South Africa. Genomic analysis of the malaria isolates revealed a high degree of heterozygosity and limited genetic relatedness between the isolates supporting the hypothesis of limited local malaria transmission within the province. New potential vector breeding sites, potential vector populations with reduced insecticide susceptibility and areas with sub-optimal vector intervention coverage were identified during the entomological investigations. CONCLUSION: If KwaZulu-Natal is to successfully halt local malaria transmission and prevent the re-introduction of malaria, greater efforts need to be placed on detecting and treating malaria carriers at both formal and informal border crossings with transmission blocking anti-malarials, while ensuring optimal coverage of vector control interventions is achieved.
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Enfermedades Transmisibles Importadas/epidemiología , Enfermedades Transmisibles Importadas/transmisión , Malaria/epidemiología , Malaria/transmisión , Infecciones Asintomáticas/epidemiología , Erradicación de la Enfermedad , Enfermedades Endémicas/estadística & datos numéricos , Humanos , Prevalencia , Sudáfrica/epidemiologíaRESUMEN
Acute intermittent porphyria (AIP) is the most common and severe form of porphyrias. This is a dominant inherited disorder with low penetrance, caused by mutations in gene coding hydroxymethylbilane synthase (HMBS). We present the results of our long-term genetic study of AIP patients and their relatives (N = 153 and 302, respectively). We detected 88 HMBS gene mutations, 24 of which never described before. To identify additional factors conditioning AIP manifestation, we carried out whole exome sequencing on the group of AIP patients (N = 6). Mutation spectra of different patients virtually did not overlap. In 5 out of 6 patients, we found defects in genes regulating nervous system (UNC13A, ALG8, FBXO38, AGRN, DOK7, SCN4A). As usually acute AIP attacks have various neurological symptoms, we proposed a hypothesis of possible contribution of mutations in such genes in AIP manifestation.
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Predisposición Genética a la Enfermedad , Hidroximetilbilano Sintasa/genética , Mutación , Penetrancia , Porfiria Intermitente Aguda/diagnóstico , Porfiria Intermitente Aguda/genética , Alelos , Sustitución de Aminoácidos , Frecuencia de los Genes , Estudios de Asociación Genética , Genotipo , Humanos , Fenotipo , Federación de Rusia , Secuenciación del ExomaRESUMEN
Clostridioides difficile infection (CDI) is an emerging public health threat and C. difficile is the most common cause of antimicrobial-associated diarrhea worldwide and the leading cause of hospital-associated infections in the US, yet the burden of community-acquired infections (CAI) is poorly understood. Characterizing C. difficile isolated from canines is important for understanding the role that canines may play in CAI. In addition, several studies have suggested that canines carry toxigenic C. difficile asymptomatically, which may imply that there are mechanisms responsible for resistance to CDI in canines that could be exploited to help combat human CDI. To assess the virulence potential of canine-derived C. difficile, we tested whether toxins TcdA and TcdB (hereafter toxins) derived from a canine isolate were capable of causing tight junction disruptions to colonic epithelial cells. Additionally, we addressed whether major differences exist between human and canine cells regarding C. difficile pathogenicity by exposing them to identical toxins. We then examined the canine gut microbiome associated with C. difficile carriage using 16S rRNA gene sequencing and searched for deviations from homeostasis as an indicator of CDI. Finally, we queried 16S rRNA gene sequences for bacterial taxa that may be associated with resistance to CDI in canines. Clostridioides difficile isolated from a canine produced toxins that reduced tight junction integrity in both human and canine cells in vitro. However, canine guts were not dysbiotic in the presence of C. difficile. These findings support asymptomatic carriage in canines and, furthermore, suggest that there are features of the gut microbiome and/or a canine-specific immune response that may protect canines against CDI. We identified two biologically relevant bacteria that may aid in CDI resistance in canines: 1) Clostridium hiranonis, which synthesizes secondary bile acids that have been shown to provide resistance to CDI in mice; and 2) Sphingobacterium faecium, which produces sphingophospholipids that may be associated with regulating homeostasis in the canine gut. Our findings suggest that canines may be cryptic reservoirs for C. difficile and, furthermore, that mechanisms of CDI resistance in the canine gut could provide insights into targeted therapeutics for human CDI.
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Biota , Clostridioides difficile/crecimiento & desarrollo , Infecciones por Clostridium/veterinaria , Enfermedades de los Perros/microbiología , Disbiosis , Tracto Gastrointestinal/microbiología , Animales , Proteínas Bacterianas/toxicidad , Toxinas Bacterianas/toxicidad , Células CACO-2 , Supervivencia Celular/efectos de los fármacos , Clostridioides difficile/patogenicidad , Infecciones por Clostridium/microbiología , Perros , Enterotoxinas/toxicidad , Células Epiteliales/efectos de los fármacos , Células Epiteliales/microbiología , Células Epiteliales/fisiología , Humanos , Ratones , Fosfolípidos/análisis , Uniones Estrechas/efectos de los fármacosRESUMEN
The affordability of bacterial genome sequencing has provided a helpful tool for sequencing large strain collections. Bente Børud (J. Bacteriol. 200:e00794-17, 2018, https://doi.org/doi:10.1128/JB.00794-17) recently led an effort to analyze the genomes of a collection of oropharyngeal Neisseria meningitidis isolates from 50 healthy individuals. Paired longitudinal isolates from each individual were sequenced. Genome analyses focused on (i) predicting the expression state of phase-variable loci that encode enzymes important for O-linked protein glycosylation and (ii) correlating specific genotypes with glycosylation phenotypes.
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Infecciones Meningocócicas , Neisseria meningitidis , Genotipo , Glicosilación , Humanos , Fenotipo , PolisacáridosRESUMEN
We investigated the faecal carriage prevalence of extended-spectrum ß-lactamase production in Escherichia coli (EP-EC) and/or Klebsiella pneumoniae (EP-KP) and risk factors associated with carriage among adult study subjects in Finland, Germany, Latvia, Poland, Russia and Sweden (partner countries). The aim was to get indicative data on the prevalence of ESBL-carriage in specific populations in the region. Faecal samples were collected from four study populations and screened on ChromID-ESBL and ChromID-OXA-48 plates. Positive isolates were further characterised phenotypically. Our results show a large variation in carrier prevalence ranging from 1.6% in Latvia to 23.2% in Russia for EP-EC. For the other partner countries, the prevalence of EP-EC were in increasing numbers, 2.3% for Germany, 4.7% for Finland, 6.6% for Sweden, 8.0% for Poland and 8.1% for all partner countries in total. Carriers of EP-KP were identified only in Finland, Russia and Sweden, and the prevalence was < 2% in each of these countries. No carriers of carbapenemase-producing isolates were identified. This is the first study reporting prevalence of carriers (excluding traveller studies) for Finland, Latvia, Poland and Russia. It contributes with important information regarding the prevalence of EP-EC and EP-KP carriage in regions where studies on carriers are limited.
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Infecciones Asintomáticas/epidemiología , Infecciones por Escherichia coli/epidemiología , Escherichia coli/aislamiento & purificación , Heces/microbiología , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/aislamiento & purificación , Adulto , Antibacterianos/farmacología , Proteínas Bacterianas/metabolismo , Estudios Transversales , Farmacorresistencia Bacteriana Múltiple , Escherichia coli/enzimología , Europa (Continente)/epidemiología , Femenino , Humanos , Klebsiella pneumoniae/enzimología , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Prevalencia , Factores de Riesgo , Federación de Rusia/epidemiología , Adulto Joven , beta-Lactamasas/metabolismoRESUMEN
Studies of the human pathogen group A Streptococcus (GAS) define the carrier phenotype to be an increased ability to adhere to and persist on epithelial surfaces and a decreased ability to cause disease. We tested the hypothesis that a single amino acid change (Arg135Gly) in a highly conserved sensor kinase (LiaS) of a poorly defined GAS regulatory system contributes to a carrier phenotype through increased pilus production. When introduced into an emm serotype-matched invasive strain, the carrier allele (the gene encoding the LiaS protein with an arginine-to-glycine change at position 135 [liaSR135G]) recapitulated a carrier phenotype defined by an increased ability to adhere to mucosal surfaces and a decreased ability to cause disease. Gene transcript analyses revealed that the liaS mutation significantly altered transcription of the genes encoding pilus in the presence of bacitracin. Elimination of pilus production in the isogenic carrier mutant decreased its ability to colonize the mouse nasopharynx and to adhere to and be internalized by cultured human epithelial cells and restored the virulence phenotype in a mouse model of necrotizing fasciitis. We also observed significantly reduced survival of the isogenic carrier mutant compared to that of the parental invasive strain after exposure to human neutrophils. Elimination of pilus in the isogenic carrier mutant increased the level of survival after exposure to human neutrophils to that for the parental invasive strain. Together, our data demonstrate that the carrier mutation (liaSR135G) affects pilus expression. Our data suggest new mechanisms of pilus gene regulation in GAS and that the invasiveness associated with pilus gene regulation in GAS differs from the enhanced invasiveness associated with increased pilus production in other bacterial pathogens.
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Portador Sano/microbiología , Fimbrias Bacterianas/genética , Histidina Quinasa/genética , Mutación Missense , Biogénesis de Organelos , Infecciones Estreptocócicas/microbiología , Streptococcus pyogenes/patogenicidad , Animales , Adhesión Bacteriana , Células Cultivadas , Células Epiteliales/microbiología , Femenino , Perfilación de la Expresión Génica , Interacciones Huésped-Patógeno , Humanos , Ratones , Viabilidad Microbiana , Nasofaringe/microbiología , Neutrófilos/inmunología , Neutrófilos/microbiología , Streptococcus pyogenes/fisiología , Transcripción GenéticaRESUMEN
A 9-month-old infant died from Ebola virus (EBOV) disease with unknown epidemiological link. While her parents did not report previous illness, laboratory investigations revealed persisting EBOV RNA in the mother's breast milk and the father's seminal fluid. Genomic analysis strongly suggests EBOV transmission to the child through breastfeeding.
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Ebolavirus/aislamiento & purificación , Fiebre Hemorrágica Ebola/transmisión , Transmisión Vertical de Enfermedad Infecciosa , Leche Humana/virología , Adulto , Análisis por Conglomerados , Femenino , Humanos , Lactante , Masculino , Filogenia , ARN Viral/genética , ARN Viral/aislamiento & purificación , Semen/virología , Análisis de Secuencia de ADN , Homología de Secuencia , Adulto JovenRESUMEN
BACKGROUND: Malaria in Senegal is due essentially to infections by Plasmodium falciparum and, to a lesser extent to Plasmodium malariae and Plasmodium ovale. By the use of molecular methods, detection of Plasmodium vivax has been recently reported in the region of Kedougou, raising the question of appraisal of its potential prevalence in this setting. METHODS: A retrospective serological study was carried out using 188 samples taken from 2010 to 2011 in a longitudinal school survey during which 48 asymptomatic children (9-11 years) were recruited. Four collections of samples collected during two successive dry and rainy seasons were analysed for antibody responses to P. vivax and P. falciparum. Recombinant P. falciparum and P. vivax MSP1 antigens and total P. falciparum schizont lysate from African 07/03 strain (adapted to culture) were used for ELISA. Nested PCR amplification was used for molecular detection of P. vivax. RESULTS: A surprising high prevalence of IgG responses against P. vivax MSP1 was evidenced with 53% of positive samples and 58% of the individuals that were found positive to this antigen. There was 77% of responders to P. falciparum outlined by 63% of positive samples. Prevalence of responders did not differ as function of seasons. Levels of antibodies to P. falciparum fluctuated with significant increasing between dry and rainy season (P < 0.05), contrary to responses to P. vivax. There was a significant reciprocal relationship (P < 10-3) between antibody responses to the different antigens, but with weak coefficient of correlation (Rho around 0.3) underlining a variable profile at the individual level. Clear molecular signature was found in positive IgG to P. vivax msp1 samples by PCR. CONCLUSION: This cross-sectional longitudinal study highlights the unexpected high circulation of P. vivax in this endemic area. Sero-immunology and molecular methods are powerful additive tools to identify endemic sites where relevant control measures have to be settled and monitored.
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Anticuerpos Antiprotozoarios/sangre , Infecciones Asintomáticas/epidemiología , Malaria Vivax/sangre , Malaria Vivax/epidemiología , Plasmodium vivax/aislamiento & purificación , Niño , Estudios Transversales , ADN Protozoario/genética , Ensayo de Inmunoadsorción Enzimática , Femenino , Humanos , Inmunoglobulina G/sangre , Estudios Longitudinales , Malaria Falciparum/sangre , Malaria Falciparum/epidemiología , Malaria Falciparum/inmunología , Malaria Falciparum/parasitología , Malaria Vivax/inmunología , Malaria Vivax/parasitología , Masculino , Plasmodium falciparum/genética , Plasmodium vivax/genética , Plasmodium vivax/inmunología , Reacción en Cadena de la Polimerasa , Prevalencia , Estudios Retrospectivos , Senegal/epidemiología , Pruebas SerológicasRESUMEN
BACKGROUND: Group A Streptococcus (GAS; Streptococcus pyogenes) causes a range of mild to severe infections in humans. It can also colonize healthy persons asymptomatically. Therefore, it is important to study GAS carriage in healthy populations, as carriage of it might lead to subsequent disease manifestation, clonal spread in the community, and/or diversification of the organism. Throat swab culture is the gold standard method for GAS detection. Advanced culture-independent methods provide rapid and efficient detection of microorganisms directly from clinical samples. We investigated the presence of GAS in throat swab samples from healthy adults in Japan using culture-dependent and culture-independent methods. RESULTS: Two throat swab samples were collected from 148 healthy volunteers. One was cultured on selective medium, while total DNA extracted from the other was polymerase chain reaction (PCR) amplified with two GAS-specific primer pairs: one was a newly designed 16S rRNA-specific primer pair, the other a previously described V-Na+-ATPase primer pair. Although only 5 (3.4 %) of the 148 samples were GAS-positive by the culture-dependent method, 146 (98.6 %) were positive for the presence of GAS DNA by the culture-independent method. To obtain serotype information by emm typing, we performed nested PCR using newly designed emm primers. We detected the four different emm types in 25 (16.9 %) samples, and these differed from the common emm types associated with GAS associated diseases in Japan. The different emm types detected in the healthy volunteers indicate that the presence of unique emm types might be associated with GAS carriage. CONCLUSIONS: Our results suggest that culture-independent methods should be considered for profiling GAS in the healthy hosts, with a view to obtaining better understanding of these organisms. The GAS-specific primers (16S rRNA and V-Na+-ATPase) used in this study can be used to estimate the maximum potential GAS carriage in people.
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Faringe/microbiología , Streptococcus pyogenes/genética , Streptococcus pyogenes/aislamiento & purificación , Adulto , Proteínas Bacterianas/genética , Técnicas de Tipificación Bacteriana/métodos , Cartilla de ADN , ADN Bacteriano/análisis , Genotipo , Humanos , Japón , Persona de Mediana Edad , Tipificación Molecular/métodos , Reacción en Cadena de la Polimerasa/métodos , ARN Ribosómico 16S/genética , Serotipificación , Infecciones Estreptocócicas/diagnóstico , Infecciones Estreptocócicas/microbiología , Adulto JovenRESUMEN
Because asymptomatic carriage of extended-spectrum beta-lactamase (ESBL) producers is a risk factor for infection, data on colonization dynamics are important when planning infection control. This study investigated fecal colonization with ESBL producers among inpatients, outpatients and medical students and compares the characteristics of ESBL producers among these groups. Carriage rates were investigated in 5581 fecal samples; 4343 from inpatients (330, 1397, 619 and 1864 from adult ICUs [intensive care units], adult non-ICUs, pediatric ICUs and pediatric non-ICUs, respectively), 814 from outpatients and 424 from screening of medical students. ESBL producers were characterized by co-resistance, integrons carried, and aminoglycoside resistance and ESBL genes. Dynamic regression models were built to identify relationships between combinations of time series of monthly antibiotic consumption, prevalence of carriers and infected subjects. Inpatients, ICU patients and adults showed higher prevalence than outpatients, non-ICU patients or children (7.4%, 9.3% and 12.0% vs. 3.1%, 6.1% and 4.1%, respectively). Klebsiella pneumoniae was more frequent in ICU patients; dominance of CTX-M-15 producers was more marked in adult than in pediatric inpatients. ESBL carriage was shown to be a consequence of infection in adults in the time-series analysis; antibiotic consumption had little effect. The epidemiology of colonization with ESBL producers differed between pediatric ICU, adult ICU and adult non-ICU patients. In adults, carriage of ESBL producers seems to be the consequence of infection, especially in ICU patients; the main source of colonization is nosocomial acquisition. In contrast, children are less likely to acquire colonizer strains in hospitals; importation of ESBL producers by colonized children seems to be significant.
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Portador Sano/epidemiología , Infecciones por Enterobacteriaceae/epidemiología , Enterobacteriaceae/enzimología , Heces/microbiología , beta-Lactamasas/análisis , Antibacterianos/uso terapéutico , Portador Sano/microbiología , Utilización de Medicamentos , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/aislamiento & purificación , Infecciones por Enterobacteriaceae/microbiología , Humanos , Pacientes Internos , Integrones , Pruebas de Sensibilidad Microbiana , Pacientes Ambulatorios , Prevalencia , Estudiantes de MedicinaRESUMEN
The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies ("pool-seq"), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286 S. aureus culture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
RESUMEN
The most common approach to sampling the bacterial populations within an infected or colonized host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. Sequencing a mixture of several colonies (pool-seq) is a better approach to detect population heterogeneity, but it is more complex to analyse due to different types of heterogeneity, such as within-clone polymorphisms, multi-strain mixtures, multi-species mixtures and contamination. Here, we compared 8 single-colony isolates (singles) and pool-seq on a set of 2286 Staphylococcus aureus culture samples to identify features that can distinguish pure samples, samples undergoing intraclonal variation and mixed strain samples. The samples were obtained by swabbing 3 body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
Asunto(s)
Staphylococcus aureus Resistente a Meticilina , Infecciones Estafilocócicas , Humanos , Staphylococcus aureus , Genómica , Frecuencia de los Genes , Resistencia a la MeticilinaRESUMEN
Pertussis (whooping cough) is an important cause of morbidity and mortality in infants world-wide, and continues to be a public health concern despite high vaccination coverage. The disease, caused by bacterium Bordetella pertussis, is present in all countries. Before vaccines became widely available in the 1950s, pertussis was one of the most common childhood diseases worldwide. According to WHO, estimation of deaths was 4 millions/year in 1950 and 100 000/year in 2015. But morbidity remains important with a high circulation of the bacterium determining atypical clinical forms after whole cell or acellular vaccines use. This is due mainly to the absence of booster doses in adolescents and adults. Major progress are generalisation of PCR and vaccination of mother during pregnancy. A resurgence of pertussis is observed after generalisation of acellular vaccines use. In China the progression of allele ptxPl was found in all areas following the use of acellular vaccine. This allele, rare before acellullar vaccine, is linked to a macrolide resistance, and reaches more than 30% of strains isolated in hospitalised children.These evolutions must be evaluated in clinical forms and genotyping of all strains, in all areas.