ABSTRACT
OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment. RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.
Subject(s)
Metagenomics , Respiratory Tract Infections , Metagenomics/methods , Humans , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/diagnosis , Metagenome/genetics , Computational Biology/methods , Reproducibility of Results , Nasopharynx/microbiology , Nasopharynx/virologyABSTRACT
In previous studies, it was demonstrated that Corynebacterium pseudodiphtheriticum 090104, isolated from the human nasopharynx, modulates respiratory immunity, improving protection against infections. Here, the antagonistic effect of the 090104 strain on respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, was explored. In a series of in vitro studies, the capacity of C. pseudodiphtheriticum 090104, its bacterium-like particles, and its culture supernatants to coaggregate, inhibit the growth, and change the virulent phenotype of pathogenic bacteria was evaluated. The results showed that the 090104 strain was able to exert a bacteriostatic effect on K. pneumoniae and S. pneumoniae growth. In addition, C. pseudodiphtheriticum 090104 coaggregated, inhibited biofilm formation, and induced phenotypic changes in all the respiratory pathogens evaluated. In conclusion, this work demonstrated that, in addition to its beneficial effects exerted by host-microbe interactions, C. pseudodiphtheriticum 090104 can enhance protection against respiratory pathogens through its microbe-microbe interactions. The mechanisms involved in such interactions should be evaluated in future research.
ABSTRACT
Viral respiratory infections may predispose to co-infections with other pathogenic microorganisms. In this study, pathogenic respiratory bacteria were detected using commercial kit Allplex™ Respiratory Panel 4 from nasopharyngeal samples from individuals suffering respiratory symptoms with and without severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients without respiratory symptoms were included as controls. Haemophilus influenzae and Streptococcus pneumoniae were detected from 12 patients (6%) in both, patients with respiratory symptoms (including hospitalized) (n = 6) and individual without symptoms (n = 6). Pathogenic bacteria possibly proliferate due to the limited immune response of patients with SARS-CoV-2, perhaps due to dysbiosis generated by the viral infection.
Subject(s)
COVID-19 , Pneumonia , Humans , SARS-CoV-2 , Colombia/epidemiology , Streptococcus pneumoniaeABSTRACT
Objective: The aim of this study was to assess the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in the oral cavity of pediatric patients hospitalized at an intensive care unit (ICU). Methodology: Thirty ICU patients (group 1) and 30 healthy patients (group 2), between 1 and 12 years of age, matched by sex and age, were selected from a public hospital in Brazil. After oral examinations, biological specimens (nostril swab, oral mucosa, and supragingival biofilm) were collected from both groups to verify the presence of Staphylococcus aureus. Identification occurred after growth in Tryptic Soy Broth with 7.5% of NaCl for 48 hours, growth in Mannitol Salt Agar, gram staining, catalase, and coagulase tests. S. aureus isolates were submitted to antibiotic sensitivity test. Results: Only 36.7% of patients in the ICU perform oral hygiene during the hospitalization period and 41.7% presented high level of dental biofilm accumulation. The presence of S. aureus was similar in patients from group 1 (43.3%, 13) and group 2 (50.0%, 15) (p = 0.60). Both groups presented 18 samples each that tested positive for S. aureus. However, when considering patients infected by MRSA, the prevalence was higher in group 1 (eight; 26.7%) than in group 2 (five; 16.7%) but no statistical difference was observed (p = 0.53). In group 1, nine MRSA samples were resistant to erythromycin and seven to clindamycin. In group 2, two MRSA samples were resistant to erythromycin and two to clindamycin. Conclusions: Although ICU children did not show a significant higher carriage of MRSA when compared with the healthy group in the population studied, the number of highly resistant strains in the oral cavity isolated from ICU patients adds an important risk factor to be considered by the medical team as possible source of systemic infections, extended hospital stay, and poor outcomes.
Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Anti-Bacterial Agents/pharmacology , Child , Clindamycin , Erythromycin/pharmacology , Humans , Intensive Care Units , Microbial Sensitivity Tests , Mouth , Staphylococcal Infections/drug therapy , Staphylococcal Infections/epidemiology , Staphylococcus aureusABSTRACT
In recent decades there have been multiple pathogens, viruses and bacteria, which have emerged as causal agents of pneumonia affecting adults, albeit less frequently, to children. For the purposes of this article we have classified emerging pathogens as follows: True emerging, to pathogens identified for the very first time affecting human population (SARS-CoV-1, SARS-CoV-2, MERS-CoV, avian influenza, and hantavirus); Re-emerging, to known pathogens which circulation was controlled once, but they have reappeared (measles, tuberculosis, antimicrobial resistant bacteria such as CA-MRSA, Mycoplasma pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and new serotypes of post-vaccine pneumococcal); and finally, those that we have called old known with new presentations, including common pathogens that, in particular condition, have changed their form of presentation (rhinovirus, and non-SARS coronavirus). We will review for each of them their epidemiology, forms of presentation, therapy, and prognosis in children compared to the adult with the aim of being able to recognize them to establish appropriate therapy, prognostics, and effective control measures.
ABSTRACT
During the 2018 breeding season, an outbreak of respiratory disease occurred among Galapagos sea lions (Zalophus wollebaeki) that inhabit rookeries near urban areas with introduced fauna such as dogs and cats. Several sea lions had nasal discharge and respiratory distress and were in poor body condition. Eighteen sea lions were captured for a general health assessment including collection of blood for serology and nasal discharge for culture and PCR. Samples were analyzed for 15 respiratory pathogens known to infect cats, dogs, and marine mammals. There was no evidence for interspecies pathogen transmission between Galapagos sea lions and domestic animals. Several bacterial pathogens associated with respiratory tract infection in the California sea lion (Zalophus californianus) were isolated. Mycoplasma spp. were identified by PCR in nasal discharge samples but were not the species commonly found in cats and dogs.
Subject(s)
Cat Diseases , Dog Diseases , Mycoplasma , Sea Lions , Animals , Cats , DogsABSTRACT
The bovine respiratory disease (BRD) complex is a multifactorial and multietiological disease entity described in all geographic regions of Brazil. This brief review discusses aspects related to epidemiology, etiologic agents, clinical and pathological manifestations, and challenges in the diagnosis of BRD in Brazil. The main infectious disease agents associated with respiratory outbreaks in cattle from Brazil are bovine alphaherpesvirus type 1, bovine viral diarrhea virus, bovine respiratory syncytial virus, and Mycoplasma bovis. Ovine gammaherpesvirus-2 and HoBi-like pestivirus have been associated with the development of pneumonia in adult cattle and calves, respectively in Brazil, and should be considered as possible causes of BRD. Additionally, studies using epidemiological data, histopathological and molecular associations with morbidity and mortality should be carried out in Brazil, to demonstrate the real impacts of BRD on livestock.(AU)
O complexo da doença respiratória bovina (DRB) é uma enfermidade multifatorial e multietiológica descrita em todas as regiões geográficas do Brasil. Essa breve revisão discute os aspectos relacionados epidemiologia, aos agentes etiológicos, as manifestações clínicas e patológicas e os desafios no diagnóstico da DRB no Brasil. Os principais agentes associados a surtos respiratórios brasileiros são: alfaherpesvírus bovino tipo 1, vírus da diarreia viral bovina, vírus sincicial respiratório bovino e Mycoplasma bovis. Gammaherpesvirus ovino tipo-2 e HoBi-like pestivírus foram associados ao desenvolvimento de pneumonia em bovinos adultos e bezerros no país, respectivamente, e devem ser considerados como possíveis agentes no desenvolvimento da DRB. Adicionalmente, mais estudos utilizando dados epidemiológicos, associação histopatológica e molecular com morbidade e mortalidade devam ser realizados no Brasil, para demonstrar os verdadeiros efeitos de DRB em bovinos confinados.(AU)
Subject(s)
Animals , Cattle , Cattle Diseases/virology , Bovine Respiratory Disease Complex/diagnosis , Bovine Respiratory Disease Complex/epidemiology , Bovine Respiratory Disease Complex/etiology , Bovine Respiratory Disease Complex/pathologyABSTRACT
The bovine respiratory disease (BRD) complex is a multifactorial and multietiological disease entity described in all geographic regions of Brazil. This brief review discusses aspects related to epidemiology, etiologic agents, clinical and pathological manifestations, and challenges in the diagnosis of BRD in Brazil. The main infectious disease agents associated with respiratory outbreaks in cattle from Brazil are bovine alphaherpesvirus type 1, bovine viral diarrhea virus, bovine respiratory syncytial virus, and Mycoplasma bovis. Ovine gammaherpesvirus-2 and HoBi-like pestivirus have been associated with the development of pneumonia in adult cattle and calves, respectively in Brazil, and should be considered as possible causes of BRD. Additionally, studies using epidemiological data, histopathological and molecular associations with morbidity and mortality should be carried out in Brazil, to demonstrate the real impacts of BRD on livestock.
O complexo da doença respiratória bovina (DRB) é uma enfermidade multifatorial e multietiológica descrita em todas as regiões geográficas do Brasil. Essa breve revisão discute os aspectos relacionados epidemiologia, aos agentes etiológicos, as manifestações clÃnicas e patológicas e os desafios no diagnóstico da DRB no Brasil. Os principais agentes associados a surtos respiratórios brasileiros são: alfaherpesvÃrus bovino tipo 1, vÃrus da diarreia viral bovina, vÃrus sincicial respiratório bovino e Mycoplasma bovis. Gammaherpesvirus-ovino tipo-2 e HoBi-like pestivÃrus foram associados ao desenvolvimento de pneumonia em bovinos adultos e bezerros no paÃs, respectivamente, e devem ser considerados como possÃveis agentes no desenvolvimento da DRB. Adicionalmente, mais estudos utilizando dados epidemiológicos, associação histopatológica e molecular com morbidade e mortalidade devam ser realizados no Brasil, para demonstrar os verdadeiros efeitos de DRB em bovinos confinados.
ABSTRACT
The bovine respiratory disease (BRD) complex is a multifactorial and multietiological disease entity described in all geographic regions of Brazil. This brief review discusses aspects related to epidemiology, etiologic agents, clinical and pathological manifestations, and challenges in the diagnosis of BRD in Brazil. The main infectious disease agents associated with respiratory outbreaks in cattle from Brazil are bovine alphaherpesvirus type 1, bovine viral diarrhea virus, bovine respiratory syncytial virus, and Mycoplasma bovis. Ovine gammaherpesvirus-2 and HoBi-like pestivirus have been associated with the development of pneumonia in adult cattle and calves, respectively in Brazil, and should be considered as possible causes of BRD. Additionally, studies using epidemiological data, histopathological and molecular associations with morbidity and mortality should be carried out in Brazil, to demonstrate the real impacts of BRD on livestock.(AU)
O complexo da doença respiratória bovina (DRB) é uma enfermidade multifatorial e multietiológica descrita em todas as regiões geográficas do Brasil. Essa breve revisão discute os aspectos relacionados epidemiologia, aos agentes etiológicos, as manifestações clínicas e patológicas e os desafios no diagnóstico da DRB no Brasil. Os principais agentes associados a surtos respiratórios brasileiros são: alfaherpesvírus bovino tipo 1, vírus da diarreia viral bovina, vírus sincicial respiratório bovino e Mycoplasma bovis. Gammaherpesvirus-ovino tipo-2 e HoBi-like pestivírus foram associados ao desenvolvimento de pneumonia em bovinos adultos e bezerros no país, respectivamente, e devem ser considerados como possíveis agentes no desenvolvimento da DRB. Adicionalmente, mais estudos utilizando dados epidemiológicos, associação histopatológica e molecular com morbidade e mortalidade devam ser realizados no Brasil, para demonstrar os verdadeiros efeitos de DRB em bovinos confinados.(AU)
Subject(s)
Animals , Cattle , Cattle , Bovine Respiratory Disease Complex/classification , Bovine Respiratory Disease Complex/epidemiology , Mycoplasma bovisABSTRACT
The bovine respiratory disease (BRD) complex is a multifactorial and multietiological disease entity described in all geographic regions of Brazil. This brief review discusses aspects related to epidemiology, etiologic agents, clinical and pathological manifestations, and challenges in the diagnosis of BRD in Brazil. The main infectious disease agents associated with respiratory outbreaks in cattle from Brazil are bovine alphaherpesvirus type 1, bovine viral diarrhea virus, bovine respiratory syncytial virus, and Mycoplasma bovis. Ovine gammaherpesvirus-2 and HoBi-like pestivirus have been associated with the development of pneumonia in adult cattle and calves, respectively in Brazil, and should be considered as possible causes of BRD. Additionally, studies using epidemiological data, histopathological and molecular associations with morbidity and mortality should be carried out in Brazil, to demonstrate the real impacts of BRD on livestock.
O complexo da doença respiratória bovina (DRB) é uma enfermidade multifatorial e multietiológica descrita em todas as regiões geográficas do Brasil. Essa breve revisão discute os aspectos relacionados epidemiologia, aos agentes etiológicos, as manifestações clínicas e patológicas e os desafios no diagnóstico da DRB no Brasil. Os principais agentes associados a surtos respiratórios brasileiros são: alfaherpesvírus bovino tipo 1, vírus da diarreia viral bovina, vírus sincicial respiratório bovino e Mycoplasma bovis. Gammaherpesvirus-ovino tipo-2 e HoBi-like pestivírus foram associados ao desenvolvimento de pneumonia em bovinos adultos e bezerros no país, respectivamente, e devem ser considerados como possíveis agentes no desenvolvimento da DRB. Adicionalmente, mais estudos utilizando dados epidemiológicos, associação histopatológica e molecular com morbidade e mortalidade devam ser realizados no Brasil, para demonstrar os verdadeiros efeitos de DRB em bovinos confinados.
Subject(s)
Animals , Cattle , Cattle , Bovine Respiratory Disease Complex/classification , Bovine Respiratory Disease Complex/epidemiology , Mycoplasma bovisABSTRACT
The bovine respiratory disease (BRD) complex is a multifactorial and multietiological disease entity described in all geographic regions of Brazil. This brief review discusses aspects related to epidemiology, etiologic agents, clinical and pathological manifestations, and challenges in the diagnosis of BRD in Brazil. The main infectious disease agents associated with respiratory outbreaks in cattle from Brazil are bovine alphaherpesvirus type 1, bovine viral diarrhea virus, bovine respiratory syncytial virus, and Mycoplasma bovis. Ovine gammaherpesvirus-2 and HoBi-like pestivirus have been associated with the development of pneumonia in adult cattle and calves, respectively in Brazil, and should be considered as possible causes of BRD. Additionally, studies using epidemiological data, histopathological and molecular associations with morbidity and mortality should be carried out in Brazil, to demonstrate the real impacts of BRD on livestock.
O complexo da doença respiratória bovina (DRB) é uma enfermidade multifatorial e multietiológica descrita em todas as regiões geográficas do Brasil. Essa breve revisão discute os aspectos relacionados epidemiologia, aos agentes etiológicos, as manifestações clínicas e patológicas e os desafios no diagnóstico da DRB no Brasil. Os principais agentes associados a surtos respiratórios brasileiros são: alfaherpesvírus bovino tipo 1, vírus da diarreia viral bovina, vírus sincicial respiratório bovino e Mycoplasma bovis. Gammaherpesvirus ovino tipo-2 e HoBi-like pestivírus foram associados ao desenvolvimento de pneumonia em bovinos adultos e bezerros no país, respectivamente, e devem ser considerados como possíveis agentes no desenvolvimento da DRB. Adicionalmente, mais estudos utilizando dados epidemiológicos, associação histopatológica e molecular com morbidade e mortalidade devam ser realizados no Brasil, para demonstrar os verdadeiros efeitos de DRB em bovinos confinados.
Subject(s)
Animals , Cattle , Bovine Respiratory Disease Complex/diagnosis , Bovine Respiratory Disease Complex/epidemiology , Bovine Respiratory Disease Complex/etiology , Bovine Respiratory Disease Complex/pathology , Cattle Diseases/virologyABSTRACT
In December 2019, a novel beta (ß) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.
Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , COVID-19 , COVID-19 Testing , Coronavirus Infections/virology , Humans , Microscopy, Electron , Pandemics , Pneumonia, Viral/virology , Polymerase Chain Reaction/methods , SARS-CoV-2 , Sequence Analysis , Serologic Tests/methods , Specimen Handling/methodsABSTRACT
The etiology and pathologic findings of bovine respiratory disease (BRD) in adult dairy cows (n = 35) from a commercial dairy herd in Southern Brazil were investigated. Pulmonary samples were examined for histopathologic patterns and specific features within these patterns, while immunohistochemical (IHC) assays were designed to detect the intralesional antigens of viral infectious disease agents and Mycoplasma bovis. Pneumonia was diagnosed in 91.4% (32/35) of these cases; neither pneumonia nor any of the infectious disease pathogens evaluated occurred in three cows. The presence of multiple respiratory pathogens in 75% (24/32) of these cases indicated the complex origin of pneumonia in cattle. Interstitial pneumonia, necrosuppurative bronchopneumonia and suppurative bronchopneumonia were the principal patterns of pulmonary disease identified by histopathology. The most frequent pathogens identified by IHC were bovine viral diarrhea virus (BVDV; n = 18), M. bovis (n = 16) and bovine alphaherpesvirus type 1 (BoHV-1; n = 14), followed by bovine respiratory syncytial virus (BRSV; n = 11) and bovine parainfluenza virus type 3 (BPIV-3; n = 5). Obliterative bronchiolitis and peribronchial lymphocytic cuffings were the characteristic histopathologic features associated with M. bovis. Necrohemorrhagic bronchitis with bronchial angiogenesis was associated with BoHV-1. Necrotizing bronchitis and bronchiolitis were associated with BVDV, BoHV-1 and BRSV. Ballooning degeneration of the bronchial and bronchiolar epithelia was associated with BRSV and BoHV-1. This is the first report from Brazil that correlated the histopathologic findings of BRD with the associated infectious disease agents by immunohistochemistry. M. bovis was frequently detected in the tissues of cows with fatal pulmonary disease during this study and may be a possible primary disease pathogen associated with the development of BRD in dairy cows. Additionally, the histopathologic features identified within patterns of pulmonary disease during this investigation may be an efficient diagnostic tool to associate histopathologic findings with specific agents of BRD in dairy cows.
Subject(s)
Bovine Respiratory Disease Complex/virology , Herpesvirus 1, Bovine/isolation & purification , Mycoplasma Infections/microbiology , Mycoplasma bovis/isolation & purification , Parainfluenza Virus 3, Bovine/isolation & purification , Respiratory Syncytial Virus, Bovine/isolation & purification , Animals , Antibodies, Viral/blood , Bovine Respiratory Disease Complex/diagnosis , Brazil , Cattle , Enzyme-Linked Immunosorbent Assay/veterinary , Female , Herpesvirus 1, Bovine/immunology , Mycoplasma Infections/diagnosis , Parainfluenza Virus 3, Bovine/immunology , Respiration Disorders/veterinary , Respiratory Syncytial Virus, Bovine/immunologyABSTRACT
Mycoplasma hyopneumoniae and Mycoplasma flocculare are genetically similar bacteria, which coinhabit the porcine respiratory tract. These mycoplasmas share most of the known virulence factors, but, while M. hyopneumoniae causes porcine enzootic pneumonia (PEP), M. flocculare is a commensal species. To identify potential PEP determinants and provide novel insights on mycoplasma-host interactions, the whole cell proteomes of two M. hyopneumoniae strains, one pathogenic (7448) and other non-pathogenic (J), and M. flocculare were compared. A cell fractioning approach combined with mass spectrometry (LC-MS/MS) proteomics was used to analyze cytoplasmic and surface-enriched protein fractions. Average detection of ~ 50% of the predicted proteomes of M. hyopneumoniae 7448 and J, and M. flocculare was achieved. Many of the identified proteins were differentially represented in M. hyopneumoniae 7448 in comparison to M. hyopneumoniae J and M. flocculare, including potential PEP determinants, such as adhesins, proteases, and redox-balancing proteins, among others. The LC-MS/MS data also provided experimental validation for several genes previously regarded as hypothetical for all analyzed mycoplasmas, including some coding for proteins bearing virulence-related functional domains. The comprehensive proteome profiling of two M. hyopneumoniae strains and M. flocculare provided tens of novel candidates to PEP determinants or virulence factors, beyond those classically described.
Subject(s)
Host Microbial Interactions , Mycoplasma hyopneumoniae/metabolism , Mycoplasma/metabolism , Pneumonia of Swine, Mycoplasmal/microbiology , Proteome/metabolism , Adhesins, Bacterial/analysis , Animals , Bacterial Proteins/analysis , Mass Spectrometry , Mycoplasma hyopneumoniae/pathogenicity , Peptide Hydrolases/analysis , Species Specificity , Swine , Virulence FactorsABSTRACT
OBJECTIVE: To assess risk factors for nasopharyngeal carriage of potential pathogens in geographically isolated Warao Amerindians in Venezuela. METHODS: In this point prevalence survey, nasopharyngeal swabs were obtained from 1064 Warao Amerindians: 504 children aged 0-4 years, 227 children aged 5-10 years and 333 caregivers. Written questionnaires were completed to obtain information on demographics and environmental risk factors. Anthropometric measurements were performed in children aged 0-4 years. RESULTS: Carriage rates of Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Moraxella catarrhalis were 51%, 7%, 1% and 13%, respectively. Crowding index, method of cooking and tobacco exposure were not associated with increased carriage. In multivariable analysis, an increase in height-for-age Z score (i.e. improved chronic nutritional status) was associated with decreased odds of S. pneumoniae colonisation (OR 0.76, 95% CI 0.70-0.83) in children aged 0-4 years. CONCLUSIONS: Better knowledge of demographic and environmental risk factors facilitates better understanding of the dynamics of colonisation with respiratory bacteria in an Amerindian population. Poor chronic nutritional status was associated with increased pathogen carriage in children <5 years of age. The high rates of stunting generally observed in indigenous children may fuel the acquisition of respiratory bacteria that can lead to respiratory and invasive disease.
Subject(s)
Carrier State , Gram-Negative Bacteria/growth & development , Growth Disorders/complications , Indians, South American , Nasopharynx/microbiology , Respiratory Tract Infections/etiology , Staphylococcus/growth & development , Adolescent , Adult , Body Height , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Nutritional Status , Prevalence , Respiratory Tract Infections/microbiology , Risk Factors , Surveys and Questionnaires , Venezuela , Young AdultABSTRACT
El manejo clínico y epidemiológico de los pacientes con fibrosis quística (FQ) con exacerbaciones pulmonares agudas o infecciones pulmonares crónicas demanda una actualización permanente de procedimientos médicos y microbiológicos, estos se asocian con la constante evolución de los agentes patógenos durante la colonización de su hospedador. Para poder monitorear la dinámica de estos procesos es fundamental disponer de sistemas expertos que permitan almacenar, extraer y utilizar la información generada a partir de estudios realizados sobre el paciente y los microorganismos aislados de aquel. En este trabajo hemos diseñado y desarrollado una base de datos on-line basada en un sistema informático que permite el almacenamiento, el manejo y la visualización de la información proveniente de estudios clínicos y de análisis microbiológicos de bacterias obtenidas del tracto respiratorio del paciente con FQ. Este sistema informático fue designado como Cystic Fibrosis Cloud database (CFC database) y está disponible en el sitio http://servoy.infocomsa.com/cfc_database. Está compuesto por una base de datos principal y una interfaz on-line, la cual emplea la arquitectura de productos Servoy basada en tecnología Java. Si bien el sistema CFC database puede ser implementado como un programa local de uso privado en los centros de asistencia a pacientes con FQ, admite también la posibilidad de ser empleado, actualizado y compartido por diferentes usuarios, quienes pueden acceder a la información almacenada de manera ordenada, práctica y segura. La implementación del CFC database podría tener una gran impacto en la monitorización de las infecciones respiratorias, la prevención de exacerbaciones, la detección de organismos emergentes y la adecuación de las estrategias de control de infecciones pulmonares en pacientes con FQ
The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients
Subject(s)
Information Storage and Retrieval/methods , Cystic Fibrosis/physiopathology , Cystic Fibrosis/microbiology , Data Visualization , Database , Data Management/organization & administration , Monitoring, Physiologic/methodsABSTRACT
The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients.
Subject(s)
Cloud Computing , Cystic Fibrosis , Databases, Factual , Cystic Fibrosis/complications , Humans , Respiratory Tract Infections/etiologyABSTRACT
Para determinar la frecuencia de bacterias patógenas y su susceptibilidad antimicrobiana en muestras nasofaringeas de niños indígenas waraos de la comunidad María López, municipio Benítez del estado Sucre, con edades comprendidas entre 0 y 10 años, se procesaron 49 muestras recolectadas durante el período enero-marzo de 2008. La identificación bacteriana se realizó aplicando estudios bacteriológicos convencionales y la susceptibilidad antimicrobiana mediante el método de difusión en disco, siguiendo lineamientos del Instituto de Estándares de Laboratorios Clínicos (CLSI). Los resultados indicaron la presencia de Moraxella catarrhalis (28,6%), Streptococcus pneumoniae (26,5%), Staphylococcus aureus (14,3%) y Haemophilus influenzae (6,1%) en niños con y sin sintomatología. Las bacterias patógenas aisladas del tracto respiratorio superior fueron más frecuentes en el grupo de 0 a 5 años de edad, identificándose, principalmente, S. pneumoniae. Con respecto a la susceptibilidad antimicrobiana, S. pneumoniae mostró resistencia a tetraciclina (46,2%), trimetoprim-sulfametoxazol (38,5%), clindamicina (33,3%) y penicilina (23,1%). Los aislados de S. aureus expresaron sensibilidad a todos los antimicrobianos ensayados. El total de aislados de M. catarrhalis mostró resistencia a ampicilina y penicilina, además, resultaron productores de β-lactamasas. La presencia de bacterias patógenas a nivel nasofaríngeo en la población infantil, representa un riesgo para el desarrollo de infecciones severas del tracto respiratorio.
We collected and `processed 49 nasopharynx samples taken from indigenous Warao children 0-10 years old who lived at the María Lopez community of the Benitez Municipalit at Sucre State, with the purpose of determining the frequency of pathogenic bacteria and their antimicrobial sensitivity in samples collected from these children during the January-March 2008 period. The bacterial identification was obtained by applying conventional bacteriological methods and the antimicrobial sensitivity was determined by the disc diffusion method, following the guidelines of the Clinical Laboratory Standards Institute. The results showed presence of Moraxella catarrhalis (28.6%), Streptococcus pneumoniae (26.5%), Staphylococcus aureus (14.3%) and Haemophilus influenza (6.1%) in children with and without symptoms. The pathogenic bacteria isolated from the upper respiratory tract were more frequent in the 0-5 year old group and the most frequent identification was S. pneumoniae. Regarding antimicrobial sensitivity, S. pneumoniae was resistant to tetracycline (46.2%), trimetoprim-sulphametoxazol (38.5%), clindamicyn (33.3%) and penicillin (23.1%). The S. aureus isolates were sensitive to all the antimicrobials studied. All the M. catarrhalis isolates were resistant to ampicillin and penicillin and were also β-lactamase producers. The presence of pathogenic bacteria at the nasopharynx level in child populations signifies a risk for the development of severe respiratory tract infections.