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1.
Medicine (Baltimore) ; 100(13): e25362, 2021 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-33787640

RESUMEN

ABSTRACT: We investigated the vaginal flora diversity of preschool-aged (ie, 4-6-year-old) girls in southwest China.Fourteen preschool-aged girls were enrolled in this study. The statuses and differences in their vaginal flora were evaluated by Gram staining, bacterial culturing, and sequencing analysis.Gram staining and microbial culturing showed that the main vaginal flora of the preschool-aged girls were Gram-negative bacilli, whereas the main vaginal flora of healthy adult controls were large Gram-positive bacilli such as Lactobacillus crispatus. Shannon and Simpson indexes indicated that the bacterial diversity tended to decrease with age. The species abundance heat map showed that the vaginal microecology of the girls differed slightly at different ages but mainly comprised Pseudomonas, Methylobacterium, Sphingomona,s and Escherichia. The functional abundance heat map indicated that the bacterial functions increased with age.The vaginal microecology of preschool-aged girls differs from that of adults. A comprehensive understanding of the vaginal flora diversity of preschool-aged girls will aid in clinically diagnosing vulvovaginitis in preschool-aged girls.


Asunto(s)
Bacterias/aislamiento & purificación , Microbiota/genética , Vagina/microbiología , Vulvovaginitis/diagnóstico , Adulto , Factores de Edad , Bacterias/genética , Estudios de Casos y Controles , Niño , Preescolar , China , ADN Bacteriano/aislamiento & purificación , Femenino , Voluntarios Sanos , Humanos , Tipificación Molecular/métodos , Análisis de Secuencia de ADN , Frotis Vaginal , Vulvovaginitis/microbiología
2.
Methods Mol Biol ; 2259: 167-179, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33687714

RESUMEN

Metaproteomics of host-microbiome interfaces comprises the analysis of complex mixtures of bacteria, archaea, fungi, and viruses in combination with its host cells. Microbial niches can be found all over the host including the skin, oral cavity, and the intestine and are considered to be essential for the homeostasis. The complex interactions between the host and diverse commensal microbiota are poorly characterized while of great interest as dysbiosis is associated with the development of various inflammatory and metabolic diseases. The metaproteomics workflows to study these interfaces are currently being established, and many challenges remain. The major challenge is the large diversity in species composition that make up the microbiota, which results in complex samples that require extended mass spectrometry analysis time. In addition, current database search strategies are not developed to the size of the search space required for unbiased microbial protein identification.Here, we describe a workflow for the proteomics analysis of microbial niches with a focus on intestinal mucus layer. We will cover step-by-step the sample collection, sample preparation, liquid chromatography-mass spectrometry, and data analysis.


Asunto(s)
Bacterias/aislamiento & purificación , Proteínas Bacterianas/análisis , Proteínas Fúngicas/análisis , Hongos/aislamiento & purificación , Microbioma Gastrointestinal , Proteómica/métodos , Animales , Cromatografía Liquida/métodos , Intestinos/microbiología , Espectrometría de Masas/métodos , Ratones , Péptidos/análisis , Flujo de Trabajo
3.
Methods Mol Biol ; 2259: 205-213, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33687717

RESUMEN

Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the characterization of bacterial strains.Here, we describe the analysis of tryptic digestion peptides by LC-ESI-MS/MS to search for specific biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other hand, the physiological and biochemical characteristics such as the expression of virulence factors, including toxins, immune-modulatory factors, and exoenzymes.


Asunto(s)
Bacterias/aislamiento & purificación , Proteínas Bacterianas/análisis , Microbiología de Alimentos , Proteómica/métodos , Proteínas Bacterianas/aislamiento & purificación , Cromatografía Liquida/métodos , Programas Informáticos , Espectrometría de Masa por Ionización de Electrospray/métodos , Espectrometría de Masas en Tándem/métodos
4.
BMC Infect Dis ; 21(1): 303, 2021 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-33765944

RESUMEN

BACKGROUND: Proper detection of disease-causing organisms is very critical in controlling the course of outbreaks and avoiding large-scale epidemics. Nonetheless, availability of resources to address these gaps have been difficult due to limited funding. This report sought to highlight the importance of in-country partners and non-governmental organizations in improving detection of microbiological organisms in Ghanaian Public Health Laboratories (PHLs). METHODS/CONTEXT: This study was conducted between June, 2018 to August, 2019. U. S CDC engaged the Centre for Health Systems Strengthening (CfHSS) through the Association of Public Health Laboratories to design and implement strategies for strengthening three PHLs in Ghana. An assessment of the three PHLs was done using the WHO/CDS/CSR/ISR/2001.2 assessment tool. Based on findings from the assessments, partner organizations (CfHSS/APHL/CDC) serviced and procured microbiological equipment, laboratory reagents and logistics. CfHSS provided in-house mentoring and consultants to assist with capacity building in detection of epidemic-prone infectious pathogens by performing microbiological cultures and antimicrobial susceptibility tests. RESULTS: A total of 3902 samples were tested: blood (1107), urine (1742), stool (249) and cerebrospinal fluid (CSF) (804). All-inclusive, 593 pathogenic bacteria were isolated from blood cultures (70; 11.8%); urine cultures (356; 60%); stool cultures (19; 3.2%) and from CSF samples (148; 25%). The most predominant pathogens isolated from blood, urine and stool were Staphylococcus aureus (22/70; 31%), Escherichia coli (153/356; 43%) and Vibrio parahaemolyticus (5/19; 26.3%), respectively. In CSF samples, Streptococcus pneumoniae was the most frequent pathogen detected (80/148; 54.1%). New bacterial species such as Pastuerella pneumotropica, Klebsiella oxytoca, Vibrio parahaemolyticus, and Halfnia alvei were also identified with the aid of Analytical Profile Index (API) kits that were introduced as part of this implementation. Streptococcus pneumoniae and Neisseria meningitidis detections in CSF were highest during the hot dry season. Antimicrobial susceptibility test revealed high rate of S. aureus, K. pneumoniae and E. coli resistance to gentamicin (35-55%). In urine, E. coli was highly resistant to ciprofloxacin (39.2%) and ampicillin (34%). CONCLUSION: Detection of epidemic-prone pathogens can be greatly improved if laboratory capacity is strengthened. In-country partner organizations are encouraged to support this move to ensure accurate diagnosis of diseases and correct antimicrobial testing.


Asunto(s)
Bacterias/aislamiento & purificación , Infecciones Bacterianas/diagnóstico , Antibacterianos/farmacología , Bacterias/efectos de los fármacos , Infecciones Bacterianas/microbiología , Sangre/microbiología , Líquido Cefalorraquídeo/microbiología , Farmacorresistencia Bacteriana/efectos de los fármacos , Heces/microbiología , Ghana , Humanos , Laboratorios , Pruebas de Sensibilidad Microbiana , Organizaciones , Estudios Retrospectivos , Estaciones del Año , Orina/microbiología
5.
Sensors (Basel) ; 21(4)2021 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-33670022

RESUMEN

Conventional pathogenic bacteria-detection methods are lab-bound, time-consuming and need trained personnel. Microelectrodes can be used to recognize harmful microorganisms by dielectric impedance spectroscopy. However, crucial for this spectroscopy method are the spatial dimensions and layout of the electrodes, as the corresponding distribution of the electric field defines the sensor system parameters such as sensitivity, SNR, and dynamic range. Therefore, a variety of sensor models are created and evaluated. FEM simulations in 2D and 3D are conducted for this impedimetric sensor. The authors tested differently shaped structures, verified the linear influence of the excitation amplitude and developed a mathematical concept for a quality factor that practically allows us to distinguish arbitrary sensor designs and layouts. The effect of guard electrodes blocking outer influences on the electric field are investigated, and essential configurations are explored. The results lead to optimized electronic sensors in terms of geometrical dimensions. Possible material choices for real sensors as well as design and layout recommendations are presented.


Asunto(s)
Bacterias/aislamiento & purificación , Técnicas Biosensibles , Espectroscopía Dieléctrica , Microelectrodos , Impedancia Eléctrica
6.
BMC Plant Biol ; 21(1): 127, 2021 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-33663379

RESUMEN

BACKGROUND: Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. RESULTS: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. CONCLUSIONS: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.


Asunto(s)
Bacterias/aislamiento & purificación , Dendrobium/microbiología , Plantas Medicinales/microbiología , Rizosfera , Microbiología del Suelo , Bacterias/clasificación , Biodiversidad , Medicamentos Herbarios Chinos , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota
7.
BMC Infect Dis ; 21(1): 152, 2021 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-33546631

RESUMEN

BACKGROUND: Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms. METHODS: BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified. RESULTS: The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P = 0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4% of the cases co-detection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens. CONCLUSION: Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.


Asunto(s)
Líquido del Lavado Bronquioalveolar/microbiología , Líquido del Lavado Bronquioalveolar/virología , Infecciones del Sistema Respiratorio/diagnóstico , Adolescente , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Niño Hospitalizado , Preescolar , Coinfección/diagnóstico , Coinfección/microbiología , Coinfección/virología , Pruebas Diagnósticas de Rutina , Femenino , Humanos , Lactante , Masculino , Reacción en Cadena de la Polimerasa , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación
8.
Int J Food Microbiol ; 343: 109086, 2021 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-33631605

RESUMEN

The importance of leaf integrity, i.e. the effects of bruising (mechanical damage), and sanitisation with peroxyacetic acid (PAA) on bacterial communities of ready-to-eat baby spinach remains unclear. Two shelf-life studies were conducted at 4 °C to investigate the effect of bruising and sanitisation on the growth of spoilage microorganisms. In the first experiment, both bruising treatments (100% and 40% of leaves) halved shelf life to 12 d, whereas intact leaves had a shelf-life of 23 d. Bruising had no influence on bacterial diversity during shelf-life, though some differences in the relative abundance of minor genera were observed. Pseudomonas and Pantoea were the most dominant bacterial genera, regardless of bruising treatment. High throughput amplicon sequencing also identified other spoilage bacteria including Chryseobacterium, Stenotrophomonas, Bacillus, Sphingobacterium, Erwinia and Flavobacterium. In the second experiment, washing of intact baby spinach with a sanitiser (80 mg/L: PAA) reduced microbial load as determined by aerobic plate count but did not immediately affect the presence/relative abundance of most of the genera of spoilage bacteria observed. During shelf-life, the bacterial diversity of sanitised leaves was significantly lower than on water-washed leaves. Although sanitisation resulted in a higher initial log reduction in microbial load compared to control (portable tap water), sanitisation did not extend the shelf life of baby spinach (23 d). Sanitised spinach had reduced bacterial diversity however, by the end of shelf life, both sanitised and water-washed spinach was dominated by Pseudomonas and Pantoea spoilage bacteria. This study demonstrated for the first time that the shorter shelf life of bruised leaves was related to faster microbial growth rather than changes in bacterial diversity or community composition.


Asunto(s)
Desinfectantes/farmacología , Almacenamiento de Alimentos/métodos , Microbiota/efectos de los fármacos , Ácido Peracético/farmacología , Spinacia oleracea/microbiología , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/crecimiento & desarrollo , Bacterias/aislamiento & purificación , Recuento de Colonia Microbiana , Microbiología de Alimentos , Hojas de la Planta/microbiología , Agua/farmacología
9.
BMC Infect Dis ; 21(1): 230, 2021 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-33639884

RESUMEN

BACKGROUND: Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children. METHODS: Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated. RESULTS: A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0-2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3-5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6-14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05). CONCLUSIONS: This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.


Asunto(s)
Técnicas Microbiológicas/métodos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones del Sistema Respiratorio/diagnóstico , Virología/métodos , Adolescente , Edad de Inicio , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Preescolar , Diagnóstico Diferencial , Femenino , Humanos , Lactante , Recién Nacido , Unidades de Cuidado Intensivo Pediátrico , Masculino , Nasofaringe/microbiología , Nasofaringe/virología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Valor Predictivo de las Pruebas , Reproducibilidad de los Resultados , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Virus/genética , Virus/aislamiento & purificación
10.
BMC Infect Dis ; 21(1): 190, 2021 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-33602178

RESUMEN

BACKGROUND: PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger's sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients' treatments according to different sample types. METHODS: From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. RESULTS: Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients' management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). CONCLUSION: In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.


Asunto(s)
Infecciones Bacterianas/diagnóstico , Toma de Decisiones Clínicas , Técnicas de Diagnóstico Molecular/métodos , ARN Ribosómico 16S/genética , Antibacterianos/uso terapéutico , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Infecciones Bacterianas/tratamiento farmacológico , Humanos , Reacción en Cadena de la Polimerasa , Estudios Retrospectivos , Análisis de Secuencia de ADN
11.
Microbiome ; 9(1): 55, 2021 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-33622394

RESUMEN

BACKGROUND: The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS: We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS: We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.


Asunto(s)
Proteínas Bacterianas/análisis , Proteínas Bacterianas/química , Comunicación Celular , Microbioma Gastrointestinal , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Bacterias/metabolismo , Proteínas Bacterianas/genética , Microbioma Gastrointestinal/genética , Humanos , Intestinos/química , Intestinos/microbiología , Metagenoma/genética , Espectrometría de Masas en Tándem
12.
BMC Infect Dis ; 21(1): 216, 2021 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-33632144

RESUMEN

BACKGROUND: HIV-associated chronic lung disease (CLD) is common among children living with HIV (CLWH) in sub-Saharan Africa, including those on antiretroviral therapy (ART). However, the pathogenesis of CLD and its possible association with microbial determinants remain poorly understood. We investigated the prevalence, and antibiotic susceptibility of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) among CLWH (established on ART) who had CLD (CLD+), or not (CLD-) in Zimbabwe and Malawi. METHODS: Nasopharyngeal swabs (NP) and sputa were collected from CLD+ CLWH (defined as forced-expiratory volume per second z-score < - 1 without reversibility post-bronchodilation with salbutamol), at enrolment as part of a randomised, placebo-controlled trial of azithromycin (BREATHE trial - NCT02426112 ), and from age- and sex-matched CLD- CLWH. Samples were cultured, and antibiotic susceptibility testing was conducted using disk diffusion. Risk factors for bacterial carriage were identified using questionnaires and analysed using multivariate logistic regression. RESULTS: A total of 410 participants (336 CLD+, 74 CLD-) were enrolled (median age, 15 years [IQR = 13-18]). SP and MC carriage in NP were higher in CLD+ than in CLD- children: 46% (154/336) vs. 26% (19/74), p = 0.008; and 14% (49/336) vs. 3% (2/74), p = 0.012, respectively. SP isolates from the NP of CLD+ children were more likely to be non-susceptible to penicillin than those from CLD- children (36% [53/144] vs 11% [2/18], p = 0.036). Methicillin-resistant SA was uncommon [4% (7/195)]. In multivariate analysis, key factors associated with NP bacterial carriage included having CLD (SP: adjusted odds ratio (aOR) 2 [95% CI 1.1-3.9]), younger age (SP: aOR 3.2 [1.8-5.8]), viral load suppression (SP: aOR 0.6 [0.4-1.0], SA: 0.5 [0.3-0.9]), stunting (SP: aOR 1.6 [1.1-2.6]) and male sex (SA: aOR 1.7 [1.0-2.9]). Sputum bacterial carriage was similar in both groups (50%) and was associated with Zimbabwean site (SP: aOR 3.1 [1.4-7.3], SA: 2.1 [1.1-4.2]), being on ART for a longer period (SP: aOR 0.3 [0.1-0.8]), and hot compared to rainy season (SP: aOR 2.3 [1.2-4.4]). CONCLUSIONS: CLD+ CLWH were more likely to be colonised by MC and SP, including penicillin-non-susceptible SP strains, than CLD- CLWH. The role of these bacteria in CLD pathogenesis, including the risk of acute exacerbations, should be further studied.


Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana , Infecciones por VIH/microbiología , Enfermedades Pulmonares/microbiología , Adolescente , Antirretrovirales/uso terapéutico , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Femenino , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/epidemiología , Humanos , Enfermedades Pulmonares/tratamiento farmacológico , Enfermedades Pulmonares/epidemiología , Malaui/epidemiología , Masculino , Microbiota , Nasofaringe/microbiología , Prevalencia , Factores de Riesgo , Zimbabwe/epidemiología
13.
Food Chem ; 349: 129131, 2021 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-33581434

RESUMEN

Soy sauce is a traditional fermented soy food for enhancing the umami taste in Asian cuisines. In this study, 16S rRNA gene throughput sequencing analysis showed the bacterial communities and the changes in soy sauce during fermentation. Weissella, Bacillus and Lactococcus were the most abundant at genus level. The uncultured bacterium Weissella and Lactococcus had relatively high abundance at species level. Alpha diversity analysis indicated the bacterial community diversity increased at fermentation initiation, while decreased as fermentation progressed. Based on beta-diversity analysis, four clusters including cluster I (time point A-F), cluster II (G,H), cluster III (I,J) and cluster IV(K) were distinctly separated, indicating the fermentation time significantly affected bacterial community diversity. Also, close associations were found between the bacterial communities in soy sauce and its amino acid nitrogen, organic acid and reducing sugar contents during fermentation. Therefore, it will provide important information for optimization of the soy sauce production process.


Asunto(s)
Aminoácidos/análisis , Bacterias/genética , Fermentación , Secuenciación de Nucleótidos de Alto Rendimiento , Alimentos de Soja/análisis , Alimentos de Soja/microbiología , Azúcares/análisis , Aminoácidos/química , Bacterias/aislamiento & purificación , Bacterias/metabolismo , Nitrógeno/química , ARN Ribosómico 16S/genética , Gusto
14.
Cell Mol Life Sci ; 78(6): 2585-2606, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33582841

RESUMEN

Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.


Asunto(s)
Bacterias/genética , Infección Hospitalaria/patología , Farmacorresistencia Bacteriana Múltiple/genética , Antibacterianos/uso terapéutico , Bacterias/clasificación , Bacterias/aislamiento & purificación , Infección Hospitalaria/tratamiento farmacológico , Infección Hospitalaria/microbiología , Transferencia de Gen Horizontal , Humanos , Metagenómica , Plásmidos/genética , Plásmidos/metabolismo , ARN Ribosómico 16S/química , ARN Ribosómico 16S/clasificación , ARN Ribosómico 16S/metabolismo , Secuenciación Completa del Genoma
15.
Int J Mol Sci ; 22(3)2021 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-33540521

RESUMEN

Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.


Asunto(s)
Código de Barras del ADN Taxonómico , Microbiota , Paenibacillus/fisiología , Rizosfera , Microbiología del Suelo , Zea mays/microbiología , Bacterias/aislamiento & purificación , Bacterias/metabolismo , Hongos/aislamiento & purificación , Micobioma , Fijación del Nitrógeno , Paenibacillus/metabolismo , Raíces de Plantas/microbiología
16.
Int J Nanomedicine ; 16: 895-904, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33603358

RESUMEN

Purpose: Worldwide water contamination treatment and water security are essential for all living organisms. Among various water contaminants, dye, and bacteria pollution needs to be solved urgently. Methods and Results: In this work, a ceramic sheet from monodisperse, porous silica nanospheres (SiO2 NSs) with an average diameter of 220 was prepared. The prepared SiO2 ceramic sheets were investigated as a "filtration" material in removing dyes (alcian blue, AB; and methylene blue, MB) and bacteria (E. coli and S. aureus). The obtained sheets had efficient adsorption efficiency of 98.72% (for AB) and 97.35% (for MB), and a high adsorption capacity for AB is 220 (mg/g), for MB is 176 (mg/g). Furthermore, these SiO2 ceramic sheets had a high recycling capability for removing dyes by calcination. Being modified by Ag nanoclusters, the ceramic sheets present a strong bactericidal function. Conclusion: Our results demonstrated that the obtained SiO2 non-sintered ceramic sheets is rapid and efficient in the filtration of dyes and bacteria from polluted water.


Asunto(s)
Bacterias/aislamiento & purificación , Cerámica/química , Colorantes/aislamiento & purificación , Nanosferas/química , Dióxido de Silicio/química , Plata/química , Contaminantes Químicos del Agua/aislamiento & purificación , Adsorción , Azul Alcián/química , Antibacterianos/farmacología , Colorantes/química , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Azul de Metileno/química , Pruebas de Sensibilidad Microbiana , Nanosferas/ultraestructura , Porosidad , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/aislamiento & purificación , Agua
17.
Ecotoxicol Environ Saf ; 212: 112006, 2021 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-33556810

RESUMEN

Particulate matter (PM) is a carrier of many substances. Microorganisms are vital constituents contained in PM, and their varieties and concentrations are closely connected to human health and animal production. This study aimed to investigate the distribution characteristics of bioaerosols inside a pig house and in the respiratory tract of pigs. Environmental indices inside a nursery pig house were monitored in winter, including temperature, relative humidity, total suspended particulate (TSP), PM10, PM2.5, NH3, CO2, CO and NO. The concentrations of airborne culturable bacteria, fungi and Escherichia coli were detected. Then, 16S rRNA sequencing technology was applied to identify different-sized bioaerosols and bacteria in the respiratory tract of piglets. The results showed that the concentration of airborne culturable bacteria inside the pig house was significantly higher than that outside, and no significant difference was found among culturable fungi and Escherichia coli. The 16S rRNA results showed that the bacterial aerosols presented high similarity to the bacteria in the respiratory tract of piglets. The airborne bacterial aerosols within the size range of 1.1-3.3 µm showed high similarity to the bacteria in the lower respiratory tract (bronchus and lung) of piglets. In addition, four potential pathogenic bacterial genera (Escherichia-Shigella, Streptococcus, Acinetobacter, Pseudomonas) were identified both in the bacterial aerosols and the respiratory tract of piglets. These results will provide a significant scientific basis for exploring the potential risk of aerosols from animal houses to human and animal health.


Asunto(s)
Microbiología del Aire/normas , Contaminantes Atmosféricos/análisis , Bacterias/aislamiento & purificación , Monitoreo del Ambiente/métodos , Material Particulado/análisis , Sistema Respiratorio/microbiología , Aerosoles , Animales , China , Polvo , Humanos , ARN Ribosómico 16S , Estaciones del Año , Porcinos , Temperatura
18.
Microbiome ; 9(1): 50, 2021 02 18.
Artículo en Inglés | MEDLINE | ID: mdl-33602336

RESUMEN

BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen. METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort. RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites. CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.


Asunto(s)
Exobiología , Ambientes Extremos , Microbiota/fisiología , Anaerobiosis , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Metagenoma , Microbiota/genética
19.
Microbiome ; 9(1): 52, 2021 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-33612109

RESUMEN

BACKGROUND: Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. RESULTS: In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. CONCLUSIONS: Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.


Asunto(s)
Microbioma Gastrointestinal/genética , Redes Reguladoras de Genes , Porcinos/genética , Porcinos/microbiología , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Femenino , Estudio de Asociación del Genoma Completo , Masculino , Porcinos/clasificación , Simbiosis/genética
20.
BMC Infect Dis ; 21(1): 173, 2021 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-33579205

RESUMEN

BACKGROUND: Blood cultures are one of the most important tests performed by microbiology laboratories. Many hospitals, particularly in low and middle-income countries, lack either microbiology services or staff to provide 24 h services resulting in delays to blood culture incubation. There is insufficient guidance on how to transport/store blood cultures if delays before incubation are unavoidable, particularly if ambient temperatures are high. This study set out to address this knowledge gap. METHODS: In three South East Asian countries, four different blood culture systems (two manual and two automated) were used to test blood cultures spiked with five common bacterial pathogens. Prior to incubation the spiked blood culture bottles were stored at different temperatures (25 °C, in a cool-box at ambient temperature, or at 40 °C) for different lengths of time (0 h, 6 h, 12 h or 24 h). The impacts of these different storage conditions on positive blood culture yield and on time to positivity were examined. RESULTS: There was no significant loss in yield when blood cultures were stored < 24 h at 25 °C, however, storage for 24 h at 40 °C decreased yields and longer storage times increased times to detection. CONCLUSION: Blood cultures should be incubated with minimal delay to maximize pathogen recovery and timely result reporting, however, this study provides some reassurance that unavoidable delays can be managed to minimize negative impacts. If delays to incubation ≥ 12 h are unavoidable, transportation at a temperature not exceeding 25 °C, and blind sub-cultures prior to incubation should be considered.


Asunto(s)
Cultivo de Sangre/normas , Manejo de Especímenes/normas , Asia Sudoriental , Bacterias/clasificación , Bacterias/aislamiento & purificación , Cultivo de Sangre/estadística & datos numéricos , Servicios de Laboratorio Clínico/normas , Servicios de Laboratorio Clínico/estadística & datos numéricos , Humanos , Manejo de Especímenes/estadística & datos numéricos , Temperatura , Factores de Tiempo
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