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1.
Database (Oxford) ; 20192019 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-31868882

RESUMEN

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

2.
Front Microbiol ; 10: 2464, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31736907

RESUMEN

Resistance in Mycobacterium tuberculosis is a major obstacle for effective treatment of tuberculosis. Multiple studies have shown promising results for predicting drug resistance in M. tuberculosis based on whole genome sequencing (WGS) data, however, these tools are often limited to this single species. We have previously developed a common platform for resistance prediction in multiple species. This platform detects acquired resistance genes (ResFinder) and species-specific chromosomal mutations (PointFinder) associated with resistance, all based on WGS data. In this study, we present a new version of PointFinder together with an updated M. tuberculosis database. PointFinder now includes predictions based on insertions and deletions, and it explicitly reports frameshift mutations and premature stop codons. We found that premature stop codons in four resistance-associated genes (katG, ethA, pncA, and gidB) were over-represented in resistant strains, and we saw an increased prediction performance when including premature stop codons in these genes as resistance markers. Different M. tuberculosis resistance prediction tools vary in performance mostly due to the mutation library used. We found that a well-established mutation library included non-predictive linage markers, and through forward feature selection we eliminated those from the mutation library. Compared to other similar web-based tools, PointFinder performs equally good. The advantages of PointFinder is that together with ResFinder it serves as a common web-based and downloadable platform for resistance detection in multiple species. It is easy to use for clinicians and already widely used in the research community.

3.
Front Microbiol ; 10: 1937, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31507556

RESUMEN

Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.

4.
Microbiome ; 7(1): 131, 2019 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-31519210

RESUMEN

BACKGROUND: Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including cancers such as acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g., at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. RESULTS: In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) high concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state. CONCLUSIONS: We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution, and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine.

5.
PLoS One ; 14(8): e0220261, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31381579

RESUMEN

Excessive use of antibiotics, especially watch group antibiotics such as ceftriaxone leads to emergence and spread of antimicrobial resistance (AMR). In low and middle-income countries (LMICs), antibiotics are overused but data on consumption is scarcely available. We aimed at determining the extent and predictors of ceftriaxone use in a tertiary care university teaching hospital in Kilimanjaro, Tanzania. A hospital-based cross-sectional study was conducted from August 2013 through August 2015. Patients admitted in the medical, surgical wards and their respective intensive care units, receiving antimicrobials and other medications for various ailments were enrolled. Socio-demographic and clinical data were recorded in a structured questionnaire from patients' files and logistic regression was performed to determine the predictors for ceftriaxone use. Out of the 630 patients included in this study, 322 (51.1%) patients were on ceftriaxone during their time of hospitalization. Twenty-two patients out of 320 (6.9%) had been on ceftriaxone treatment without evidence of infection. Ceftriaxone use for surgical prophylaxis was 44 (40.7%), of which 32 (72.7%) and 9 (20.5%) received ceftriaxone prophylaxis before and after surgery, respectively. Three (6.8%) received ceftriaxone prophylaxis during surgery. Predicting factors for that the health facility administered ceftriaxone were identified as history of any medication use before referral to hospital [OR = 3.4, 95% CI (1.0-11.4), p = 0.047], bacterial infection [OR = 18.0, 95% CI (1.4-225.7, p = 0.025)], surgical ward [OR = 2.9, 95% CI (0.9-9.4), p = 0.078] and medical wards [OR = 5.0, 95% CI (0.9-28.3), p = 0.070]. Overall, a high ceftriaxone use at KCMC hospital was observed. Antimicrobial stewardship programs are highly needed to monitor and regulate hospital antimicrobial consumption, which in turn could help in halting the rising crisis of antimicrobial resistance.

6.
Malar J ; 18(1): 252, 2019 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-31349834

RESUMEN

BACKGROUND: Large-scale surveillance of molecular markers of anti-malarial drug resistance is an attractive method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. METHODS: Between 2014 and 2017, this study sampled malaria rapid diagnostic tests (RDTs), used in routine clinical care, from two health centres in Bissau, Guinea-Bissau. In order to obtain epidemiological insights, RDTs were collected together with patient data on age and sex. A subset of positive RDTs from one of the two sites (n = 2184) were tested for Plasmodium DNA content. Those testing positive for Plasmodium DNA by PCR (n = 1390) were used for library preparation, custom designed dual indexing and next generation Miseq targeted sequencing of Plasmodium falciparum genes pfcrt, pfmdr1, pfdhfr, pfdhps and pfk13. RESULTS: The study found a high frequency of the pfmdr1 codon 86N at 88-97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33 to 51% between 2014 and 2017. No polymorphisms indicating artemisinin tolerance were discovered. The demographic data indicate a large proportion of young adults (66%, interquartile range 11-28 years) presenting with P. falciparum infections. While a total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell, PCR-positivity from the library preparation varied considerably from 13 to 87% for different amplicons. Furthermore, pre-screening of samples for Plasmodium DNA content proved necessary prior to library preparation. CONCLUSIONS: This study serves as a proof of concept for using leftover clinical material (used RDTs) for large-scale molecular surveillance, encompassing the inherent complications regarding to methodology and analysis when doing so. Factors such as RDT storage prior to DNA extraction and parasitaemia of the infection are likely to have an effect on whether or not parasite DNA can be successfully analysed, and are considered part of the reason the data yield is suboptimal. However, given the necessity of molecular surveillance of anti-malarial resistance in settings where poor infrastructure, poor economy, lack of educated staff and even surges of political instability remain major obstacles to performing clinical studies, obtaining the necessary data from used RDTs, despite suboptimal output, becomes a feasible, affordable and hence a justifiable method.


Asunto(s)
Pruebas Diagnósticas de Rutina/estadística & datos numéricos , Monitoreo Epidemiológico , Malaria Falciparum/diagnóstico , Plasmodium falciparum/genética , Prueba de Estudio Conceptual , Adolescente , Adulto , Niño , Preescolar , Femenino , Guinea Bissau , Humanos , Lactante , Recién Nacido , Masculino , Adulto Joven
7.
J Infect Dis ; 220(8): 1312-1324, 2019 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-31253993

RESUMEN

BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

8.
J Antimicrob Chemother ; 74(6): 1484-1493, 2019 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-30843063

RESUMEN

BACKGROUND: Reliable phenotypic antimicrobial susceptibility testing can be a challenge in clinical settings in low- and middle-income countries. WGS is a promising approach to enhance current capabilities. AIM: To study diversity and resistance determinants and to predict and compare resistance patterns from WGS data of Acinetobacter baumannii with phenotypic results from classical microbiological testing at a tertiary care hospital in Tanzania. METHODS AND RESULTS: MLST using Pasteur/Oxford schemes yielded eight different STs from each scheme. Of the eight, two STs were identified to be global clones 1 (n = 4) and 2 (n = 1) as per the Pasteur scheme. Resistance testing using classical microbiology determined between 50% and 92.9% resistance across all drugs. Percentage agreement between phenotypic and genotypic prediction of resistance ranged between 57.1% and 100%, with coefficient of agreement (κ) between 0.05 and 1. Seven isolates harboured mutations at significant loci (S81L in gyrA and S84L in parC). A number of novel plasmids were detected, including pKCRI-309C-1 (219000 bp) carrying 10 resistance genes, pKCRI-43-1 (34935 bp) carrying two resistance genes and pKCRI-49-1 (11681 bp) and pKCRI-28-1 (29606 bp), each carrying three resistance genes. New ampC alleles detected included ampC-69, ampC-70 and ampC-71. Global clone 1 and 2 isolates were found to harbour ISAba1 directly upstream of the ampC gene. Finally, SNP-based phylogenetic analysis of the A. baumannii isolates revealed closely related isolates in three clusters. CONCLUSIONS: The validity of the use of WGS in the prediction of phenotypic resistance can be appreciated, but at this stage is not sufficient for it to replace conventional antimicrobial susceptibility testing in our setting.

9.
Plants (Basel) ; 8(3)2019 Mar 22.
Artículo en Inglés | MEDLINE | ID: mdl-30909408

RESUMEN

Unscientific use of synthetic fungicides in plant disease management has environmental ramifications, such as disease resurgence and serious health problems due to their carcinogenicity. This has prompted the identification and development of eco-friendly greener alternatives. Eclipta alba extract was evaluated for its antifungal activity in in vitro and in vivo against sorghum fungal pathogens Fusarium thapsinum, Alternaria alternata, Epicoccum sorghinum, and Curvularia lunata. The column purified methanolic extract of E. alba exhibited good antifungal activity against the target pathogens. The MIC was observed at 80 mg/mL for all tested pathogenic fungi, whereas MFC was 80 mg/mL for E. sorghinum, 100 mg/mL for F. thapsinum, A. alternata, and C. lunata. In vitro germination percentage was significantly high in seeds treated with E. alba extract (98%) over untreated control (91%). Significant disease protection of 95% was observed in greenhouse and 66% disease protection was noticed in field experiments. The efficacy of E. alba extract in field conditions was improved with the use of E. alba extract formulation. The profile of phytochemicals in E. alba methanol fractions was obtained by ultra-performance liquid chromatography (UPLC) mass spectroscopy. The [M-H]- at m/z 313.3, m/z 797.9, and m/z 269.0 revealed the presence of wedelolactone, eclalbasaponin II, and apigenin, respectively. The H-nuclear magnetic resonance spectroscopy (¹H-NMR) chemical shift value supported the findings of the mass spectrometry. The results highlighted the possible use of E. alba methanolic extract as alternative to chemical fungicide in sorghum disease management.

10.
Nat Commun ; 10(1): 1124, 2019 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-30850636

RESUMEN

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.


Asunto(s)
Bacterias/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Genes Bacterianos , Metagenoma , Aguas del Alcantarillado/microbiología , África , Asia , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Monitoreo Epidemiológico , Europa (Continente) , Humanos , Metagenómica/métodos , Consorcios Microbianos/efectos de los fármacos , Consorcios Microbianos/genética , América del Norte , Oceanía , Salud Poblacional , Factores Socioeconómicos , América del Sur
11.
J Antimicrob Chemother ; 74(6): 1473-1476, 2019 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-30863844

RESUMEN

OBJECTIVES: In enterococci, resistance to linezolid is often mediated by mutations in the V domain of the 23S rRNA gene (G2576T or G2505A). Furthermore, four genes [optrA, cfr, cfr(B) and poxtA] encode linezolid resistance in enterococci. We aimed to develop a Web tool for detection of the two mutations and the four genes encoding linezolid resistance in enterococci from whole-genome sequence data. METHODS: LRE-Finder (where LRE stands for linezolid-resistant enterococci) detected the fraction of Ts in position 2576 and the fraction of As in position 2505 of the 23S rRNA and the cfr, cfr(B), optrA and poxtA genes by aligning raw sequencing reads (fastq format) with k-mer alignment. For evaluation, fastq files from 21 LRE isolates were submitted to LRE-Finder. As negative controls, fastq files from 1473 non-LRE isolates were submitted to LRE-Finder. The MICs of linezolid were determined for the 21 LRE isolates. As LRE-negative controls, 26 VRE isolates were additionally selected for linezolid MIC determination. RESULTS: LRE-Finder was validated and showed 100% concordance with phenotypic susceptibility testing. A cut-off of 10% mutations in position 2576 and/or position 2505 was set in LRE-Finder for predicting a linezolid resistance phenotype. This cut-off allows for detection of a single mutated 23S allele in both Enterococcus faecalis and Enterococcus faecium, while ignoring low-level sequencing noise. CONCLUSIONS: A Web tool for detection of the 23S rRNA mutations (G2576T and G2505A) and the optrA, cfr, cfr(B) and poxtA genes from whole-genome sequences from enterococci is now available online.

12.
Toxins (Basel) ; 10(10)2018 09 27.
Artículo en Inglés | MEDLINE | ID: mdl-30261694

RESUMEN

Antivenom cross-reactivity has been investigated for decades to determine which antivenoms can be used to treat snakebite envenomings from different snake species. Traditionally, the methods used for analyzing cross-reactivity have been immunodiffusion, immunoblotting, enzyme-linked immunosorbent assay (ELISA), enzymatic assays, and in vivo neutralization studies. In recent years, new methods for determination of cross-reactivity have emerged, including surface plasmon resonance, antivenomics, and high-density peptide microarray technology. Antivenomics involves a top-down assessment of the toxin-binding capacities of antivenoms, whereas high-density peptide microarray technology may be harnessed to provide in-depth knowledge on which toxin epitopes are recognized by antivenoms. This review provides an overview of both the classical and new methods used to investigate antivenom cross-reactivity, the advantages and disadvantages of each method, and examples of studies using the methods. A special focus is given to antivenomics and high-density peptide microarray technology as these high-throughput methods have recently been introduced in this field and may enable more detailed assessments of antivenom cross-reactivity.


Asunto(s)
Antivenenos/inmunología , Venenos de Serpiente/inmunología , Animales , Reacciones Cruzadas , Péptidos/inmunología
13.
BMC Bioinformatics ; 19(1): 307, 2018 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-30157759

RESUMEN

BACKGROUND: As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates. RESULTS: The functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory. CONCLUSION: With KMA, it was possible map raw reads directly against redundant databases with high accuracy, speed and memory efficiency.


Asunto(s)
Algoritmos , Biología Computacional/métodos , Bases de Datos Factuales , Genoma Humano , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Simulación por Computador , Humanos , Alineación de Secuencia
15.
Methods Mol Biol ; 1822: 115-122, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30043300

RESUMEN

Successful application of virus-induced gene silencing for functional genomics requires a virus vector that can initiate a systemic infection of the host plant. Agroinoculation of the pea early browning virus vectors pCAPE1 and pCAPE2 can establish infection in several genotypes of Medicago truncatula and can reduce target gene RNA levels to an extent that allows investigation of gene function.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Silenciador del Gen , Medicago truncatula/genética , Interferencia de ARN , Genoma de Planta , Genómica/métodos , Medicago truncatula/microbiología , Fenotipo , Plantas Modificadas Genéticamente , Plásmidos/genética
16.
Eur J Clin Microbiol Infect Dis ; 37(10): 1901-1914, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-30030694

RESUMEN

This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.


Asunto(s)
Farmacorresistencia Bacteriana/genética , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/patogenicidad , Adulto , Anciano , Anciano de 80 o más Años , Antibacterianos/farmacología , Niño , Estudios Transversales , Farmacorresistencia Bacteriana/efectos de los fármacos , Femenino , Hospitales , Humanos , Infecciones por Klebsiella/tratamiento farmacológico , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/genética , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Filogenia , Plásmidos/genética , Tanzanía , Virulencia/genética , beta-Lactamasas/genética
17.
Artículo en Inglés | MEDLINE | ID: mdl-29977533

RESUMEN

Background: Limited information regarding the clonality of circulating E. coli strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of E. coli isolated from patients in a tertiary care hospital in Tanzania. Methods: E. coli isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain E. coli relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance. Results: Out of 38 E. coli isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes. On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and p = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and p = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote E. coli immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs. Conclusion: There is a high diversity of E. coli isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.


Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Escherichia coli/epidemiología , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Hospitales/estadística & datos numéricos , Centros de Atención Terciaria/estadística & datos numéricos , Resistencia betalactámica/genética , Combinación Amoxicilina-Clavulanato de Potasio/farmacología , Estudios Transversales , Escherichia coli/clasificación , Escherichia coli/genética , Genoma Bacteriano/genética , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Filogenia , Tanzanía/epidemiología , Combinación Trimetoprim y Sulfametoxazol/farmacología , Factores de Virulencia , Secuenciación Completa del Genoma , beta-Lactamasas/genética
18.
Nat Microbiol ; 3(8): 898-908, 2018 08.
Artículo en Inglés | MEDLINE | ID: mdl-30038308

RESUMEN

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.


Asunto(s)
Bacterias/clasificación , Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana , Heces/microbiología , Animales , Bacterias/efectos de los fármacos , Bacterias/genética , Biodiversidad , Pollos , Europa (Continente) , Perfilación de la Expresión Génica/veterinaria , Metagenómica/métodos , Análisis de Secuencia de ADN/veterinaria , Especificidad de la Especie , Porcinos
19.
Biomed Res Int ; 2018: 2087693, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29487865

RESUMEN

Objective: To determine molecular epidemiology of methicillin-resistant S. aureus in Tanzania using whole genome sequencing. Methods: DNA from 33 Staphylococcus species was recovered from subcultured archived Staphylococcus isolates. Whole genome sequencing was performed on Illumina Miseq using paired-end 2 × 250 bp protocol. Raw sequence data were analyzed using online tools. Results: Full susceptibility to vancomycin and chloramphenicol was observed. Thirteen isolates (43.3%) resisted cefoxitin and other antimicrobials tested. Multilocus sequence typing revealed 13 different sequence types among the 30 S. aureus isolates, with ST-8 (n = seven, 23%) being the most common. Gene detection in S. aureus stains were as follows: mecA, 10 (33.3%); pvl, 5 (16.7%); tst, 2 (6.7%). The SNP difference among the six Tanzanian ST-8 MRSA isolates ranged from 24 to 196 SNPs and from 16 to 446 SNPs when using the USA300_FPR3757 or the USA500_2395 as a reference, respectively. The mutation rate was 1.38 × 10-11 SNPs/site/year or 1.4 × 10-6 SNPs/site/year as estimated by USA300_FPR3757 or the USA500_2395, respectively. Conclusion: S. aureus isolates causing infections in hospitalized patients in Moshi are highly diverse and epidemiologically unrelated. Temporal phylogenetic analysis provided better resolution on transmission and introduction of MRSA and it may be important to include this in future routines.


Asunto(s)
Staphylococcus aureus Resistente a Meticilina/genética , Infecciones Estafilocócicas/epidemiología , Infecciones Estafilocócicas/microbiología , Antibacterianos/uso terapéutico , Cloranfenicol/uso terapéutico , Humanos , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Epidemiología Molecular/métodos , Filogenia , Polimorfismo de Nucleótido Simple/genética , Infecciones Estafilocócicas/tratamiento farmacológico , Tanzanía/epidemiología , Centros de Atención Terciaria , Vancomicina/uso terapéutico , Secuenciación Completa del Genoma/métodos
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