| 1. |
- Tilevik, Diana, 1975-, et al.
(författare)
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Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden
- 2022
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Ingår i: Microbial Pathogenesis. - : Elsevier. - 0882-4010 .- 1096-1208. ; 173:Part A
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Tidskriftsartikel (refereegranskat)abstract
- Extra-intestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a large number of human infections globally. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance, most importantly the increasing recognition of isolates producing extended-spectrum β-lactamases (ESBL). Herein, we used whole-genome sequencing (WGS) on ExPEC isolates for a comprehensive genotypic characterization. Twenty-one ExPEC isolates, nine with and 12 without ESBL-production, from 16 patients with suspected sepsis were sequenced on an Illumina MiSeq platform. Analysis of WGS data was performed with widely used bioinformatics software and tools for genotypic characterization of the isolates. A higher number of plasmids, virulence and resistance genes were observed in the ESBL-producing isolates than the non-ESBL-producing, although not statistically significant due to the low sample size. All nine ESBL-producing ExPEC isolates presented with at least one bla gene, as did three of the 12 without ESBL-production. Multi-locus sequence typing analysis revealed a diversity of sequence types whereas phylogroup A prevailed among isolates both with and without ESBL-production. In conclusion, this limited study shows that analysis of WGS data can be used for genotypic characterization of ExPEC isolates to obtain in-depth information of clinical relevance.
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| 2. |
- Shebehe, Jacques, 1983-, et al.
(författare)
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Knowledge about infections is associated with antibiotic use : cross-sectional evidence from the health survey Northern Ireland
- 2021
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Ingår i: BMC Public Health. - : Springer Nature. - 1471-2458. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Antibiotic overuse is the main modifiable driver of antibiotic resistance. Factors associated with overuse have been inconsistently reported and vary across populations. Given the burgeoning occurrence of infectious diseases around the world, there remains a great need to identify barriers and solutions to the control of infections. We examined whether knowledge about infections and antibiotic resistance is associated with antibiotic use in a northern European population sample. Methods: The Health Survey Northern Ireland 2014/15 was completed by a cross-sectional sample of 4135 participants aged > 16 years. Participants were asked whether they had taken an antibiotic in the past 12 months; and six questions were asked concerning knowledge about infections and antibiotic resistance. Correct answers to the six knowledge questions defined a knowledge score (score range 0–6 correct answers). We used multivariable logistic regression to estimate odds of self-reported antibiotic use during the last 12 months in association with knowledge score (lowest score, 0/6, as referent), and response to each knowledge question. Covariates included sex, age group, smoking, alcohol drinking, deprivation index, self-rated health, and satisfaction with life. Results were outputted as Odds Ratios (OR) and 95% Confidence Intervals (CI). Results: Antibiotic use in the past 12 months was reported by 39.0% (1614/4135); and 84.2% (3482/4135) scored < 6/6 correct on knowledge statements. Compared to the lowest knowledge score (0/6 correct), the highest knowledge score (6/6 correct) was associated with higher odds of antibiotic use (adjusted OR 2.03, 95% CI [1.46, 2.81], p < 0.001), with a P-value < 0.001 for trend with increasing knowledge score. Female sex, age, high deprivation, and poor general health, were independently associated with higher odds of antibiotic use. Stratified analyses showed sex and age group differences. Conclusion: Knowledge, and other modifiable and non-modifiable risk factors, were positively associated with antibiotic use in the past 12 months. While the causal direction of these associations could not be determined, given the high prevalence of lesser knowledge, as well as independent contributions of other factors including socioeconomic characteristics, health literacy campaigns to raise awareness of antibiotic resistance should take a multi-pronged approach. © 2021, The Author(s).
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| 3. |
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| 4. |
- Shemirani, Mahnaz Irani, 1976, et al.
(författare)
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Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis
- 2023
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Ingår i: Bmc Infectious Diseases. - : Springer Science and Business Media LLC. - 1471-2334. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory.MethodsWhole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement.ResultsThere was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates.ConclusionsAltogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.
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| 5. |
- Futo, M., et al.
(författare)
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Embryo-Like Features in Developing Bacillus subtilis Biofilms
- 2021
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Ingår i: Molecular Biology and Evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:1, s. 31-47
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Tidskriftsartikel (refereegranskat)abstract
- Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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| 6. |
- Nyberg, Lena, 1979, et al.
(författare)
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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The rapid spread of antibiotic resistance - currently one of the greatest threats to human health according to WHO - is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.
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| 7. |
- Ekström, Linnea, et al.
(författare)
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Vaginal flora and urinary and vaginal group B streptococci in early pregnancy
- 2013
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Ingår i: Gynecology. - : Herbert Publications Limited. - 2052-6210. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Bacterial vaginosis (BV) is a risk factor for premature birth and group B streptococci (GBS) colonizing the vagina are etiological agents of neonatal infections. Significant growth of GBS in the vagina has been assumed to be detectable through urinary culture. The aim was to investigate the correlation between BV and the presence of GBS in qualitative vaginal or quantitative urinary culture, since this could predict a higher risk for perinatal morbidity.Design and setting: A consecutive prospective study of women in early pregnancy included 3101 women between 2007 and 2010, in a region of south-western Sweden.Methods: Vaginal and urine samples were obtained from women in early pregnancy at maternity health care clinics. BV was diagnosed according to the Ison/Hay classification. GBS in urine were detected in amounts as low as 100 CFU/ml. Vaginal culturing for GBS was obtained from a selected group of 481 women.Results: There was no difference in the prevalence of GBS in the urine among women with BV compared with women with lactobacilli flora (OR 0.7; 95% CI 0.4-1.1). Vaginal presence of GBS was found among 17.3% of women with BV and among 23.5% of women with lactobacilli flora (OR 0.7; 95% CI 0.3-1.4). Among the 105 women who had vaginal GBS, the urine culture of GBS was positive in only 21.9% of cases.Conclusions: Even though women with BV. have much higher concentration of bacteria in the vagina, they do not necessarily have more GBS in the vagina or urine. The modest correlation between positive vaginal culture and positive urine culture of GBS question the value of urinary culture for detection of vaginal GBS.
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| 8. |
- Sundell, Timothy, et al.
(författare)
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Single-cell RNA sequencing analyses : interference by the genes that encode the B-cell and T-cell receptors
- 2023
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Ingår i: Briefings in Functional Genomics & Proteomics. - : Oxford University Press. - 2041-2649 .- 2041-2657. ; 22:3, s. 263-273
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Tidskriftsartikel (refereegranskat)abstract
- B and T cells are integral parts of the immune system and are implicated in many diseases, e.g. autoimmunity. Towards understanding the biology of B and T cells and subsets thereof, their transcriptomes can be analyzed using single-cell RNA sequencing. In some studies, the V(D)J transcripts encoding the variable regions of the B- and T-cell antigen receptors have been removed before the analyses. However, a systematic analysis of the effects of including versus excluding these genes is currently lacking. We have investigated the effects of these transcripts on unsupervised clustering and down-stream analyses of single-cell RNA sequencing data from B and T cells. We found that exclusion of the B-/T-cell receptor genes prior to unsupervised clustering resulted in clusters that represented biologically meaningful subsets, such as subsets of memory B and memory T cells. Furthermore, pseudo-time and trajectory inference analyses of early B-lineage cells resulted in a developmental pathway from progenitor to immature B cells. In contrast, when the B-/T-cell receptor genes were not removed, with the PCs used for clustering consisting of up to 70% V-genes, this resulted in some clusters being defined exclusively by V-gene segments. These did not represent biologically meaningful subsets; for instance in the early B-lineage cells, these clusters contained cells representing all developmental stages. Thus, in studies of B and T cells, to derive biologically meaningful results, it is imperative to remove the gene sequences that encode B- and T-cell receptors.
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| 9. |
- Bennet, Sean M. P., et al.
(författare)
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Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs
- 2018
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Ingår i: Gut. - : BMJ Publishing Group Ltd. - 0017-5749 .- 1468-3288. ; 67:5, s. 872-881
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Tidskriftsartikel (refereegranskat)abstract
- Objective The effects of dietary interventions on gut bacteria are ambiguous. Following a previous intervention study, we aimed to determine how differing diets impact gut bacteria and if bacterial profiles predict intervention response. Design Sixty-seven patients with IBS were randomised to traditional IBS (n=34) or low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) (n=33) diets for 4 weeks. Food intake was recorded for 4 days during screening and intervention. Faecal samples and IBS Symptom Severity Score (IBS-SSS) reports were collected before (baseline) and after intervention. A faecal microbiota dysbiosis test (GA-map Dysbiosis Test) evaluated bacterial composition. Per protocol analysis was performed on 61 patients from whom microbiome data were available. Results Responders (reduced IBS-SSS by >= 50) to low FODMAP, but not traditional, dietary intervention were discriminated from non-responders before and after intervention based on faecal bacterial profiles. Bacterial abundance tended to be higher in non-responders to a low FODMAP diet compared with responders before and after intervention. A low FODMAP intervention was associated with an increase in Dysbiosis Index (DI) scores in 42% of patients; while decreased DI scores were recorded in 33% of patients following a traditional IBS diet. Non-responders to a low FODMAP diet, but not a traditional IBS diet had higher DI scores than responders at baseline. Finally, while a traditional IBS diet was not associated with significant reduction of investigated bacteria, a low FODMAP diet was associated with reduced Bifidobacterium and Actinobacteria in patients, correlating with lactose consumption. Conclusions A low FODMAP, but not a traditional IBS diet may have significant impact on faecal bacteria. Responsiveness to a low FODMAP diet intervention may be predicted by faecal bacterial profiles.
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| 10. |
- Suzuki, Kazushi, et al.
(författare)
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Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli
- 2002
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Ingår i: Journal of Bacteriology. - 0021-9193 .- 1098-5530. ; 184:18, s. 5130-5140
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Tidskriftsartikel (refereegranskat)abstract
- The global regulator CsrA (carbon storage regulator) is an RNA binding protein that coordinates centralcarbon metabolism, activates flagellum biosynthesis and motility, and represses biofilm formation in Escherichiacoli. CsrA activity is antagonized by the untranslated RNA CsrB, to which it binds and forms a globularribonucleoprotein complex. CsrA indirectly activates csrB transcription, in an apparent autoregulatory mechanism.In the present study, we elucidate the intermediate regulatory circuitry of this system. Mutationsaffecting the BarA/UvrY two-component signal transduction system decreased csrB transcription but did notaffect csrA-lacZ expression. The uvrY defect was severalfold more severe than that of barA. Both csrA and uvrYwere required for optimal barA expression. The latter observation suggests an autoregulatory loop for UvrY.Ectopic expression of uvrY suppressed the csrB-lacZ expression defects caused by uvrY, csrA, or barA mutations;csrA suppressed csrA or barA defects; and barA complemented only the barA mutation. Purified UvrY proteinstimulated csrB-lacZ expression approximately sixfold in S-30 transcription-translation reactions, revealing adirect effect of UvrY on csrB transcription. Disruption of sdiA, which encodes a LuxR homologue, decreased theexpression of uvrY-lacZ and csrB-lacZ fusions but did not affect csrA-lacZ. The BarA/UvrY system activatedbiofilm formation. Ectopic expression of uvrY stimulated biofilm formation by a csrB-null mutant, indicative ofa CsrB-independent role for UvrY in biofilm development. Collectively, these results demonstrate that uvrYresides downstream from csrA in a signaling pathway for csrB and that CsrA stimulates UvrY-dependentactivation of csrB expression by BarA-dependent and -independent mechanisms.
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