| 1. |
- Ahrens, Peter, et al.
(författare)
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Changes in the vaginal microbiota following antibiotic treatment forMycoplasma genitalium,Chlamydia trachomatisand bacterial vaginosis
- 2020
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- The human vagina harbor a rich microbiota. The optimal state is dominated by lactobacilli that help to maintain health and prevent various diseases. However, the microbiota may rapidly change to a polymicrobial state that has been linked to a number of diseases. In the present study, the temporal changes of the vaginal microbiota in patients treated for sexually transmitted diseases or bacterial vaginosis (BV) and in untreated controls were studied for 26 days. The patients included 52 women treated with azithromycin, tetracyclines or moxifloxacin for present or suspected infection withChlamydia trachomatisorMycoplasma genitalium. Women with concurrent BV were also treated with metronidazole. The controls were 10 healthy women of matching age. The microbiota was analyzed by 16S rRNA gene deep sequencing, specific qPCRs and microscopy. There was generally good correlation between Nugent score and community state type (CST) and qPCR confirmed the sequencing results. By sequencing, more than 600 different taxa were found, but only 33 constituted more than 1 parts per thousand of the sequences. In both patients and controls the microbiota could be divided into three different community state types, CST-I, CST-III and CST-IV. Without metronidazole, the microbiota remained relatively stable regarding CST although changes were seen during menstrual periods. Administration of metronidazole changed the microbiota from CST-IV to CST-III in approximately 50% of the treated patients. In contrast, the CST was generally unaffected by azithromycin or tetracyclines. In 30% of the BV patients,Gardnerella vaginaliswas not eradicated by metronidazole. The majority of women colonized withUreaplasma parvumremained positive after azithromycin whileU.urealyticumwas eradicated.
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| 2. |
- Baig, Sharmin, et al.
(författare)
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Evolution and Population Dynamics of Clonal Complex 152 Community-Associated Methicillin-Resistant Staphylococcus aureus
- 2020
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Ingår i: mSphere. - : AMER SOC MICROBIOLOGY. - 2379-5042. ; 5:4
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Tidskriftsartikel (refereegranskat)abstract
- Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s. The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe. IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.
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| 3. |
- Nielsen, Karen Leth, et al.
(författare)
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Escherichia coli causing recurrent urinary tract infections: Comparison to non-recurrent isolates and genomic adaptation in recurrent infections
- 2021
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Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 9:7
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Tidskriftsartikel (refereegranskat)abstract
- Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.
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| 5. |
- Sagerfors, Susanna, et al.
(författare)
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In the eye of the ophthalmologist : the corneal microbiome in microbial keratitis
- 2024
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Ingår i: Graefe's Archives for Clinical and Experimental Ophthalmology. - : Springer. - 0721-832X .- 1435-702X. ; 262:5, s. 1579-1589
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: To describe the bacterial findings by a targeted sequencing approach from corneal samples of patients with microbial keratitis and factors influencing culture outcome of indirectly inoculated corneal specimen.METHODS: Prospective inclusion of patients fulfilling predefined criteria of microbial keratitis. Samples from the corneal lesion were collected and dispensed in liquid transport medium, from which both culture and targeted amplification and sequencing of the V3-V4 region of the 16S rRNA gene were carried out. Additional standard corneal culture from the corneal lesions was also performed. Factors influencing culture outcome of indirectly inoculated corneal samples were identified by a multivariate regression model incorporating quantitative data from sequencing.RESULTS: Among the 94 included patients with microbial keratitis, contact lens wear (n = 69; 73%) was the most common risk factor. Contact lens wearers displayed significant differences in the bacterial community composition of the corneal lesion compared to no lens wearers, with higher abundance of Staphylococcus spp., Corynebacterium spp., and Stenotrophomonas maltophilia. Targeted sequencing detected a potential corneal pathogen in the highest proportional abundance among 9 of the 24 (38%) culture-negative patients with microbial keratitis. Age, bacterial density in the sample, and prior antibiotic treatment significantly influenced culture outcome of indirectly inoculated corneal samples.CONCLUSION: Targeted sequencing may provide insights on pathogens in both culture negative episodes of microbial keratitis and among subgroups of patients with microbial keratitis as well as factors influencing culture outcome of indirectly inoculated corneal samples.
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| 6. |
- Sagerfors, Susanna, 1977-, et al.
(författare)
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What targeted sequencing can tell us, that culture cannot : The corneal microbiome in infectious keratitis
- 2023
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Ingår i: Investigative Ophthalmology and Visual Science. - : Association for Research in Vision and Ophthalmology. - 0146-0404 .- 1552-5783. ; 64:8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Purpose: To describe the corneal microbiome in infectious keratitis in relation to contact lens wear or not, and culture outcome. To explore if targeted sequencing may provide information concerning: i) culture negative episodes, ii) variables influencing culture outcome of corneal samples dispensed in transport medium.Methods: Prospective inclusion of patients fulfilling predefined criteria of infectious keratitis. Corneal samples were dispensed in liquid Amies medium, from which both culture and targeted sequencing of the V3-V4 region of the 16S rRNA gene were carried out. Additional standard corneal culture was also performed. Main outcome measures were bacterial findings by targeted sequencing in relation to contact lens wear and culture outcome, and identification of variables influencing corneal culture outcome of indirectly inoculated corneal samples, using quantitative data from the PCR.Results: In all, 94 episodes of infectious keratitis were included, of which 70 (74%) had bacterial growth on corneal culture. In median, 15 (range 8-30) different bacterial genera per episode of infectious keratitis were detected by targeted sequencing. The contact lens wearers (69/94; 73%) displayed significant (p=0.01) differences in the bacterial community composition of the corneal lesion compared to non-wearers, with higher abundance of Staphylococcus spp. Corynebacterium spp. and Stenotrophomonas maltophilia. Among the culture negative episodes (n=24) Brevundimonas was found to be significantly (adjusted p<0.05) enriched. Sequencing detected a potential corneal pathogen such as Clostridium, Staphylococcus, Brevundimonas, Pseudomonas and Veillonella, with a relative abundance of at least 20% in more than half of the culture negative episodes (14/24; 58%). Bacterial density in the sample had the highest impact on culture outcome (OR 6.3; p=0.009) but also age increased the odds for a positive culture outcome (OR 1.04; p=0.034), while prior antibiotic treatment significantly reduced the odds of a positive corneal culture to a fifth (OR 0.2; p=0.031).Conclusions: Targeted sequencing can provide a potential corneal pathogen in case of a negative culture outcome in patients with infectious keratitis, as well as providing insights on the corneal microbiome of infectious keratitis and factors influencing its composition.
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