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ObjectiveThe aim was to compare rapid antigen detection test (RADT) and throat culture for group A streptococci (GAS) among patients recently treated with penicillin V for GAS pharyngotonsillitis.Design and settingThe study was a secondary analysis within a randomized controlled trial comparing 5 versus 10 days of penicillin V for GAS pharyngotonsillitis. Patients were recruited at 17 primary health care centres in Sweden.SubjectsWe included 316 patients >= 6 years of age, having 3-4 Centor criteria, a positive RADT and a positive throat culture for GAS at inclusion, and also having a RADT and throat culture for GAS taken at a follow-up visit within 21 days.Main outcome measuresRADT and conventional throat culture for GAS.ResultsThis prospective study showed 91% agreement between RADT and culture at follow-up within 21 days. Only 3/316 participants had negative RADT with a positive throat culture for GAS at follow-up, and 27/316 patients with positive RADT had a negative culture for GAS. Log rank test did not reveal any difference in the decline over time of positive tests between RADT and throat culture (p = 0.24). Agreement between RADT and throat culture for GAS at the follow-up was not associated with treatment duration, number of days from inclusion until follow-up, throat symptoms at follow-up, gender, or age.ConclusionRADT and culture for GAS agreed to a high extent also after recent penicillin V treatment. RADT for GAS means a low risk for missing the presence of GAS.

BackgroundInvasive infections caused by Staphylococcus aureus have high clinical and epidemiological relevance. It is therefore important to monitor the S. aureus trends using suitable methods.AimThe study aimed to describe the trends of bloodstream infections (BSI) caused by meticillin-resistant S. aureus (MRSA) and meticillin-susceptible S. aureus (MSSA) in the European Union (EU) and the European Economic Area (EEA).MethodsAnnual data on S. aureus BSI from 2005 to 2018 were obtained from the European Antimicrobial Resistance Surveillance Network (EARS-Net). Trends of BSI were assessed at the EU/EEA level by adjusting for blood culture set rate (number of blood culture sets per 1,000 days of hospitalisation) and stratification by patient characteristics.ResultsConsidering a fixed cohort of laboratories consistently reporting data over the entire study period, MRSA percentages among S. aureus BSI decreased from 30.2% in 2005 to 16.3% in 2018. Concurrently, the total number of BSI caused by S. aureus increased by 57%, MSSA BSI increased by 84% and MRSA BSI decreased by 31%. All these trends were statistically significant (p

Clostridioides difficile infection represents a growing clinical challenge. The new compound omadacycline is a potential treatment alternative, as many antibiotics have limited activity or are rarely used due to costs and side effects. The activity of omadacycline and five comparators was assessed with agar dilution on a 2015-to-2018 collection of 65 C. difficile isolates from Sweden. Omadacycline demonstrated in vitro activity against the contemporary ribotypes of C. difficile, and further clinical investigation is needed. IMPORTANCE Evaluating the activity of novel antimicrobials like omadacycline is of great interest, as a reliable and efficient antimicrobial treatment for Clostridioides difficile infections is in demand.

Additional file 3: Figure S1. A) The genetic environment of blaOXA-48 and blaNDM-1 in 14 colistin-resistant OXA-48-producing K. pneumoniae strains. blaOXA-48 was identified in all strains except for P26. The lysR and blaOXA-48 complex was found in all strains. No transposase element was detected surrounding the lysR and blaOXA-48 complex in P6, P7, P40, P42 and P43. Two blaOXA-48 with different genetic arrangement were found on P32 plasmid. In P36, P37, P38 and P44; the lysR and blaOXA-48 complex was flanked upstream by IS91, IS4 and IS110 family transposase genes, respectively. B) blaNDM-1 was detected only in P6 and P26. blaNDM-1 was flanked upsteram by bleomycin binding protein and trpF genes and downstream by the IS91 family transposase.

Additional file 2: Table S2. Extrachromosomal Genetic and resistome information of 14 colistin-resistant OXA-48-producing K. pneumoniae strains.

Additional file 1: Table S1. Genotypic, resistome profile and capsular and O-typing of 14 colistin-resistant OXA-48-producing K. pneumoniae strains.

Over the past few decades, extensively drug resistant (XDR) resistant Klebsiella pneumoniae has become a notable burden to healthcare all over the world. Especially carbapenemase-producing strains are problematic due to their capability to withstand even last resort antibiotics. Some sequence types (STs) of K. pneumoniae are significantly more prevalent in hospital settings in comparison to other equally resistant strains. This provokes the question whether or not there are phenotypic characteristics that may render certain K. pneumoniae more suitable for epidemic dispersal between patients, hospitals, and different environments. In this study, we selected seven epidemic and non-epidemic carbapenem resistant K. pneumoniae isolates for extensive systematic characterization for phenotypic and genotypic qualities in order to identify potential factors that precede or emerge from epidemic successfulness. Studied characteristics include growth rates and densities in different conditions (media, temperature, pH, resource levels), tolerance to alcohol and drought, inhibition between strains, ability to compensate pH, as well as various genomic features. Overall, there are clear differences between isolates, yet, only drought tolerance was found to notably associate with non-epidemic K. pneumoniae strains. We further report a preliminary study on the potential to control K. pneumoniae ST11 with an antimicrobial component produced by a non-epidemic K. pneumoniae. This component initially restricts bacterial growth, but stable resistance develops rapidly in vitro. peerReviewed

The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.

ObjectivesThe aim of this study was to investigate the epidemiology of bloodstream infections (BSI) in a Swedish setting, with focus on risk factors for BSI-associated mortality.MethodsA 9-year (2008-2016) retrospective cohort study from electronic records of episodes of bacteremia amongst hospitalized patients in the county of Östergötland, Sweden was conducted. Data on episodes of BSI including microorganisms, antibiotic susceptibility, gender, age, hospital admissions, comorbidity, mortality and aggregated antimicrobial consumption (DDD /1,000 inhabitants/day) were collected and analyzed. Multidrug resistance (MDR) was defined as resistance to at least three groups of antibiotics. MDR bacteria and MRSA, ESBL-producing Enterobacteriaceae, vancomycin-resistant enterococci not fulfilling the MDR criteria were all defined as antimicrobial-resistant (AMR) bacteria and included in the statistical analysis of risk factors for mortality.ResultsIn all, 9,268 cases of BSI were found. The overall 30-day all-cause mortality in the group of patients with BSI was 13%. The incidence of BSI and associated 30-day all-cause mortality per 100,000 hospital admissions increased by 66% and 17% respectively during the nine-year study period. The most common species were Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae and Enterococcus faecalis. Independent risk factors for 30-day mortality were age (RR: 1.02 (CI: 1.02-1.03)) and 1, 2 or ≥3 comorbidities RR: 2.06 (CI: 1.68-2.52), 2.79 (CI: 2.27-3.42) and 2.82 (CI: 2.31-3.45) respectively. Almost 3% (n = 245) of all BSIs were caused by AMR bacteria increasing from 12 to 47 per 100,000 hospital admissions 2008-2016 (p = 0.01), but this was not associated with a corresponding increase in mortality risk (RR: 0.89 (CI: 0.81-0.97)).ConclusionComorbidity was the predominant risk factor for 30-day all-cause mortality associated with BSI in this study. The burden of AMR was low and not associated with increased mortality. Patients with BSIs caused by AMR bacteria (MDR, MRSA, ESBL and VRE) were younger, had fewer comorbidities, and the 30-day all-cause mortality was lower in this group.

BackgroundAntibiotic resistance, either intrinsic or acquired, is a major obstacle for treating bacterial infections.AimOur objective was to compare the country-specific species distribution of the four Gram-negative species Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter species and the proportions of selected acquired resistance traits within these species.MethodWe used data reported for 2016 to the European Antimicrobial Resistance Surveillance Network (EARS-Net) by 30 countries in the European Union and European Economic Area.ResultsThe country-specific species distribution varied considerably. While E. coli accounted for 31.9% to 81.0% (median: 69.0%) of all reported isolates, the two most common intrinsically resistant species P. aeruginosa and Acinetobacter spp. combined (PSEACI) accounted for 5.5% to 39.2% of isolates (median: 10.1%). Similarly, large national differences were noted for the percentages of acquired non-susceptibility to third-generation cephalosporins, carbapenems and fluoroquinolones. There was a strong positive rank correlation between the country-specific percentages of PSEACI and the percentages of non-susceptibility to the above antibiotics in all four species (rho > 0.75 for 10 of the 11 pairs of variables tested).ConclusionCountries with the highest proportion of P. aeruginosa and Acinetobacter spp. were also those where the rates of acquired non-susceptibility in all four studied species were highest. The differences are probably related to national differences in antibiotic consumption and infection prevention and control routines.