Staphylococcus aureus is a commensal colonizing the skin and mucous membranes. it can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs. Worldwide, millions of patients undergo arthroplasty surgery every year, with an expected increase in the coming years 1. Staphylococcus aureus is a major cause of both community-acquired and nosocomial infections, and is regularly reported to be the most common pathogen in prosthetic joint infections (PJIs) 2,3. Risk factors for developing PJIs are related to deficiencies in host defense due to age, obesity, previous surgery, smoking, and immune deficiencies (e.g. rheumatoid arthritis, diabetes mellitus), as well as exogenous factors such as timing and selection of antibiotic prophylaxis, extended operation time, and blood transfusions 4-8. Implant-sparing curative treatment of acute PJIs, whether occurring early in the postoperative period or later through hematogenous seeding, relies on a regimen of debridement, antibiotics, irrigation, and retention of the prosthesis (DAIR) 9. This is possible, provided that the infection has not persisted for more than approximately three weeks and that the isolate is susceptible to biofilm-active antibiotic treatment (i.e. rifampin for staphylococcal infections) 10. However, there are reports suggesting an even shorter time to intervention is needed for a successful treatment 11,12. The impact of risk factors on outcome of treatment has not been fully explored, but recent reports have proposed new risk scores to better guide the choice of treatment 13-15. S. aureus is a commensal of the human skin, nares, and mucous membranes, but also a human pathogen due to its invasive capacity. S. aureus infections occur among both otherwise-healthy individuals and those with co-morbidities, and nasal carriage...

Background and objectiveResistance in the sexually transmitted bacterium Mycoplasma genitalium to all recommended therapeutic antimicrobials have rapidly emerged. However, to date, internationally reported resistance surveillance data for M. genitalium strains circulating in Eastern Europe are entirely lacking. The aim of this study was to estimate the prevalence of macrolide and fluoroquinolone resistance-associated mutations in M. genitalium in four cities in Russia and one in Estonia, 2013–2016.Materials and methodsConsecutive urogenital samples found positive for M. genitalium during diagnostic testing were retrospectively analyzed for resistance-associated mutations in the 23S rRNA and parC genes using pyrosequencing and conventional Sanger sequencing, respectively.ResultsIn total, 867 M. genitalium positive samples from 2013–2016 were analyzed. Macrolide resistance-associated mutations were detected in 4.6% of the samples from Russia (0.7–6.8% in different cities) and in 10% of the samples from Estonia. The mutations A2059G and A2058G were highly predominating in both Russia and Estonia, accounting together for 90.9% of the cases positive for nucleotide substitutions in the 23S rRNA gene. The rates of possible fluoroquinolone resistance-associated mutations were 6.2% in Russia (2.5–7.6% in different cities) and 5% in Estonia. The mutations S83I and S83N were the most frequent ones in Russia (24.4% each), whereas D87N highly predominated in Estonia (83.3% of all fluoroquinolone resistance-associated mutations). Approximately 1% of the samples in both countries harbored both macrolide and possible fluoroquinolone resistance-associated mutations, with A2058G and S83I being the most frequent combination (37.5%).ConclusionsThe prevalence of macrolide and fluoroquinolone resistance-associated mutations in M. genitalium was 4.6% and 6.2%, respectively, in Russia, and 10% and 5%, respectively, in Estonia. Despite the relatively low rates of macrolide and fluoroquinolone resistance in these countries, antimicrobial resistance surveillance and testing for resistance-associated mutations in M. genitalium positive cases would be valuable.

Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003–2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0–5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.

Mycoplasma genitalium, causing non-gonococcal non-chlamydial urethritis and associated with cervicitis, has developed antimicrobial resistance (AMR) to both the macrolide azithromycin (first-line treatment) and the fluoroquinolone moxifloxacin (second-line treatment). Our aim was to estimate the prevalence of resistance, based on genetic AMR determinants, to these antimicrobials in the M. genitalium population in two Swedish counties, Örebro and Halland, 2011-2015. In total, 672 M. genitalium positive urogenital samples were sequenced for 23S rRNA and parC gene mutations associated with macrolide and fluoroquinolone resistance, respectively. Of the samples, 18.6% and 3.2% in Örebro and 15.2% and 2.7% in Halland contained mutations associated with macrolide and fluoroquinolone resistance, respectively. The predominating resistance-associated mutations in the 23S rRNA gene was A2059G (n = 39) in Örebro and A2058G (n = 13) and A2059G (n = 13) in Halland. The most prevalent possible resistance-associated ParC amino acid alterations were S83I (n = 4) in Örebro and S83N (n = 2) in Halland. Resistance-associated mutations to both macrolides and fluoroquinolones were found in 0.7% of samples. Our findings emphasize the need for routine AMR testing, at a minimum for macrolide resistance, of all M. genitalium-positive samples and regular national and international surveillance of AMR in M. genitalium, to ensure effective patient management and rational antimicrobial use.