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Knowledge of zoonotic links between bovine and human isolates of Staphylococcus epidermidis remains limited. The primary aim of this study was to assess the genetic relatedness of S. epidermidis isolates from bovine subclinical mastitis (SCM), bovine milk filters, healthy dairy farmers or farm personnel, and human hospital patients in Sweden, and to detect and compare genes encoding antimicrobial resistance (AMR) and virulence factors. A secondary aim was to explore the epidemiology of bovine S. epidermidis intramammary infections (IMI) by examining associations between genotypes and geographic location, persistence of IMI, severity of inflammatory response, and the persistence of S. epidermidis strains over time. A total of 283 S. epidermidis isolates were analyzed using whole genome sequencing (WGS): 128 SCM milk isolates, 55 milk filter isolates, 13 farmer/personnel isolates, and 87 human patient isolates. Sixty unique sequence types (STs) of S. epidermidis were identified. ST99, ST100, and ST570 were the most common among bovine isolates, collectively accounting for 49% (63/128) of the milk isolates and detected on multiple farms, while ST2 and ST215 were the most prevalent among human isolates. Only four STs (ST59, ST73, ST184, and ST218), representing a total of 13 isolates, were found in both bovine and human samples. Genes conferring AMR were more frequently identified in human patient isolates compared to bovine isolates. However, penicillin resistance, identified by presence of the blaZ gene, was detected in 42% of bovine S. epidermidis isolates. The average number of potential virulence factors (pVF) per isolate was 23.8 with 23.1 in milk isolates, 23.4 in milk filter isolates, 23.0 in farmer/personnel isolates, and 25.2 in human patient isolates. There was some variation in the total number of pVFs and the presence of specific pVFs or functional groups of pVFs between sample types and STs. In conclusion, the results indicate that the overlap of STs and AMR genes between human and bovine samples was minimal. However, the persistence of certain STs across multiple dairy farms suggests inter-farm transmission. This study provides new insights into the epidemiology of bovine S. epidermidis IMI, with implications for the control of these infections.

Objectives: Previous research has suggested antiviral properties for lithium, including potential effectiveness against COVID-19 in vitro. This study aimed to investigate the impact of lithium and other psychotropic drugs on the risks of mortality, hospitalization, and ICU admission due to COVID-19 among individuals with bipolar disorder. The primary objective was to assess whether lithium was beneficial in COVID-19-infection in a real-world population.

Methods: Retrospective register study using data from multiple Swedish patient registers, including 39,063 individuals in Sweden with bipolar disorder and prescribed mood stabilizers. Outcomes included COVID-19-associated death, hospitalization, and ICU admission between 11 March 2020 and 10 March 2021. Multivariate logistic regression adjusted for age, sex, and somatic comorbidities was conducted.

Results: Lithium were prescribed to 44.2 % of patients, either as mono- or combination therapy; other mood stabilizers were prescribed to 55.8 %. There were no significant associations between lithium and COVID-19-associated death, hospitalization, or ICU admission. Atypical antipsychotics were associated with increased odds ratios for COVID-19-associated death (OR 1.58 [95 % CI 1.01–2.47]), hospitalization (OR 1.80 [95 % CI 1.49–2.18]), and ICU admission (OR 2.25 [95 % CI 1.33–3.80]). Benzodiazepines were associated with a significant increase in COVID-19-associated death (OR 1.54 [95 % CI 1.01–2.35]) and hospitalization OR 1.26 [95 % CI 1.03–1.53]). In an ad hoc analysis, lithium monotherapy was, however, associated with reduced hospitalizations and ICU admissions.

Conclusions: Our findings weaken the hypothesis that lithium reduces the risk of severe events associated with COVID-19 infection in bipolar disorder.

In 2010, a Cryptosporidium hominis outbreak resulted in 27,000 clinical cryptosporidiosis cases (45% of the population) in Östersund, Sweden. Long-term abdominal and joint symptoms are common following cryptosporidiosis in adults, and it can affect the development of children in low-income countries. We investigated the potential consequences for children in a high-income setting. In 2011, we prospectively surveyed 600 randomly selected children aged 0-5 years from Östersund. Cases were defined as respondents reporting new episodes of diarrhoea during the outbreak. After 10 years, respondents received a follow-up questionnaire about long-term symptoms (n = 423). We used X2 and Mann-Whitney U tests to assess between-group differences in demographics and the mean number of symptoms. Logistic regressions adjusted for sex, age, and prior issues with loose stools were used to examine associations between case status and symptoms reported at follow-up. We retrieved data on healthcare visits from patient records. In total, 121 cases and 174 non-cases responded to the follow-up questionnaire (69.7%). Cases reported 1.74 (median 1.00, range 0-14) symptoms and non-cases 1.37 (median 0.00, range 0-11) symptoms (p = 0.029). Cases were more likely to report joint symptoms (aOR 4.0, CI 1.3-12.0) and fatigue (aOR 1.9, CI 1.1-3.4), but numbers were generally low. We found no between-group differences in abdominal symptoms, healthcare utilization, or disease diagnoses. Children aged 0-5 years from high-income countries may experience long-term symptoms after cryptosporidiosis, but may not be affected to the same extent as adults or their peers living in low-income countries.

Background: A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.

Results: We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination’s role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30–50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.

Conclusions: This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.

Background: Reports at the beginning of the COVID-19 pandemic suggested differences in COVID-19-associated mortality between individuals with serious mental disorders (SMD) and the population at large.

Aim: To compare the pattern of COVID-19-associated mortality in individuals with and without SMD in Sweden over the two main pandemic years.

Methods: We compared the pattern of COVID-19-associated mortality in individuals with and without SMD in Sweden during 2020 and 2021. For SMD, we included psychotic disorder, bipolar disorder, and severe depression. The analysis was based on summary data from the Swedish Board of Health and Welfare covering the entire adult Swedish population.

Results: The overall relative risk (RR) for experiencing a COVID-19-associated death was 1.66 (CI 1.50–1.83; p < 0.001) for individuals with SMD versus individuals without SMD. The corresponding RRs were 3.25 (CI 2.84–3.71; p < 0.001) for individuals with psychotic disorder, 1.06 (CI 0.88–1.26; p = 0.54) for individuals with bipolar disorder, and 1.03 (CI 0.80–1.32; p = 0.80) for individuals with severe depression. Compared to their respective counterparts in the non-SMD group, in the psychotic disorder and severe depression group, the RR were higher in women than in men. In the bipolar disorder group, the RR was higher in men than in women. The RR of COVID-19-associated death was generally higher in younger individuals with SMD. Individuals with psychosis between 18 and 59 years had the highest RR of COVID-19-associated death with 7.25 (CI 4.54–11.59; p<0.001).

Conclusions: Individuals with SMD, and particularly those with psychotic disorders, had a higher risk of COVID-19-associated death than the general population. As this is a pattern also seen with other infections, people with SMD may be similarly vulnerable in future pandemics.

In September 2022, the Public Health Agency of Sweden observed an increase in domestic Salmonella Typhimurium cases through the Swedish electronic notification system, and an outbreak strain was identified with whole genome sequencing. Overall, 109 cases with symptom onset between 17 September and 24 November 2022 were reported from 20 of 21 Swedish regions. The median age of cases was 52 years (range 4-87 years) and 62% were female. A case-control study found cases to be associated with consumption of rocket salad (adjusted odds ratio (aOR) = 4.9; 95% confidence interval (CI): 2.4-10, p value < 0.001) and bagged mixed salad (aOR = 4.0; 95% CI: 1.9-8.1, p value < 0.001). Traceback, supported by Finnish authorities who identified the Swedish outbreak strain in a Finnish cluster during the same time period, identified rocket salad, cultivated, pre-washed and pre-packed in Sweden as the likely source of the outbreak. No microbiological analyses of rocket salad were performed. Our investigation indicates that bagged leafy greens such as rocket salad, regardless of pre-washing procedures in the production chain, may contain Salmonella and cause outbreaks, posing a health risk to consumers. We emphasise the need for primary producers of leafy greens to identify possible contamination points to prevent outbreaks.

Background: Fluoroquinolones lack approval for treatment of tularemia but have been used extensively for milder illness. Here, we evaluated fluoroquinolones for severe illness.

Methods: In an observational study, we identified case-patients with respiratory tularemia from July to November 2010 in Jämtland County, Sweden. We defined severe tularemia by hospitalization for >24 hours and severe bacteremic tularemia by Francisella tularensis subsp. holarctica growth in blood or pleural fluid. Clinical data and drug dosing were retrieved from electronic medical records. Chest images were reexamined. We used Kaplan-Meier curves to evaluate time to defervescence and hospital discharge.

Results: Among 67 case-patients (median age, 66 years; 81% males) 30-day mortality was 1.5% (1 of 67). Among 33 hospitalized persons (median age, 71 years; 82% males), 23 had nonbacteremic and 10 had bacteremic severe tularemia. Subpleural round consolidations, mediastinal lymphadenopathy, and unilateral pleural fluid were common on chest computed tomography. Among 29 hospitalized persons with complete outcome data, ciprofloxacin/levofloxacin (n = 12), ciprofloxacin/levofloxacin combinations with doxycycline and/or gentamicin (n = 11), or doxycycline as the single drug (n = 6) was used for treatment. One disease relapse occurred with doxycycline treatment. Treatment responses were rapid, with median fever duration 41.0 hours in nonbacteremic and 115.0 hours in bacteremic tularemia. Increased age-adjusted Charlson comorbidity index predicted severe bacteremic tularemia (odds ratio, 2.7 per score-point; 95% confidence interval, 1.35-5.41). A 78-year-old male with comorbidities and delayed ciprofloxacin/gentamicin treatment died.

Conclusions: Fluoroquinolone treatment is effective for severe tularemia. Subpleural round consolidations and mediastinal lymphadenopathy were typical findings on computed tomography among case-patients in this study.

Objectives: Blood culture is a key method for diagnosing bloodstream infections. In this prospective study, we aimed to investigate whether blood cultures collected with the one-puncture method results in fewer contaminants, i.e. microorganisms from the skin or the environment, and the same detection of relevant pathogens compared to the two-puncture method. Further, we aimed to investigate if the time to blood culture positivity could be useful in evaluating contaminants.

Methods: Patients planned for blood cultures were asked to participate in the study. From each recruited patient, six blood culture bottles were drawn, bottles 1–4 from the first venipuncture and bottles 5–6 from the second venipuncture. Within each patient, bottles 1–4 were compared to bottles 1, 2, 5, and 6 for contaminants and relevant pathogens. A sub-analysis was conducted on patients admitted to the ICU and those in the haematology department. We also assessed time-to-positivity for coagulase-negative staphylococci.

Results: In the final analysis, 337 episodes from 312 patients were included. Relevant pathogens were identified in 62/337 (18.4%) episodes in both methods. Contaminants were detected in 12 (3.6%) and 19 episodes (5.6%) using the one-puncture and two-puncture method (p =.039), respectively. Corresponding results were observed in the sub-analysis. Notably, relevant coagulase-negative staphylococci demonstrated a shorter time-to-positivity compared to contaminant coagulase-negative staphylococci.

Conclusion: Blood cultures obtained using the one-puncture method resulted in significantly fewer contaminants and detected relevant pathogens equally to the two-puncture method. Time-to-positivity may be a useful additive indicator for predicting coagulase-negative staphylococci contamination in blood cultures.

We report a sudden increase in the number of cases of C. canimorsus bacteremia during 3 months in 2022 at Östersund Hospital, Sweden. Prior to these cases, the most recent one in the region occurred in 2015. Among the five cases, one suffered from meningitis and one was diagnosed as endocarditis. Dog contact was present in all cases, although dog bites could only be verified in two. Improved diagnostics could not be an explanation to the surge, since the analysis method for blood culture had been the same since 2015. No corresponding increase was noted nationally, according to the Public Health Agency of Sweden. The isolates have been included in the ongoing global study with the aim to explore Capnocytophaga in humans and animals using comparative genomics and genome wide association studies. The study is supported by several ESCMID (European Society of Clinical Microbiology and Infectious Diseases) study groups.

Sepsis orsakad av Capnocytophaga canimorsus  förekommer även hos individer som inte är immunsup­primerade. Majoriteten av dem som drabbas har nyligen haft kontakt med hund, men hundbett är inte nödvändigt. Blododlingar före antibiotikabehandling är avgörande för diagnostiken. Förstahandsbehandling vid hundbett är cefotaxim vid allvarlig infektion och amoxicillin–klavulansyra vid peroral behandling. C canimorsus är inte känslig för flukloxacillin. Rapporteringssystemet Svebar kan ge information om förekomsten av olika patogener på de mikrobiologiska laboratorierna.

Staphylococcus chromogenes and Staphylococcus simulans are commonly found in intramammary infections (IMI) associated with bovine subclinical mastitis, but little is known about genotypic variation and relatedness within species. This includes knowledge about genes encoding antimicrobial resistance (AMR) and potential virulence factors (pVF). The aim of this study was therefore to investigate these aspects by whole-genome sequencing of milk isolates from Swedish dairy cows with subclinical mastitis in an observational study. We also wanted to study if specific genotypes were associated with persistent IMI and the inflammatory response at udder quarter level. In total, 105 and 118 isolates of S. chromogenes and S. simulans, respectively, were included. Isolates were characterized using a 7-locus multilocus sequence typing (7-MLST), core genome analysis and in-silico analysis of AMR and pVF genes. Forty-seven sequence types (ST) and 7 core genome clusters of S. chromogenes were identified, and the most common ST were ST-6 and ST-109, both belonging to cluster VII. A 7-locus MLST scheme for S. simulans was not available, but 3 core genome clusters and 5 subclusters were described. Overall, substantial variation in ST and clusters among cows and herds were found in both species. Some ST of S. chromogenes were found in several herds, indicating spread between herds. Moreover, within-herd spread of the same genotype was observed for both species. Only a few AMR genes [blaZ, strpS194, vga(A)] were detected in a limited number of isolates, with the exception of blaZ coding for β-lactamase, which was identified in 22% of the isolates of S. chromogenes with ST-19, ST-102, and ST-103 more commonly carrying this gene compared with other ST. However, the blaZ gene was not identified in S. simulans. The average total number of pVF detected per isolate was similar in S. chromogenes (n = 30) and S. simulans (n = 33), but some variation in total numbers and presence of specific pVF or functional groups of pVF, was shown between ST/clusters within species. Differences in inflammatory response and potentially in persistent IMI at udder quarter level were found between S. chromogenes subtypes but not between S. simulans subtypes. In conclusion, the results from the present study generates new insight into the epidemiology of bovine S. chromogenes and S. simulans IMI, which can have implications for future prevention and antimicrobial treatment of infections related to these species.