Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway.

Vaccination against SARS-CoV-2 has greatly mitigated the impact of the COVID-19 pandemic. However, concerns have been raised about the degree to which vaccination might drive the emergence and selection of immune escape mutations that will hamper the efficacy of the vaccines. In this study, we investigate whether vaccination impacted the micro-scale adaptive evolution of SARS-CoV-2 in the Oslo region of Norway, during the first nine months of 2021, a period in which the population went from near-zero to almost 90 per cent vaccine coverage in the population over 50 years old. Weekly aggregated data stratified by age on vaccine uptake and number of SARS-CoV-2 cases in the area were obtained from the National Immunization Registry and the Norwegian Surveillance System for Communicable Diseases, respectively. A total of 6,438 virus sequences (7.5 per cent of the registered cases) along with metadata were available. We used a causal-driven approach to investigate the relationship between vaccination progress and changes in the frequency of 362 mutations present in at least ten samples, conditioned on the emergence of new lineages, time, and population vaccination coverage. After validating our approach, we identified 21 positive and 12 negative connections between vaccination progress and mutation prevalence, and most of them were outside the Spike protein. We observed a tendency for the mutations that we identified as positively connected with vaccination to decrease as the vaccinated population increased. After modelling the fitness of different competing mutations in a population, we found that our observations could be explained by a clonal interference phenomenon in which high fitness mutations would be outcompeted by the emergence or introduction of other high-fitness mutations.

Longitudinal whole blood transcriptomic analysis characterizes neutrophil activation and interferon signaling in moderate and severe COVID-19.

A maladaptive inflammatory response has been implicated in the pathogenesis of severe COVID-19. This study aimed to characterize the temporal dynamics of this response and investigate whether severe disease is associated with distinct gene expression patterns. We performed microarray analysis of serial whole blood RNA samples from 17 patients with severe COVID-19, 15 patients with moderate disease and 11 healthy controls. All study subjects were unvaccinated. We assessed whole blood gene expression patterns by differential gene expression analysis, gene set enrichment, two clustering methods and estimated relative leukocyte abundance using CIBERSORT. Neutrophils, platelets, cytokine signaling, and the coagulation system were activated in COVID-19, and this broad immune activation was more pronounced in severe vs. moderate disease. We observed two different trajectories of neutrophil-associated genes, indicating the emergence of a more immature neutrophil phenotype over time. Interferon-associated genes were strongly enriched in early COVID-19 before falling markedly, with modest severity-associated differences in trajectory. In conclusion, COVID-19 necessitating hospitalization is associated with a broad inflammatory response, which is more pronounced in severe disease. Our data suggest a progressively more immature circulating neutrophil phenotype over time. Interferon signaling is enriched in COVID-19 but does not seem to drive severe disease.

Phylodynamic signatures in the emergence of community-associated MRSA.

Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (Re) and sustained transmission (Re > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia, and Europe. Surges in Re were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.

A tale of two STs: molecular and clinical epidemiology of MRSA t304 in Norway 2008-2016.

The purpose of this study was to investigate the epidemiological, molecular, and clinical characteristics of MRSA t304/ST8 and t304/ST6 in Norway from 2008 to 2016. Clinical and epidemiological data were collected for each case included in the study. Strains were characterized by PCR, spa typing, antimicrobial susceptibility testing, and whole genome sequencing. The overall number of cases of MRSA t304 increased from 27 in 2008 to 203 in 2016. Most MRSA t304/ST8 cases were defined as HA-MRSA (89.9%) and diagnosed in persons with Norwegian background, many of them living in nursing homes (62.3%). The number of t304/ST8 cases declined throughout the study period and it has not been reported in Norway since 2014. The increasing MRSA t304/ST6 genotype has mainly been introduced to Norway by immigration from the Middle East, but also from other parts of the world. The t304/ST6 clone is mostly classified as CA-MRSA (75.1%), does not seem to cause serious infections, is not multi-resistant, and has not yet caused outbreaks in Norway. This study provides an example of two MRSA clones with the same spa type found in different epidemiological settings. This is very unusual, but still a reminder that spa typing in some cases may have insufficient discriminatory power for surveillance of MRSA. Our results highlight the importance of active surveillance and characterization of emerging MRSA clones with high potential for spread in the community, which may potentially cause outbreaks in healthcare facilities.

Exploring the evolution and epidemiology of European CC1-MRSA-IV: tracking a multidrug-resistant community-associated meticillin-resistant Staphylococcus aureus clone.

This study investigated the evolution and epidemiology of the community-associated and multidrug-resistant Staphylococcus aureus clone European CC1-MRSA-IV. Whole-genome sequences were obtained for 194 European CC1-MRSA-IV isolates (189 of human and 5 of animal origin) from 12 countries, and 10 meticillin-susceptible precursors (from North-Eastern Romania; all of human origin) of the clone. Phylogenetic analysis was performed using a maximum-likelihood approach, a time-measured phylogeny was reconstructed using Bayesian analysis, and in silico microarray genotyping was performed to identify resistance, virulence-associated and SCCmec (staphylococcal cassette chromosome mec) genes. Isolates were typically sequence type 1 (190/204) and spa type t127 (183/204). Bayesian analysis indicated that European CC1-MRSA-IV emerged in approximately 1995 before undergoing rapid expansion in the late 1990s and 2000s, while spreading throughout Europe and into the Middle East. Phylogenetic analysis revealed an unstructured meticillin-resistant S. aureus (MRSA) population, lacking significant geographical or temporal clusters. The MRSA were genotypically multidrug-resistant, consistently encoded seh, and intermittently (34/194) encoded an undisrupted hlb gene with concomitant absence of the lysogenic phage-encoded genes sak and scn. All MRSA also harboured a characteristic ~5350 nt insertion in SCCmec adjacent to orfX. Detailed demographic data from Denmark showed that there, the clone is typically (25/35) found in the community, and often (10/35) among individuals with links to South-Eastern Europe. This study elucidated the evolution and epidemiology of European CC1-MRSA-IV, which emerged from a meticillin-susceptible lineage prevalent in North-Eastern Romania before disseminating rapidly throughout Europe.

Comparison of SARS-CoV-2 infections in healthcare workers with high and low exposures to Covid-19 patients in a Norwegian University Hospital.

INTRODUCTION: A year into the pandemic, the knowledge of SARS-CoV-2 infection risks among healthcare workers remains limited. In this cross-sectional study, we examined whether healthcare workers with high exposure to Covid-19 patients had a higher risk of SARS-CoV-2 infection than other healthcare workers in a Norwegian University Hospital. We also investigated the prevalence of asymptomatic healthcare workers in a ward with a SARS-CoV-2 outbreak. METHODS: Healthcare workers from five wards at Akershus University Hospital were included between May 11 and June 11, 2020. Blood samples were analyzed for SARS-CoV-2 antibodies and seroprevalences compared between participants with high and low exposure to Covid-19 patients. Demographic data and SARS-CoV-2 infection risk factors were recorded in a questionnaire. Naso-/oropharyngeal swabs from participants from the outbreak ward were analyzed by reverse transcriptase-polymerase chain reaction. RESULTS: 360/436 (82.6%) healthcare workers participated. 9/262 (3.4%) participants from wards with high exposure to Covid-19 patients were SARS-CoV-2 seropositive versus 3/98 (3.1%) from wards with low exposure (OR 1.13; 95%CI 0.3-4.26, p = .861). SARS-CoV-2 antibodies were found in 11/263 (4.2%) participants who had worked one or more shifts caring for Covid-19 patients versus in 1/85 (1.2%) without any known occupational Covid-19 exposure (OR 3.67; 95%CI 0.46-29.06, p = .187). SARS-CoV-2 was detected in naso-/oropharyngeal swabs from 2/78 (2.6%) participants. CONCLUSION: We found no significantly increased risk of SARS-CoV-2 infection in healthcare workers with high exposure to COVID-19 patients. Five healthcare workers had either serologic or molecular evidence of past or present unrecognized SARS-CoV-2 infection.

Severe Acute Respiratory Syndrome Coronavirus 2 RNA in Plasma Is Associated With Intensive Care Unit Admission and Mortality in Patients Hospitalized With Coronavirus Disease 2019.

The clinical significance of severe acute respiratory syndrome coronavirus 2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58 of 123 (47%) patients hospitalized with coronavirus disease 2019. RNA was detected more frequently, and levels were higher, in patients who were admitted to the intensive care unit and/or died.

Is increased Staphylococcus aureus colonization during military service caused by specific genotypes? Molecular examination of long-term carriage in a prospective cohort study.

A 22% increase in Staphylococcus aureus colonization was observed in Norwegian recruits during first year of military service. The aim was to determine whether specific genotypes caused the increase and to examine carriage status based on genotyping. Characterization of S. aureus from nose, throat and perineum sampled at enrolment and discharge included spa typing, MLVA, detection of PVL genes and antimicrobial susceptibility testing. spa typing demonstrated high and stable genetic diversity. The three most frequent spa types were found in 15% of recruits at enrolment and in 29% at discharge. Only t084 increased significantly (p = 0.02). Subtyping revealed that t084, t065 and t002 consisted of 13, 6 and 11 different MLVA types, respectively, at discharge. The military cohort (n = 265) consisted of S. aureus carriers of identical genotype (n = 99, 38%), carriers of non-identical genotype (n = 52, 20%), intermittent carriers (n = 86, 33%) and non-carriers (n = 27, 10%). Carrier status was indefinable for one recruit due to unavailable isolates for genotyping. Antibiotic resistance towards erythromycin, fusidic acid and clindamycin increased significantly and above national surveillance levels. The observed increase in S. aureus colonization during military service was caused by many different genotypes implying many transmission routes. Genotype did not correlate with colonization niche or carriage status.

Predictors of one-year all-cause mortality and infection-related mortality in patients with Staphylococcus aureus bacteraemia.

OBJECTIVES: Staphylococcus aureus bacteraemia (SAB) is a common infection associated with significant short-term mortality. Little is known about long-term prognosis. The aim of this study was to determine one-year all-cause mortality and infection-related mortality and associated predictors. METHODS: Data from 303 consecutive patients with SAB were prospectively collected from March 2011 to February 2014. All patients were followed one year or until death. RESULTS: One-year all-cause- and infection-related mortality were 36.7% and 20.8%, respectively. For all-cause mortality, in multivariable logistic regression analysis, age 70-79 years (OR 3.9; 95% CI 1.7-9.1; p = .001), Charlson Comorbidity index ≥3 (OR 6.9; 95% CI 2.7-17.3; p < .001), healthcare-associated infection (OR 2.3; 95% CI 1.1-4.9; p = .03) and severe sepsis (OR 3.6; 95% CI 1.8-7.1; p < .001) were independent predictors of outcome. For infection-related mortality, the predictors were similar, except for healthcare-associated infection that lost significance. The vast majority (89%) of infection-related deaths occurred within 30 days. CONCLUSIONS: This study demonstrates additional significant all-cause mortality in patients with SAB beyond 30 days to one year, mainly driven by high age and comorbidity. As a result, SAB can be considered an indirect marker of high risk of death in these patients. Follow-up beyond 30 days does not add significant information with respect to infection-related mortality.

No associations established between single nucleotide polymorphisms in human Toll-like receptor 2 and Toll-interacting protein and Staphylococcus aureus bloodstream infections.

Staphylococcus aureus bloodstream infections (SABSI) are associated with high morbidity and mortality. The Toll-like receptor 2 (TLR2) and Toll-interacting protein (TOLLIP) are important in recognition and regulation of human innate immunity response to S. aureus. Single nucleotide polymorphisms (SNPs) in the TLR2 and TOLLIP encoding genes have been associated with disease, including BSI. The aim of this study was to examine potential associations between a selection of SNPs in the genes encoding TLR2 and TOLLIP, and predisposition, severity, and outcome of SABSI. All patients ≥18 years of age with at least one S. aureus positive blood culture collected from March 2011 through February 2014 at Akershus University Hospital, Lørenskog, Norway, were considered for inclusion. Patients attending elective orthopaedic surgery (total hip and knee replacements, lumbar surgery) served as a control group. The TLR2 Arg753Gln, TLR2 Pro631His, TOLLIP rs5743942, and rs5743867 polymorphisms were analysed using TaqMan SNP Genotyping Assays. A total of 209 SABSI patients and 295 controls were included. The TLR2 Arg753Gln and TLR2 Pro631His polymorphisms were infrequent with no homozygotes and <10% heterozygotes. The included TLR2 and TOLLIP polymorphisms were not associated with susceptibility to SABSI, severity, 30-day all-cause mortality, or SABSI caused by the clonal complex 30 (CC30) genotype.

Can MLVA Differentiate among Endemic-Like MRSA Isolates with Identical Spa-Type in a Low-Prevalence Region?

The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Norway is low, but an endemic-like MRSA clone with Staphylococcal protein A (spa)-type t304 has been established especially in nursing homes in the Oslo region causing several large outbreaks. The challenge was that spa-typing and the gold standard Pulsed-Field Gel Electrophoresis (PFGE) were inadequate in discriminating isolates in outbreak investigations. Additional higher resolution genotyping methods were needed. The aims of this study were a) to evaluate whether Multiple-Locus Variable number of tandem repeat Analysis (MLVA) could differentiate within the PFGE clusters between epidemiologically related and unrelated endemic-like ST8-MRSA-IV-t304-PVL-neg (MRSA-t304) isolates and b) investigate the evolution of the endemic-like MRSA-t304 clone over a 15-year time period. All MRSA-t304 isolates detected in the region from 1998 through April 2013 were included. In total, 194 of 197 isolates were available for PFGE and MLVA analyses. PFGE results on isolates from 1998-2010 have been published previously. Two PFGE clusters subdivided into eight MLVA types were detected. One major outbreak clone (PFGE cluster C2/ MLVA type MT5045) appeared from 2004 to 2011 causing long-lasting and large outbreaks in seven nursing homes and one hospital. Five new MLVA types (N = 9 isolates) differing in only one VNTR compared to the outbreak clone C2/MT5045 were detected, but only one (C2/MT5044) was seen after 2011. We suggest that MLVA can replace PFGE analysis, but MLVA may not be the optimal method in this setting as it did not discriminate between all epidemiologically unrelated isolates. The results may indicate that all eight outbreaks in different locations within the PFGE C2 cluster may be branches of one large regional outbreak. The major outbreak strain C2/MT5045 may now, however, be under control, extinguished or has moved geographically.

[Cases of MRSA in nursing homes in Oslo 2005-11]. / MRSA-funn i sykehjem i Oslo 2005-11.

BACKGROUND: The number of infections caused by MRSA has increased substantially in Norway in the past decade. It is an objective to prevent MRSA from becoming established in nursing homes and hospitals. The purpose of the article is to describe the features of the development of MRSA cases found in nursing homes in Oslo. MATERIALS AND METHOD: We carried out a retrospective study of registered cases of MRSA (both sufferers and carriers) in Oslo in 2005-11. Data were obtained from the City of Oslo municipal health services' MRSA database and from genotyping carried out at Akershus University Hospital. RESULTS: The annual number of cases of MRSA found in Oslo increased during the period 2005-11 from 92 in 2005 to 268 in 2011, a total of 1198 cases. Of these, 224 cases (19%) were registered in nursing homes, distributed among 22 institutions, 158 residents and 66 staff, with an average of 32 cases annually (14-58 spread). Twenty-eight of 50 nursing homes had no cases of MRSA, while 159 of the cases were related to outbreaks of MRSA. Three of 20 outbreaks affected residents only. The nursing home isolates consisted of 40 different spa types, of which 160 (71%) of the isolates were clustered in three clonal complexes. The most common spa type t304 was found in 116 (52%) of the cases. INTERPRETATION: Cases of MRSA in Oslo in total increased sharply from 2005 to 2011, while the number of cases in nursing homes was stable. It is, however, uncertain whether this reflects the actual incidence.

Molecular characterization of methicillin-sensitive Staphylococcus aureus isolates from bacteremic patients in a Norwegian University Hospital.

Staphylococcus aureus bacteremia is common in both nosocomial and community settings, and the pathogenicity of the microbe depends upon a large repertoire of virulence factors. S. aureus bacteremia isolates (n = 126) were characterized using DNA microarrays. Clonal complexes 5, 8, 15, 30, and 45 accounted for 74.6% of the isolates. We identified geographical differences in dominating clones and toxin gene profiles. One isolate was methicillin resistant. Potential associations between age and genotype were detected.

Genotyping of 353 Staphylococcus aureus bloodstream isolates collected between 2004 and 2009 at a Norwegian university hospital and potential associations with clinical parameters.

We analyzed 353 Staphylococcus aureus bloodstream isolates from 2004 to 2009 to identify dominant genotypes, changes over time, and associations between genotype, phenotype, and clinical parameters. The isolates were genotyped with regard to spa type and presence of Panton-Valentine leukocidin and toxic shock syndrome toxin 1-encoding genes. A high level of genetic diversity was detected. All but three isolates were methicillin sensitive. Interestingly, spa clonal complex 021 showed a weak association with higher all-cause hospital mortality.

A diet rich in coconut oil reduces diurnal postprandial variations in circulating tissue plasminogen activator antigen and fasting lipoprotein (a) compared with a diet rich in unsaturated fat in women.

The effects of high and low fat diets with identical polyunsaturated/saturated fatty acid (P/S) ratios on plasma postprandial levels of some hemostatic variables and on fasting lipoprotein (a) [Lp(a)] are not known. This controlled crossover study compared the effects of a high fat diet [38.4% of energy (E%) from fat; HSAFA-diet, P/S ratio 0.14], a low fat diet (19.7 E% from fat; LSAFA-diet, P/S ratio 0.17), both based on coconut oil, and a diet with a high content of monounsaturated fatty acids (MUFA) and PUFA (38.2 E% from fat; HUFA-diet, P/S ratio 1.9) on diurnal postprandial levels of some hemostatic variables (n = 11) and fasting levels of Lp(a) (n = 25). The postprandial plasma concentration of tissue plasminogen activator antigen (t-PA antigen) was decreased when the women consumed the HSAFA-diet compared with the HUFA-diet (P = 0.02). Plasma t-PA antigen was correlated with plasminogen activator inhibitor type 1 (PAI-1) activity when the participants consumed all three diets (Rs = 0.78, P < 0.01; Rs = 0.76, P < 0.01; Rs = 0.66, P = 0.03; on the HSAFA-, the LSAFA- and the HUFA-diet, respectively), although the diets did not affect the PAI-1 levels. There were no significant differences in postprandial variations in t-PA activity, factor VII coagulant activity or fibrinogen levels due to the diets. Serum fasting Lp(a) levels were lower when women consumed the HSAFA-diet (13%, P < 0.001) and tended to be lower when they consumed the LSAFA-diet (5.3%, P = 0.052) than when they consumed the HUFA-diet. Serum Lp(a) concentrations did not differ when the women consumed the HSAFA- and LSAFA-diets. In conclusion, our results indicate that a coconut oil-based diet (HSAFA-diet) lowers postprandial t-PA antigen concentration, and this may favorably affect the fibrinolytic system and the Lp(a) concentration compared with the HUFA-diet. The proportions of dietary saturated fatty acids more than the percentage of saturated fat energy seem to have a beneficial influence on Lp(a) levels.