Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. While SNP variant calling is currently considered as the most suitable method, the choice of a ...representative reference genome and the isolate dependency of results limit standardization and affect resolution in an unknown manner. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. Here, we assess the accuracy of wg- and cg-MLST by comparing results of four
Pseudomonas aeruginosa
datasets for which epidemiological and genomic data were previously described. Three datasets included 155 isolates from three different sequence types (ST) of
P. aeruginosa
collected in our ICUs over a 5-year period. The fourth dataset consisted of 10 isolates from an investigation of
P. aeruginosa
contaminated hand soap. All isolates were previously analyzed by a core SNP approach. In this study, wg- and cg-MLST were performed in BioNumerics
TM
using a scheme developed by Applied-Maths. Correlation between SNP calling and wg- or cg-MLST results were evaluated by calculating linear regressions and their coefficient of correlations (
R
2
) between the number of SNPs and the number of allele differences in pairwise comparison of isolates. The number of SNPs and allele difference between isolates with close epidemiological linkage varies between 0–26 and 0–13, respectively. When compared to core-SNP calling, a higher coefficient of correlation was obtained with cgMLST (
R
2
of 0.92–0.99) than with wgMLST (0.78–0.99). In one dataset, a putative homologous recombination of a large DNA fragment (202 loci) was identified among these isolates, affecting its phylogeny, but with no impact on the epidemiological analysis of outbreak isolates. In conclusion, we showed that the
P. aeruginosa
wgMLST scheme in BioNumerics
TM
is as discriminatory as the core-SNP calling approach and apparently useful for outbreak investigations. We also showed that epidemiological linked isolates showed less than 26 SNPs or 13 allele differences. These are important figures for the distinction between outbreak and non-outbreak isolates when interpreting WGS results. However, as
P. aeruginosa
is highly recombinant, a cgMLST approach is preferable and caution should be addressed to possible recombination of large DNA fragments.
This study aims to describe the epidemiology of COVID-19 patients in a Swiss university hospital.
This retrospective observational study included all adult patients hospitalized with a laboratory ...confirmed SARS-CoV-2 infection from March 1 to March 25, 2020. We extracted data from electronic health records. The primary outcome was the need to mechanical ventilation at day 14. We used multivariate logistic regression to identify risk factors for mechanical ventilation. Follow-up was of at least 14 days.
145 patients were included in the multivariate model, of whom 36 (24.8%) needed mechanical ventilation at 14 days. The median time from symptoms onset to mechanical ventilation was 9·5 days (IQR 7.00, 12.75). Multivariable regression showed increased odds of mechanical ventilation with age (OR 1.09 per year, 95% CI 1.03-1.16, p = 0.002), in males (OR 6.99, 95% CI 1.68-29.03, p = 0.007), in patients who presented with a qSOFA score ≥2 (OR 7.24, 95% CI 1.64-32.03, p = 0.009), with bilateral infiltrate (OR 18.92, 3.94-98.23, p<0.001) or with a CRP of 40 mg/l or greater (OR 5.44, 1.18-25.25; p = 0.030) on admission. Patients with more than seven days of symptoms on admission had decreased odds of mechanical ventilation (0.087, 95% CI 0.02-0.38, p = 0.001).
This study gives some insight in the epidemiology and clinical course of patients admitted in a European tertiary hospital with SARS-CoV-2 infection. Age, male sex, high qSOFA score, CRP of 40 mg/l or greater and a bilateral radiological infiltrate could help clinicians identify patients at high risk for mechanical ventilation.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Candida auris, a globally emerging pathogen, has been repeatedly introduced into European healthcare settings, leading to large and long-lasting nosocomial outbreaks. The pathogen has already been ...isolated in Switzerland, requiring clinicians and microbiologists to become alert. This is the first comprehensive guidance document on prevention and control of C. auris in Swiss acute care hospitals. It brings to light the most recent evidence from published original articles and reviews. We emphasise the importance of quickly identifying this yeast by means of screening in order to prevent an outbreak that could be difficult to contain. Key containment strategies include reinforcing early detection, hand hygiene, application of strict contact precautions for colonised and infected patients, and thorough specific environmental cleaning and disinfection.
This article reviews the available evidence on the effectiveness of gloves in preventing infection during care provided to patients under contact precautions, and analyses the risks and benefits of ...their systematic use. Although hand hygiene with alcohol-based handrub was shown to be effective in preventing nosocomial infections, many publications put the effectiveness and usefulness of gloves into perspective. Instead, literature and various unpublished experiences point towards reduced hand hygiene compliance and increased risk of spreading pathogens with routine glove use. Therefore, hospitals should emphasise hand hygiene in their healthcare staff and, instead of the routine use of gloves when caring for patients under contact precautions, limit their use to the indications of standard precautions, i.e., mainly for contact with body fluids. Wide and easy access to alcohol-based handrub and continual teaching are essential. If such conditions are met and adherence to hand hygiene is excellent and regularly assessed, the routine use of gloves for patients under contact precautions seems no longer indicated.
Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for ...patients' cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q
, Panbio
and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q
, Panbio
and BD Veritor™, respectively, for viral loads above 10
copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 10
copies/mL and 100% for viral loads above 10
copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.
Invasive mould infections are life-threatening complications in patients with haematologic cancer and chemotherapy-induced neutropenia. While invasive aspergillosis represents the main cause of ...invasive mould infections, non-Aspergillus mould infections, such as mucormycosis, are increasingly reported. Consequently, their local epidemiology should be closely monitored. The aim of this study was to investigate the causes of an increased incidence of non-Aspergillus mould infections in the onco-haematology unit of a Swiss tertiary care hospital.
All cases of proven and probable invasive mould infections were retrospectively identified via a local registry for the period 2007-2021 and their incidence was calculated per 10,000 patient-days per year. The relative proportion of invasive aspergillosis and non-Aspergillus mould infections was assessed. Factors that may affect invasive mould infections' incidence, such as antifungal drug consumption, environmental contamination and changes in diagnostic approaches, were investigated.
A significant increase of the incidence of non-Aspergillus mould infections (mainly mucormycosis) was observed from 2017 onwards (Mann and Kendall test p = 0.0053), peaking in 2020 (8.62 episodes per 10,000 patient-days). The incidence of invasive aspergillosis remained stable across the period of observation. The proportion of non-Aspergillus mould infections increased significantly from 2017 (33% vs 16.8% for the periods 2017-2021 and 2007-2016, respectively, p = 0.02). Building projects on the hospital site were identified as possible contributors of this increase in non-Aspergillus mould infections. However, novel diagnostic procedures may have improved their detection.
We report a significant increase in non-Aspergillus mould infections, and mainly in mucormycosis infections, since 2017. There seems to be a multifactorial origin to this increase. Epidemiological trends of invasive mould infections should be carefully monitored in onco-haematology units in order to implement potential corrective measures.
Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant Staphylococcus aureus (MRSA) sequence type 228 (ST228) ...SCCmec I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient admission and movement confirmed that the outbreak was due to the transmission of a single clonal variant of ST228, rather than repeated introductions of this clone into the hospital. We note that this clone is significantly more frequently recovered from groin and rectal swabs than other clones (P < 0.0001) and is also significantly more transmissible between roommates (P < 0.01). Unrecognized MRSA carriers, together with movements of patients within the hospital, also seem to have played a major role. These atypical colonization and transmission dynamics can help explain how the outbreak was maintained over the long term. This "stealthy" asymptomatic colonization of the gut, combined with heightened transmissibility (potentially reflecting a role for environmental reservoirs), means the dynamics of this outbreak share some properties with enteric pathogens such as vancomycin-resistant enterococci or Clostridium difficile.
Using whole-genome sequencing, we showed that a large and prolonged outbreak of methicillin-resistant Staphylococcus aureus was due to the clonal spread of a specific strain with genetic elements adapted to the hospital environment. Unrecognized MRSA carriers, the movement of patients within the hospital, and the low detection with clinical specimens were also factors that played a role in this occurrence. The atypical colonization of the gut means the dynamics of this outbreak may share some properties with enteric pathogens.
Infective endocarditis (IE) is a common complication of
bacteremia (SAB). The study aimed to develop and validate a prediction score to determine IE risk among SAB.
This retrospective study included ...adults with SAB (2015-2021) and divided them into derivation and validation cohorts. Using the modified 2015 European Society of Cardiology modified Duke Criteria for definite IE, the LAUSTAPHEN score was compared to previous scores.
Among 821 SAB episodes, 419 and 402 were divided into derivation and validation cohorts, respectively. Transthoracic and transoesophageal echocardiography (TOE) were performed in 77.5 and 42.1% of episodes, respectively. Definite IE was diagnosed in 118 episodes (14.4%). Derivation cohort established that cardiac predisposing factors, such as cardiac implantable electronic devices, prolonged bacteremia ≥48 h, and vascular phenomena were independently associated with IE. In addition to those parameters, native bone and joint infections were used to constitute the LAUSTAPHEN score. LAUSTAPHEN and VIRSTA scores misclassified <4% of IE cases as low risk. Misclassification using POSITIVE and PREDICT scores was >10%. The number of TOEs required to safely exclude IE were 66.9 and 51.6% with VIRSTA and LAUSTAPHEN, respectively.
LAUSTAPHEN and VIRSTA scores exhibited the lowest misclassification rate of IE cases to the low-risk group. However, the number of patients requiring TOE was higher for VIRSTA than for LAUSTAPHEN.
We previously reported an increase in meropenem prescriptions for Pseudomonas aeruginosa infections in our hospital after the implementation of the 10th version of the EUCAST breakpoints table for P. ...aeruginosa in January 2020. As a consequence, antibiotic susceptibility testing results were adapted by masking meropenem for P. aeruginosa isolates susceptible to either ceftazidime, cefepime or piperacillin-tazobactam. We aimed to assess the changes in meropenem prescriptions after the implementation of the selective reporting.
In this retrospective single-centre observational study, we analysed antimicrobial therapies prescribed for P. aeruginosa infections after the susceptibility testing results have been made available over three periods: "before EUCAST update", "after EUCAST update without selective reporting" and "after EUCAST update with selective reporting", at Lausanne University Hospital, Switzerland. We collected epidemiological, microbiological and clinical data. The primary outcome was the prescription of meropenem to treat P. aeruginosa infections after the release of susceptibility testing results. Secondary outcomes were the use of increased dosage of non-meropenem anti-pseudomonal drugs, and IDs' consultations rates after the release of susceptibility testing results.
Among the 457 patients included, 65 (14.2%) received meropenem: 5/148 (3.4%) before EUCAST update, 51/202 (25.3%) after EUCAST update without selective reporting, and 9/107 (8.4%) after EUCAST update with selective reporting. Supervision and counselling from IDs as well as the use of increased dosages of non-carbapenem antibiotics increased in both periods after EUCAST update, compared to the first period, respectively: 40.5% (60/148) versus 61.4% (124/202) versus 51.4% (55/107) (P < 0.001), and 57.9% (84/148) versus 91.1% (183/202) versus 90.7% (97/107) (P < 0.001).
Selective reporting of antibiotic susceptibility testing results might decrease unnecessary meropenem prescriptions for the treatment of P. aeruginosa infections and could be part of multimodal antibiotic stewardship interventions.
Objective To compare intravenous (IV) amoxicillin/clavulanic acid (A/CA) to IV cefuroxime plus metronidazole (C + M) for preventing surgical site infections (SSI) in colorectal surgery. Background ...Given their spectra that include most Enterobacterales and anaerobes, C + M is commonly recommended as prophylaxis of SSI in colorectal surgery. A/CA offers good coverage of Enterobacterales and anaerobes as well, but, in contrast to C + M, it also includes Enterococcus faecalis which is also isolated from patients with SSI and could trigger anastomotic leakage. Methods Data from a Swiss SSI surveillance program were used to compare SSI rates after class II (clean contaminated) colorectal surgery between patients who received C + M and those who received A/CA. We employed multivariable logistic regression to adjust for potential confounders, along with propensity score matching to adjust for group imbalance. Results From 2009 to 2018, 27,922 patients from 127 hospitals were included. SSI was diagnosed in 3132 (11.2%): 278/1835 (15.1%) in those who received A/CA and 2854/26,087 (10.9%) in those who received C + M (p < 0.001). The crude OR for SSI in the A/CA group as compared to C + M was 1.45 CI 95% 1.21-1.75. The adjusted OR was 1.49 1.24-1.78. This finding persisted in a 1:1 propensity score matched cohort of 1835 patients pairs with an OR of 1.60 1.28-2.00. Other factors independently associated with SSI were an ASA score > 2, a longer duration of operation, and a reoperation for a non-infectious complication. Protective factors were female sex, older age, antibiotic prophylaxis received 60 to 30 min before surgery, elective operation, and endoscopic approach. Conclusions Despite its activity against enterococci, A/CA was less effective than C + M for preventing SSI, suggesting that it should not be a first choice antibiotic prophylaxis for colorectal surgery. Keywords: Surgical site infection, Antibiotic prophylaxis, Colorectal surgery, Amoxicillin/clavulanic acid, Cefuroxime, Metronidazole
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