Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection.

BACKGROUND: Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. METHODS: We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes. RESULTS: Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally. CONCLUSIONS: The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.

Efficiency evaluation of a SARS-CoV-2 diagnostic strategy combining high throughput quantitative antigen immunoassay and real time PCR.

OBJECTIVES: Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played an important role in the effort to prevent and contain local outbreaks. The aim of this study was to assess the diagnostic accuracy of a new fully automated SARS-CoV-2 laboratory-based antigen assay (CoV2Ag) and to explore the efficiency of a diagnostic algorithm combining antigen and conventional high-throughput molecular assays to address potential future challenges of the SARS-CoV-2 pandemic. METHODS: One thousand two hundred and twenty four consecutive nasopharyngeal swabs were tested using RT-PCR and CoV2Ag assay. RESULTS: The overall sensitivity and specificity of CoV2Ag were 79.1 and 97.8%, respectively. When the analysis was restricted to cases with Ct values ≤30, the sensitivity of the assay improved to 98.1%. Acceptable sensitivity was found when the analysis was limited to patients presenting within one or two to four days of symptom onset (80.5 and 84.8%, respectively). A retrospective analysis of the use of a two-step diagnostic approach combining the CoV2Ag assay and RT-PCR during an acute pandemic phase of 97 days showed a potential reduction in the number of RT-PCR tests by 36.1%, corresponding to savings in reagent costs and technician workload of approximately €8,000 and 10.5 h per day, respectively. CONCLUSIONS: Our data show that the proposed algorithm represents a valid alternative diagnostic approach to increase testing efficiency during future pandemic phases with high positivity rates (>20%) and elevated numbers of RT-PCR test requests.

Distribution of Aspergillus Species and Prevalence of Azole Resistance in Respiratory Samples From Swiss Tertiary Care Hospitals.

Among 400 Aspergillus species from respiratory samples in Switzerland, Aspergillus fumigatus was the most frequent species. Non-fumigatus Aspergillus spp were more prevalent among solid organ transplant recipients and after azole exposure. Azole resistance was detected in 4 A fumigatus isolates, 3 of them with the "environmental" mutation TR34/L98H in the cyp51A gene.

Trends of the Epidemiology of Candidemia in Switzerland: A 15-Year FUNGINOS Survey.

BACKGROUND: The increasing incidence of candidemia and emergence of drug-resistant Candida species are major concerns worldwide. Long-term surveillance studies are needed. METHODS: The Fungal Infection Network of Switzerland (FUNGINOS) conducted a 15-year (2004-2018), nationwide, epidemiological study of candidemia. Hospital-based incidence of candidemia, Candida species distribution, antifungal susceptibility, and consumption were stratified in 3 periods (2004-2008, 2009-2013, 2014-2018). Population-based incidence over the period 2009-2018 derived from the Swiss Antibiotic Resistance Surveillance System (ANRESIS). RESULTS: A total of 2273 Candida blood isolates were studied. Population and hospital-based annual incidence of candidemia increased from 2.96 to 4.20/100 000 inhabitants (P = .022) and 0.86 to 0.99/10 000 patient-days (P = .124), respectively. The proportion of Candida albicans decreased significantly from 60% to 53% (P = .0023), whereas Candida glabrata increased from 18% to 27% (P < .0001). Other non-albicans Candida species remained stable. Candida glabrata bloodstream infections occurred predominantly in the age group 18-40 and above 65 years. A higher proportional increase of C glabrata was recorded in wards (18% to 29%, P < .0001) versus intensive care units (19% to 24%, P = .22). According to Clinical and Laboratory Standards Institute, nonsusceptibility to fluconazole in C albicans was observed in 1% of isolates, and anidulafungin and micafungin nonsusceptibility was observed in 2% of C albicans and C glabrata. Fluconazole consumption, the most frequently used antifungal, remained stable, whereas use of mold-active triazoles and echinocandins increased significantly in the last decade (P < .0001). CONCLUSIONS: Over the 15-year period, the incidence of candidemia increased. A species shift toward C glabrata was recently observed, concurring with increased consumption of mold-active triazoles.

Parasitic infections in Swiss children: Are we overtesting?

BACKGROUND: A wide variation of causes can lead to gastrointestinal symptoms in children- an infection with parasites is one of them. The expansion of international travel might lead to an increase in testing children for a correspondent infection. Currently there are no guidelines available, which patients should be tested for a possible parasitical infection. The aim of the study was to characterize Swiss children suffering from intestinal parasites, in order to provide more knowledge for the clinician who should be tested. METHODS: This is a retrospective study of Swiss pediatric patients, whose stools have been tested for parasites and helminths. RESULTS: A total of 1855 stool samples, belonging to 572 different children with an average age of 7.9 years, were tested within a 10-year period. The prevalence of a positive result was 4.2%, of which all were positive for Blastocystis, and 12.5% had a co-infection with Endolimax nana. CONCLUSION: Immigrants, immune compromised children with diarrhea and pediatric patients with bloody or protracted diarrhea should have 2 different stool specimens examined for a possible parasitical infection.

The Shapiro-Procalcitonin algorithm (SPA) as a decision tool for blood culture sampling: validation in a prospective cohort study.

PURPOSE: Blood cultures (BC) are the gold standard for bacteremia detection despite a relatively low diagnostic yield and high costs. A retrospective study reported high predictive values for BC positivity when combining the clinical Shapiro score with procalcitonin (PCT). METHODS: Single-center, prospective cohort study between 01/2016 and 02/2017 to validate SPA algorithm, including a modified Shapiro score ≥ 3 points (S) PLUS admission PCT > 0.25 µg/l (P), or presence of overruling safety criteria (A) in patients with systemic inflammatory response syndrome. The diagnostic yield of SPA compared to non-standardized clinical judgment in predicting BC positivity was calculated and results presented as odds ratios (OR) with 95% confidence intervals. RESULTS: Of 1438 patients with BC sampling, 215 (15%) had positive BC which increased to 31% (173/555) in patients fulfilling SP criteria (OR for BC positivity 9.07 [6.34-12.97]). When adding 194 patients with overruling safety criteria (i.e., SPA), OR increased to 11.12 (6.99-17.69), although BC positivity slightly decreased to 26%. With an area under the receiver operating curve of 0.742, SPA indicated better diagnostic performance than its individual components. Positive BC in 689 patients not fulfilling SPA (sampling according to non-standardized clinical judgment) were rare (3%; OR for BC positivity 0.09 [0.06-0.14]). Eight out of 21 missed pathogens were still identified by sampling the primary infection focus. CONCLUSIONS: This study validates the high predictive value of SPA for bacteremia, increasing true BC positivity from 15 to 26%. Restricting BC sampling to SPA would have reduced BC sampling by 48%, while still detecting 194/215 organisms (90%), which makes SPA a valuable diagnostic stewardship tool.

Blastocystis in Swiss children: a practical approach.

Blastocystis is a parasite with a worldwide distribution and a varying prevalence in different countries. The pleomorphic nature of the protozoon and the lack of understanding a possible pathogenesis have led to confusion regarding its clinical significance. The aim of the study was to shed light on clinical characteristics of pediatric patients in Swiss children with a positive stool sample for Blastocystis, in order to provide recommendations for a practical approach for the clinician to know whom, when, and how to test. This is a retrospective study of pediatric patients, whose stool has been tested positive for Blastocystis in the last 10 years in northern Switzerland. A total of 4047 stool samples, belonging to 1887 different patients, were analyzed; 240 stool samples (of 160 patients) were tested positive for Blastocystis. On average, 2.2 (CI 1.98-2.35) stool samples per patient were analyzed, of which 1.48 (CI 1.36-1.61) were positive for Blastocystis. In 63% abdominal pain was the leading symptom, while in 17.5% it was an accidental finding without symptoms. There was a high significance in correlation of abdominal pain and chronicity (p < 0.0001) but none in diarrhea (p = 0.082) nor nausea/vomiting or other symptoms and chronicity. Followed by Entamoeba coli (8%), 26.3% of the patients with Blastocystis had a co-infection with another parasite, mostly Endolimax nana (13%).Conclusion: Carriage of Blastocystis is common; therefore, only children/teenagers at risk for a symptomatic Blastocystis infection should be tested. There is a good correlation between Blastocystis and chronic abdominal pain. Children with abdominal symptoms persisting over 4 weeks should have two different stool samples analyzed. No screening after travels/immigration is recommended.What is Known:• Blastocystis has a worldwide distribution.• The clinical significance is unclear.What is New:• Based on retrospective data, we recommend to only test children/teenagers with chronic abdominal pain for Blastocystis.• Two different stool samples should be examined by microscopy; serological investigations are not warranted.

Outcome of Clostridioides difficile infections treated in a Swiss tertiary care hospital: an observational study.

AIMS OF THE STUDY: Clostridioides difficile infection (CDI) is associated with high morbidity, recurrence rates and mortality. We assessed the local epidemiology, treatment outcomes and risk factors for recurrence and mortality. METHODS: This was a retrospective study of all adult CDI episodes treated in our tertiary care hospital between 2014 and 2016. Patients were followed up for 60 days, with recurrence and death as endpoints. Antibiotic treatment as well as epidemiological, clinical and laboratory parameters were studied using logistic regression analysis. Risk factors for recurrent CDI (age >70 years, haematological malignancy, chronic kidney disease, severe infection, continued antibiotics other than for CDI, proton pump inhibitor / antacid use) and indicators of severe CDI (temperature ≥38.5°C, leucocytes >15 × 109/l, creatinine increase ≥1.5 × baseline, albumin <25 g/l) were analysed. We considered episodes with ≥2 indicators as severe. RESULTS: We identified 210 CDI episodes (66 severe) in 191 patients with a median age of 71 years (interquartile range 59–79). Hypervirulent ribotype 027/NAP1/BI accounted for four episodes (2%). Overall, 176, 30 and 4 patients, respectively, received a first, second and third treatment. Metronidazole was used in 94% of the first episodes and in 73% and 50% of the first and second recurrences, respectively. The recurrence rate after the first metronidazole treatment was 20%. Recurrence rates were higher when ≥2 risk factors were present (25 vs 10%, p = 0.03). The 60-day mortality was 17% (4% attributable to CDI) and increased with the presence of ≥2 indicators of severe CDI. CONCLUSIONS: The high 60-day mortality suggests that CDI is a strong indicator of frailty. Metronidazole was associated with low recurrence rates at minimal costs in patients with uncomplicated CDI, but had relevant shortcomings in patients with severe CDI and/or a high risk of recurrence, suggesting that these vulnerable patients might better be treated with oral vancomycin and fidaxomicin, according to the latest guidelines.  .

Implementation of an infection prevention bundle is associated with reduced surgical site infections in cranial neurosurgery.

OBJECTIVE: The objective of this study was to quantify surgical site infection (SSI) rates after cranial neurosurgery in a tertiary care hospital, identify risk factors for SSI, and evaluate the impact of standardized surveillance and an infection prevention bundle (IPB). METHODS: The authors compared SSI rates during 7 months before and after the intervention. The IPB included standardized patient preparation, perioperative antibiotic/antiseptic use, barrier precautions, coaching of surgeons, and the implementation of a specialized technical operation assistant team. RESULTS: Three hundred twenty-two unselected consecutive patients were evaluated before the IPB, and 296 were evaluated after implementation. Infection rates after 1 year decreased from 7.8% (25/322) to 3.7% (11/296, p = 0.03) with similar mortality rates (14.7% vs 13.8%, p = 0.8). The isolated bacteria included Staphylococcus aureus (42%), Cutibacterium acnes (22%), and coagulase-negative staphylococci (14%). Organ/space infections dominated with 67%, and mostly consisted of subdural empyema and meningitis/ventriculitis. Among the 36 SSIs, 13 (36%) occurred during hospitalization, and 29 (81%) within the first 3 months of follow-up. In multivariable analysis including established risk factors described in the literature, non-CNS neoplasia (odds ratio [OR] 3.82, 95% confidence interval [CI] 1.39-10.53), postoperative bleeding (OR 4.09, 1.44-11.62), operations performed by or under supervision of a senior faculty surgeon (OR 0.38, 0.17-0.84), and operations performed after the implementation of standardized surveillance and an IPB (OR 0.38, 0.17-0.85) significantly influenced the infection rate. CONCLUSIONS: The introduction of an IPB combined with routine surveillance and personal feedback was associated with a 53% reduced infection rate. The lower infection rates of senior faculty and the strong association between postoperative bleeding and infection underline the importance of both surgical experience as well as thorough supervision and coaching of younger surgeons.

Non-Seasonal Variation of Airborne Aspergillus Spore Concentration in a Hospital Building.

Nosocomial fungal infections are gaining increased attention from infectiologists. An adequate investigation into the levels of airborne Aspergillus and other fungal spores in hospital settings, under normal conditions, is largely unknown. We monitored airborne spore contamination in a Swiss hospital building in order to establish a seasonally-dependent base-line level. Air was sampled using an impaction technique, twice weekly, at six different locations over one year. Specimens were seeded in duplicate on Sabouraud agar plates. Grown colonies were identified to genus levels. The airborne Aspergillus spore concentration was constantly low throughout the whole year, at a median level of 2 spores/m³ (inter-quartile range = IQR 1-4), and displayed no seasonal dependency. The median concentration of other fungal spores was higher and showed a distinct seasonal variability with the ambient temperature change during the different seasons: 82 spores/m³ (IQR 26-126) in summer and 9 spores/m³ (IQR 6-15) in winter. The spore concentration varied considerably between the six sampling sites in the building (10 to 26 spores/m³). This variability may explain the variability of study results in the literature.

Pulmonary tularaemia: all that looks like cancer is not necessarily cancer - case report of four consecutive cases.

BACKGROUND: Pulmonary tularaemia is a very rare disease with only a small number of cases described in the literature. So far, to our knowledge, there exists no case report of pulmonary tularaemia where PET-CT scans and follow up CT scans are available. CASE PRESENTATION: We present four consecutive cases of pulmonary tularaemia. All patients suffered from non-specific symptoms. All patients were referred to our institution with strong suspicions of malignancy, particularly lung cancer. Diagnosis of tularaemia was made by typical findings in the aspirate of EBUS guided fine needle aspiration (necrosis, epithelioid cell aggregation) and surgical biopsy respectively, and a positive serology. In three of the four cases, the diagnosis was confirmed by positive PCR results of the tissue. PET-CT scans obtained in all four cases were indistinguishable from lesions typically seen in patients suffering from lung cancer. One of the four patients suffered from recurrence of the disease after antibiotic treatment; also this patient finally recovered after initiation of a second antibiotic regimen. One case became asymptomatic spontaneously, but this patient still received an antibiotic treatment. In one case, a follow up CT scan was unchanged compared to the initial PET-CT scan; in all other cases, the lesions disappeared almost completely. CONCLUSIONS: Symptoms of patients suffering from pulmonary tularaemia are non-specific and can be of prolonged character. PET-CT scans in these cases are indistinguishable from lung cancer. The diagnosis can be established when typical findings in EBUS guided fine needle aspirates or surgical biopsies are found in combination with a positive serology. In most cases the lesions disappear in follow up CT scans after clinically successful treatment.