Högskolan i Skövde

Enligt högskolelagen (SFS 1992:1434) och högskoleförordningen (SFS 1993:100) ingår ämnesspecifika- och generiska (generella) kunskaper och färdigheter i en högskoleutbildning. Exempel på generiska färdigheter är samarbetsförmåga, problemlösning, muntlig kommunikation och informationskompetens¹ (Berg, 2017; Widestedt, 2020; Moeller, 2020). 

Hur kan vi som undervisar skapa förutsättningar för lärprocesser som tränar generiska färdigheter? I denna presentation redogörs för upplägg, erfarenheter och utvärderingar om ”Söklaboration 1b”. Detta undervisningsmoment är en studentaktiverande läraktivitet som utvecklats och anpassats för kursen ”Molekylär genetik”^2,3, men som med fördel kan anpassas och användas på andra kurser och inom andra discipliner. 

”Ökad studentaktivitet är viktig eftersom den och interaktion med andra gynnar ett djupinriktat lärande.” 

(Elmgren & Henriksson, 2016 s. 180). 

Söklaborationen bygger på konstruktivism och sociokulturell tradition i vilka språket har en nyckelroll i lärprocessen (se Elmgren & Henriksson, 2016; Säljö, 2011). Syftet med undervisningsmomentet är att introducera studenterna till att söka vetenskaplig information och att med hjälp av elaboration (se Linderoth, 2023; Jemstedt, 2024) reflektera kring resultaten och erfarenheterna. Söklaborationen är ett obligatoriskt moment på kursen och examineras med hjälp av en skriftlig inlämningsuppgift. 

Undervisningsmomentet startas med en salsföreläsning på temat informationskompetens. Sedan får studenterna söka information och utföra en uppgift på egen hand. Därefter träffas studenter och undervisande personal för en workshop i en flexibel sal. Workshopen är ett obligatoriskt moment som även innebär att studenterna får öva muntlig kommunikation och presentation samt samarbetsförmåga och problemlösning. Mycket av det som studenterna lär sig får de även tillämpa i ett senare moment på kursen, som också det examineras. I det momentet ingår att söka vetenskapliga artiklar och använda dem i en labbrapport. 

Vi som utvecklat söklaborationen är en lärare i biovetenskap och en bibliotekarie. Vårt samarbete har tydlig bäring på Högskolans utvecklingsplan (Högskolan i Skövde, 2023a) och verksamhetsstödets ledord⁴ (Högskolan i Skövde, 2023b) samt Sveriges universitets- och högskoleförbund (SUHF):s slutrapport Vägledning för integration av undervisning i medie- och informationskunnighet i högre utbildning (2024).

¹ Att kunna söka, välja och värdera information ingår i begreppet informationskompetens. 

² Kursen Molekylär genetik (BV317G) ges på grundnivå för studenter som läser termin tre på programmen Molekylär biodesign (MOLBG) och Molekylär bioinformatik (MOBIG). 

³ Biblioteket undervisar i informationskompetens i en tänkt progressionstrappa i tre steg. Kursen ”Molekylär genetik”, motsvarar progressionssteg 1b. 

⁴ Proaktivitet, professionalism, tillgänglighet, helhetsperspektiv och verksamhetsnära.

Referenser

Berg, J. (2017). Generiska färdigheter. Stockholms universitet. Kulturgeografiska institutionen. https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-148566

Högskolan i Skövde (2023a). Utvecklingsplan för Högskolan i Skövde 2023-2026 (Diarienummer HS 2023/16). https://www.his.se/globalassets/styrdokument/strategier-kvalitet-  organisation/utvecklingsplan-presentationsformat-sv.pdf 

Högskolan i Skövde (2023b). Verksamhetsstödets uppdrag och ansvarsområden (Diarienummer HS 2023/719). https://www.his.se/globalassets/styrdokument/strategier-kvalitet-  organisation/verksamhetsstodets-uppdrag-och-ansvarsomraden.pdf

Jemstedt, A. (2024). Enhancing learning with a two-page study manual. Learning and Instruction, 90. https://doi.org/10.1016/j.learninstruc.2023.101852 

Linderoth, J. (2023, 11 jan). Djupinformationsbearbetning - elaborering. I Studieteknik i högre utbildning. [Video]. YouTube. https://www.youtube.com/watch?v=m5yxrZfk61Y 

Moeller, C. M. (2020). Insert instruction here: the impact of the service model on authentic teaching. I Douglas, V. A. & Gadsby, J. (Red.). Deconstructing service in libraries:   intersections of identities and expectations (s. 237-252). Litwin Books. 

SFS 1992:1434. Högskolelag. https://www.riksdagen.se/sv/dokument-och-lagar/dokument/svensk-forfattningssamling/hogskolelag-19921434_sfs-1992-1434/ 

SFS 1993:100. Högskoleförordning. https://www.riksdagen.se/sv/dokument-och-lagar/dokument/svensk forfattningssamling/hogskoleforordning-1993100_sfs-1993-100/ 

Sveriges universitets- och högskoleförbund (SUHF). (2024). Vägledning för integration av undervisning i medie- och informationskunnighet i högre utbildning. [Slutrapport].   https://suhf.se/app/uploads/2024/02/Slutrapport-SUHF-MIK-2024-02-15.pdf 

Widestedt, K. (2020, 30 mars). Generiska färdigheter är osynliga för studenter. Stockholms universitet. Centrum för universitetslärarstudier. https://www.su.se/centrum-for-  universitetslararutbildning/akademiskt-l%C3%A4rarskap/aktuell-forskning/generiska-f%C3%A4rdigheter-%C3%A4r-osynliga-f%C3%B6r-studenter-1.492672 

BACKGROUND: The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory.

METHODS: Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement.

RESULTS: There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates.

CONCLUSIONS: Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.

Undervisningsteamet vid Högskolebiblioteket i Skövde undervisar i informationskompetens på högskolans alla program. Undervisningen sker enligt en progression i tre steg som anpassas till respektive program. Sedan några år samarbetar undervisningsteamet med ett antal lärare på högskolan. Samarbetet är en del av ett större projekt – Projekt Integrerat Stöd (PIS). Projektet syftar till att integrera verksamhetsstödets insatser i utbildningarna på högskolan. I denna presentation berättar vi dels om vårt samarbete med en programansvarig lärare inom biovetenskap och dels om hur vi tillsammans med kursansvarig lärare utvecklat nya undervisningsmoment. Vi kommer också att dela våra erfarenheter av att på kursen ”Molekylär genetik” anpassa undervisningsmoment från Zoom till nya flexibla salar. 

Extra-intestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a large number of human infections globally. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance, most importantly the increasing recognition of isolates producing extended-spectrum β-lactamases (ESBL). Herein, we used whole-genome sequencing (WGS) on ExPEC isolates for a comprehensive genotypic characterization. Twenty-one ExPEC isolates, nine with and 12 without ESBL-production, from 16 patients with suspected sepsis were sequenced on an Illumina MiSeq platform. Analysis of WGS data was performed with widely used bioinformatics software and tools for genotypic characterization of the isolates. A higher number of plasmids, virulence and resistance genes were observed in the ESBL-producing isolates than the non-ESBL-producing, although not statistically significant due to the low sample size. All nine ESBL-producing ExPEC isolates presented with at least one bla gene, as did three of the 12 without ESBL-production. Multi-locus sequence typing analysis revealed a diversity of sequence types whereas phylogroup A prevailed among isolates both with and without ESBL-production. In conclusion, this limited study shows that analysis of WGS data can be used for genotypic characterization of ExPEC isolates to obtain in-depth information of clinical relevance.

Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.

Background: Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures.

Materials and methods: During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden.

Results: The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH®assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4–98.3), when the causative agent was covered by the QuickFISH® assay.

Conclusions: The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents.