American Society For Microbiology Research Articles

Complete Genome Sequences of Four Strains ofErwiniatracheiphila: A Resource for Studying aBacterial Plant Pathogen with a Highly Complex Genome.

Complete Genome Sequences of Four Strains ofErwiniatracheiphila: A Resource for Studying aBacterial Plant Pathogen with a Highly Complex Genome.

Addressing Health Concerns Interrupted by the COVID-19 Pandemic

Addressing Health Concerns Interrupted by the COVID-19 Pandemic

How to make Microbiology Teaching interesting to students?

How to make Microbiology Teaching interesting to students?

Teaching Microscopy Remotely: Two Engaging Options.

ABSTRACTThe rapid switch to remote teaching with the onset of the COVID-19 pandemic forced educators to become resourceful and creative to meet course learning objectives. This was especially challenging for undergraduate microbiology laboratory exercises. The American Society for Microbiology (ASM) Recommended Curriculum Guidelines for Undergraduate Microbiology Education includes providing students with a microscopy experience. To meet these learning objectives in an at-home setting, we utilized two methods which we present as options for remote teaching of microscopy. One method involves students taking home microscopes equipped with oil immersion objective lenses. The other employs the remote operation of a confocal and/or scanning electron microscope through participation in the University of Toledo’s SCOPE (Scientists Changing Our Pre-College Education) program. These techniques allowed students to develop competency and confidence in the operation of a microscope. The SCOPE program provided experience with types of microscopes not commonly available to undergraduate students even when in person. In addition to these unique experiences, students can gain microscopy expertise utilizing various virtual microscopy simulations. Together these techniques provide an exciting and robust online microscopy experience for undergraduate microbiology students that can be employed for use in regularly taught online microbiology courses.

Software testing in microbial bioinformatics: a call to action

Computational algorithms have become an essential component of research, with great efforts by the scientific community to raise standards on development and distribution of code. Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics. We have developed these recommendations based on our experience from a collaborative hackathon organised prior to the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference. We also present a repository hosting examples and guidelines for testing, available from https://github.com/microbinfie-hackathon2020/CSIS.

The Diverse World of Protists—an Ideal Community with which to Introduce Microscopy in the Microbiology Teaching Laboratory

ABSTRACTProtists and other eukaryotes are present in diverse terrestrial and aquatic environments. They can easily be collected from local ponds and streams. Although they are typically larger in size than prokaryotes, making them easy to study with even basic microscopes, microbiology laboratory courses often do not discuss them in detail and may only dedicate a short time to observing preserved samples. This laboratory exercise allows students to develop microscope skills, experience real world application of collecting and processing field samples, and delve deeper into the diverse world of protists and other microbial eukaryotes. Students may also engage by sharing their findings on the website iNaturalist to contribute to the scientific knowledge collected around the world. This laboratory module was initially designed for in-person learning but has been successfully adapted to remote learning and can also be applied to a complete online learning environment.

Особливості викладання мікробіології іноземним студентам українською мовою

У статті наводиться досвід викладання мікробіології студентам-іноземцям, які навчаються українською мовою на кафедрі мікробіології та вірусології в Буковинському державному медичному університеті. Під час навчання студенти-іноземці стикаються з низкою проблем: недостатнім володінням українською мовою, часто слабкою підготовкою за профільними та спеціальними дисциплінами, відсутністю навичок самостійної роботи, несформованим алгоритмом використання на практичних заняттях теоретичного матеріалу та відчутною різницею між формами та методами навчання в українському вузі та у вищій школі на батьківщині студента. В основі організації та проведення практичних занять з іноземцями лежить принцип індивідуального підходу до кожного студента, що забезпечується використанням на заняттях завдань різного рівня складності. Самопідготовка студентів пов’язана з наявністю в них достатньої кількості навчально-методичних посібників, можливістю отримати консультативну допомогу викладача, а також з використанням технічних засобів навчання. Для кращого засвоєння студентами лекційного матеріалу викладачі наполегливо працюють над обранням оптимальної форми подання матеріалу: у вигляді схем, графологічних структур, рисунків, навчальних слайдів, відеофільмів та мультимедійних презентацій. Засвоєнню матеріалу практичного заняття сприяє комплексний контроль знань шляхом усного опитування, оцінювання виконання практичної роботи та вміння аналізувати результати досліджень та роботи висновки. З метою стандартизації оцінки знань студентів використовуються тестові питання, складені за типом ліцензійного іспиту «Крок‑1». Постійна робота над удосконаленням професійної майстерності, використання в навчальному процесі різноманітних випробованих часом та новітніх форм і методів викладання дозволяють добре розв’язувати сучасні завдання з підготовки спеціалістів із числа іноземних громадян.

Expression of Concern for Shin et al., "blaNDM-5-Bearing IncFII-Type Plasmids of Klebsiella pneumoniae Sequence Type 147 Transmitted by Cross-Border Transfer of a Patient".

The American Society for Microbiology (ASM) and Antimicrobial Agents and Chemotherapy (AAC) are issuing this Expression of Concern regarding the following publication: Shin J, Baek JY, Cho SY, Huh HJ, Lee NY, Song J-H, Chung DR, Ko KS. 2016. blaNDM-5-bearing IncFII-type plasmids of Klebsiella pneumoniae sequence type 147 transmitted by cross-border transfer of a patient. Antimicrob Agents Chemother 60:1932–1934. https://doi.org/10.1128/AAC.02722-15.

Case-Based Learning and its Application as a Teaching Tool for Medical Graduates in Competency-Based Medical Education in Clinical Microbiology

Background: Microbiology is taught using traditional methods, and its practical application is scarce among medical practitioners. As a result, “active learning” is essential to aid pupil learning. One such strategy is case-based learning (CBL), which helps to improve understanding as well as therapeutic applications of microbiology in everyday practice. Aim: CBL was first used as a teaching and learning method in clinical microbiology for medical students. Methodology: At IQ City Medical College and Hospital in Durgapur, an educational intervention study was undertaken for the 2nd phase MBBS students. A total of 82 people took part in the study, and two groups were formed. After sensitizing the faculty using CBL, the project was carried out. The first group was given a CBL, whereas the second group was given a didactic talk with crossover. A pre- and post-test was done, and student and instructor perceptions were recorded and assessed. Results: CBL was warmly received by both students and teachers. Students and teachers’ perceptions were rated on a Likert scale ranging from strongly disagree to strongly agree. In comparison to Didactic Lecture, around 76.8% of students believe that in CBL, we interact more with teachers, followed by 65.9% who believe that CBL has helped me retain the material and its clinical application, and 62.2% who believe that CBL has stimulated self-study. Conclusion: CBL in microbiology is an effective technique for improving and changing students’ attitudes toward microbiology’s applicability in clinical practice. It also helps students gain a better understanding of microbiology.

How the flipped classroom improves student learning in medical microbiology education: a meta-analysis

ABSTRACT The flipped classroom method has recently become popular in biology education. However, there is a lack of systematic and quantitative assessments on the efficiency of teaching medical microbiology using this novel approach. In this study, we performed a meta-analysis to explore the flipped classroom method’s effects versus those of traditional lectures in medical microbiology education. Six electronic databases, including PubMed, Web of Science, ERIC, China National Knowledge Infrastructure (CNKI), Wanfang Data, and Chinese Scientific Journals Database, were searched to obtain relevant articles from the first publication on this topic up to March 2021. Study selection, data extraction, and quality estimations were conducted to analyse the effects. A total of 13 studies were included in this meta-analysis, with the results revealing a significantly improved effect within the flipped classroom model on students’ theoretical [SMD = 0.56, 95% CI (0.28, 0.84), p < 0.0001] and practical examination scores [SMD = 0.70, 95% CI (0.19, 1.20), p = 0.007]. In terms of its teaching effects, the flipped classroom approach improves students’ learning interest, self-study abilities, knowledge mastery, and satisfaction, but does exacerbate their learning burden. The flipped classroom method possesses multiple advantages when compared to traditional lectures in medical microbiology education, but does increase the burden experienced by students.

INTERACTIVE METHODS IN TEACHING MICROBIOLOGY

INTERACTIVE METHODS IN TEACHING MICROBIOLOGY

Empowering Undergraduates to Fight Climate Change with Soil Microbes.

The burning of fossil fuels to meet a growing demand for energy has created a climate crisis that threatens Earth's fragile ecosystems. While most undergraduate students are familiar with solar and wind energy as sustainable alternatives to fossil fuels, many are not aware of a climate solution right beneath their feet—soil-dwelling microbes! Microbial fuel cells (MFCs) harness energy from the metabolic activity of microbes in the soil to generate electricity. Recently, the coronavirus disease 2019 (COVID-19) pandemic transformed the traditional microbiology teaching laboratory into take-home laboratory kits and online modes of delivery, which could accommodate distance learning. This laboratory exercise combined both virtual laboratory simulations and a commercially available MFC kit to challenge undergraduate students to apply fundamental principles in microbiology to real-world climate solutions.

Learner attitudes towards a virtual microbiology simulation for pharmacy student education

IntroductionSimulation for education has become popular, but much literature on this modality fails to critically examine the learner's experience, focusing instead on learning outcomes. Learner attitudes should be scrutinised and monitored to appraise a technology-enhanced learning experience as student perceived educational benefits of technology-enhanced learning is reported to be more important than the intrinsic characteristics of any particular medium or tool. This study sought to evaluate pharmacy students' attitudes toward a virtual microbiology simulation. MethodsThe virtual microbiology simulation (VUMIE) was compared with a traditional wet laboratory (lab) in a second-year integrated pharmacotherapeutics course for bachelor of pharmacy students. Data were collected using surveys deployed at baseline (pre-intervention), post-intervention (VUMIE or wet lab), and endpoint (post-interventions). Statistical and qualitative thematic analyses were performed. ResultsLearners found the simulation valuable, and outcomes suggest that it is possible for technology-enhanced learning activities to replace face-to-face instruction to some extent, which may be useful given the current challenges with in-person education resulting from COVID-19. More students reported a specific preference for the wet lab rather than VUMIE. ConclusionsAlthough technology-enhanced simulation can produce a similar learning experience to a traditional wet lab, this evidence is not sufficient to completely replace the traditional lab experience for clinical courses of study. Technology-enhanced simulation could be considered for just-in-time training before exposure to traditional lab activities, for specific skill acquisition using deliberate practice, and perhaps for standardised assessment for clinical microbiology education.

17. Comparative Assessment of a Machine Learning Model and Rectal Swab Surveillance to Predict Hospital Onset Clostridioides difficile

BackgroundHospital onset Clostridioides difficile infection (HO-CDI) is associated with significant morbidity and mortality. Screening individuals at risk could help limit transmission, however swab-based surveillance for HO-CDI is resource intensive. Applied to electronic health records (EHR) data, machine learning (ML) models present an efficient approach to assess patient risk. We compare the effectiveness of swab surveillance against daily risk estimates produced by a ML model in detecting patients who will develop HO-CDI.MethodsPatients presenting to Michigan Medicine’s ICUs and oncology wards between June 6th and October 8th 2020 had rectal swabs collected on admission, weekly, and at discharge from the unit, as part of VRE surveillance. We performed anaerobic culture on the residual media followed by a custom, multiplex PCR on isolates to identify toxigenic C. difficile. Risk of HO-CDI was calculated daily for each patient using a previously validated EHR-based ML model. Swab results and model risk scores were aggregated for each admission and assessed as predictors of HO-CDI. Holding sensitivity equal, we evaluated both approaches in terms of accuracy, specificity, and positive predictive value (PPV).ResultsOf 2,044 admissions representing 1,859 patients, 39 (1.9%) developed HO-CDI. 23.1% (95% CI: 11.1–37.8%) of HO-CDI cases had at least one positive swab. At this sensitivity, model performance was significantly better than random but worse compared to swab surveillance—accuracy: 87.5% (86.0–88.9%) vs. 94.3% (93.3–95.3%), specificity: 88.7% (87.3–90.0%) vs. 95.7% (94.8–96.6%), PPV: 3.8% (1.6–6.4%) vs. 9.4% (4.3–16.1%). Combining swab AND model yielded lower sensitivity 2.6% (0.0–8.9%) compared to combining swab OR model at 43.6% (27.3–60.0%), and yielded PPV 7.1% (0.0–25.0%) vs. 43.6% (27.3–60.0%) respectively (Figure 1).Figure 1. Surveillance & risk score performance. Binary classification performance metrics of ML model (Model), toxigenic C. difficile rectal swab surveillance (Swab), and combination approaches (Model AND Swab and Model OR Swab), reported in terms of percentage points. Bold numbers highlight the best performing approach for a given performance metric. The combined approach of monitoring the Model AND Swab yielded the highest accuracy 97.5% (95% confidence interval: 96.8%, 98.1%), it also had the highest specificity 99.4% (99.0%, 99.7%). The combined approach of monitoring the Model OR Swab yielded the highest sensitivity 43.6% (27.3%, 60.0%) and negative predictive value (NPV) 98.7% (98.2, 99.2%). Using the Swab alone yielded the highest PPV 9.4% (4.3%, 16.1%) and F1 score 13.3% (6.2%, 21.8%). These results highlight the complementarity of the model and swab-based approaches.ConclusionCompared to swab surveillance using a ML model for predicting HO-CDI results in more false positives. The ML model provides daily risk scores and can be deployed using different thresholds. Thus, it can inform varied prevention strategies for different risk categories, without the need for resource intensive swabbing. Additionally, the approaches may be complimentary as the patients with HO-CDI identified by each approach differ.Disclosures Vincent B. Young, MD, PhD, American Society for Microbiology (Other Financial or Material Support, Senior Editor for mSphere)Vedanta Biosciences (Consultant) Krishna Rao, MD, MS, Bio-K+ International, Inc. (Consultant)Merck & Co., Inc. (Grant/Research Support)Roche Molecular Systems, Inc. (Consultant)Seres Therapeutics (Consultant)

Difficulty in Assigning Fungal Identity Based on DNA Sequences.

The Comment Letter by Houbraken et al. (1) correctly points out the need for accurate fungal taxonomical identification in biological research and the difficulty confronted by scientists in assigning genus and species identity due to the high genome sequence similarity of related individuals and the low availability of full fungal genome sequences in DNA data repositories with which to perform sequence comparisons. The Comment Letter accurately presents the need to revise or even update previously assigned fungal classifications as more DNA sequences and full genomes become available over time. The Comment Letter highlights that currently, the internal transcribed spacer (ITS) region is most often used to identify fungi, and the authors argue that some short regions of genes such as benA, caM, and tef1-alpha may be better suited for accurate species identification of close relatives. Based on that premise, the authors used the partial beta-tubulin (benA) and partial calmodulin (caM) gene sequences to reassess the taxonomical identity of multiple fungal isolates published in journals such as MRA (previously known as Genome Announcements) using phylogenetic trees. The authors argue that upon analysis of the short regions of the benA or caM genes, 21 published papers in MRA had incorrectly assigned the fungal identity of their isolates. While we agree that assigned fungal taxa should be revised as more DNA sequence information becomes available, this does not mean that the classification provided at the time of publication was erroneous based on the available sequence information at the time. Furthermore, we argue that the authors actually contradicted their own argument when they ignored available ITS sequences, 18S rRNA gene sequences, and even full genome sequences and relied on a very short 65-amino acid region of the benA gene to assign fungal identity. Based on the 65-amino acid region of benA, Houbraken et al. (1) claimed that our paper (2) misidentified the isolate as Byssochlamys sp., when it should have been Monascus floridanus.

A Simple and Affordable Biofilm Assay for the Undergraduate Microbiology Classroom

Through experience and surveying undergraduate microbiology curriculum, we found that most schools discuss biofilms in lecture classes but not laboratory courses. Biofilms are a concern for both industry and the medical field and should be studied in student laboratories. To study this at an institution, there would need to be an affordable method to assay them. As a sample specimen, Pseudomonas aeruginosa was used as it proliferates into biofilms when it is starved for nutrients, which can be easily simulated in a laboratory environment. Known assays for studying biofilms are expensive, and most departments do not have the materials. In Trypticase Soy Broth (TSB), P. aeruginosa can also be induced to form a biofilm, but the technique is not seen very often because it has not been sufficiently standardized for undergraduate microbiology education laboratories. To account for the absence of specialized reagents, we incubated bacteria for longer periods of time as a means to diminish nutrients or starve the specimen. Using a two-tailed t-test, we were able to show that glass tubes inoculated with P. aeruginosa in TSB for 48 hours were forming distinct biofilms on the glass surface, which is appropriate for undergraduate microbiology laboratory studies.

What you need to know about children's COVID-19: a systematic review.

The aim of the systematic review is to describe clinical features of coronavirus disease 2019 (COVID-19) in children with a focus on the possible reasons why children are less susceptible to COVID-19 and whether their immune response works better than adults. The three research questions below were determined. (1) Why do pediatric COVID-19 cases have milder clinical symptoms than adults? (2) What are clinical manifestations, diagnosis, and treatment of COVID-19 in children? (3) How long lasts viral shedding after recovery? We searched MEDLINE, Embase, Cochrane Central Register of Controlled Trials, and Cochrane Database of Abstracts of Reviews of Effects, as well as foreign literature with English translations. Extra information and data have been collected from Google Scholar and the American Society for Microbiology. Information on patients' age, comorbidities, methods of treatment, and effects on mortality and morbidity were extracted. It is concluded that children are less susceptible to COVID-19 than adults and that the symptoms in children are less severe than in adults. A low incidence of COVID-19 in children and milder disease than in adults might be attributed to many theories and reasons; however, the mechanisms involved are not fully understood.

Innovative Instructional Reform and Practice of Oral Microbiology-A Course in Undergraduate Stomatology Curriculum

Oral Microbiology is a vital component of the basic science of stomatology and an important compulsory course for undergraduate students of stomatology, focusing on the oral microbiology and microecology, the pathogenesis of oral infectious diseases, and the relationship between oral microbes and human health. Our faculty team have made reforms of the theory and laboratory teaching of the course Oral Microbiology. We have introduced in the classroom the concept of Three Comprehensive Approaches to Education-the full involvement of everyone, the through-course approach and all-round education-and offered inquiry-based instruction through a combination of extracting the core information from every chapter, using the core information as the foundation, integrating the core information with clinical problems, and using experiment operation to foster in the students an attitude of solving clinical problems through research. These teaching innovations improved the undergraduate students'motivation to learn. We evaluated the teaching effect with questionnaire surveys. The results suggested that the students showed high interest in learning and were satisfied with our teaching innovations. In addition, student performance evaluation for the course showed significant improvement, indicating that the instructional reform program of Oral Microbiology was conducive to students'understanding and mastery of the course content, improved student motivation to learn and their grades, and received positive reviews from the students. We report herein, from three aspects, the course innovations and the experiences gained. We discussed the significance of integrating ideological and political theories teaching in all courses and using innovative teaching materials and teaching models and, highlighted their importance in the education of stomatology students, and proposed suggestions to further improve the course design of Oral Microbiology.

General microbiology teaching adaptation in the covid-19 period: Pre-service teacher perspectives and experiences

As a result of the COVID-19 global pandemic, teaching activity for pre-service teachers enrolled in the second year of a teacher education program from mid-March of 2020/2021 at the Universitas Sultan Ageng Tirtayasa were changed in a remote learning setting. This study's objective was to investigate pre-service students' perceptions and personal experience toward the transition of General microbiology lecture to online learning during the global COVID-19 pandemic. The results described the efforts and adaptation to an online teaching model of the General Microbiology course using both online synchronous and asynchronous learning. The perspectives of the Pre-Service Teacher about this strategy were analyzed and showed positive responses. Despite some challenges, they could adapt to the new learning methods. In addition, the study also provided an analysis of faculty readiness and experiences through a process that can use as a foundation to tackle the pandemic situation in the future.

A Side-by-Side Comparison of Clinical versus Current Good Manufacturing Practices (cGMP) Microbiology Laboratory Requirements for Sterility Testing of Cellular and Gene Therapy Products

Over the last few years, there have been numerous discussions on the American Society for Microbiology’s clinical listservs (DivC, and ClinMicroNet) regarding sterility testing of cell and gene therapy products and environmental monitoring and gloved fingertip testing for hospital pharmacies. Clinical microbiology laboratories have often been asked to assist with testing due to the on-site proximity of laboratory equipment and microbiological expertise within the hospital environment. The role of the clinical microbiology laboratory in this setting, however, is questionable due to major differences in test requirements and regulatory oversight. Here, we provide a side-by-side comparison of clinical versus current good manufacturing practices microbiology laboratories to provide guidance to those that are currently assisting with or have been asked to assist with sterility testing of manufactured biopharmaceutical products that have become common frontline treatments in modern medicine.