Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting

BACKGROUND

Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2.

METHODS

We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs.

RESULTS

Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001).

CONCLUSIONS

IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

Evaluation of an Infectious Diseases Elective for Early Clinical Medical Students on their Internal Medicine Clerkship

Background

Early medical subspecialty training is an emerging trend in medical education. These electives are still rare for Early Clinical Medical Students (ECMS). We describe the introduction of an Infectious Disease (ID) inpatient consult rotation elective for ECMS.

Methods

In addition to seeing patients and rounding with the inpatient ID consult team, we created a supplemental curriculum to provide added support for ECMS that included a checklist of clinical skills learning objectives, self-directed, publicly available mini-lectures on ID topics, and an ID Coach who provided directed and personalized tutoring for students. We surveyed ECMS, ID fellows and attendings on service, and ID Coaches to evaluate the acceptability, feasibility, and effectiveness of this rotation and curriculum.

Results

The majority of ECMS reported that the rotation was a useful educational experience and that the ID Coach was one of the most valuable aspects of the rotation. The majority of ID fellows and attendings reported that working with ECMS improved their job satisfaction and well-being.

Conclusions

This multifaceted approach to early medical subspecialty training was valuable for ECMS, ID fellows, and faculty. Ongoing improvements in this curriculum will provide a useful tool for medical education.

83. ID Coaches Contribute to a Highly Effective Learning Experience for Third-Year Medical Students Rotating on the Infectious Diseases Consult Service

Background

Education on infections in hospitalized patients, antimicrobial selection, and principles of antimicrobial stewardship are foundational to all clinicians. Incorporating early learners into Infectious Diseases (ID) consult services has the potential to build a strong fund of knowledge in these content domains, but also poses potential challenges. We evaluated the impact of a novel clinical rotation and supporting curriculum on third-year medical students rotating on the ID consult service for 2 weeks during their 12-week Internal Medicine clerkship at the University of California, San Diego.

Methods

Third-year medical students who selected to rotate on the ID consult service were given an hour-long orientation about the service and common infectious syndromes. They were provided with a checklist of clinical skills to complete during the rotation. In addition to daily rounds and clinical care, ID Coaches (ID faculty and senior ID fellows) met with students weekly for 1-2 hours to review ID topics, practice oral presentations, and/or conduct physical exam finding rounds. We surveyed medical students to assess the effectiveness of the rotation.

Results

Forty third-year medical students participated in the 2-week ID consult rotation between June 2020-May 2021; 31 (77%) completed the rotation evaluation. Seventy percent or more of students reported that the ID rotation facilitated their learning across 8 of 10 ID-content domains (Figure 1). More students reported that the ID Coach facilitated learning (71%) compared to the clinical skills checklist (42%). Students highlighted learning about antimicrobial selection, stewardship, and clinical reasoning on the rotation but reported that teaching was limited when the service census was high (Figure 2).

Figure 1: Percent of Students Rating the ID Consult Rotation as Extremely or Very Effective in Facilitating Learning Across 10 Domains

Conclusion

Third-year medical students found that a 2-week rotation on the ID consult service was highly effective in teaching foundational ID content and general medicine skills. Incorporating early learners into a busy and complex subspecialty consult service can be facilitated through the use of supplemental curricular tools such as ID Coaches.

Disclosures

Darcy Wooten, MD, MS, Nothing to disclose

Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests

Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms preferentially inhibit bacterial test organisms over eukaryotic organisms. rDNA sequence analysis indicates that these organisms are not equivalent to any other cultured deposits in GenBank. Our results provide evidence of the untapped biodiversity in the form of biologically active microbes present within the tissues of higher plants.

Bioactive endophytes warrant intensified exploration and conservation

Background

A key argument in favor of conserving biodiversity is that as yet undiscovered biodiversity will yield products of great use to humans. However, the link between undiscovered biodiversity and useful products is largely conjectural. Here we provide direct evidence from bioassays of endophytes isolated from tropical plants and bioinformatic analyses that novel biology will indeed yield novel chemistry of potential value.

Methodology/Principal Findings

We isolated and cultured 135 endophytic fungi and bacteria from plants collected in Peru. nrDNAs were compared to samples deposited in GenBank to ascertain the genetic novelty of cultured specimens. Ten endophytes were found to be as much as 15–30% different than any sequence in GenBank. Phylogenetic trees, using the most similar sequences in GenBank, were constructed for each endophyte to measure phylogenetic distance. Assays were also conducted on each cultured endophyte to record bioactivity, of which 65 were found to be bioactive.

Conclusions/Significance

The novelty of our contribution is that we have combined bioinformatic analyses that document the diversity found in environmental samples with culturing and bioassays. These results highlight the hidden hyperdiversity of endophytic fungi and the urgent need to explore and conserve hidden microbial diversity. This study also showcases how undergraduate students can obtain data of great scientific significance.