Comparing transmission reconstruction models with Mycobacterium tuberculosis whole genome sequence data

Pathogen genomic epidemiology is now routinely used worldwide to interrogate infectious disease dynamics. Multiple computational tools that reconstruct transmission networks by coupling genomic data with epidemiological modelling have been developed. The resulting inferences are often used to inform outbreak investigations, yet to date, the performance of these transmission reconstruction tools has not been compared specifically for tuberculosis, a disease process with complex epidemiology that includes variable latency periods and within-host heterogeneity. Here, we carried out a systematic comparison of seven publicly available transmission reconstruction tools, evaluating their accuracy in predicting transmission events in both simulated and real-world Mycobacterium tuberculosis outbreaks. No tool was able to fully resolve transmission networks, though both the single-tree and multi-tree input implementations of TransPhylo identified the most epidemiologically supported transmission events and the fewest false positive links. We observed a high degree of variability in the transmission networks inferred by each approach. Our findings may inform the choice of tools in future tuberculosis transmission analyses and underscore the need for caution when interpreting transmission networks produced using probabilistic approaches.

Application of high throughput sequencing in veterinary science

High throughput sequencing (HTS) creates an opportunity for comprehensive genomic studies. It can be applied in veterinary science, bacteriology and virology, diagnostics of animal diseases, food safety, examinations of the composition of environmental samples, and even in veterinary vaccinology. Thus HTS a wide-ranging method that can be applied in different areas of the One Health approach. In particular, the whole genome sequencing (WGS) of bacteria is routinely used in food hygiene and outbreak investigations for phylogenetic analysis of pathogenic bacteria isolated from various sources across timeline, molecular characterisation of bacteria, plasmids, antibiotic resistance and identification of virulence factors. Metagenomics can be used to characterize the composition of microbiota in environmental samples. It makes it possible to obtain a taxonomic identification of bacteria, fungi or plants present in a metasample. It can also be used for the monitoring and epidemiological tracing of viruses, such as SARS-CoV-2. The transcriptomic approach makes it possible to study the expression of genes associated with various infections and diseases. HTS is a highly versatile method, but the selection of the proper application is crucial to obtain expected outcomes. The paper presents some HTS approaches and examples of research in veterinary science.

Biosecurity Levels and Farm Characteristics of African Swine Fever Outbreak and Unaffected Farms in Estonia—What Can Be Learned from Them?

Risk factors related to external biosecurity have been considered to play a major role in the introduction and spread of African swine fever (ASF) in domestic pig populations. The aim of the study was to describe the biosecurity levels and management practices of ASF outbreak and uninfected herds and to identify potential risk factors for ASF introduction. Data collected from the outbreak herds during outbreak investigations and from the randomly selected uninfected herds were analyzed. The biosecurity score in ASF outbreak herds was significantly lower compared to uninfected herds. However, this may reflect general improvement in the application of biosecurity measures in pig farms over time as the data on uninfected herds were collected later, at a time when intensified official controls may have had their effect. Larger herds were more at risk of being outbreak herds compared to smaller herds. The biosecurity parameters significantly associated with the outbreak herd status in multiple correspondence analysis were mostly related to indirect contacts with the outside farm environment. The biosecurity barriers applied in Estonian pig farms have not been sufficient to avoid ASF introduction and need critical evaluation and improvement. Reduction of all contacts between the farm and the external environment should be emphasized in a situation where ASF is circulating in wild boar populations close to pig farms.

Analysis of an IncR Plasmid Carrying bla NDM-1 Linked to an Azithromycin Resistance Region in Enterobacter hormaechei Involved in an Outbreak in Quebec

Analyzing the genetic environment of clinically relevant MDR genes can provide information on the way in which such genes are maintained and disseminated. Understanding this phenomenon is of interest for clinicians as it can also provide insight on where these genes might have been sourced, possibly supporting outbreak investigations.

Healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (HALT NTM) study: Rationale and study design

Background Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been reported and is of increasing concern. No standardized epidemiologic investigation tool has been published for healthcare-associated NTM outbreak investigations. This report describes the design of an ongoing observational study to standardize the approach to NTM outbreak investigation among pwCF. Methods This is a parallel multi-site study of pwCF within a single Center who have respiratory NTM isolates identified as being highly-similar. Participants have a history of positive airway cultures for NTM, receive care within a single Center, and have been identified as part of a possible outbreak based on genomic analysis of NTM isolates. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of a shared healthcare-associated encounter(s) among patients in a Center and identification of environmental isolates that are genetically highly-similar to respiratory isolates recovered from pwCF. Secondary endpoints include characterization of potential transmission modes and settings, as well as incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. Discussion We hypothesize that genetically highly-similar strains of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from environmental sources. This novel study design will establish a standardized, evidence-based epidemiologic investigation tool for healthcare-associated NTM outbreak investigation within CF Care Centers, will broaden the scope of independent outbreak investigations and demonstrate the frequency and nature of healthcare-associated NTM transmission in CF Care Centers nationwide. Furthermore, it will provide valuable insights into modeling risk factors associated with healthcare-associated NTM transmission and better inform future infection prevention and control guidelines. This study will systematically characterize clinically-relevant NTM isolates of CF healthcare environmental dust and water biofilms and set the stage to describe the most common environmental sources within the healthcare setting harboring clinically-relevant NTM isolates. Trial registration ClinicalTrials.gov NCT04024423. Date of registry July 18, 2019.

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

Streamlined Whole Genome Sequencing of Mumps for High Resolution Outbreak Analysis

Since 2015, the United States has experienced a resurgence in the number of mumps cases and outbreaks in fully vaccinated populations. These outbreaks have occurred predominantly in close quarter settings such as camps, colleges and detention centers. Phylogenetic analysis of 758 mumps positive samples from outbreaks across the United States, identified 743 (98%) as genotype G based on sequence analysis of the mumps small hydrophobic (SH) gene. Additionally, SH sequences in the genotype G samples showed almost no sequence diversity, with 675 (91%) of them having identical sequences or only one nucleotide difference. This uniformity of circulating genotype and strain created complications for epidemiologic investigations and necessitated the development of a system for rapidly generating mumps whole genome sequences for more detailed analysis. In this study, we report a novel and streamlined assay for whole genome sequencing (WGS) of mumps virus genotype G. The WGS procedure successfully generated 318 high-quality WGS sequences on nucleic acid from genotype G-positive respiratory samples collected during several mumps outbreaks in the United States between 2016-2019. Sequencing was performed by a rapid and highly sensitive custom Ion AmpliSeq mumps genotype G panel, with sample preparation performed on an Ion Chef and sequencing on an Ion S5. The WGS data generated by the AmpliSeq panel provided enhanced genomic resolution for epidemiological outbreak investigations. Translation and protein sequence analysis also identified several potentially important epitope changes in the circulating mumps genotype G strains compared to the Jeryl-Lynn strain (JL5) used in vaccines in the United States which could explain the current level of vaccine escapes.

1207. Coronavirus Disease, 2019 (COVID-19) in Long-Term Care Facilities (LTCF): One Large County’s Response, California 2020-2021

Background The coronavirus-19 disease (COVID-19) outbreak has had a particularly devasting effect on skilled nursing facility (SNF) residents and healthcare workers (HCWs). While representing only 11% of COVID-19 cases, the residents accounted for 43% of deaths in the United States. Methods We report a retrospective review of the support provided by our local health department (LHD) to long-term care facilities in response to the COVID-19 pandemic. This group comprised of staff from healthcare-associated infections (HAI); the Medical Operations Center (MOC); Testing, Tracing, and Treatment (T3); and the Healthcare Provider Status Taskforce (Table 1 outlines their functions). The HAI team with the State Public Health Department provided infection prevention and control (IPC) outbreak investigation, education, recommendations, and ongoing access to technical assistance. The T3 team focused on rapid response testing and tracing; the HPSTF team collected data and issued questionnaires; the MOC responded to staffing and PPE requests; and the Long-Term Care Facility sector presented routine telebriefings to update the facilities on public health guidance, share resources, and answer questions during and in between briefings. Table 1. Sectors and Function of Response Teams to COVID-19 Results From March 2020 through May 2021, there were 504 outbreaks in LTCFs; the HAI team performed 281 outbreak investigations (Figure 1). In the same period, 308,264 molecular tests were performed using various platforms; laboratory services were outsourced during peak testing requests (Figure 2); “strike teams were deployed to facilitate testing on 404 occasions. Self-reported fully vaccination rate for SNF staff was 73% (March 2021) and 76% for residents (April 2021). There were 568 staff requested; total orders for PPE were 4,839 and 16,892,823 PPE items were fulfilled (Figure 3). In addition to knowledge gaps in IPC, other challenges included shifting IPC guidance, PPE shortages, timeliness of test results that impacted cohorting, community acquisition of disease with transmission to residents, interfacility spread among staff, staffing shortages, and vaccine hesitancy issues. Figure 1. Number of Outbreaks and Number of Outbreak Investigations Figure 2. Number of Tests Performed by the Public Health Laboratory and the Number of Visits by “Strike Teams” Figure 3. Personal Protective Equipment Fulfillment during COVID-19 Pandemic Conclusion The management of the recent COVID-19 outbreaks required a multi-pronged approach. Lessons learned are applicable to other highly transmissible infectious diseases. Disclosures All Authors: No reported disclosures

820. Optimal Specimen Source(s) for Carbapenemase-Producing Acinetobacter Colonization Screening

Background Infection prevention (IP) strategies are implemented to limit the transmission of healthcare-associated infections (HAIs), which are estimated to occur in 1 out of 31 hospitalized patients per day in the United States. Carbapenem-resistant Acinetobacter (CRA) cause HAIs classified as an urgent threat by CDC. When carbapenemase-producing CRA (CP-CRA) are identified, containment strategies are implemented, including screening patients at high risk for colonization with CP-CRA. Point prevalence surveys (PPS) are conducted to assist with HAI outbreak investigations and identify colonized patients. Methods Herein, we describe results from culture-based CP-CRA colonization testing of multiple specimen sources (rectal, skin [axilla/groin or groin], respiratory, and/or wound). A total of 744 PPS specimens from 356 patients, across six states, were obtained from February 2019 to May 2021 for CP-CRA colonization screening including 30% (224/744) rectal, 52% (390/744) skin, 10% (73/744) respiratory, and 8% (57/744) wound sources. The specimens were plated onto both non-selective (blood agar) and selective media (MacConkey, ESBL CHROMagar, Acinetobacter CHROMagar), and RT-PCR was performed for detection of the Acinetobacter-specific carbapenemase genes blaOXA-23, blaOXA-24, and blaOXA-58. Results Twelve percent (90/744) of specimens, representing 17% (62/356) of patients, were positive for detection of blaOXA-23 and/or blaOXA-24 CP-CRA. The majority (96%) of CP-CRA harbored blaOXA-24. Of the 62 colonized patients, 52% (32/62) had more than one collection source and 47% (15/32) of those had more than one source positive for CP-CRA. There was no consensus regarding a single source type across positive specimens. However, rectal or skin swab collection alone would potentially miss 2% (4/163) or 8% (14/186) of positive specimens, respectively. Conclusion These data suggest that rectal or skin source collection alone could be sufficient for detection of CP-CRA. Overall, multiple factors should be considered to guide the source(s) for CP-CRA specimen collection, such as infection type, regional prevalence, patient factors, and/or IP gap(s) within a facility. Disclosures All Authors: No reported disclosures