State Public Health Laboratories Research Articles

Evaluation of the Laboratory Response Network and Testing Access During the First 10 Weeks of the Mpox Response, United States, May 17-July 31, 2022.

The Laboratory Response Network (LRN) consists of US and international laboratories that respond to public health emergencies, such as biothreats. We used a qualitative approach to assess the successes and challenges of the LRN during the initial 10 weeks of the 2022 mpox outbreak (May 17-July 31, 2022). We conducted 9 unstructured interviews, which included 3 interviews with subject matter experts from the Centers for Disease Control and Prevention (CDC) and 6 interviews with state and local public health laboratories and epidemiologists and Association of Public Health Laboratories (APHL) staff. We asked guiding questions on investments in preparedness, successes, and challenges during the initial mpox response and asked for suggestions to improve future LRN responses to infectious disease outbreaks. We also reviewed data from 2 contemporaneous APHL surveys conducted in June and July 2022 in 84 LRN public health laboratories. Notable successes included availability of an assay that had received clearance from the US Food and Drug Administration (FDA) for testing orthopoxviruses (non-variola Orthopoxvirus [NVO] assay) and a trained workforce; strong relationships among FDA, CDC, and the LRN; and strong communications between LRN laboratories and CDC. Challenges included variability among LRN laboratories in self-reported testing capacity, barriers to accessing the NVO assay for health care providers, and gaps in LRN function during surges of testing needs. The LRN system plays an essential role in the response to emerging infectious disease outbreaks in the United States. Lessons learned from the LRN's initial response to the mpox outbreak can help guide improvements to better position the LRN for future responses, including continued engagement with health care providers, commercial laboratories, and laboratories in health care settings.

Navigating the network: a narrative overview of AMR surveillance and data flow in the United States.

The antimicrobial resistance (AMR) surveillance landscape in the United States consists of a data flow that starts in the clinical setting and is maintained by a network of national and state public health laboratories. These organizations are well established, with robust methodologies to test and confirm antimicrobial susceptibility. Still, the bridge that guides the flow of data is often one directional and caught in a constant state of rush hour that can only be refined with improvements to infrastructure and automation in the data flow. Moreover, there is an absence of information in the literature explaining the processes clinical laboratories use to coalesce and share susceptibility test data for AMR surveillance, further complicated by variability in testing procedures. This knowledge gap limits our understanding of what is needed to improve and streamline data sharing from clinical to public health laboratories. Successful models of AMR surveillance display attributes like 2-way communication between clinical and public health laboratories, centralized databases, standardized data, and the use of electronic health records or data systems, highlighting areas of opportunity and improvement. This article explores the roles and processes of the organizations involved in AMR surveillance in the United States and identifies current knowledge gaps and opportunities to improve communication between them through standardization, communication, and modernization of data flow.

1703. Pseudo-Outbreak of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit: Implications for Surveillance

Abstract Background We conduct weekly surveillance screening for methicillin-resistant Staphylococcus aureus (MRSA) in our neonatal intensive care unit (NICU). In September 2021, we noted an increase in positive MRSA screening results and identified 2 patients with MRSA wound infection. We conducted an investigation to explore the possibility of in-unit transmission. Methods We launched a multi-pronged investigation that included additional patient screening. Surveillance isolates were assessed for the presence of MRSA using chromogenic agar. Additional antimicrobial sensitivity testing was performed on an automated bacterial identification system if chromogenic agar results were inconclusive, fig 1 & 2. We also conducted audits of staff hand hygiene, enhanced cleaning and disinfection of shared patient-care equipment, implemented standardized chlorhexidine gluconate (CHG) scrub use for NICU staff upon unit entry, and added new CHG bathing for certain patients. Positive control chromogenic agar plate Ambiguous chromogenic agar results Results Over the course of a 6-week long investigation, 18 neonates were found to be MRSA-positive on surveillance swabs using chromogenic agar. In the first 2 weeks of the investigation, PFGE showed that 9 MRSA isolates were genetically distinct. Over the next weeks, additional MRSA-positive surveillance swabs were collected and ultimately 15 isolates underwent whole genome sequencing at the Mass. State Public Health Laboratory. Only 2 pairs of isolates appeared related. Antimicrobial resistance genes were identified and revealed only 6 of the 15 isolates contained the mecA gene consistent with MRSA. As a result, all 18 positive surveillance swabs obtained during the investigation underwent full identification and sensitivity testing confirming only 6 samples contained MRSA and 12 contained methicillin-sensitive Staphylococcus aureus (MSSA). Testing discordance with breakthrough MSSA growth was reported to the chromogenic agar manufacturer. Conclusion Our investigation identified that an increase in MRSA-positive surveillance swabs was a pseudo-outbreak due to false-positive MSSA growth on MRSA selective media. At the conclusion of this investigation, the need for ongoing surveillance swabs was re-evaluated and ultimately discontinued. Clinical NICU specimens are now monitored in real-time by Infection Control. Disclosures James Kirby, MD, D(ABMM), Abbott Molecular: Educational Grant

Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade of Salmonella enterica serovar Enteritidis in Queensland, Australia.

Salmonellosis is a significant public health problem globally. In Australia, Salmonella enterica serovar Enteritidis is one of the main causes of salmonellosis. This study reports how the implementation of routine genetic surveillance of isolates from human S. Enteritidis cases enabled identification of the likely source of an outbreak that occurred in a remote town in Far North Queensland, Australia. This study included patient, food and water samples collected during an outbreak investigation. S. Enteritidis of the novel sequence type 5438 was isolated from all seven patient samples and one bore water sample but not any of the food samples. Both whole-genome single nucleotide polymorphism (SNP) and core-genome multilocus sequence typing analysis revealed that S. Enteritidis isolated from outbreak-related patient samples and the bore water isolates clustered together with fewer than five SNP differences and ten allelic differences. This genetic relatedness informed the outbreak response team around public health interventions and no further cases were identified post-treatment of the bore water. This disease cluster was identified through the routine sequencing of S. Enteritidis performed by the state public health laboratory in an actionable time frame. Additionally, genomic surveillance captured a case with unknown epidemiological links to the affected community, ruled out a simultaneous outbreak in an adjacent state as the source and provided evidence for the likely source preventing further transmission. Therefore, this report provides compelling support for the implementation of whole-genome sequencing based genotyping methods in public health microbiology laboratories for better outbreak detection and management.

Assessment of carbapenem-resistant Acinetobacter baumannii–colonized patients: Which specimens produce the highest yield?

Background: Carbapenem-resistant Acinetobacter (CRA) bacteria are an urgent public health threat. Accurate and timely testing of CRA is important for proper infection control practices to minimize spread. In 2017, the CDC estimated 8,500 CRA cases among hospitalized patients, 700 deaths, and $281 million in attributable healthcare costs. Treatment options are extremely limited for carbapenem-resistant Acinetobacter baumannii (CRAB) infections, making CRAB a unique concern. Colonization screening is a valuable tool for containment but requires sampling of 4 body sites. Identifying a reliable specimen collection site for CRAB is important to inform public health recommendations as screening can cost healthcare facilities valuable time and resources. Methods: Results of all screening specimens of patients with at least 1 site positive for CRAB on a unique collection date were extracted from the Southeast Regional data of Antimicrobial Resistance Lab Network (SEARLN) data. Non-CRAB screening and screenings that did not yield at least 1 positive result on a single collection date were excluded. We also limited our data to include only the following screening sites, which have been validated by the Tennessee Department of Health’s State Public Health Laboratory: axilla and groin, rectal, sputum, and wound. For each specimen source, we calculated the percentage of positive specimen among CRAB-colonized patients. Data were extracted and analyzed using SAS version 9.4 software. Results: The SEARLN data contained 594 CRAB screening specimens collected over 4 years, 2018 through 2021, and 486 of those specimens yielded CRAB. For CRAB-colonized patients screened in this study, wound specimens had the highest positivity rate at 93.4% (95% CI, 89.9%–96.9%) of samples culturing CRAB. Sputum followed at 87.7%, then axilla and groin at 77.6% and rectal at 59.7%. Conclusions: Wound specimens produced the highest proportion of positive cultures among CRAB-positive patients, making them the sample type with the highest prevalence in our study. For healthcare facilities with limited time and resources seeking to optimize their CRAB screening process, wound specimens may be the most reliable single site for detecting CRAB colonization in patients with an open wound. When a wound is not present, sputum may be a good alternative single-source collection site. More research should be conducted before CRAB screening recommendations are updated.Disclosures: None

Carbapenem-resistant Enterobacterales susceptibility patterns to new antimicrobials: A single-center analysis

Background: Multidrug-resistant bacteria are of high concern, and empiric antimicrobial choice for infections caused by these pathogens, while awaiting susceptibilities, is increasingly encountered. We describe the susceptibility patterns of ceftazidime-avibactam (CZA), imipenem-rel-ebactam (I-R), meropenem-vaborbactam (MVB), cefiderocol (FDC), ceftolozone-tazobactam (C/T), minocycline (MIN), and tigecycline (TGC) for carbapenem-resistant Enterobacterales at an academic medical center. Methods: We performed a single-center analysis of Enterobacterales isolates from 110 hospitalized adult patients who had CZA, I-R, MVB, FDC, MIN, or TGC susceptibility testing performed between October 2020 and September 2022. The study included 1 isolate per patient per infection site per year. Isolates were divided into carbapenem susceptible and non susceptible categories. For carbapenem nonsusceptible isolates, phenotypic confirmatory testing of carbapenem nonsusceptibility was performed using disk diffusion, gradient diffusion, and/or broth microdilution. Interpretive categories were applied using CLSI- or FDA-approved break-points where applicable. Carbapenemase testing was also performed using the modified carbapenem inactivation method (mCIM) and, where applicable, this testing was confirmed at the Massachusetts State Public Health Laboratory using genotypic methods. Results: In total, 125 unique isolates were reviewed: 34 meropenem-susceptible and 91 meropenem-intermediate or resistant isolates. CZA, I-R, MVB, and FDC were active against all tested meropenem-susceptible isolates; however, 50% of tested isolates were susceptible to C/T. MIN and TGC, when tested, were active against 2 of 11 isolates (18%) and 14 of 16 isolates (86%), respectively. Of 91 meropenem-nonsusceptible isolates, most tested isolates were susceptible to MVB (59 of 72, 82%), followed by CZA (63 of 82, 77%), I-R (8 of 11, 73%), FDC (9 of 16, 56%), and C/T (1 of 12, 8%). TGC retained activity against 78 of 81 (96%) tested isolates. In contrast, MIN retained activity against 8 of 45 isolates (18%). Additionally, all (28 of 28, 100%) isolates that were nonsusceptible to at least 1 novel agent (CZA, I-R, MVB, FDC, or C/T) remained susceptible to TGC. State laboratory confirmatory testing was available for 75 isolates. Of 43 mCIM-positive isolates, all 28 KPC-producing isolates were susceptible to CZA, I-R, MVB, FDC and TGC. Conclusions: Among Enterobacterales, CZA, MVB, and I-R retained activity against most non-NDM CRE isolates in this local analysis, with comparable susceptibilities. TGC demonstrated excellent susceptibility for CRE and meropenem-susceptible isolates, offering an alternative for nonbloodstream infections. Choice of empiric agent with a newβ-lactam, β-lactam–β-lactamase inhibitors, or TGC appear to be reasonable empiric therapeutic options at our institution. CT and MIN warrant confirmatory testing prior to use due to low susceptibility rates among meropenem nonsusceptible isolates.Disclosures: None

Mass Human Exposures to One Rabid Kitten

On October 22, 1994, a State public health laboratory diagnosed rabies in a kitten that had been purchased from a pet store in the State capital. On October 19, the animal developed seizures, then died of unknown causes during the night of October 20–21. Approximately 665 persons received rabies postexposure prophylaxis because of exposure to this kitten and other cats from the same pet store. This case is intended to walk the reader through the situation as it actually happened and identify potential opportunities for interventions that would have resulted in fewer people exposed, fewer rabies prophylaxis administrations, lower costs, and reduced community concern.© The Author 2023

The Ongoing Impact of COVID-19 on Testing for and Diagnoses of HIV and Bacterial Sexually Transmitted Infections in Oregon.

The COVID-19 pandemic has disrupted HIV and sexually transmitted infection (STI) testing accessibility. We sought to assess the longer-term impacts of COVID-19 on HIV and STI testing and diagnosis in Oregon. First, we examined HIV, Neisseria gonorrhoeae / Chlamydia trachomatis (CT), and syphilis tests conducted at the Oregon State Public Health Laboratory (public sector) and a large commercial laboratory (private sector) and HIV, N. gonorrhoeae , CT, and primary and secondary (P&S) syphilis diagnoses in Oregon from January 1, 2019, to December 31, 2021. We compared monthly testing and diagnosis rates in 5 prespecified periods: pre-COVID-19 (January 2019-February 2020), stay-at-home order (March 2020-May 2020), reopening (June 2020-December 2020), vaccine availability (January 2021-June 2021), and Delta/early Omicron spread (July 2021-December 2021). Second, we calculated the number of HIV and STI diagnoses per test in the public and private sectors. Finally, we used seasonal autoregressive integrated moving average models to predict expected HIV and STI diagnoses for comparison to those observed. Both public and private sector HIV and bacterial STI testing fell to nadirs in April 2020 with incomplete recovery to 2019 levels by the close of 2021. Compared with pre-COVID-19, public sector and private sector testing was significantly lower in all subsequent periods. Compared with pre-COVID-19, P&S syphilis cases were 52%, 75%, and 124% greater in the reopening, vaccine availability, and Delta/early Omicron periods, respectively. From March 2020 to December 2021, we observed an excess of P&S syphilis cases (+37.1%; 95% confidence interval, 22.2% to 52.1%) and a deficit in CT cases (-10.7%; 95% confidence interval, -15.4% to -6.0%). By December 2021, HIV/STI testing had not recovered to pre-COVID-19 levels, and HIV/STI continues to be underdiagnosed. Despite decreased testing, P&S syphilis cases have increased substantially.

Defining County-Level Terrestrial Rabies Freedom Using the US National Rabies Surveillance System: Surveillance Data Analysis

Rabies is a deadly zoonotic disease with nearly 100% fatality rate. In the United States, rabies virus persists in wildlife reservoirs, with occasional spillover into humans and domestic animals. The distribution of reservoir hosts in US counties plays an important role in public health decision-making, including the recommendation of lifesaving postexposure prophylaxis upon suspected rabies exposures. Furthermore, in surveillance data, it is difficult to discern whether counties have no cases reported because rabies was not present or because counties have an unreported rabies presence. These epizootics are monitored by the National Rabies Surveillance System (NRSS), to which approximately 130 state public health, agriculture, and academic laboratories report animal rabies testing statistics. Historically, the NRSS classifies US counties as free from terrestrial rabies if, over the previous 5 years, they and any adjacent counties did not report any rabies cases and they tested ≥15 reservoir animals or 30 domestic animals. This study aimed to describe and evaluate the historical NRSS rabies-free county definition, review possibilities for improving this definition, and develop a model to achieve more precise estimates of the probability of terrestrial rabies freedom and the number of reported county-level terrestrial rabies cases. Data submitted to the NRSS by state and territorial public health departments and the US Department of Agriculture Wildlife Services were analyzed to evaluate the historical rabies-free definition. A zero-inflated negative binomial model created county-level predictions of the probability of rabies freedom and the expected number of rabies cases reported. Data analyzed were from all animals submitted for laboratory diagnosis of rabies in the United States from 1995 to 2020 in skunk and raccoon reservoir territories, excluding bats and bat variants. We analyzed data from 14,642 and 30,120 county-years in the raccoon and skunk reservoir territories, respectively. Only 0.85% (9/1065) raccoon county-years and 0.79% (27/3411) skunk county-years that met the historical rabies-free criteria reported a case in the following year (99.2% negative predictive value for each), of which 2 were attributed to unreported bat variants. County-level model predictions displayed excellent discrimination for detecting zero cases and good estimates of reported cases in the following year. Counties classified as rabies free rarely (36/4476, 0.8%) detected cases in the following year. This study concludes that the historical rabies freedom definition is a reasonable approach for identifying counties that are truly free from terrestrial raccoon and skunk rabies virus transmission. Gradations of risk can be measured using the rabies prediction model presented in this study. However, even counties with a high probability of rabies freedom should maintain rabies testing capacity, as there are numerous examples of translocations of rabies-infected animals that can cause major changes in the epidemiology of rabies.

2003. Comparison of Confirmed and Probable Cases of Vibriosis, Tennessee, 2017–2021

Abstract Background Vibriosis causes an estimated 80,000 illnesses and 100 deaths in the United States each year. Commonly reported exposures include consuming raw or undercooked seafood and contact with seawater. To facilitate case ascertainment and better understand the epidemiology of vibriosis, CDC requested inclusion of positive culture-independent diagnostic testing (CIDT) cases to the 2017 case definition. We reviewed confirmed (culture positive) and probable (CIDT positive) cases in Tennessee (TN) from 2017-2021. Methods Vibrio reports from clinical and state public health laboratories were reviewed. Demographic, clinical, and exposure data were collected through routine case interviews using The Cholera and Other Vibrio Illness Surveillance (COVIS) Report. Confirmed and probable cases were described and compared using Epi Info 7. Results A total of 164 Vibrio cases were reported from 44 counties across TN. In total, 135 (82%) cases were interviewed including 72 (53%) confirmed cases (all sources) and 63 (47%) probable cases. Half of cases from each case status were 40-69 years old. Twenty-four percent of probable cases versus 7% of confirmed cases were under 10 years old. Of confirmed cases, 64% were males compared to 51% of probable cases. Most cases (90% of confirmed and 75% of probable cases) were among non-Hispanic white population. Almost all probable cases (97%) reported gastrointestinal (GI) symptoms. Among confirmed cases, 70% reported non-GI symptoms such as cellulitis. Thirty three percent of both confirmed and probable cases were hospitalized. Confirmed cases were more likely to report travel out of state (OR 5.1, p-value < 0.0001) and exposure to seawater (OR 3.4, p-value 0.002) compared to probable cases. When comparing confirmed cases from stool specimens (27 cases) to probable cases, travel out of state remained significant (OR 4.8, p-value 0.0001) as well as seafood consumption (OR 6.8, p-value 0.0008). Conclusion Demographic and clinical features differed between confirmed and probable cases. Out of state travel, seafood consumption, and exposure to seawater were reported more often by confirmed cases. Reflex culturing is recommended to better facilitate case ascertainment and understand the epidemiology of vibriosis. Disclosures All Authors: No reported disclosures.

16. Evaluation of a Monkeypox virus PCR assay and suggestions for future improvement

Abstract Background Monkeypox virus is an Orthopoxvirus in the Poxviridae family currently responsible for an ongoing global epidemic including active transmission in all 50 US states. To date, nearly 12,000 US cases have been confirmed, with the largest case count in New York State, where over 2,500 cases have been confirmed. Of these, the vast majority (greater than 90%) of cases are residents of New York City (NYC). Nearly all described cases have been identified in men, predominantly in men who have sex with men. Until recently, laboratory testing for Monkeypox virus was limited to state and local public health laboratories or the US Centers for Disease Control (CDC). Northwell Health is the largest healthcare provider in the NYC region and is responsible for molecular PCR testing for over 25 hospitals in the area. Methods We describe the evaluation of two real-time PCR assays developed by the CDC: one specific for Monkeypox virus and the other a generic Orthopoxvirus assay. We describe performance characteristics in a high-prevalence patient population, identify room for improvement in future assay iterations, and discuss potential scalability of the assay and portability to an ultra high-throughput platform. Results We evaluated the CDC Orthopoxvirus and Monkeypox virus PCR assays using 50 clinical specimens collected from patients presenting with lesions. We determined the limit of detection for both assays is 250 copies/mL. Additionally the assays are highly specific with no cross-reactivity with other viruses tested, including HSV-1, HSV-2, and VZV. One significant limitation is the high rate of indeterminate results due to the use of an RNase P specimen control. Indeterminate results were not the result of assay inhibition and may be from inadequate specimen collection. However, since RNase P signal was often absent in positive specimens, the clinical impact of the RNase P result is questionable. Conclusion The CDC Orthopoxvirus and Monkeypox virus PCR assays were useful tools for clinical laboratories to launch rapid testing capacity for these viruses early in the course of the outbreak. However, limitations of the assays prevent them from being expanded to more high-throughput testing platforms. Moving forward, additional work is needed to optimize these PCR assays for more widespread clinical use. Disclosures All Authors: No reported disclosures.

2055. Trends in the Incidence of Carbapenem-Resistant Enterobacterales (CRE) and Carbapenemase Producing CRE (CP-CRE) in Davidson and Surrounding Counties, Tennessee, 2016-2021

Abstract Background The spread of Carbapenem-resistant Enterobacterales (CRE) continue to be a public health threat. Tennessee has participated in the Multidrug-Resistant Gram-Negative Bacilli Surveillance Initiative (MuGSI) since 2014. We investigated our data to describe the trends of CRE and CP-CRE and their changes during the COVID-19 outbreak. Methods Population-based surveillance targeting selected CRE organisms was conducted in Davidson County and seven surrounding counties in Tennessee. A CRE case was defined as isolation of Escherichia coli, Klebsiella spp., or Enterobacter spp. resistant to ≥1 carbapenem from a normally sterile body site or urine, in a surveillance area resident. A case was identified as incident if it was reported for the first time in the surveillance year or was a subsequent report of a case ≥30 days after the last report. The Tennessee state public health laboratory tests for carbapenemase production on CRE isolates received from clinical laboratories. The data analysis was conducted using SAS software version 9.4. Results 474 incident CRE cases were reported from 2016 to 2021. Females made up 68.63% and the average age was 65 years for both sexes. The incidence rate of CRE cases increased throughout study period and the rate in 2021 was 1.8-fold of 2016 (lowest rate for the study period) (P-value< 0.001). The incidence rate of CP-CRE increased in 2017 and 2018 compared to 2016 (p-value=0.01). The incidence rate for CP-CRE declined to the lowest level in 2020 (0.3 per 100,000 population). In 2021, the CP-CRE rate significantly increased compared to 2020 (p-value=0.02). The carbapenemase production (CP) positivity rate was also significantly higher in 2017(28.8%), 2018 (26.6%), and 2021 (25.8%) compared to the year 2020 where the positivity rate was the lowest (10.0%) (P-value< 0.05). Conclusion The transmission of CP-CRE cases decreased during the years prior to the COVID-19 outbreak despite the steady increase in CRE cases. The transmission of CP-CRE gained momentum during the COVID outbreak as evidenced by an increased infection rate and CP positivity rate in 2021. Renewed focus on implementing coordinated infection prevention strategies is likely to contribute to reducing the spread of antimicrobial-resistant pathogens. Disclosures All Authors: No reported disclosures.

Identifying Operational Challenges and Solutions During the COVID-19 Response Among US Public Health Laboratories.

Context:The ability to diagnose and screen for infection is an important component of the US COVID-19 response and is facilitated by public health laboratories (PHLs). Anecdotal media reports and limited case studies have described some of the challenges faced by PHLs during the pandemic, particularly initial challenges related to developing and deploying tests to PHLs, but there has not been a systematic evaluation of the experience of PHLs during the pandemic.Objective:To document challenges and lessons learned experienced by local and state PHLs during the COVID-19 pandemic to support generation of best practices for current and future similar emergencies.Design, Setting, and Participants:From February to June 2021, researchers conducted 24 interviews with 68 leaders and staff representing 28 local and state PHLs across 27 states. Thematic analysis of interview content documented operational challenges and any identified solutions or preventive measures used or proposed.Main Outcome Measures:Analysis identified the following themes regarding challenges faced among PHLs: strategic decision making and determining the mandate of the PHL; political interference by jurisdictional leadership; federal mismanagement of the emergency; regulatory challenges; managing partnerships with other laboratories; acquisition of appropriate supplies; insufficient information systems; acquiring and retaining workforce; and difficulty accessing sufficient funding.Results:Within the identified themes, key informants provided further elaboration regarding how PHLs experienced, evaded, or solved these challenges. In addition, PHLs described how challenges evolved throughout the course of the COVID-19 pandemic and made proposals regarding how challenges could be prevented or further addressed in the future by laboratories or other decision makers and stakeholders.Conclusions:While fellow laboratories and political leadership may gain inspiration from creative solutions employed by PHLs, recognition of long-standing gaps related to funding, laboratory workforce, and consideration of laboratory needs in preparedness policies must be addressed for future large-scale outbreaks.

Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012-2019.

Pathogen detection has changed with increased use of culture-independent diagnostic tests (CIDTs). CIDTs do not yield isolates, which are necessary to detect outbreaks using whole-genome sequencing. The Foodborne Diseases Active Surveillance Network (FoodNet) monitors clinical laboratory testing practices to improve interpretation of surveillance data and assess availability of isolates. We describe changes in practices over 8 years. During 2012-2019, 10 FoodNet sites collected standardized data about practices in clinical laboratories (range, 664-723 laboratories) for select enteric pathogens. We assessed changes in practices. During 2012-2019, the percentage of laboratories that used only culture methods decreased, with the largest declines for Vibrio (99%-57%) and Yersinia (99%-60%). During 2019, the percentage of laboratories using only CIDTs was highest for Shiga toxin-producing Escherichia coli (43%), Campylobacter (34%), and Vibrio (34%). From 2015 to 2019, the percentage of laboratories that performed reflex culture after a positive CIDT decreased, with the largest declines for Shigella (75%-42%) and Salmonella (70%-38%). The percentage of laboratories that routinely submitted isolates to a public health laboratory decreased for all bacterial pathogens examined from 2015 to 2019. By increasing use of CIDTs and decreasing reflex culture, clinical laboratories have transferred the burden of isolate recovery to public health laboratories. Until technologies allow for molecular subtyping directly from a patient specimen, state public health laboratories should consider updating enteric disease reporting requirements to include submission of isolates or specimens. Public health laboratories need resources for isolate recovery.

Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020

BackgroundThe implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020.ResultsThe New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination.ConclusionsWGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.

Transmission of Pan-resistant and Echinocandin-resistant Candida Auris Between Healthcare Facilities During the COVID-19 Pandemic

BackgroundCandida auris is a Texas notifiable condition requiring isolate submission to the state public health laboratory. C. auris spreads in healthcare through contact with contaminated surfaces and unclean hands. During the COVID-19 pandemic, pan-resistant and echinocandin-resistant C. auris were identified in Texas for the first time.MethodsIn January 2021, a long-term acute care hospital patient's isolate was identified as C. auris. Retrospective surveillance identified a 2020 case. Remote and onsite infection control assessments (ICARs) were conducted at healthcare facilities (HCFs) where the cases received care. Colonization screenings were conducted until the HCFs achieved two rounds of negative results. Cases and those pending screening results were placed on contact precautions. Epidemiologists provided education and resources to HCFs to mitigate identified infection prevention gaps. Antifungal susceptibility testing (AST) was performed at the Antibiotic Resistance (AR) Laboratory Network laboratory. Whole genome sequencing (WGS) was performed by the Centers for Disease Control and Prevention (CDC) Laboratory.ResultsThere were 47 C. auris cases with collection dates from November 20, 2020, to September 27, 2021, including 15 clinical and 32 colonized cases from 22 years to 89 years old with a mean age of 63. Sixty-six percent (n=31) were males. Common gaps from the 46 ICARs conducted at 42 HCFs included using ineffective disinfectants, not following manufacturer's instructions, reusing disposable personal protective equipment, and not conducting audits. There were 59 colonization screenings at 20 HCFs. AST revealed two pan-resistant, seven echinocandin-resistant, and thirty-one fluconazole resistant cases. CDC performed WGS on 16 isolates, revealing clusters within and between HCFs, including a cluster of resistant cases.ConclusionsWGS supported transmission of pan-resistant or echinocandin-resistant C. auris for the first time in the United States. The pandemic presented new infection control risks. Rapid surveillance detection, colonization screenings, infection control assessments, and education are instrumental to outbreak containment.

Mortality rates among non-Hispanic Black and White persons in carbapenemase-producing Enterobacterales, Tennessee, 2015–2019

Background: Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat, particularly those that produce carbapenemase (CP-CRE). Certain risk factors associated with CRE acquisition have been well described, such as older age, indwelling devices, prior hospitalizations, and underlying conditions. However, data are limited regarding the association of CRE and health disparities, such as race and ethnicity. Published literature has consistently shown that minority groups, including but not limited to Non-Hispanic Black persons, have higher risks of developing adverse health outcomes. To better understand the impact of race and ethnicity in CP-CRE cases, we compared 1-year mortality rates among Non-Hispanic Blacks and Non-Hispanic Whites. Methods: CRE are reportable in Tennessee; isolates must be sent to the State Public Health Laboratory for carbapenemase detection and resistance mechanism testing. We linked 2015–2019 CP-CRE surveillance cases and laboratory data from our statewide surveillance system, the National Disease Surveillance System (NEDDS)-Base System, with the Tennessee Hospital Discharge Data System (HDDS) and vital records databases. Database linkage and data analyses were performed using SAS version 9.4 software. Results: Among 615 CP-CRE cases, the mean age was lower among non-Hispanic Blacks (59 years; SD, 16.6) compared to non-Hispanic Whites (mean, 65 years; SD, 15.7). Among 156 non-Hispanic Blacks with CP-CRE, 101 (64.7%) were nursing home residents, whereas 281 (71.1%) among the 395 non-Hispanic Whites were nursing home residents. Also, 64 Non-Hispanic Blacks (41%) died within 1 year of their first specimen collection date compared to 92 Non-Hispanic Whites (23.3%). Non-Hispanic Blacks with CP-CRE who died within 1 year had a mortality rate of 5.6 per 100,000 (95% CI, 4.21–6.94) Black population, which was 1.6 times higher than Non-Hispanic White persons at 3.5 per 100,000 (95% CI, 2.94–3.95; χ2P < .001) White population. Conclusions: Despite a lower mean age, non-Hispanic Black CP-CRE cases had a higher 1-year mortality rate than non-Hispanic Whites. Racial and ethnicity data often are missing or incomplete from surveillance data. Data linkages can be a valuable tool to gather additional clinical and demographic data that may be missing from public health surveillance data to improve our understanding of health disparities. Recognition of these health disparities among CRE can provide an opportunity for public health to create more targeted interventions and educational outreach.Funding: NoneDisclosures: None

VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.

ABSTRACTNext-generation sequencing (NGS) is a powerful tool for detecting and investigating viral pathogens; however, analysis and management of the enormous amounts of data generated from these technologies remains a challenge. Here, we present VPipe (the Viral NGS Analysis Pipeline and Data Management System), an automated bioinformatics pipeline optimized for whole-genome assembly of viral sequences and identification of diverse species. VPipe automates the data quality control, assembly, and contig identification steps typically performed when analyzing NGS data. Users access the pipeline through a secure web-based portal, which provides an easy-to-use interface with advanced search capabilities for reviewing results. In addition, VPipe provides a centralized system for storing and analyzing NGS data, eliminating common bottlenecks in bioinformatics analyses for public health laboratories with limited on-site computational infrastructure. The performance of VPipe was validated through the analysis of publicly available NGS data sets for viral pathogens, generating high-quality assemblies for 12 data sets. VPipe also generated assemblies with greater contiguity than similar pipelines for 41 human respiratory syncytial virus isolates and 23 SARS-CoV-2 specimens.IMPORTANCE Computational infrastructure and bioinformatics analysis are bottlenecks in the application of NGS to viral pathogens. As of September 2021, VPipe has been used by the U.S. Centers for Disease Control and Prevention (CDC) and 12 state public health laboratories to characterize >17,500 and 1,500 clinical specimens and isolates, respectively. VPipe automates genome assembly for a wide range of viruses, including high-consequence pathogens such as SARS-CoV-2. Such automated functionality expedites public health responses to viral outbreaks and pathogen surveillance.

Assessing an Adaptation of the Universal Parasite Diagnostic Assay for Bloodborne Parasites in a US State Public Health Laboratory.

For complex clinical cases where a parasitic infection is suspected, it can be difficult for clinicians to recommend an appropriate laboratory test. These tests are usually pathogen-specific and require a certain degree of suspicion for the precise etiology. A recently described assay, the universal parasite diagnostic (UPDx) can potentially provide a diagnosis of any parasite present in a specimen. Using primers that amplify DNA from all eukaryotes, UPDx differentiates several parasitic infections in blood by amplicon-based next-generation sequencing (NGS) of the 18S rDNA locus. As the state's public health reference laboratory, the Parasitology Laboratory at the Wadsworth Center (Albany, NY) receives specimens from patients who have potentially encountered a wide variety of parasites. As such, the ability to differentiate several blood parasites using a single assay is of interest. We assessed UPDx for its ability to confirm parasitic infections for 20 specimens that were previously identified by real-time PCR (RT-PCR). This included specimens positive for Babesia microti, Trypanosoma cruzi, Leishmania tropica, various Plasmodium species, and specimens comprising mixed Plasmodium sp. infections. Results obtained using UPDx were largely concordant with the RT-PCR assays. A T. cruzi positive specimen was negative by UPDx and for two mixed Plasmodium sp. infections only one species was detected. The results obtained for other specimens were concordant. We conclude that UPDx shows promise for the detection of blood parasites in diagnostic laboratories. As NGS becomes cheaper, assays like UPDx will become increasingly amenable to use in clinical settings.

Analysis of the initial lot of the CDC 2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel.

At the start of the COVID-19 pandemic, the Centers for Disease Control and Prevention (CDC) designed, manufactured, and distributed the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel for SARS-CoV-2 detection. The diagnostic panel targeted three viral nucleocapsid gene loci (N1, N2, and N3 primers and probes) to maximize sensitivity and to provide redundancy for virus detection if mutations occurred. After the first distribution of the diagnostic panel, state public health laboratories reported fluorescent signal in the absence of viral template (false-positive reactivity) for the N3 component and to a lesser extent for N1. This report describes the findings of an internal investigation conducted by the CDC to identify the cause(s) of the N1 and N3 false-positive reactivity. For N1, results demonstrate that contamination with a synthetic template, that occurred while the “bulk” manufactured materials were located in a research lab for quality assessment, was the cause of false reactivity in the first lot. Base pairing between the 3’ end of the N3 probe and the 3’ end of the N3 reverse primer led to amplification of duplex and larger molecules resulting in false reactivity in the N3 assay component. We conclude that flaws in both assay design and handling of the “bulk” material, caused the problems with the first lot of the 2019-nCoV Real-Time RT-PCR Diagnostic Panel. In addition, within this study, we found that the age of the examined diagnostic panel reagents increases the frequency of false positive results for N3. We discuss these findings in the context of improvements to quality control, quality assurance, and assay validation practices that have since been improved at the CDC.