Understanding the factors that contribute to the similarities and differences in SARS-CoV-2 testing strategies across Europe

Background Since the beginning of the COVID-19 outbreak, the importance of testing suspected cases has been stressed by various governments and international organizations. Early in the pandemic, the WHO's Secretary General emphasized the need to ‘test, test, test'. Nonetheless, there were some evident differences between European Member States' testing strategies. In order to get an understanding of why and how these differences developed we conducted a mixed methods study in several EU member states. Methods We conducted semi-structured interviews with 11 professionals with expertise in public health, laboratory diagnostics and policymaking in 8 European countries, namely Croatia, Italy, Latvia, Malta, the Netherlands, Spain, Latvia, Italy, Slovenia. Based on interview results, a questionnaire is developed to quantify to which degree a larger audience of public health, laboratory and policy-making professionals believe identified factors played a role in the national SARS-CoV-2 testing strategy. Preliminary results 3 factors seem to play an important role in the diagnostic capacity and testing strategy. Firstly, differences in the countries' available stockpile and their ability to efficiently procure diagnostic equipment influenced testing strategies. Secondly, the variation in institutions that took ownership of the issues of developing, executing and developing the policies led to differences in the testing strategies. Lastly, all countries aimed to follow international advice and guidelines, which led to the convergence of testing strategies over time. Conclusions In order to be prepared for a pandemic of COVID-19's scale and make necessary adjustments in capacity building, it is important that Member States understand the factors that play an important role in both their own and other European countries' diagnostic preparedness strategies.

A summary of surveillance, morbidity and microbiology of laboratory-confirmed cases of infant botulism in Canada, 1979–2019

Background: Infant botulism is a rare toxicoinfectious disease caused by colonization of the infant’s intestine with botulinum neurotoxin-producing clostridia (i.e. Clostridium botulinum or neurotoxigenic strains of C. butyricum or C. baratii). Our goal was to examine data from laboratory-confirmed cases of infant botulism reported in Canada to summarize incidence over time, over geographic distribution by province or territory, and by sex, and to compare these parameters with data from the Canadian Notifiable Disease Surveillance System (CNDSS). The average age of onset, serotype of botulinum neurotoxin (BoNT), case outcomes, length of hospitalization and suitability of clinical specimens for laboratory confirmation were also determined. Methods: We examined laboratory records from the Health Canada Botulism Reference Service and the British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory. The Discharge Abstract Database (DAD) and the Hospital Morbidity Database (HMDB) of the Canadian Institute of Health Information (CIHI) were queried for data on hospitalization of infant botulism cases. The CNDSS was queried for data on reported cases of infant botulism. Results: From 1979 to 2019, 63 laboratory-confirmed cases of infant botulism were confirmed by the Health Canada Botulism Reference Service and the BCCDC Public Health Laboratory for an annual rate of 4.30 cases per million live births. From 1983 to 2018, 57 cases of infant botulism were reported to the CNDSS. Of the 63 cases confirmed by the reference laboratories, the median age of onset was 16 weeks with a range of 2 to 52 weeks. The majority of cases were type A (76%) and B (21%), with single cases of type F and type AB. Of the 23 laboratory-confirmed cases with matched hospital records, 13 were transferred to special care and eight needed ventilator support; no deaths were reported. Conclusion: Spores of C. botulinum are present naturally in the environment, thus diagnosis of infant botulism does not require a history of exposure to high-risk foods such as honey. Stool samples are the most useful diagnostic specimen.

Verona Integron-Encoded Metallo-Beta-Lactamase (VIM)–Producing Pseudomonas aeruginosa Outbreak Associated with Acute Care

Background: Contaminated healthcare facility plumbing is increasingly recognized as a source of carbapenemase-producing organisms (CPOs). In August 2019, the Tennessee State Public Health Laboratory identified Tennessee’s twelfth VIM-producing carbapenem-resistant Pseudomonas aeruginosa (VIM-CRPA), from a patient in a long-term acute-care hospital. To determine a potential reservoir, the Tennessee Department of Health (TDH) reviewed healthcare exposures for all cases. Four cases (33%), including the most recent case and earliest from March 2018, had a history of admission to intensive care unit (ICU) room X at acute-care hospital A (ACH A), but the specimens were collected at other facilities. The Public Health Laboratory collaborated with ACH A to assess exposures, perform environmental sampling, and implement control measures. Methods: TDH conducted in-person infection prevention assessments with ACH A, including a review of the water management program. Initial recommendations included placing all patients admitted to room X on contact precautions, screening for CPO on room discharge, daily sink basin and counter cleaning, and other sink hygiene measures. TDH collected environmental and water samples from 5 ICU sinks (ie, the handwashing and bathroom sinks in room X and neighboring room Y [control] and 1 hallway sink) and assessed the presence of VIM-CRPA. Moreover, 5 patients and 4 environmental VIM-CRPA underwent whole-genome sequencing (WGS). Results: From February to June 2020, of 21 patients admitted to room X, 9 (43%) underwent discharge screening and 4 (44%) were colonized with VIM-CRPA. Average room X length of stay was longer for colonized patients (11.3 vs 4.8 days). Drain swabs from room X’s bathroom and handwashing sinks grew VIM-CRPA; VIM-CRPA was not detected in tap water or other swab samples. VIM-CRPA from the environment and patients were sequence type 253 and varied by 0–13 single-nucleotide variants. ACH A replaced room X’s sinks and external plumbing in July. Discharge screening and contact precautions for all patients were discontinued in November, 5 months following the last case and 12 consecutive negative patient discharge screens. Improved sink hygiene and mechanism testing for CRPA from clinical cultures continued, with no new cases identified. Conclusions: An ICU room with a persistently contaminated sink drain was a persistent reservoir of VIM-CRPA. The room X attack rate was high, with VIM-CRPA acquisition occurring in >40% of patients screened. The use of contaminated plumbing fixtures in ACH have the potential to facilitate transmission to patients but may be challenging to identify and remediate. All healthcare facilities should follow sink hygiene best practices.Funding: NoDisclosures: None

COVID-19 Response Efforts of Washington State Public Health Laboratory: Lessons Learned

Laboratory diagnostics play an essential role in pandemic preparedness. In January 2020, the first US case of COVID-19 was confirmed in Washington State. At the same time, the Washington State Public Health Laboratory (WA PHL) was in the process of building upon and initiating innovative preparedness activities to strengthen laboratory testing capabilities, operations, and logistics. The response efforts of WA PHL, in conjunction with the Centers for Disease Control and Prevention, to the COVID-19 outbreak in Washington are described herein—from the initial detection of severe acute respiratory syndrome coronavirus 2 through the subsequent 2 months. Factors that contributed to an effective laboratory response are described, including preparing early to establish testing capacity, instituting dynamic workforce solutions, advancing information management systems, refining laboratory operations, and leveraging laboratory partnerships. We also report on the challenges faced, successful steps taken, and lessons learned by WA PHL to respond to COVID-19. The actions taken by WA PHL to mount an effective public health response may be useful for US laboratories as they continue to respond to the COVID-19 pandemic and may help inform current and future laboratory pandemic preparedness activities. (Am J Public Health. Published online ahead of print March 18, 2021: e1–e9. https://doi.org/10.2105/AJPH.2021.306212 )

Candida auris Direct Detection from Surveillance Swabs, Blood, and Urine Using a Laboratory-Developed PCR Method

Candida auris is an emerging fungal pathogen with cases reported in countries around the world and in 19 states within the United States as of August 2020. The CDC has recommended that hospitals perform active surveillance upon admission for patients with the appropriate risk factors. Currently, active surveillance requires that local hospitals send surveillance swabs to a public health laboratory for analysis. In this work, a real-time PCR assay was developed for the specific detection of C. auris from surveillance swabs, blood, and urine to enable rapid detection of this pathogen. The assay uses commercially available primers and reporter probes and it was verified on the LightCycler 480 PCR platform. Contrived specimens and prospectively collected composite groin/axilla surveillance swabs were used to validate the assay. The performance of the PCR assay on surveillance swabs was also compared to a second PCR assay targeting C. auris that was performed at the Minnesota Department of Health–Public Health Laboratory (MDH-PHL). Our PCR assay is able to detect and differentiate C. auris from closely related Candida species such as C. duobushaemulonii, C. haemulonii, and C. pseudohaemulonii on the basis of melting curve temperature differences.

Roles and challenges of coordinated public health laboratory response against COVID-19 pandemic in Africa

As the incidence of Coronavirus Disease 19 (COVID-19) continues to rise, many countries have been seeking for medical assistance such as donation or procurement of laboratory test kits and strips. These consumables are largely intended for use in the laboratory investigations of COVID-19 cases, suspected contacts, asymptomatic persons and in discharging cured persons. Thus, this article was instigated to update and remind healthcare providers and policymakers (especially those in developing countries) on the principles of sample collections, storage, transportation, laboratory protocols and networks needed for appropriate public health response against COVID-19 pandemic in Africa and other developing countries. In addition, this article presents challenges that hinder adequate COVID-19 laboratory response and discuss some possible solutions that could ameliorate these constrains.