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The COVID-19 pandemic is having a significant impact on the diagnosis of infectious diseases and clinical laboratory operations far beyond shortages of reagents and supplies. The increase in workload forced laboratories to mobilize personnel and resources to support SARS-CoV-2 testing, affecting diagnostic testing of other infectious diseases of public health importance, such as sexually transmitted infections (STIs) and healthcare-associated infections (HAIs). Clinical and public health laboratories have come a long way since the beginning of the pandemic in their attempts to develop strategies to deal with daily challenges brought on by COVID-19. With so much uncertainty ahead, it is important to look back at these challenges and identify lessons learned to develop more efficient approaches to maintaining laboratory operation and ensuring the quality of patient care as the fight against COVID-19 continues.

COVID-19’s Impact on Respiratory Disease Diagnosis and Incidence

Dr. Marie-Claire Rowlinson, who chaired the World Microbe Forum session “,” presented a case study of a patient with respiratory symptoms who returned to the U.S. after a trip to a province near Wuhan, China in Feb. 2020. Due to concerns about COVID-19, much of the initial diagnostic effort was focused on ruling out SARS-CoV-2 infection and necessary imaging studies were postponed. The possibility of the patient having tuberculosis (TB) was not considered until imaging studies demonstrated the presence of pleural effusion, a manifestation not commonly seen in COVID-19 patients.

TB test results from the Florida Public Health Laboratory later confirmed the diagnosis of a multi-drug resistant tuberculosis (MDR-TB) infection. The clinical presentation of an active pulmonary TB infection can be non-specific and often leads to a misdiagnosis. In this case, the challenge of TB diagnosis was compounded by the salience of COVID-19 and limited access to COVID-19 testing in the U.S. at that time, resulting in delayed diagnosis of MDR-TB.

Rowlinson discussed another case where a patient presented with respiratory symptoms later in the pandemic (June 2020).  Bacterial culture (and specifically, Legionella culture) played an important role in the diagnosis of Legionellosis.  However, multiple specimens were submitted for COVID-19 testing during the hospital course, many of which may not have been clinically necessary.

Rowlinson also discussed the unusually low prevalence of influenza during 2020-2021 season, with the peak positivity rate of 0.4% compared to 30.3% in the year prior. The reduction in number of cases could be the and a change in people’s behavior during the pandemic. Nobody knows for certain what this coming respiratory season holds for influenza, and it may be wise to be ready for any possibility. Many public health laboratories have prepared by implementing diagnostic tests that can detect influenza and COVID-19 at the same time.

Sexually Transmitted Infection (STI) Patient Care Suffered

Dr. Megan Crumpler described the effect of COVID-19 on the diagnosis of sexually transmitted infections (STIs). At the beginning of the pandemic, the numbers of individuals seeking STI testing at the Orange County STD clinic dropped dramatically. These numbers have increased slowly, albeit not to pre-pandemic levels.

shows that, in the spring of 2020, 83% of STI programs had to defer STI services or field visits due to decreased clinic capacity. Several factors affected laboratory operation, including shortages of supplies and lab equipment, inventory challenges and personnel issues. While Orange County Public Health Laboratory was able to maintain STI testing throughout the pandemic, laboratories that were not able to perform STI testing inevitably affected downstream patient care. Lack of STI testing probably resulted in delayed epidemiological intervention and missed opportunities to treat the patients and their partners in some cases.

Crumpler presented a case of disseminated gonorrhea infection, where the patient was reluctant to seek medical care during the pandemic, despite ongoing symptoms, due to fear of COVID-19. A case of an HIV patient with ocular syphilis was also presented, where the development of this unusual clinical presentation may have been partly due to delay in medical care. Self-collection and self-testing are potential solutions to these STI testing issues, but they are not without their own challenges. The tests must be validated per U.S. Food and Drug Administration (FDA) regulations, are potentially high cost, and linkage to care and means of reporting to public health departments must be addressed.

Pandemic Influenced Spread and Diagnosis of Healthcare-Associated Infections and Antimicrobial Resistance

Dr. Carol Rauch discussed the impact of COVID-19 on healthcare-associated infection (HAI) antimicrobial resistance (AR) spread and testing. Many HAI outbreaks, some of which involved multi-drug resistant organisms (MDROs), have been reported to the U.S. Centers for Disease Control and Prevention during the COVID-19 pandemic. However, the ability of laboratories to perform testing for HAI organisms and antimicrobial susceptibility testing (AST) have been negatively affected by factors identified by a survey of infectious diseases physicians and laboratory directors from the Infectious Diseases Society of America. These included shortages of reagents and supplies, and insufficient testing devices. Weekly surveys on supply shortages in laboratories conducted by ASM in the fall of 2020 indicated shortages across many types of testing, including routine bacterial pathogen detection.

The Antimicrobial Resistant Laboratory Network (ARLN) is a national initiative that enables state public health labs and state health departments to collaborate with local healthcare facilities and clinical labs to detect, respond to and contain emerging MDRO threats. ARLN sent out surveys to its regional laboratories to assess the effect of COVID-19 on testing. In addition to shortages of supplies, ARLN regional laboratories also reported receiving fewer isolates from clinical laboratories and STI clinics, along with personnel shortages due to mobilization of staff to support COVID-19 testing.

Interestingly, despite the shortages of collection kits and test supplies, Candida auris testing increased, with reports of outbreaks during the pandemic. For example, in a special care unit dedicated to COVID-19, where 35 out of 67 admitted patients tested positive for the organism during point prevalence surveys. Shortages of personnel, supplies and personal protective equipment (PPE), and suboptimal infection prevention practices, such as extended used of PPE, failure to disinfect equipment like mobile computers and inadequate hand hygiene, may have contributed to this outbreak. Rauch recommended that laboratories learn about this emerging HAI fungal organism and how to identify it.

As with C. auris, the pandemic may be aiding the spread of antimicrobial resistance. Co-infection of COVID-19 and other infectious diseases has been a topic of interest throughout the pandemic. Due to concerns about co-infection and secondary bacterial infections, hospitalized COVID-19 patients often receive broad-spectrum antibiotics, potentially promoting the spread of antimicrobial resistance. However, the highly unusual characteristics of the most recent respiratory season led to decreased numbers of AST tests performed by ARLN laboratories on respiratory pathogens, including Streptococcus pneumoniae. Overall, the full impact of the pandemic on HAI and antimicrobial resistance is not fully understood, but awareness of the issues and having preventive measures in place with support from laboratory testing are critical.

With the development of novel variants and the constantly shifting dynamics of disease transmission, it seems that the COVID-19 pandemic is here for the foreseeable future. It is important to remember that, in addition to the ongoing community transmission of SARS-CoV-2, other infectious diseases of public health important are still very much present in the population. Speakers in this session presented real-life cases, survey results and personal insights into the effect of the pandemic on testing in clinical and public health laboratories. In these unprecedented times, there has never been a greater need for laboratories to develop preparedness and surge operation plans that are tailored to their own needs and challenges. Clinical and public health laboratories should work closely with federal and local public health agencies to maintain situational awareness of any emerging infectious disease and request assistance when needed. Additionally, to ensure accurate and timely diagnosis of infectious diseases, laboratories and healthcare providers must work collaboratively with a common goal of providing the best care for their patients.