“ Generally , healthcare personnel are unaware and lack understanding of the complex nature of microbial outbreaks . This is primarily due to lack of training in microbiology , epidemiology and the factors associated with outbreaks / pandemics .” — Paul J . Pearce , PhD
The average turnaround times during the study period were 6.7 hours for PCR ( ranging from 1.3 hours to 8.1 hours ) and 1.4 hours for antibody testing ( range , 57 minutes to 1.9 hours ). Overall , the CML costs increased 114.8 percent , with personnel hiring and extended shifts and laboratory materials accounting for most of the additional expenditures . The most expensive items were PCR reagents , reagents for SARS-CoV-2 IgG detection , SARS-CoV-2 extraction and purification , and nasopharyngeal sampling swabs and transport media .
Not only were CMLs impacted significantly , but COVID-19 reverberated through all hospital departments . “ One must remember that SARS-CoV-2 was a novel virus ,” Rohde emphasizes . “ Our healthcare system had not faced this type of ongoing , novel virus in recent history and that means the impact for clinical lab services was felt from multiple angles . The healthcare system was in war on multiple fronts . For example , an immediate lack of adequate capacity to handle the surging patient volume , compounded by the lack of PPE , which led to an ongoing and devastating reduction of healthcare professionals in both patient facing areas ( nursing , physicians , respiratory care ) as well as those behind the scenes ( laboratory , front-office , support areas ).”
“ Many clinical laboratories added methods , means and equipment to test for COVID ,” Pearce says . “ Prior to the pandemic there was a minimum amount
CML Best Practices
Benbachir ( 2018 ) outlines some best practices for the CML , including the importance of a representative of the microbiology laboratory department serving as an active member of the infection control committee ( ICC ) and a consultant to the infection prevention and control ( IP &) program . As Benbachir ( 2018 ) explains , “ In many hospitals , the ICC is chaired by a microbiologist , and a key function is to improve collaboration between clinical , laboratory and ICC personnel . All healthcare institutions should have a committee / team responsible for antimicrobial stewardship . A members list would be a clinician , a clinical pharmacologist , a clinical microbiologist and an infection preventionist , not to mention a nurse , and all should serve as standing members of the ICC . If necessary , the microbiologist gives training in basic microbiology to ICC and antimicrobial stewardship members and provides expertise ( e . g ., quality of pre-analytical phase , interpretation of culture and antimicrobial susceptibility results , ready to use microbiological strategies to deal with each specific infection control situation , evaluation of resources needed ).”
Additionally , Benbachir ( 2018 ) points out that laboratory-based surveillance is an essential part of the hospital wide surveillance : “ Surveillance of healthcare-associated infections can be active or passive and comprehensive or focused ( patient units , specific sites of infections , selected pathogens ). Active focused surveillance is the preferred method because it is more feasible and more efficient . Routine surveillance of nosocomial infections is based both on daily review and on periodic reports of microbiology records . These reports would be analyzed preferably during daily meetings between the IP & C team and the laboratory staff .”
Surveillance data should be analyzed and reported promptly on a regular basis , and the ICC and the antimicrobial stewardship working group and the microbiology laboratory should articulate a reporting policy .
Benbachir ( 2018 ) adds that “ The microbiology laboratory is also a sentinel system . Prompt notification to clinical wards and to ICC initiate epidemiological investigation which may lead to preventive measures to halt the spread of causative microorganisms . The microbiology laboratory is responsible for the early detection of clusters of microorganisms with the same phenotypic characteristics . Laboratory and epidemiological studies of suspected outbreaks should be conducted in parallel . During outbreaks the microbiology laboratory collaborates with the ICC to elaborate case definitions , choose the specimens to collect , the isolates to fingerprint , and the relevant isolates to store . All this work should be done timely .”
Finally , to assess and improve antimicrobial usage , the antimicrobial stewardship working group should elaborate and implement an antimicrobial stewardship plan that can be adapted from the SHEA / IDSA and Centers for Diseases Control and Prevention ( CDC ) models . As Benbachir ( 2018 ) explains , “ Rapid diagnosis coupled to antimicrobial stewardship have positive impact on patient care and economical outcome . The overall objective of the microbiology laboratory contribution to the AMS plan is to guide the antimicrobial choice to support successful patient outcome and minimize adverse impacts in terms of toxicity , antimicrobial selective pressure , and costs … Data on antimicrobial resistance should be periodically available to the medical staff , at least annually . These data are helpful for generating hospital treatment guidelines , which are useful in situations where empirical therapy is often given before the microbiology results are available . The laboratory contribution is multi-modal from advice for appropriate sampling advice , to rapid diagnostic testing , selective reporting , early notification , antibiotic data compilation and feedback .”