Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

Clinical predictors of donor antibody titre and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial

BACKGROUND

Convalescent plasma therapy for COVID-19 relies on transfer of anti-viral antibody from donors to recipients via plasma transfusion. The relationship between clinical characteristics and antibody response to COVID-19 is not well defined. We investigated predictors of convalescent antibody production and quantified recipient antibody response in a convalescent plasma therapy clinical trial.

METHODS

Multivariable analysis of clinical and serological parameters in 103 confirmed COVID-19 convalescent plasma donors 28 days or more following symptom resolution was performed. Mixed-effects regression models with piecewise linear trends were used to characterize serial antibody responses in 10 convalescent plasma recipients with severe COVID-19.

RESULTS

Donor antibody titres ranged from 0 to 1 : 3892 (anti-receptor binding domain (RBD)) and 0 to 1 : 3289 (anti-spike). Higher anti-RBD and anti-spike titres were associated with increased age, hospitalization for COVID-19, fever and absence of myalgia (all P < 0.05). Fatigue was significantly associated with anti-RBD (P = 0.03). In pairwise comparison amongst ABO blood types, AB donors had higher anti-RBD and anti-spike than O donors (P < 0.05). No toxicity was associated with plasma transfusion. Non-ECMO recipient anti-RBD antibody titre increased on average 31% per day during the first three days post-transfusion (P = 0.01) and anti-spike antibody titre by 40.3% (P = 0.02).

CONCLUSION

Advanced age, fever, absence of myalgia, fatigue, blood type and hospitalization were associated with higher convalescent antibody titre to COVID-19. Despite variability in donor titre, 80% of convalescent plasma recipients showed significant increase in antibody levels post-transfusion. A more complete understanding of the dose-response effect of plasma transfusion amongst COVID-19-infected patients is needed.

Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

Comparison of 3 Nucleic Acid Amplification Tests and a Rapid Antigen Test with Culture for the Detection of Group A Streptococci from Throat Swabs

Background

Recently, the US Food and Drug Administration cleared 3 nucleic acid amplification test (NAAT) assays for detection of Streptococcus pyogenes [group A Streptococcus (GAS)] in pharyngeal specimens. However, there are limited studies evaluating the performance of these NAAT assays.

Methods

We compared the results of 3 NAATs (cobas Liat, Luminex Aries, and Cepheid Xpert Xpress) and a rapid antigen assay (Quidel QuickVue in-line strep A) with the accepted gold standard method, bacterial culture.

Results

Sixty-eight throat swab specimens collected between August and October 2017 were tested. Compared to bacterial culture, the sensitivities, specificities, positive predictive value, and negative predictive value for detecting GAS were as follows: cobas Liat: 100%, 97.4%, 96.7%, and 100%; Cepheid Xpert: 100%, 97.4%, 96.7%, and 100%; Luminex Aries: 95.2%, 100%, 100%, and 95.5%. The Quidel QuickVue in-line strep A assay showed poor sensitivity, detecting only 5.2% of culture-positive specimens.

Conclusion

The 3 NAATs have high sensitivity when compared with bacterial culture for detection of GAS. With rapid turnaround time and ease of use, these tests can be considered as reliable point-of-care tests for the diagnosis of GAS, replacing the need for back-up culture.

1996. Enteric Multiplex PCR Testing: Antimicrobial Stewardship Friend or Foe

Background

There are advantages and challenges associated with enteric multiplex PCR testing. Fast turnaround time can lead to prompt pathogen identification and antibiotic initiation, decreased length of stay and decreased time in isolation. Challenges include identification of multiple organisms, carrier state detection, and detection of organisms with uncertain pathogenic potential, which can lead to unnecessary antibiotic use.

Methods

Two institutions transitioned from stool culture to stool PCR testing for identification of diarrheal pathogens. On February 1, 2016, Center 1 employed the BioFire® FilmArray® GI Panel, which detects 22 organisms and includes targets of unclear clinical significance. Center 2 implemented the BD MAX™ Enteric Bacterial Panel on 3/6/2019, which reports 4 bacterial known pathogens. Fluoroquinolone (FQ) and third-generation cephalosporin (TGC) prescribing in response to positive PCR testing was assessed over a 1 month period. Antibiotics were counted when prescribed within 72 hours of the collection date.

Results

At Center 1, 332 GI PCR panels were ordered, 94 (28.3%) were positive and 15 (16%) were treated; 4 received an FQ (26%), and 11 (73%) received a TGC. Center 1 organisms included 44 Clostridioides difficile, 27 Norovirus, 8 Enteropathogenic E. coli, 7 Sapovirus, 4 Campylobacter species, 2 Giardia lamblia, 2 Rotavirus, 1 Shigella/Enteroinvasive E. coli and 1 Salmonella species. Of 642 PCR tests ordered at Center 2, 16 (2.5%) were positive and 11 (69%) were treated; 10 (91%) received a FQ, and 1 (9%) received a TGC. Center 2 organisms included 8 non-typhoidal Salmonella species, 5 Aeromonas species, 2 Shigella sonnei and 1 Salmonella typhi.

Conclusion

Implementation of an enteric multiplex PCR test with targets of uncertain clinical significance is more likely to yield an abnormal result than a PCR test with only known pathogens. However, careful interpretation of results can avoid unnecessary antimicrobial use. Antimicrobial stewardship teams should work in tandem with microbiology laboratories to implement enteric multiplex PCR tests and monitor the impact on antibiotic use. Larger studies are needed to definitively assess the impact of the GI panel on antimicrobial prescribing within the context of patient comorbidities and institutional practices.

Disclosures

All authors: No reported disclosures.

Variability in assessing for BK viremia: whole blood is not reliable and plasma is not above reproach - a retrospective analysis

Polyomavirus nephropathy (PVN) is a major complication of kidney transplantation. Most reports describe polyomavirus viremia either precedes or is detectable at the time of diagnosis of PVN. This association is the basis of current screening recommendations. We retrospectively reviewed the PCR results of blood and urine samples from 29 kidney transplant recipients with biopsy-proven PVN. Biopsies were performed for a rise in serum creatinine or persistent high-level BK viruria. All biopsies showed polyoma virus large T-antigen expression in tubular epithelium using immunohistochemistry. All had viruria preceding or at the time of biopsy (range, 5.2 × 10⁴ to >25 × 10⁶ BKV DNA copies/ml). Twenty (69%) had viremia ranging from 2.5 × 10³ to 4.3 × 10⁶ copies/ml at the time of the biopsy. Via blood BK PCR assay, nine (31%) had no BK viremia detected either preceding or at the time of the biopsy. In five recipients where sufficient specimen permitted, additional plasma BK assessment revealed positive detection of viremia. A comparative analysis of assays from two centres was performed with spiked samples. BK DNA may not be detected in the blood of some kidney transplant recipients with histologically confirmed PVN. This may reflect limitation of whole blood as opposed to plasma-based BK DNA assessment.

Optimizing empirical antimicrobial therapy for infection due to gram-negative pathogens in the intensive care unit: utility of a combination antibiogram

OBJECTIVE

To determine whether the use of dual antimicrobial therapy based on the results of a combination antibiotic susceptibility report (antibiogram) increases the likelihood of selecting adequate empirical coverage in critically ill patients with infection due to potentially resistant gram-negative pathogens.

DESIGN

Retrospective data analysis.

SETTING

Urban academic medical center.

METHODS

An analysis of culture results and susceptibility data from intensive care unit patients determined by the clinical microbiology laboratory was performed. The proportion of 5 common gram-negative pathogens susceptible to monotherapy with 1 of 3 antipseudomonal antibiotics (piperacillin-tazobactam, ceftazidime, or imipenem) was compared with the proportion susceptible to each of these 3 "backbone" agents plus 1 of 4 additional antimicrobial agents used in combination.

RESULTS

More than 5,000 clinical isolates were examined. When all isolates recovered during the entire study period were included, the addition of any of the second antibiotics studied to each of the 3 backbone agents significantly increased the likelihood of covering the causative pathogen (P < .01 for each). The benefit of combination therapy was variable when results for each of the 5 organisms were examined individually. When temporal trends in susceptibility were examined, the decrease in the proportion of organisms susceptible to monotherapy was statistically significant for both imipenem and ceftazidime (P < .01).

CONCLUSIONS

Reporting antibiotic susceptibility data in the form of a combination antibiogram may be useful to clinicians who are considering empirical antimicrobial therapy in the intensive care unit.

Multicenter clinical evaluation of a continuous monitoring blood culture system using fluorescent-sensor technology (BACTEC 9240)

The BACTEC 9240 (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) is a new continuous-monitoring blood culture system that uses internal, fluorescent-CO2 sensors. In a multicenter clinical trial, organism yield and times to detection with the prototype BACTEC 9240 system were compared with those of the BACTEC NR 660 system. Equal volumes of blood were inoculated into the bottles included in the study blood culture sets (aerobic and anaerobic 9240 and NR6A and NR7A bottles). A total of 9,391 aerobic and 8,951 anaerobic bottle pairs were inoculated with 9,801 blood specimens. A total of 587 clinically significant positive blood cultures and 415 cases of sepsis were studied. The standard 9240 aerobic bottle detected significantly more Staphylococcus aureus (P < 0.05), coagulase-negative staphylococci (P < 0.01), and total microorganisms (P < 0.001) than the NR6A bottle. The standard 9240 anaerobic bottle detected significantly more coagulase-negative staphylococci (P < 0.001), members of the family Enterobacteriaceae (P < 0.01), and total microorganisms (P < 0.001) than the NR7A bottle. A total of 420 positive cultures were detected in both systems; for 284, the time to detection was equivalent with both systems (within 12 h); for 123, the 9240 system was faster; and for 13, the NR 660 system was faster (P < 0.001). The average times to detection for the 9240 and the NR 660 systems were 20.2 and 27.5 h, respectively. Ninety-nine cultures were positive only in the 9240 system, and 68 cultures were positive only in the NR 660 system (P < 0.02). The 9240 system also detected significantly more episodes of bacteremia (P < 0.001). The false-positive rates for the 9240 and NR 660 systems were 2.2 and 2.3%, respectively. The false-negative rates for the two systems after 5 days of incubation did not differ significantly. The contamination rates for the 9240 and NR 660 systems were 1.9 and 1.5%, respectively (P < 0.05). In conclusion, the prototype 9240 system detected more clinically significant positive blood cultures and did so sooner than the NR 660 system, with the additional advantages of full automation, continuous monitoring, and noninvasive sampling.