Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.

Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.

Incidence of COVID-19 and Identification of Possible Risk Factors Associated with COVID-19 in Acute Renal Transplant Recipients in Pakistan.

BACKGROUND Renal transplant recipients are susceptible to increased mortality with COVID-19 infection. There is insufficient data regarding risk factors for COVID-19 disease acquisition. We aimed to identify them here. MATERIAL AND METHODS We enrolled Pakistani renal transplant recipients from February 10, 2020, to March 18, 2021, and actively tracked their baseline health status, transplant characteristics, comorbidities, immunosuppressive therapies, and post-transplant follow-ups until September 2021. Furthermore, we formulated 2 questionnaires for their compliance assessment with COVID-19-preventive measures. We also identified COVID-19 disease acquisition, symptomatology, and management. RESULTS Among the 50 enrolled patients, 14 (28%) patients developed COVID-19, which is higher than the incidence observed in general Pakistani population (0.55%). Their mean age was 35.38 years ±11.69 SD years, and 82% of patients were males. The following factors were independently associated with COVID-19 disease: female gender (P value: 0.042), diabetes mellitus (P value: 0.002), anti-thymocyte globulin (ATG) induction (P value: 0.006), in-person follow-ups (P value: 0.000), prolonged immediate and late post-transplant hospital stays (P value: 0.019 and 0.000, respectively), raised post-transplant serum creatinine (P value: 0.019), and COVID-19 protective measures non-compliance (P value: 0.000). Out of 14 infected recipients, 92.85% required symptomatic management and overall mortality was 0%. CONCLUSIONS Female gender, diabetes mellitus, ATG induction, in-person follow-ups, prolonged hospital stays, raised post-transplant serum creatinine, and COVID-19-protective measures non-compliance were associated with the higher acquisition of SARS-CoV-2 infection. By taking concrete measures against these risk factors, we can continue renal transplants, as overall mortality was lower than in the general Pakistani population (2%).

SARS-CoV-2 surveillance and outbreak response on an urban American college campus.

OBJECTIVE: The George Washington University (GW) in Washington, D.C., USA established the Public Health Laboratory and Campus COVID-19 Support Team (CCST) to develop and implement its SARS-CoV-2 surveillance testing and outbreak response for the 2020-2021 academic year. PARTICIPANTS AND METHODS: Approximately 4,000 GW members had access to campus for living accommodations, limited in-person instruction, athletics, research, and university operations. The outbreak response included daily risk assessment surveys, weekly surveillance testing, symptomatic and voluntary testing, case investigation, and contact tracing. RESULTS: Between August 17 - November 24, 2020, 42,350 SARS-CoV-2 PCR tests were performed, and 194 (0.46%) of tests were positive. Surveillance testing identified 59 (30.4%); voluntary testing 97 (50%); and symptomatic testing 30 (15.5%) of the cases, respectively. CONCLUSIONS: Robust testing of asymptomatic people and rapid isolation and quarantine of members who are exposed or infected effectively limited the spread of SARS-CoV-2 during the Fall 2020 semester.