Combining Gram stain and 16S qPCR improved diagnostic accuracy for suspected pneumonia and could become a new metric in the rapid diagnosis of lower respiratory tract infections.

Introduction. The frequency of multidrug-resistant organisms (MDROs) in hospitals and the risk of delaying effective treatment result in the culture of respiratory secretions for nearly all patients with suspected pneumonia. Culture delays contribute to over prescribing and use of broader spectrum antibiotics.Gap statement. The need for improved rapid diagnostics for early assessment of suspected hospital pneumonia.Aim. To validate a new metric, enhanced Gram stain (EGS), to provide a rapid diagnostic test of high diagnostic accuracy that could be assessed in clinical trials of the use of antibiotics in suspected pneumonia.Methodology. Ninety-two residual lower respiratory samples previously tested by culture and Gram stain were re-tested by 16S ribosomal DNA real-time polymerase chain reaction (16S qPCR) and reported as a combined metric with Gram stain termed EGS. The EGS was assessed for diagnostic accuracy, standard performance measurements and correlation against culture. For samples with discordance between culture and EGS, 16S ribosomal DNA whole operon sequencing (16S rDNA WOS) was used for test resolution. An amended EGS (A-EGS was reassessed against culture.Results. Gram stain, 16S qPCR, EGS and A-EGS had respective diagnostic accuracies of 77.01 %, 82.76 %, 84.04 % and 94.19 %. The same platforms had respective correlation with culture of r = 0.67, r = 0.71, r = 0.81 and r = 0.89. EGS had the highest negative predictive value (NPV) of 93.18 % (81.99 %-97.62 %). Adding an 16S qPCR result is achievable in most routine laboratories and, combined with Gram stain, could improve early decision-making in patients with suspected hospital pneumonia.Conclusion. EGS could improve early decision-making in patients with suspected hospital pneumonia and could be assessed in clinical trials. The 16S rDNA WOS results in the A-EGS also supported the use of pathogen genomic sequencing in early decision making of suspected pneumonia.

One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar.

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

Diffuse Large B-Cell Breast Lymphoma: A Case Series.

Primary breast lymphoma (PBL) is a rare disease, and few clinicohistopathologic features of the disease have been discussed in previous studies. It represents 2.2% of extranodal lymphomas and constitutes 0.04% to 0.5% of malignant breast neoplasms, despite the clinical and radiographic similarities between breast lymphoma and carcinoma, the prognosis, as reported in the literature, varies. No consensus exists on the best way to treat PBL. However, radiotherapy and chemotherapy were used alone or in combination to treat various cases of PBL. We retrospectively studied 3 cases of PBL of the breast seen in patients attending a tertiary cancer center in Qatar, between 2012 and 2015, in an attempt to determine the common clinical features, therapy, and prognosis of PBL.