[IMPACT ON TUBERCULOSIS DIAGNOSTIC DURING COVID-19 PANDEMIC IN A TERTIARY CARE HOSPITAL]. / IMPACTO DE LA PANDEMIA COVID-19 EN EL DIAGNOSTICO DE TUBERCULOSIS EN UN HOSPITAL DE TERCER NIVEL.

INTRODUCTION: The aim of this study is to review how did the first three COVID-19 waves affected the diagnostic of tuberculosis and to describe the extra-pulmonary Mycobacterium tuberculosis complex (TB) diagnosis. MATERIALS AND METHODS: A retrospective observational study was done during the first three waves of pandemic to ascertain the impact on TB samples and to recover the extra-pulmonary TB cases we included the first two years of COVID-19. All relevant data was recovered from hospital and Clinical Microbiology records. RESULTS: Prepandemic period showed an average of 44 samples per week for TB study; during the first three waves this number dropped to 23.1 per week. A reduction of 67.7% of pulmonary TB diagnosis was observed and an increase of 33.3% diagnosis of extra-pulmonary TB was noted when comparing pre-pandemic and pandemic period. DISCUSSION: The number of declared cases and samples for TB diagnosis dropped during the first three COVID-19 waves due to the overstretched Public Health System which could lead to a delay in diagnosis, treatment and to the spread of TB disease in the general population. Surveillance programs should be reinforced to avoid this.

Impact on tuberculosis diagnostic during COVID-19 pandemic in a tertiary care hospital.

INTRODUCTION: The aim of this study is to review how did the first three COVID-19 waves affected the diagnostic of tuberculosis and to describe the extra-pulmonary Mycobacterium tuberculosis complex (TB) diagnosis. MATERIALS AND METHODS: A retrospective observational study was done during the first three waves of pandemic to ascertain the impact on TB samples and to recover the extra-pulmonary TB cases we included the first two years of COVID-19. All relevant data was recovered from hospital and Clinical Microbiology records. RESULTS: Prepandemic period showed an average of 44 samples per week for TB study; during the first three waves this number dropped to 23.1 per week. A reduction of 67.7% of pulmonary TB diagnosis was observed and an increase of 33.3% diagnosis of extra-pulmonary TB was noted when comparing pre-pandemic and pandemic period. DISCUSSION: The number of declared cases and samples for TB diagnosis dropped during the first three COVID-19 waves due to the overstretched Public Health System which could lead to a delay in diagnosis, treatment and to the spread of TB disease in the general population. Surveillance programs should be reinforced to avoid this.

Isolation of Aspergillus spp. in respiratory samples of patients with COVID-19 in a Spanish Tertiary Care Hospital.

BACKGROUND: Invasive pulmonary aspergillosis (IPA) is a complication of respiratory bacterial and viral infections such as coronavirus disease 2019 (COVID-19). PATIENTS/METHODS: In University Hospital La Paz (Madrid, Spain), we reviewed the clinical and demographic characteristics of 10 patients with positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PCR and Aspergillus spp. isolate in respiratory samples. We also recovered results of galactomannan tests in serum and/or bronchoalveolar lavage (BAL) samples. RESULTS: Eight male and two female from 51 to 76 years were recovered. They had reported risk factors to develop IPA (haematological malignancies, immunosuppression, diabetes, obesity, intensive care unit stay, among others). Azole susceptible Aspergillus fumigatus was isolated in nine patients and Aspergillus nidulans was isolated in one patient. Only one case was classified as probable aspergillosis, seven cases as putative aspergillosis, and two cases were not classifiable. Eight patients received antifungal treatment. Seven patients died (70%), two are still inpatient due to nosocomial infections and one was discharged referred to another institution. CONCLUSIONS: This clinical entity has high mortality, and therefore, it should be performed surveillance with early galactomannan tests and cultures in respiratory samples in order to improve the outcome of the patients with this condition.

Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution.

The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.

Bacterial co-infections in COVID-19 pneumonia in a tertiary care hospital: Surfing the first wave.

The aim of this study is to review bacterial isolates from respiratory samples of patients with severe COVID-19 disease during the first 2 months of the first wave in our hospital. A single-center retrospective observational study in critically ill adult patients was performed. A total of 1251 respiratory samples from 1195 patients were processed. Samples from 66 patients (5.52%) were determined to be microbiologically significant by a semi-quantitative culture. All patients received broad spectrum antibiotherapy as an empirical treatment. The isolated bacteria were mainly Enterobacterales followed by Staphylococcus aureus and Pseudomonas aeruginosa. Bacterial co-infections in ICU stay could seem not dependent on the virus that has produced the viral pneumonia similarly as with other respiratory viruses such as Influenza virus.

Evaluation of three commercial assays for SARS-CoV-2 molecular detection in upper respiratory tract samples.

The increasing COVID-19 widespread has created the necessity to assess the diagnostic accuracy of newly introduced (RT-PCR based) assays for SARS-CoV-2 RNA detection in respiratory tract samples. We compared the results of the Allplex™ 2019-nCoV assay with those of the Simplexa™ COVID-19 Direct assay and the Quanty COVID-19 assay, respectively, all performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 suspicion. Fifty-four samples were positive, and 71 were negative with the Allplex™ assay, whereas 47 of 54 samples were also positive with the Simplexa™ assay. The Quanty assay detected 55 positive samples, including the 54 positive samples with the Allplex™ assay and 1 sample that was Allplex™ negative but Simplexa™ positive. Using a consensus result criterion as the reference standard allowed to resolve the eight samples with discordant results (one Allplex™ negative and seven Simplexa™ negative) as truly false negative. Interestingly, a Spearman's negative association was found between the viral RNA loads quantified by the Quanty assay and the CT values of RT PCRs performed with either the Allplex™ assay or the Simplexa™ assay. However, the strength of this association was higher for the Allplex™ assay (N gene, ρ = - 0.92; RdRP gene, ρ = - 0.91) than for the Simplexa™ assay (ORF1ab gene, ρ = - 0.65; S gene, ρ = - 0.80). The Allplex™ 2019-nCoV, the Simplexa™ COVID-19 Direct, and the Quanty COVID-19 assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies.