Respiratory Samples Research Articles

Performance of rapid antigen tests to detect SARS-CoV-2 variant diversity and correlation with viral culture positivity: implication for diagnostic development and future public health strategies.

Despite the availability of vaccines, COVID-19 continues to be a major health concern, and antigen-based rapid diagnostic tests (Ag-RDTs) are commonly used as point-of-care or at-home diagnostic tests. In this study, we evaluated the performance of two commercially available Ag-RDTs and a research Ag-RDT to detect multiple SARS-CoV-2 variants using upper respiratory tract swab samples from clinical COVID-19 cases. Furthermore, we determined whether Ag-RDT results correlated with culture positivity, a potential proxy of viral transmissibility. Our results have important implications to inform future testing and response strategies during periods of high COVID-19 transmission with new variants.

Contribution of Other Respiratory Viruses During Influenza Epidemic Activity in Catalonia, Spain, 2008–2020

Background: During seasonal influenza activity, circulation of other respiratory viruses (ORVs) may contribute to the increased disease burden that is attributed to influenza without laboratory confirmation. The objective of this study was to characterize and evaluate the magnitude of this contribution over 12 seasons of influenza using the Acute Respiratory Infection Sentinel Surveillance system in Catalonia (PIDIRAC). Methods: A retrospective descriptive study of isolations from respiratory samples obtained by the sentinel surveillance network of physicians was carried out from 2008 to 2020 in Catalonia, Spain. Information was collected on demographic variables (age, sex), influenza vaccination status, epidemic activity weeks each season, and influenza laboratory confirmation. Results: A total of 12,690 samples were collected, with 46% (5831) collected during peak influenza seasonal epidemic activity. In total, 49.6% of the sampled participants were male and 51.1% were aged <15 years. Of these, 73.7% (4298) of samples were positive for at least one respiratory virus; 79.7% (3425 samples) were positive for the influenza virus (IV), with 3067 samples positive for one IV type, 8 samples showing coinfection with two types of IV, and 350 showing coinfection of IV with more than one virus. The distribution of influenza viruses was 64.2% IVA, 35.2% IVB, and 0.1% IVC. Of the other respiratory viruses identified, there was a high proportion of human rhinovirus (32.3%), followed by human adenovirus (24.3%) and respiratory syncytial virus (18; 7%). Four percent were coinfected with two or more viruses other than influenza. The distribution of coinfections with ORVs and influenza by age groups presents a significant difference in proportions for 0–4, 5–14, 15–64 and >64 (21.5%, 10.8%, 8.2% and 7.6%: p < 0.001). A lower ORVs coinfection ratio was observed in the influenza-vaccinated population (11.9% vs. 17.4% OR: 0.64 IC 95% 0.36–1.14). Conclusions: During the weeks of seasonal influenza epidemic activity, other respiratory viruses contribute substantially, either individually or through the coinfection of two or more viruses, to the morbidity attributed to influenza viruses as influenza-like illness (ILI). The contribution of these viruses is especially significant in the pediatric and elderly population. Identifying the epidemiology of most clinically relevant respiratory viruses will aid the development of models of infection and allow for the development of targeted treatments, particularly for populations most vulnerable to respiratory viruses-induced diseases.

Respiratory Carriage of Methicillin-Resistant Staphylococcus aureus-Encoding Gene in Hajj Pilgrims.

To assess the carriage of methicillin-resistant Staphylococcus aureus-encoding genes (MRSA) among French Hajj pilgrim cohorts. A prospective cohort study was conducted on pilgrims from Marseille during the 2014 to 2018 Hajj. Respiratory samples were collected before and after the pilgrimage. S. aureus and then MRSA-encoding genes were identified using real-time PCR. A total of 606 pilgrims were included with a sex ratio of 1:1.3 with a median age of 61 years (interquartile = 56-66 years, range = 21-88 years). A total of 511/606 (84.3%) pilgrims presented at least one respiratory symptom during their pilgrimage. Cough was the most frequent symptom occurring in 76.2% of pilgrims, followed by sore throat (57.6%), rhinitis (54.6%), and voice failure (36.3%). 87 (14.4%) were positive with S. aureus before travelling. On return, 130/606 (21.4%) participants were positive. The acquisition rate of S. aureus was 13.0% (79/606). The prevalence of MRSA pre- and post-travel and acquisition rate was 4.1% (25/606), 10.6% (62/606), and 8.2% (50/606), respectively. All MRSA were positive with mecA gene. No case was positive with mecC. Our study highlights the importance of surveillance and infection control measures during mass gatherings such as the Hajj to mitigate the spread of infectious pathogens, including antimicrobial-resistant bacteria like MRSA. Further research is warranted to elucidate the specific factors contributing to S. aureus and MRSA transmission during the pilgrimage and to inform targeted interventions aimed at reducing the burden of MRSA infection among pilgrims.

Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019

BackgroundHuman respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium.MethodsIn this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011–2012 until 2018–2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature.ResultsHRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011–2012 season and replaced all other circulating strains from 2014 to 2015 onwards.

Isavuconazole and Amphotericin B Synergic Antifungal Activity: In Vitro Evaluation on Pulmonary Aspergillosis Molds Isolates

Background/Objectives. Pulmonary aspergillosis is a severe respiratory infection caused by Aspergillus spp., whose resistance profiles and invasive attitude complicate therapeutical strategies. Several aspergillosis cases emerged as superinfections during the SARS-CoV-2 pandemic when isavuconazole and amphotericin B became essential antifungal alternatives. The main purpose of the present study was to investigate a possible synergic activity between these molecules against Aspergillus spp. isolated from respiratory samples. Methods. The gradient test method detected isavuconazole and amphotericin B MIC values, prompting an arrangement of their combination into an R.P.M.I. agar medium. According to Liofilchem s.r.l. instructions, the FIC index was used to establish synergy, additivity, indifference, or antagonism. Results. Among 36 Aspergillus spp. isolates, only A. fumigatus strains showed both synergy and additivity episodes. A. niger reported the highest antagonism percentage, while A. terreus revealed several indifference episodes. Conclusions. Isavuconazole and amphotericin B remain fundamental therapeutical alternatives, including a possible synergic effect against A. fumigatus. On the basis of this species-related difference, further studies will be essential to investigate different antifungal drug combinations against filamentous fungi isolates.

Effects of COVID-19 pandemic on epidemiological features of viral respiratory tract infections in children: a single-centre study.

The epidemiology of respiratory infections may vary depending on factors such as climate changes, geographical features, and urbanization. Pandemics also change the epidemiological characteristics of not only the relevant infectious agent itself but also other infectious agents. This study aims to assess the impact of the COVID-19 pandemic on the epidemiology of viral respiratory infections in children. We retrospectively reviewed the medical records of children aged ≤18years with laboratory-confirmed viral respiratory infections other than COVID-19 from January 2018 to March 2023. Data on demographic characteristics, month and year of admission, and microbiological results were collected. During the study period, 1,829 respiratory samples were sent for polymerase chain reaction testing. Rhinovirus was identified in 24% of the patients, mixed infections in 21%, influenza virus in 20%, and respiratory syncytial virus in 12.5%. A 38.6% decrease in viral respiratory infections was observed in 2020, followed by a 188% increase in 2021. The respiratory syncytial virus was significantly more common in the post-pandemic period (13.8%) compared to the pre-pandemic period (8.1%), but no seasonal shift in respiratory syncytial virus infection was observed. There was also a yearly increase in influenza infections in the post-pandemic period compared to the pre-pandemic period. After the COVID-19 pandemic, the frequency of parainfluenza virus infections increased during the summer months, and this finding provides a new contribution to the existing literature.

Experience of microbiological monitoring of the respiratory tract microflora in patients with cystic fibrosis during therapy with the combination drug elexacaftor/tezacaftor/ivacaftor + ivacaftor

Bacterial complications of the respiratory tract are negative prognostic factors leading to a decrease in pulmonary function, duration, and quality of life of patients with cystic fibrosis. To date, a sufficient number of studies have not been accumulated to reliably prove or reject microbiological improvement during targeted therapy. The aim of the study was to collect continuous microbiological data from patients with cystic fibrosis in the Samara region receiving treatment with elexacaftor/tezacaftor/ivacaftor + ivacaftor from November-December 2021. The article presents eight clinical observations. At the time of therapy initiation, seven patients had chronic respiratory tract infection associated with Burkholderia cenocepacia ST 208, combined with chronic Pseudomonas aeruginosa infection in two of them. One patient had a chronic P. aeruginosa infection in association with Aspergillus fumigatus. Conclusion. An expansion of the species composition in the respiratory samples was demonstrated in all cases. The majority of patients showed microbiological improvement. Thus, biochemical and, as a result, microecological changes in the lungs against the normalization of chlorine channel function allow suggesting that key pathogens may be eradicated during the therapy with elexacaftor/tezacaftor/ivacaftor + ivacaftor.

Radio-Biological Confrontation in the Diagnosis of Invasive Aspergillosis: About Two Cases and Review of Literature

Invasive pulmonary aspergillosis due to Aspergillus fumigatus is an often serious mycosis, usually occurring in severely immunocompromised patients. It is accompanied by a high mortality rate due to its often difficult and late diagnosis. Diagnosis is based on early chest computed tomography and mycological examination of respiratory samples. Both patients had presented with acute respiratory distress, developing in a context of fever and deterioration of the general condition despite the initiation of broad-spectrum empirical treatment. In each of them, a chest CT scan was performed, objectifying atypical cavitary images not suggesting pulmonary aspergillosis. Cytobacteriological examination of sputum and search for Mycobacterium tuberculosis were negative. Serology for aspergillus antigens and a sample of bronchoalveolar lavage fluid for a mycological study were requested. Direct examination of bronchoalveolar lavage fluid was negative, but culture allowed the identification of Aspergillus fumigatus. Galactomannan testing was positive. Given these results, treatment with injectable voriconazole was initiated in our two cases. The evolution was marked by a clinical improvement of one patient and the death of the other patient. Invasive pulmonary aspergillosis is a major concern due to the frequency of its complications. Its diagnosis must be early to ensure adequate management for a better prognosis.

Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.

Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics.

A Retrospective Analysis of Broad-Range Microbial PCR-Sequencing Findings and Culture Results in 101 Bronchoalveolar Lavage Specimens

Abstract Introduction/Objective Pneumonia is a significant cause of illness and death, identifying its cause is challenging and critical for effective antibiotic treatment and for reducing the length of stay. Bronchoalveolar lavage is commonly performed to obtain high-quality lower respiratory tract samples. While traditional culture methods have been the standard for pathogen detection, microbial rRNA broad-range polymerase chain reaction (BR-PCR) has emerged as an alternative method. Methods/Case Report A retrospective analysis was conducted on 101 patients suspected of severe pulmonary infections at Oregon Health and Science University (OHSU). Results (if a Case Study enter NA) When important microbial etiology is considered, culture detected 26%, while BR- PCR detected 20%. Both methods proved effective in detecting common pathogens; however, culture demonstrated superiority in detecting fungal pathogens due to potential sampling biases associated with PCR. Furthermore, culture holds the advantages of being faster and more cost-effective, although it may fail to detect difficult to non-cultivable organisms, like Legionella spp. Culture is indispensable for susceptibility testing and strain typing purposes. More often than not, BR-PCR captures airway microbiota indiscriminately with minimal clinical significance, potentially confusing clinical interpretation. Conclusion Novel technologies like Biofire Pneumonia Panel (BPP), a multiplex PCR, have shown promise in the rapid detection of pneumonia pathogens including bacteria, viruses, and resistance genes (< 2 hours), complementing the traditional culture methods for microbiological diagnosis. Based on this analysis we recommend introducing BPP at OHSU.

Alterations in the Antimicrobial Resistance Profile of Acinetobacter baumannii Strains Isolated from Intensive Care Unit Patients: Five-Year Follow-up in Cappadocia

Background: This study aims to determine alterations in the antibiotic resistance status of Acinetobacter baumannii strains isolated from lower respiratory tract samples of patients in intensive care units over the years. Methods: In this comprehensive study, A. baumannii strains isolated from aspirate and sputum samples of patients hospitalized in intensive care units of a second-stage state hospital between January 2018 and December 2022 were meticulously and retrospectively investigated and analyzed for antimicrobial resistance. Results: The rate of aspirate and sputum samples in the study was 18.1% (754/4151); The positivity rate of cultures was 51.7% (390/754); The rate of those associated with A. baumannii was found to be 65.6% (256/390).. 90.2% of the isolates were isolated from the general intensive care unit (231/256). The rates of A. baumannii isolated from aspirate and sputum samples were 67.4% (213/316) and 58.1% (43/74), respectively. The carbapenem resistance rate in A. baumannii isolates grown in aspirate samples was 96.5%, fluoroquinolone resistance was 91.7%; The carbapenem resistance rate in sputum samples was 96.1% and fluoroquinolone resistance was 90.9%. The most effective antibiotics against A. baumannii strains isolated from both aspirate and sputum samples were colistin 100% (n=256), TMP/SXT 55.8% (143/256), tigecycline 50.3% (129/256), respectively. Conclusion: Our study reveals a concerning trend-a high frequency of multidrug-resistant A. baumannii isolates are being identified in the Central Anatolia region of our country. This high prevalence, which is a cause for immediate concern, underscores the urgent and immediate need for robust infection control measures to curb the spread of A. baumannii in hospitals.

Males are at Higher Risk for Colonizations and Infections with Multidrug Resistant Organisms than Females

Global rise of multidrug-resistant organisms (MDRO) is alarming and antimicrobial resistance (AMR) poses a significant public health threat globally. Although certain risk factors are known including recent antimicrobial therapy, inappropriate use and hospitalization, the focus on gender-specific aspects in MDRO is scarce. Our aim was to show gender-specific differences in colonization and infections of multiple MDRO and their detection sites. For this multicentre, retrospective cohort study surveillance data between 2015 and 2020 was collected in 86 hospitals of the Helios group, Germany. The following multidrug-resistant bacteria were analysed according to sample site: MRSA, Enterococcus spp., Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa and Acinetobacter baumannii. Out of the 7,081,708 cases in the database, 187,656 patients were found to be colonized with MDRO (2.65%). A documented infection with MDRO was identified in 33,023 patients (0.466%), with the origin of infection known in 24,231 cases. Male gender was a risk factor for both infection and colonization of any MDRO (p< .001). Males exhibited a higher likelihood of MDRO detection in superficial skin/soft tissue, blood cultures (p < .001), and respiratory samples (p = .002). Additionally, gender-specific differences in MDRO detection site and pathogens were found with slightly higher proportion of MRSA infection in deep skin/soft tissue and respiratory samples for females. Our study reinforces the existing hypothesis that male gender is a risk factor for MDRO, supported by our large dataset. It highlights the need to acknowledge gender-specific MDRO susceptibility in clinical practice.

Evaluating the Efficacy of a Polymerase Chain Reaction Assay for Pneumocystis carinii Detection in Respiratory Samples

Abstract Introduction: Accurately identifying patients with pneumocystis pneumonia (PCP) presents considerable challenges, primarily relying on clinical suspicion. The manifestations of PCP lack specificity, encompassing symptoms such as cough, dyspnoea, fever, hypoxaemia, malaise and weight loss. Therefore, this study assesses the efficacy of a polymerase chain reaction (PCR) assay intended for use in clinical microbiology laboratories for the identification of Pneumocystis carinii from respiratory specimens. Materials and Methods: In this retrospective study, the medical records of patients aged 18 years and above were examined, focusing on those assessed using pneumocystis PCR-based tests. The study spanned from 2019 to 2022 in our tertiary care centre at Max Hospital, Saket. In this study, sputum and bronchoalveolar lavage (BAL) samples were proceeded for both staining and PCR for multi-copy mtLSU gene and single-copy dihydropteroate synthase polymorphisms (DHPS) fas gene of P. jirovecii. Results: In the analysis of 112 BAL specimens, 17 were identified as positive for P. carinii through both Grocott-Gomori’s Methenamine Silver Staining (GMS) staining and PCR. In addition, two BAL specimens were negative through GMS staining but showed positive results with PCR. On reviewing the clinical details of the patients associated with these two specimens, it was discovered that both individuals were under systemic steroid treatment, yet neither exhibited clinical signs of pneumocystis pneumonia (PCP). Consequently, these instances were classified as false positives by PCR. In comparison to GMS, the PCR assay demonstrated a sensitivity of 100% and specificity of 98% for detecting P. carinii in BAL specimens. Conclusions: The study underscores the necessity for individualised approaches, with each laboratory assessing the positive and negative predictive values based on their specific prevalence rates. In the ongoing pursuit of improving PCP diagnosis, PCR emerges as a promising screening tool that when used judiciously in conjunction with confirmatory measures, can enhance diagnostic precision in immunosuppressed populations.

A large number of autofluorescent crystals with hyphae in respiratory samples

A large number of autofluorescent crystals with hyphae in respiratory samples

Bronchoscopic Diagnosis of Severe Respiratory Infections

The diagnosis of severe respiratory infections in intensive care remains an area of uncertainty and involves a complex balancing of risks and benefits. Due to the frequent colonisation of the lower respiratory tract in mechanically ventilated patients, there is an ever-present possibility of microbiological samples being contaminated by bystander organisms. This, coupled with the frequency of alveolar infiltrates arising from sterile insults, risks over-treatment and antimicrobial-associated harm. The use of bronchoscopic sampling to obtain protected lower respiratory samples has long been advocated to overcome this problem. The use of bronchoscopy further enables accurate cytological assessment of the alveolar space and direct inspection of the proximal airways for signs of fungal infection or alternative pathologies. With a growing range of molecular techniques, including those based on nucleic acid amplification and even alveolar visualisation and direct bacterial detection, the potential for bronchoscopy is increasing concomitantly. Despite this, there remain concerns regarding the safety of the technique and its benefits versus less invasive sampling techniques. These discussions are reflected in the lack of consensus among international guidelines on the topic. This review will consider the benefits and challenges of diagnostic bronchoscopy in the context of severe respiratory infection.

Analysis of Stenotrophomonas maltophilia infections in lower respiratory tract samples at a university hospital: 5 year data

Objectives Patients with reported Stenotrophomonas maltophilia (S. maltophilia) growth in lower respiratory tract samples were investigated. The results of these patients were assessed by clinicians as either infection or colonization. The data of patients considered to have S. maltophilia infection were compared to those considered to have colonization to explore factors associated with infection. Methods Parameters including as age, length of hospital stay, duration of S. maltophilia growth after hospital admission, sex, unit, department, specimen type, mechanical ventilation treatment status, antimicrobial susceptibility results, comorbidities, survival, and antimicrobials used during the period from hospital admission to S. maltophilia growth were investigated. Additionally, some biochemical parameters that were examined include the day of hospital admission, the day of sample collection when the bacterium was isolated (±1 day), and the day of discharge/died. Results The infection group had a significantly higher rate of admissions to internal medical departments and more cases of discharge/died. The infection group showed a lower amount of aminoglycoside antibiotic usage and significantly higher levels of BUN, creatinine, neutrophils, and neutrophil-to-lymphocyte ratio on their day of discharge/died. Conclusion Being admitted to internal medical departments and receiving aminoglycoside treatment were identified to be factors associated with S. maltophilia infection. These patients should be monitored for infection markers such as CRP and neutrophil count, as well as renal function tests. It should be noted that being infected with S. maltophilia is an independent risk factor for mortality. Bangladesh Journal of Medical Science Vol. 23 No. 04 October’24 Page : 1095-1103

A-287 Mycoplasma pneumoniae outbreak in 2023: Post pandemic resurgence of an atypical bacterial pathogen

Abstract Background Mycoplasma pnuemoniae is an atypical fastidious bacteria known to cause respiratory infections of both upper and lower tract, with a wide range of clinical presentations. M. pnuemoniae is one of the major causes of community acquired pneumonias worldwide. Almost all of the M pnuemoniae outbreak incidences have been reported in closed- community or congregate settings, such as schools, universities and colleges, and hospitals and long-term care facilities. Since the clinical symptoms of M pneumoniae overlap with other pneumonia causing pathogens, detection via multiplex PCR remains paramount for accurate and timely diagnosis to curb the infection spread. In the present study we demonstrate an unexpected increase in the detection of M. pneumoniae in the outpatient population, during 2023, as compared to the previous two years. In addition, a detailed analysis of the ICD10 diagnostic codes associated with the outbreak is also presented. Methods Respiratory samples (oropharyngeal, nasopharyngeal, sputum and EBL) summited to the HealthTrackRX laboratories were tested for the presence of M. pneumoniae and other respiratory bacterial and viral pathogens using the nanofluidic OpenArray qPCR platform (ThermoFisher, California, USA). Patient data was analyzed on the basis of age, gender and geographical location. Data was also classified in the basis of ICD10 diagnostic codes associated with the patient samples. All statistical analysis was performed using R version 3.6.0 (R Foundation for Statistical Computing). Results A total of 541,267 samples were submitted for testing at the HealthTrackRX facilities between January 1, 2021 and December 31, 2023. Only 13 samples tested positive for M. pneumoniae between 2021 (0.004%, n =3/61,498) and 2022 (0.006%, n = 10/165,423). The positivity rate of M. pneumoniae in 2023 increased to 0.19% (n = 621/314,346). The highest proportion of M. pneumoniae cases were detected from Georgia (26.8%), followed by Ohio (21.7%), Texas (8.5%) and California (6.4%). Most of the outbreak appears to be concentrated in large urban settings. Median age of the patients testing positive for M. pneumoniae was 10 (interquartile range [IQR] 8-18) years. Gender classification of the positive samples showed an almost equal distribution between females (49.8%) and males (50.1%). Co-infecting pathogens detected in samples positive for M. pneumoniae were similar in proportion to the M. pneumoniae negative population. The co-detected pathogens at a statistically significant difference were lower than the negative population. Survey of the ICD-10 codes submitted in conjunction with the samples suggest that the current outbreak is mostly associated with upper respiratory tract infections. Conclusions The present study shows an unprecedented increase in the detection of M. pneumoniae in the outpatient population in the United States during 2023. Our analysis suggests that this outbreak was not associated with any other bacterial or viral respiratory pathogen but appears to be case of “immunity debt” caused by the COVID19 pandemic. The outbreak of this atypical pathogen was concentrated in the pediatric population in large urban areas. Our study highlights the importance of performing continuous surveillance of respiratory pathogens, especially in the altered epidemiological landscape of the post COVID world.

Influenza outbreak during the surge of SARS-CoV-2 omicron in a metropolitan area from southern Brazil: genomic surveillance.

Influenza circulation was significantly affected in 2020-21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021-22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Brazil, Rio Grande do Sul (RS). The present study aimed to identify the circulation of FLUAV, FLUBV and SARS-CoV-2 and characterize the influenza genomes in respiratory samples using high-throughput sequencing technology (HTS). Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed using reverse transcriptase real-time PCR (RT-qPCR) and showed 32% (223/694) of the samples to be positive for SARS-CoV-2, 7% for FLUAV (H3) (49/694). FLUBV was not detected. RT-qPCR data also resulted in FLUAV and SARS-CoV-2 co-infections in 1.7% (4/223) of samples tested. Whole genome sequencing of FLUAV produced 15 complete genomes of the H3N2 subtype, phylogenetically classified in the 3C.2a1b.2a.2a.3 subclade and revealing the dominance of viruses in the southern region of Brazil. Mutation analysis identified 72 amino acid substitutions in all genes, highlighting ongoing genetic evolution with potential implications for vaccine effectiveness, viral fitness, and pathogenicity. This study underscores limitations in current surveillance systems, advocating for comprehensive data inclusion to enhance understanding of influenza epidemiology in southern Brazil. These findings contribute valuable insights to inform more effective public health responses and underscore the critical need for continuous genomic surveillance.

Identification of JC polyomavirus in upper respiratory samples from Portuguese children

BackgroundJC polyomavirus (JCPyV) is ubiquitous in the human population and the causative agent of a rare, fatal and demyelinating disease of the central nervous system named Progressive Multifocal Leukoencephalopathy (PML). The route of JCPyV transmission remains unclear, but high values of seroprevalence suggest an easy and frequent mode, such as respiratory route. ObjectivesThe present study aims to investigate the presence of JCPyV in upper respiratory samples and contribute to the elucidation of the JCPyV transmission pathway. Study designNasopharyngeal swabs from 587 Portuguese individuals, including 380 children (≤18 years) and 207 adults (>18 years), collected for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis between September and November 2021 were evaluated for the presence of JCPyV DNA. ResultsJCPyV DNA was detected in 3.1 % of the nasopharyngeal swabs analysed, with higher frequency of detection in samples from children (4.5 %) than from adults (0.5 %) (p = 0.005). Infection with SARS-CoV-2 does not potentiate the presence of JCPyV in upper respiratory tract, once only one adult of 28 years with confirmed SARS-CoV-2 infection showed detectable JCPyV DNA. JCPyV DNA was more frequently detected in respiratory samples from children without SARS-CoV-2 infection (6.4 %). As for this group, children under six years of age presents the highest frequency of detection (10.3 %). ConclusionsThe present study demonstrates that upper respiratory secretions of children, particularly under the age of six, may be implicated in JCPyV transmission, regardless of SARS-CoV-2 infection.

Profile of Bacterial Resistance in Emergency Wards, Hospitalization, and Intensive Care Units in Mexican Hospitals with the Antimicrobial Stewardship Program

IntroductionBacterial infections are important causes of death. Some reports have shown that the COVID-19 pandemic may have had an impact on drug resistance. AimTo compare the resistance profiles between 2019 and 2020 emergency room, hospitalization non-intensive care units (ICU), and ICU areas in Mexican hospitals. MethodDatabases from 15 hospitals from 8 states in Mexico including susceptibility results for Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa collected from blood, urine, respiratory, and intra-abdominal secretions were analyzed. Different hospital areas were included: emergency room, hospitalization non-ICU, and ICU. The databases were converted using the BacLink2 tool and analyzed using the WHOnet 2022 platform. The percentage of antibiotic resistance was compared for each species and clinical specimen among years (2019 vs 2020) by a chi-square test using the criterion of p<0.05 for statistical significance. ResultsA statistically significant decrease in resistance to imipenem was observed for P. aeruginosa recovered from respiratory specimens in the ICU (55.6% vs 39.3%) and from urine samples from hospitalization non-ICU areas (52.9% vs 37.3%). Also, an increase in resistance was detected in blood isolates from hospitalization non-ICU areas for carbapenems in P. aeruginosa imipenem, (23.3 % vs 54.5%) and meropenem (27.4 % vs 49%) and in E. coli, ertapenem (2.4% vs 10.1%), imipenem (1.9% vs 13.2%), and meropenem (1.6% vs 6.8%). Also, an increase in resistance for imipenem (20.0 % vs 57.5%) and meropenem (17.6% vs 48.7 %) was detected in the emergency room for P. aeruginosa in respiratory isolates. ConclusionA decrease in carbapenem resistance for P. aeruginosa recovered from respiratory specimens in the ICU and from urine samples from hospitalization non-ICU areas was detected. In contrast, an increase in carbapenem resistance was detected for P. aeruginosa in blood isolates from hospitalization non-ICU areas and respiratory isolates from the emergency room. Regarding respiratory samples, a higher resistance for meropenem was detected in 2020 than in 2019 for K. pneumoniae (2.6 vs 10.6%, p = 0.05). These results underline the analysis of AMR in different hospital wards to focus efforts on AMR reduction.