Oropharyngeal Swabs Research Articles

Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity

To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity. The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV). When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often. We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.

Comparison and Harmonization of Different Semi-Automated and Automated qRT-PCR Assays in the Assessment of SARS-CoV-2.

In SARS-CoV-2 diagnostics, cycle threshold (Ct) values from qRT-PCRs semi-quantitatively estimate a patient’s viral load. However, relevant analytical differences between qRT-PCR assays are often neglected. This study was designed (i) to identify such differences between five commonly used assays and (ii) to demonstrate a straightforward strategy to harmonize them. QRT-PCRs for SARS-CoV-2 were carried out in 85 oropharyngeal swab samples using three fully automated (Alinity m, cobas®6800 and GeneXpert) and two semi-automated (genesig® and RIDA®GENE) assays. Qualitative results (positive/negative) showed excellent comparability between the fully automated assays, but not between the Alinity m and semi-automated methods. Ct values significantly varied between all the methods, with the median values ranging from 22.76 (Alinity m) to 30.89 (RIDA®GENE) and 31.50 (genesig®), indicating the lowest sensitivity for semi-automated methods. Passing–Bablok analysis further revealed systemic biases. Assay-specific viral load concentration calculations—based on generated individual standard curves—resulted in much better comparability between the assays. Applying these calculations, significant differences were no longer detectable. This study highlights relevant analytical differences between SARS-CoV-2 qRT-PCR assays, leading to divergent decisions about the mandatory isolation of infected individuals. Secondly, we propose a strategy to harmonize qRT-PCR assays to achieve better comparability. Our findings are of particular interest for laboratories utilizing different assays.

Possibility of Coronavirus Disease 2019 Transmission Through Breast Milk: A Systematic Review

Context: Coronavirus disease 2019 (COVID-19) and the infection control strategies have affected breastfeeding and mother-newborn contact due to the fear of disease transmission to the baby. Objectives: This study aimed to evaluate the possibility of CPVID-19 transmission by reviewing the currently published articles. Methods: In this systematic review, 296 articles were first retrieved from IranMedex, SID, IranDoc, Magiran, Iranian Registry of Clinical Trials (IRCT), PubMed, ProQuest, Scopus, Science Direct, Medline, and Google Scholar search engine using the keywords "breastfeeding", "breast", "vertical transfer", "breast milk", "colostrum", "corona", and "COVID-19". Of the 296 retrieved articles, 16 were eligible for the review. Results: Reviewed articles included four retrospective cross-sectional studies, one cohort study, eight case reports, and three case series. Overall, the studies reported 237 RT-PCR tests on breast milk and/or nasopharyngeal or oropharyngeal swabs from mother or baby, and 156 serum antibody measurements in mother or baby. The overall findings indicated a low risk for COVID-19 transmission from mother to infant through breastfeeding, while breastfeeding was detected to transfer the antibodies to the newborn. Conclusions: Due to the low transmission risk, it was recommended that mothers with mild to moderate symptoms should breastfeed their infants with infection control measurements, while mothers with severe symptoms should use pumped breastmilk for feeding their infants.

Molecular epidemiology of human adenoviruses in children with and without respiratory symptoms: Preliminary findings from a case-control study

BackgroundHuman adenovirus (HAdV) is an important viral agent in children which can lead to severe acute respiratory infection (SARI). Reports on molecular epidemiology of HAdVs in Iran are limited. This case-control study is conducted to compare the HAdV infection rate and molecular epidemiology among two groups of children with and without respiratory symptoms in Tehran, Iran during 2018–2019.MethodsNested PCR was performed on 120 oropharyngeal swabs taken from children aged five and younger with SARI who were hospitalized as the case group, and 120 oropharyngeal swabs were collected from children of the same age without respiratory symptoms as the control group. For positive samples Sanger sequencing was done and a phylogenetic tree was drawn afterward.ResultsOut of 120 cases, 8 (6.6%) tested positive for eachHAdV types including 6 (75%) HAdV-B7, 1 (12.5%) HAdV-C2, and 1 (12.5%) HAdV-C6. Among the control group, out of 120 samples, 8 (6.6%) were positive comprising 5 (62.5%) HAdV-C5, 2 (25%) HAdV-F41, and 1 (12.5%) HAdV-C6.ConclusionThe present study indicated a different viewpoint of HAdV molecular epidemiology in which the genotypes were compared in children with and without respiratory symptoms. HAdV prevalence was equally common in cases and controls but different genotypes were detected in these two groups. HAdV-B7 was the main type among children with SARI, dissimilar to children with no respiratory symptoms where HAdV-C5 was the predominant type. Detecting HAdV-F in oropharyngeal swabs was a rare finding, which requires further investigation.

Population immunity in residents of the Kaliningrad region to current antigenic variants of influenza viruses over 2018-2021

The article presents the results of population immunity assessment in residents of the Kaliningrad region to current antigenic variants of influenza viruses over the period of 2018 to 2021. To assess spectrum of influenza types circulating in Kaliningrad region, the real-time PCR method was used using AmpliSense reagent kits. The biological material for the study was obtained from oropharyngeal swabs from the persons who applied to polyclinics with inflammatory diseases of upper respiratory tract, or underwent treatment at the out- or inpatient basis in a healthcare facilities of Kaliningrad region. Humoral immunity was assessed by testing blood sera obtained from healthy residents of Kaliningrad region during periodic prophylactic examinations at the city and regional polyclinics. The study of residents covered all age groups. For the period of 2018-2021, more than 14,000 studies have been carried out. Determination of specific serum antibody titers was carried out by staging the hemagglutination suppression reaction using local influenza antigens (LLC PPDP, St. Petersburg). Antibody titers of 1/40 and higher were considered sufficient to reduce the risk of disease by 50%. During the study period, 2165 cases of influenza were confirmed in the region by laboratory tests. Over the study period, the A(H1N1) pdm serotype proved to be the major strain causing influenza, its proportion reached 57.5%. However, along with A(H1N1) pdm, a significant contribution was also made the A(H3N2) strain to the epidemic process, being the etiological cause of influenza infection in 2019 (42.2%), type B influenza strains being actual in 2020 (42.5%). Over the period of 2018-2021, 420 samples of blood sera from vaccinated and non-vaccinated individuals were tested for specific antibodies. The sera were taken 1-2 months after vaccination and between epidemic rises of influenza (April-May). In vaccinated individuals, the antibody titer was protective in 58.3-64.5%. In this group of persons, the titer sufficient to produce immunity was maintained over the spring/summer period. Among those persons who refused vaccination, a protective antibody titer in the pre-epidemic period was noted in 41.2% of the examined, and during the off-season it was detected in 37.4% of the volunteers. Thus, the A(H1N1) pdm strain was the main etiological factor of influenza in Kaliningrad Region in 2018-2021. The protective level of antibodies in vaccinated population over the period preceding the epidemic peak, was observed 30% more often than in unvaccinated individuals. High incidence of influenza B strains noted in 2020 appears to require a change of specific vaccine preparation.

Optical reflectometric measurement of SARS-CoV-2 (COVID-19) RNA based on cationic cysteamine-capped gold nanoparticles

The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a major public health outbreak in late 2019 and was proclaimed a global pandemic in March 2020.A reflectometric-based RNA biosensor was developed by using cysteamine-stabilized gold nanoparticles (cysAuNPs) as the colorimetric probe for bioassay of COVID-19 RNA (SARS-CoV-2 RNA) sequence. The cysAuNPs aggregated in the presence of DNA probes via cationic and anionic electrostatic attraction between the positively charged cysteamine ligands and the negatively charged sugar-phosphate backbone of DNA, whilst in the presence of target RNAs, the specific recognition between DNA probes and targets depleted the electrostatic interaction between the DNA probes and cysAuNPs signal probe, leading to dispersed particles. This has rendered a remarkable shifting in the surface plasmon resonance (SPR) on the basis of visual color change of the RNA biosensor from red to purplish hue at the wavelength of 765 nm. Optical evaluation of SARS-CoV-2 RNA by means on reflectance transduction of the RNA biosensor based on cysAuNPs optical sensing probes demonstrated rapid response time of 30 min with high sensitivity, good linearity and high reproducibility across a COVID-19 RNA concentration range of 25 nM to 200 nM, and limit of detection (LOD) at 0.12 nM. qPCR amplification of SARS-CoV-2 viral RNA showed good agreement with the proposed RNA biosensor by using spiked RNA samples of the oropharyngeal swab from COVID-19 patients. Therefore, this assay is useful for rapid and early diagnosis of COVID-19 disease including asymptomatic carriers with low viral load even in the presence of co-infection with other viruses that manifest similar respiratory symptoms.

Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults

BackgroundThe composition of the digestive microbiota may be associated with outcome and infections in patients admitted to the intensive care unit (ICU). The dominance by opportunistic pathogens (such as Enterococcus) has been associated with death. However, whether this association remains all throughout the hospitalization are lacking.MethodsWe performed a single-center observational prospective cohort study in critically ill patients admitted with severe SARS-CoV-2 infection. Oropharyngeal and rectal swabs were collected at admission and then twice weekly until discharge or death. Quantitative cultures for opportunistic pathogens were performed on oropharyngeal and rectal swabs. The composition of the intestinal microbiota was assessed by 16S rDNA sequencing. Oropharyngeal and intestinal concentrations of opportunistic pathogens, intestinal richness and diversity were entered into a multivariable Cox model as time-dependent covariates. The primary outcome was death at day 90.ResultsFrom March to September 2020, 95 patients (765 samples) were included. The Simplified Acute Physiology Score 2 (SAPS 2) at admission was 33 [24; 50] and a Sequential Organ Failure Assessment score (SOFA score) at 6 [4; 8]. Day 90 all-cause mortality was 44.2% (42/95). We observed that the oropharyngeal and rectal concentrations of Enterococcus spp., Staphylococcus aureus and Candida spp. were associated with a higher risk of death. This association remained significant after adjustment for prognostic covariates (age, chronic disease, daily antimicrobial agent use and daily SOFA score). A one-log increase in Enterococcus spp., S. aureus and Candida spp. in oropharyngeal or rectal swabs was associated with a 17% or greater increase in the risk of death.ConclusionWe found that elevated oropharyngeal/intestinal Enterococcus spp. S. aureus and Candida spp. concentrations, assessed by culture, are associated with mortality, independent of age, organ failure, and antibiotic therapy, opening prospects for simple and inexpensive microbiota-based markers for the prognosis of critically ill SARS-CoV-2 patients.

Could air sampling be a substitute for individual oropharyngeal and cloacal swabs on live animals to detect avian influenza virus in Mule ducks?

Could air sampling be a substitute for individual oropharyngeal and cloacal swabs on live animals to detect avian influenza virus in Mule ducks?

Evaluation of diagnostic utility and performance of rapid SARS-CoV- 2 antigen detection assay in comparison with Real-Time RT-PCR in Kolkata, India

Background: COVID-19 has so far affected millions of people in India. The present study was undertaken to find out the performance and reliability of rapid antigen test (RAT) in compared to reverse transcription polymerase chain reaction (RT-PCR).Methods: The pre and existing medical conditions and clinical signs and symptoms were noted. The nasopharyngeal swab samples were taken for RAT, while both nasopharyngeal and oropharyngeal swab samples were mixed in a sterile viral transported medium (VTM) for RT-PCR. All patients were examined by RAT, while symptomatic negative in RAT were re-examined by RT-PCR.Results: Total 18,965 samples were examined by RAT and 3,998 samples by RT-PCR. Among them, only 5,753 patients (30.3%) were symptomatic and 1,757 patients (9.2%) were symptomatic positive. RAT showed overall 15.2% positive cases. Only 3.7% samples exhibited false negative results in RAT, which were found positive in RT-PCR. Interestingly, Ct (cycle threshold) values were >30 in all these samples.Conclusion: Hence, specific antigen-based rapid diagnostic test (RDT) will be most useful and reliable among any other qualitative tests for screening purpose.

Development of donor specific antibodies after SARS-CoV-2 vaccination in kidney and heart transplant recipients

This study examined the development of new or changes in donor specific antibodies (DSA) mean-fluorescence intensity (MFI) after SARS-CoV-2 vaccination in 100 kidney and 50 heart transplant recipients. The study was performed when the Center for Disease Control and Prevention (CDC) recommended two doses of Pfizer/BioNTech [BNT162b2] and Moderna [mRNA-1273 SARS-CoV-2] vaccine or 1 dose Johnson & Johnson/Janssen [Ad26.COV2·S] vaccines for full vaccination in transplant recipients. A novel assay bead-based platform for detecting antibodies against 4 domains of the SARS-CoV-2 spike protein to determine vaccine response (SA) and one nucleocapsid protein (NC) to determine prior SARS-CoV-2 infection was utilized. These assays were performed on the multiplex, bead-based platform utilized to assay DSA levels. 61/150 patients (40.7%) had successful vaccination. 18 patients had confirmed SARS-CoV-2 infection based on positive NC assay or previous Covid-19 oropharyngeal swab. 138 patients had no DSA prior to vaccination but 3 heart recipients developed new DSA's. Among 12 patients with known DSA prior to vaccination, 4 developed new DSA's or increased MFI. All 7 patients with new or increased DSA had stable graft function without rejection and had no changes in immunosuppression. All 8 patients with stable post vaccine DSA had stable graft function and immunosuppression was not changed. The presence of DSA before vaccination was associated with subsequent development of increased MFI or new DSA's (p = 0.001). There was no association between pre-vaccine DSA and positive vaccine response (NS). There was no association with successful vaccination or prior SARS-CoV-2 infection and DSA changes (NS).

P313 A retrospective analysis of COVID-19 - associated Mucormycosis in a tertiary care center in Northern India

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM ObjectivesTo study the prevalence of COVID-19-associated mucormycosis in a tertiary center.To analyze the factors responsible for the incidence of mucormycosis and outcome of the patients in relation to COVID 19 positive status.MethodsThis is a retrospective observational study with (n = 433) samples. Nasopharyngeal and oropharyngeal swabs were collected from clinically suspected cases of mucormycosis. These were then subjected to Xpert® Xpress SARS-CoV-2 test. Those samples which tested positive were included in this study. A history sheet form was designed and filled up for 238 patients who were admitted and could be traced properly.ResultsTotal number of SARS CoV-2 positive samples was 296 out of 433 samples. Among the tested 66% (287/433) were male and 34% (146/433) were female. Relative positivity was higher among women 74% (107/144) than men 66% (189/285). Amongst 238 admitted patients, 83.1% patients (198/238) completed treatment and were discharged while 13.9% (33/238) succumbed during management. Diabetes was found to be most common risk factor at 88.65% (211/238) followed by hypertension 36.5% (87/238), and corticosteroid use 26.89% (64/238). Type 2 DM was the most frequent with 96% (203/211) and only 4% (8/211) patients having Type 1 DM. Amongst the diabetics, 74.8% (158/211) were on medication (oral hypoglycemic agent/insulin/both), and 16.6% (35/158) of them were non-compliant to treatment. Most common clinical presentation was facial swelling 66.8% (159/238) followed by facial pain 52.52% (125/238) and headache 34.45% (82/238). Microscopy findings either nasal or palatal scraping was positive in 69.75% (166/238) cases with aseptate hyphae in 95% (157/166) patients while septate hyphae were seen in 3% (5/166). Both aseptate and septate hyphae were present in 2% (4/166 patients).Amongst the deceased patients 91% (30/33) had diabetes mellitus exclusively of Type 2 and among them, 33% (10/30) were not on any anti-diabetic medication. It was also observed that among the deceased people who were on anti-diabetic medication, 45% (9/20) were non-compliant to the treatment. Combinedly 63.33% (19/30) diabetics were on inadequate blood sugar level control which might be strongly contributing to mortality.ConclusionPercentage of clinically suspected mucor patients who were COVID-19 positive was 67%. Although male patients were twice more tested than females but females were proportionately more positive for SARS-CoV2. Type 2 diabetes mellitus was the lead risk factor, with facial swelling being the predominant presentation. Interestingly, fungal smear was positive in 166 out of 238 patients. Despite the best management, the mortality rate was 13.86% in such patients. It was also seen that untreated or non-compliance to anti-diabetic treatment resulted in increased mortality. Hence, it's necessary to review cases of COVID-19-associated mucormycosis for prompt management and to reduce morbidities and mortality.

P240 Candida nivariensis infection in South East Asia: series of case reports from Selayang Hospital, Malaysia and South East Asia Region

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Introduction Candida nivariensis, first described from Spain in 2005 is an emerging fungal pathogen. Malaysia has captured a total of 11 cases since its first reported here in 2014. Indonesia, Thailand, and Vietnam are among South East Asia countries that reported its occurrence too.ObjectivesThe occurrence and characteristics of Candida nivariensis in South East Asia are studied. We would like to highlight two cases from Selayang Hospital, Malaysia that occurred during pandemic COVID-19 in 2020 and 2022.Case DescriptionIn July 2020, a 60-year-old lady underlying poorly controlled diabetes mellitus, CKD stage V approaching ESRD, congestive cardiac failure, hypertension, and dyslipidemia was diagnosed as complicated MSSA bacteremia secondary to right gluteal carbuncle. Appropriate antibiotics were commenced. Aggressive source control including incision and drainage, cauterization of right gluteal carbuncle, and multiple wound debridement for the infected gluteal wound was performed. She underwent a trephine sigmoid loop colostomy. Tracheostomy was done following prolong ventilation. Anidulafungin as empirical fungal coverage was commenced in ICU as she further deteriorated. Candida nivariensis was isolated later from her blood culture.In February 2022, a 74-year-old man underlying Diabetes mellitus, chronic kidney disease, hypertension, ischemic heart disease with two vessels disease stented, post-Whipple's procedure due to necrotizing pancreatitis in 2014 complicated with chronic abdominal pain with hyperalgesia admitted to the ward for acute right lacunar infarct with failed swallowing test and neurogenic bladder. His general condition deteriorated with worsening of biochemical and septic parameters. His blood culture grew C. nivariensis following which anidulafungin was started. No distant seeding and no signs of endophthalmitis. He then required mechanical ventilatory support complicated with multiorgan failure, leading to ICU admission.MethodsFor both cases, yeast isolates were subcultured on Sabouraud dextrose agar and CHROMagar. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) with molecular testing was performed for confirmation of isolates. Phylogenetic tree among isolates from Malaysia was analyzed. Antifungal susceptibility test (AFST) to study the minimum inhibitory concentration (MIC) among treatment options was performed using the e-test method.ResultsWide use of MALDI-TOF MS with molecular testing increased the detection rate of the species. Isolation sites in Malaysia and South East Asia region include blood culture, peritoneal fluid, high vaginal swab, and oropharyngeal swab. Risk factors namely immunocompromised status, indwelling vascular catheter, abdominal surgeries, renal failure or on dialysis support, polymicrobial usage, and prolonged stay in ICU. AFST established susceptibility towards fluconazole, high MIC to itraconazole and low MIC against amphotericin B, anidulafungin and voriconazole for both patients who unfortunately succumbed to their illness.ConclusionDiagnosing C. nivariensis is challenging due to its closely related phylogenetic with C. glabrata, and C. bracarensis, thus molecular testing is vital. Inadequate antifungal coverage or delay of treatment could be detrimental to patient's outcome. Continuous epidemiological surveillance is crucial to address this potential invasive fungal pathogen and to observe emerging of drug resistance.

Clinical Performance of Self-Collected Nasal Swabs and Antigen Rapid Tests for SARS-CoV-2 Detection in Resource-Poor Settings.

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3–85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3–85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2–63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5–82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.

CASE REPORT : LOW LEVEL IMMUNOGLOBULING (IGG) IN REINFECTION COVID-19 CASE

Million people have infected the SARS-CoV-2 epidemic, which is currently spreading. We describe a confirmed COVID-19 patient whose oropharyngeal swab test for SARS-CoV-2 RNA and have positive PCR test results after 8 weeks proclaim negative result of PCR test for SARS-COV-2. ImmunoglobulinG was not detected during the initial illness. In this study, we discuss the potential role of low IgG in cases of reinfection.

Neisseria meningitidis carriage rate, antibiotic susceptibility profile, and associated factors among prisoners at Jimma zonal correction facility in Jimma Town, Southwestern Ethiopia: a cross-sectional study

BackgroundNeisseria meningitidis causes severe life-threatening meningococcal disease with a case fatality rate of 10–15% even with proper treatment. In Ethiopia, particularly in our study area, inadequate information is found on meningococcal disease. So, this study aimed to assess N. meningitidis carriage rate, antibiotic susceptibility profile, and associated factors among prisoners in Jimma Town, Southwestern Ethiopia.MethodsA cross-sectional study was conducted in Jimma town, Southwest Ethiopia, from May to October 2019. A stratified sampling technique was used and proportional allocation was done. A total of 550 oropharyngeal swabs were collected, processed, isolated, and identified N. meningitidis using standard microbiological techniques. Antibiotics susceptibility test was done for isolates using the disk diffusion method. Data on demographic and associated factors for carriage were collected using a structured questionnaire. Data were summarized using frequency, percentage, graph, and table. A logistic regression model was used to see the association between the dependent and independent variables. Variables with a p-value < 0.25 during bivariate analysis were included in multivariate analysis to identify factors significantly associated with the meningococcal carriage and, a p-value < 0.05 was considered statistically significant.ResultOut of the 550 study participants, 76(13.8%) with (CI: 7.20–18.20) were found carriers of N meningitidis. The predominant isolates were non-serogroupable 26(34.2%) and serogroup W/Y 22(28.9%), respectively. N. meningitidis isolates showed highest sensitivity to chloramphenicol 74(97.4%). Meningococcal carriage rate was significantly associated with being age group of 16–20 years; having respiratory symptoms within 3 months and active cigarette smoking within 3 months.ConclusionsThe majority of participants harbor most of the serogroups responsible for invasive cases of meningococcal disease. Respiratory symptoms, active cigarette smoking, and age group of 16–20 years increased the risk of N. meningitidis pharyngeal carriage rate. This study suggests providing better health education to control respiratory symptoms, smoking, and providing antibiotic prophylaxis for prisoners.

Prospective population-level validation of the Abbott ID NOW severe acute respiratory syndrome coronavirus 2 device implemented in multiple settings for testing asymptomatic and symptomatic individuals

ObjectiveDiagnostic evaluation of the ID NOW coronavirus disease 2019 (COVID-19) assay in various real-world settings among symptomatic and asymptomatic individuals. MethodsDepending on the setting, the ID NOW testing was performed using oropharyngeal swabs (OPSs) taken from patients with symptoms suggestive of COVID-19, asymptomatic close contacts, or asymptomatic individuals as part of outbreak point prevalence screening. From January to April 2021, a select number of sites switched from using OPS to combined oropharyngeal and nasal swab (O + NS) for ID NOW testing. For every individual tested, two swabs were collected by a health care worker: one swab (OPS or O + NS) for ID NOW testing and a separate swab (OPS or nasopharyngeal swab) for RT-PCR. ResultsA total of 129 112 paired samples were analysed (16 061 RT-PCR positive). Of these, 81 697 samples were from 42 COVID-19 community collection sites, 16 924 samples were from 69 rural hospitals, 1927 samples were from nine emergency shelters and addiction treatment facilities, 23 802 samples were from six mobile units that responded to 356 community outbreaks, and 4762 O + NS swabs were collected from three community collection sites and one emergency shelter. The ID NOW assay sensitivity was the highest among symptomatic individuals presenting to community collection sites (92.5%; 95% CI, 92.0–93.0%) and the lowest for asymptomatic individuals associated with community outbreaks (73.9%; 95% CI, 69.8–77.7%). Specificity was >99% in all populations tested. DiscussionThe sensitivity of ID NOW severe acute respiratory syndrome coronavirus 2 testing is the highest when used in symptomatic community populations not seeking medical care. Sensitivity and positive predictive value drop by approximately 10% when tested on asymptomatic populations. Using combined oropharyngeal and nasal swabs did not improve the performance of ID NOW assay.

Epidemiological characteristics of a local cluster epidemic caused by 2019-nCoV Delta variant in Ningbo, 2021

Objective: To understand the epidemiological characteristics of a local clustered epidemic caused by 2019-nCoV Delta variant in Ningbo and provide reference for the improvement of COVID-19 epidemic prevention and control. Methods: Case finding was conducted based on case definitions, and field epidemiological investigation of COVID-19 cases was carried out. In which Nasal and oropharyngeal swabs of the cases were collected for pathogen testing, and the results were analyzed with descriptive epidemiological methods. Results: A total of 74 COVID-19 cases were reported in this epidemic, and the cases were mainly mild ones, accounting for 87.84% (65/74), and there were no severe or critical cases. The epidemic curve showed a human-to-human transmission mode, indicating that a transmission for at least six generations had occurred. The age of the COVID-19 patients ranged from 2 years to 80 years, and 27.03% (20/74) of the cases were older than 60 years. The cases were mainly workers (55.41%, 41/74) and housework/the unemployed (27.03%, 20/74). The COVID-19 epidemic was limited, and no further spread to other areas occurred. The transmission chain among the cases was clear, and the gene sequencing results confirmed that the current epidemic was caused by 2019-nCoV Delta variant, which was highly homologous to the strains from other province. Conclusion: The local COVID-19 epidemic in Ningbo was caused by imported cases of COVID-19 from other province, and local community spread occurred through daily contacts between cases and contacts.

Evaluation of Virulence in Cynomolgus Macaques Using a Virus Preparation Enriched for the Extracellular Form of Monkeypox Virus.

The 2022 global human monkeypox outbreak emphasizes the importance of maintaining poxvirus research, including enriching a basic understanding of animal models for developing and advancing therapeutics and vaccines. Intravenous administration of monkeypox virus in macaques is arguably one of the best animal models for evaluating the efficacy of medical countermeasures. Here we addressed one criticism of the model, a requirement for a high-titer administration of virus, as well as improving our understanding of monkeypox virus pathogenesis. To do so, we infected macaques with a challenge dose containing a characterized inoculum enriched for the extracellular form of monkeypox virus. Although there were some differences between diseases caused by the enriched preparation compared with a relatively similar unpurified preparation, we were unable to reduce the viral input with the enriched preparation and maintain severe disease. We found that inherent factors contained within the serum of nonhuman primate blood affect the stability of the monkeypox extracellular virions. As a first step to study a role of the extracellular form in transmission, we also showed the presence of this form in the oropharyngeal swabs from nonhuman primates exposed to monkeypox virus.

The prevalence and influencing factors of the oropharyngeal carriage of Haemophilus influenzae in healthy children in a high-altitude area of China: A cross-sectional study.

Haemophilus influenzae is a common commensal organism of the human upper respiratory tract and an important cause of human disease. No data on H influenzae carriage rate has been carried out on the Qinghai-Tibet Plateau of China. This study aims to present the H influenzae carriage rate and influencing factors of H influenzae in healthy children <15 years of age in Qinghai Province, an area located on the Qinghai-Tibet Plateau in China. Oropharyngeal swabs for the detection of H influenzae DNA were collected between September and October 2019. Taqman real-time polymerase chain reaction was used to detect the nucleic acids from the oropharyngeal swabs. Self-designed questionnaires were used to investigate the related information among this group of children. A number of 284 children were enrolled in this study. The carriage rate of H influenzae was 44.7%. The carriage rate in cities was 47.5%, in rural areas was 21.9%, and in pastoral areas was 52.8%. The carriage rate was found to be higher among children of minority ethnic groups than those of Han ethnicity (55.6% vs 38.1%). H influenzae carriage rate was influenced by tobacco smoke exposure (adjusted odds ratio [aOR] = 2.31, 95% CI [confidence interval]: 1.14-4.70), having siblings <5 years of age (aOR = 2.36, 95% CI: 1.21-4.59), respiratory infections during the last 30 days (aOR = 2.37, 95% CI: 1.11-5.06), and parent/guardian education level (aOR = 0.08, 95% CI: 0.02-0.27). H influenzae was highly prevalent in healthy children in Qinghai Province, especially among children of minority ethnicities and those living in pastoral areas. Tobacco smoke exposure, having siblings <5 years of age, and respiratory infections during the last 30 days were risk factors for H influenzae carriage. Parents or guardians having education levels of college or higher was a protective factor for H influenzae carriage. It is of critical importance that the government take effective measures to reduce the carriage rate and the occurrence of H influenzae related diseases in susceptible populations.

Detection of SARS-CoV-2 in Air and on Surfaces in Rooms of Infected Nursing Home Residents.

There is an ongoing debate on airborne transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a risk factor for infection. In this study, the level of SARS-CoV-2 in air and on surfaces of SARS-CoV-2 infected nursing home residents was assessed to gain insight in potential transmission routes. During outbreaks, air samples were collected using three different active and one passive air sampling technique in rooms of infected patients. Oropharyngeal swabs (OPS) of the residents and dry surface swabs were collected. Additionally, longitudinal passive air samples were collected during a period of 4 months in common areas of the wards. Presence of SARS-CoV-2 RNA was determined using RT-qPCR, targeting the RdRp- and E-genes. OPS, samples of two active air samplers and surface swabs with Ct-value ≤35 were tested for the presence of infectious virus by cell culture. In total, 360 air and 319 surface samples from patient rooms and common areas were collected. In rooms of 10 residents with detected SARS-CoV-2 RNA in OPS, SARS-CoV-2 RNA was detected in 93 of 184 collected environmental samples (50.5%) (lowest Ct 29.5), substantially more than in the rooms of residents with negative OPS on the day of environmental sampling (n = 2) (3.6%). SARS-CoV-2 RNA was most frequently present in the larger particle size fractions [>4 μm 60% (6/10); 1-4 μm 50% (5/10); <1 μm 20% (2/10)] (Fischer exact test P = 0.076). The highest proportion of RNA-positive air samples on room level was found with a filtration-based sampler 80% (8/10) and the cyclone-based sampler 70% (7/10), and impingement-based sampler 50% (5/10). SARS-CoV-2 RNA was detected in 10 out of 12 (83%) passive air samples in patient rooms. Both high-touch and low-touch surfaces contained SARS-CoV-2 genome in rooms of residents with positive OPS [high 38% (21/55); low 50% (22/44)]. In one active air sample, infectious virus in vitro was detected. In conclusion, SARS-CoV-2 is frequently detected in air and on surfaces in the immediate surroundings of room-isolated COVID-19 patients, providing evidence of environmental contamination. The environmental contamination of SARS-CoV-2 and infectious aerosols confirm the potential for transmission via air up to several meters.