Pharyngeal Swabs Research Articles

Clinical aspects of human Bocavirus 1 in a sample of Egyptian infants with acute lower respiratory tract infection: A pilot study

Background/aim The recent advance in molecular technology permitted a comprehensive range of novel viral etiological causes to be detected in respiratory tract specimens. The human Bocavirus 1 (HBoV1) as a virus of the Parvoviridae family recently was defined as a human pathogen mainly linked to acute respiratory infection in children. Our aim was to identify the rate and seasonal variation of Bocavirus 1 infection and their correlation with the different clinical presentations in Egyptian infants less than 2 years old with acute lower respiratory tract infection. Patients and methods This study enrolled 100 infants aged from 4 weeks to 2 years presenting with symptoms of acute respiratory infection from Materia Hospital and Alzahraa University Hospital. Full medical history, general and local examination of the chest focusing on respiratory rate and plain chest radiograph were collected from each infant. In addition, pharyngeal swabs were collected from participated infants and were subjected to DNA extraction followed by PCR using different viral protein-targeted primer sets. Results Bronchopneumonia was the prominent diagnosis in the enrolled infants (38%) followed by bronchiolitis (34%) and bronchitis (28%) subsequently. The presence of HBoV1 among studied patients was 8% and the peak of the infection was in January (37.5%) followed by April (25%) and July (25%). Most of patients with HBoV1 positive were presented with respiratory distress and refusal of feeding. Seven percent of all patients were presented with diarrhea. Conclusions HBoV1 infection may be considered as a risk factor for lower respiratory tract infections in Egyptian children less than 2 years old.

Antimicrobial susceptibility of Moraxella catarrhalis in Russia: results of the PEGAS 2010–2021 multicenter study

Objective. To study the antimicrobial susceptibility profile of Moraxella catarrhalis isolates from different regions of Russia in 2010–2021. Materials and Methods. The study included 352 isolates of M. catarrhalis isolated in 11 cities of Russia (Volgograd, Irkutsk, Kazan, Kirov, Moscow, Murmansk, Perm, Seversk, Togliatti, Tomsk, and Ulan-Ude) in 2010–2021. Identification was done by MALDI-TOF mass spectrometry. Antimicrobial susceptibility testing was determined by broth microdilution method in accordance with the ISO 20776-1:2020. Interpretation of results was done in accordance with EUCAST guidelines (v.14.0). Results. Most of the isolates were isolated from respiratory specimens: 225 (63.9%) from sputum, 49 (13.9%) from nasal swabs, 41 (11.6%) from sinus aspirates, 17 (4.8%) from bronchoalveolar lavage, 8 (2.3%) from middle ear fluid, 6 (1.7%) from pharyngeal swabs, and 5 (1.4%) from conjunctival secretions. All tested isolates were susceptible to beta-lactams for which interpretive criteria have been established (amoxicillin-clavulanate, cefixime, ceftriaxone, cefuroxime). The susceptibility to clarithromycin and azithromycin was 99.7% and 100%, respectively. Ciprofloxacin, levofloxacin and moxifloxacin were active against 98.9%, 99.2% and 99.7% of isolates tested, respectively. Susceptibility to tetracycline was 99.7% and to trimethoprim-sulfamethoxazole was 99.4% (92% of isolates susceptible, 7.4% – susceptible at increased exposure). Conclusions. In the Russian Federation there is a favorable situation regarding the susceptibility of M. catarrhalis to antimicrobials. Amoxicillin-clavulanic acid, cefixime, ceftriaxone, azithromycin, clarithromycin, ciprofloxacin, levofloxacin, moxifloxacin and tetracycline retain high in vitro activity

Macrolide resistance of Mycoplasma pneumoniae in several regions of China from 2013 to 2019.

This paper retrospectively analysed the prevalence of macrolide-resistant Mycoplasma pneumoniae (MRMP) in some parts of China. Between January 2013 and December 2019, we collected 4,145 respiratory samples, including pharyngeal swabs and alveolar lavage fluid. The highest PCR-positive rate of M. pneumoniae was 74.5% in Beijing, the highest resistance rate was 100% in Shanghai, and Gansu was the lowest with 20%. The highest PCR-positive rate of M. pneumoniae was 74.5% in 2013, and the highest MRMP was 97.4% in 2019; the PCR-positive rate of M. pneumoniae for adults in Beijing was 17.9% and the MRMP was 10.48%. Among the children diagnosed with community-acquired pneumonia (CAP), the PCR-positive and macrolide-resistant rates of M. pneumoniae were both higher in the severe ones. A2063G in domain V of 23S rRNA was the major macrolide-resistant mutation, accounting for more than 90%. The MIC values of all MRMP to erythromycin and azithromycin were ≥64 μg/ml, and the MICs of tetracycline and levofloxacin were ≤ 0.5 μg/ml and ≤ 1 μg/ml, respectively. The macrolide resistance varied in different regions and years. Among inpatients, the macrolide-resistant rate was higher in severe pneumonia. A2063G was the common mutation, and we found no resistance to tetracycline and levofloxacin.

A multiplex recombinase polymerase amplification assay combined with CRISPR/Cas12a for the detection of respiratory syncytial virus and respiratory adenovirus.

Respiratory syncytial virus (RSV) and respiratory adenovirus (ADV) are two common pathogens that cause acute respiratory tract infections in children. We aimed to develop a rapid method for detecting both pathogens simultaneously. The recombinase polymerase isothermal amplification (RPA) method was combined with the CRISPR/Cas detection system. The assay's specificity and sensitivity were explored by designing RPA primers and CRISPR RNAs (crRNAs) through multi-sequence comparisons, optimizing the reaction conditions, and using a fluorescent reading device. The consistency of the test results of 160 clinical pharyngeal swab samples was studied using quantitative polymerase chain reaction (qPCR) results as a comparative control. RSV and ADV could be detected at levels as low as 104 copies/mL and 103 copies/mL, respectively, within 50 minutes with no cross-reactivity with other similar pathogens. For the clinical samples, compared with the qPCR method, the sensitivities for RSV and ADV were 98.1% and 91.4%, respectively, and the detection specificities were both 100%. The Kappa values were greater than 0.95, suggesting a high degree of consistency. This method for detecting RSV and ADV is rapid, sensitive, and specific. It can accurately detect mixed infections in a timely manner, making it suitable for use in areas with scarce healthcare resources.

Design and numerical-phase analysis of an SPR system for direct detection of SARS-CoV-2 virus in pharyngeal swab solution

An ultrasensitive differential-phase SPR biosensor has been successfully established, capable of direct detection of SARS-CoV-2 virus.

Evaluation of Hospitalized Patients with Community-Acquired Influenza-Like Illness During Two Influenza Seasons.

Influenza is among the most important respiratory infections affecting all age groups and can lead to hospitalizations. We aimed to determine the frequency of influenza infections among acute admissions with influenza-like illness (ILI) and evaluate the demographic, clinical findings, and outcomes of patients with influenza. This prospective, active surveillance study was conducted in a university hospital between 2015 and 2017. Patients hospitalized for at least 24 hours in the selected units with community-acquired ILI were screened according to certain influenza-predicting ICD-10 codes. Nasopharyngeal and pharyngeal swab samples were taken from patients who were eligible for the study. Patients tested for influenza with real-time polymerase chain reaction. Univariate and multivariate analyses were performed for data. Among 440 patients screened according to influenza-related ICD-10 codes, 112 were included. Influenza positivity was detected in 37 of the 112 patients. Clinical findings were similar between influenza positive and negative groups and also between influenza subtypes, excluding sore throat, which was more common in the H1N1 group. Alanine transaminase (ALT), aspartate transaminase (AST), and creatine kinase (CK) elevations were found to be significantly higher in the influenza-positive group. When influenza-positive patients with and without pneumonia were compared, the rate of vaccination in the same season was higher in patients without pneumonia than in patients with pneumonia (38.8% and 10.5%, respectively; p=0.04). Integrating molecular tests detecting both influenza and other respiratory viruses into influenza surveillance programs can increase the efficacy and quality of these programs. The elevation of AST, ALT, and CK in influenza cases can be considered in distinguishing influenza from other ILI cases. Vaccination in the same season can reduce the risk of pneumonia in influenza-positive patients.

Full Blood Count Parameters in COVID-19 Patients With Disease Severity, Patient Outcome and Vaccination Status

Introduction: A link between full blood count (FBC) parameters with the severity and prognosis of individuals with coronavirus disease 2019 (COVID-19) infection is shown. We aim to identify changes in FBC parameters depending on patients’ characteristics, the severity of the disease and vaccination status. Methods: A cross-sectional retrospective laboratory study is done on 208 respondents who were selected from February 2021 to December 2022 in the Pathology Department of the Tuanku Ja’afar Hospital in Negeri Sembilan. All patients are confirmed COVID-19 positive by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of pharyngeal and nasal swab specimens. Patients are further classified based on their COVID clinical stages, severity, vaccination status and outcome. The statistical data are analysed using IBM SPSS version 27. Results: Severe patients have significantly lower absolute lymphocyte count (ALC), absolute monocyte count (AMC), absolute eosinophil count (AEC) and absolute basophil count (ABC) but higher mean platelet volume (MPV), absolute neutrophil count (ANC), neutrophil to lymphocyte ratio (NLR) and immature granulocytes (IG) compared to non-severe patients (p < 0.05). Similar findings are seen among non-survivors (p < 0.05). Fully vaccinated patients have significantly lower NLR and MPV but higher ALC, AMC, AEC and ABC than unvaccinated or partially vaccinated patients (p < 0.05). Conclusion: Selected FBC parameters of COVID-19 patients (platelets, ANC, NLR, MPV, ALC, AMC, AEC, and ABC) are significantly different depending on patients’ severity, outcome and vaccination status. These results might give a clear insight for clinicians to anticipate the severity and outcome of patients based on the patient’s FBC parameters.

A semi-quantitative upconversion nanoparticle-based immunochromatographic assay for SARS-CoV-2 antigen detection.

The unprecedented public health and economic impact of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been met with an equally unprecedented scientific response. Sensitive point-of-care methods to detect SARS-CoV-2 antigens in clinical specimens are urgently required for the rapid screening of individuals with viral infection. Here, we developed an upconversion nanoparticle-based lateral flow immunochromatographic assay (UCNP-LFIA) for the high-sensitivity detection of SARS-CoV-2 nucleocapsid (N) protein. A pair of rabbit SARS-CoV-2 N-specific monoclonal antibodies was conjugated to UCNPs, and the prepared UCNPs were then deposited into the LFIA test strips for detecting and capturing the N protein. Under the test conditions, the limit of detection (LOD) of UCNP-LFIA for the N protein was 3.59 pg/mL, with a linear range of 0.01-100 ng/mL. Compared with that of the current colloidal gold-based LFIA strips, the LOD of the UCNP-LFIA-based method was increased by 100-fold. The antigen recovery rate of the developed method in the simulated pharyngeal swab samples ranged from 91.1 to 117.3%. Furthermore, compared with the reverse transcription-polymerase chain reaction, the developed UCNP-LFIA method showed a sensitivity of 94.73% for 19 patients with COVID-19. Thus, the newly established platform could serve as a promising and convenient fluorescent immunological sensing approach for the efficient screening and diagnosis of COVID-19.

КЛИНИЧЕСКИЙ СЛУЧАЙ ЛОНГ ИНФЕКЦИИ SARS-COV-2

Вackground. Coronavirus (COVID-19) infection caused by SARS-CoV-2 virus is associated with a wide spectrum of clinical respiratory syndromes ranging from mild upper respiratory tract symptoms to progressive viral pneumonia and systemic multinflammatory syndrome, as well as endothelial dysfunction and thrombotic complications. Despite the decline of the pandemic, the problem of the prolonged course of SARS-CoV-2 remains relevant. Aim of the study. To present a clinical case of Sars-Cov-2 long infection with development of severe lung and myocardial damage with negative results of PCR-analysis of pharyngeal and nasal swabs. Characteristics of patients and methods of research. A clinical case demonstrating a variant of prolonged course of coronavirus infection accompanied by the development of pneumonitis and myocarditis is presented in this work. Blood smear morphometry, monocyte analysis (flow cytometry), T lymphocyte analysis were performed in addition to standard methods of examination. Results and Conclusion. The presented clinical case demonstrates a variant of prolonged course of coronavirus infection, in which SARS-CoV-2 virus was encapsulated in the lungs and avoided the formation of a specific immune response. Severe lung and myocardial damage with negative results of PCR analysis of pharyngeal and nasal swabs was observed. Pulse therapy with corticosteroids resulted in regression of the disease.

Efficacy and viral dynamics of tecovirimat in patients with MPOX: A multicenter open-label, double-arm trial in Japan

IntroductionTecovirimat's application in treating mpox remains under-researched, leaving gaps in clinical and virological understanding. MethodsThe Tecopox study in Japan evaluated the efficacy and safety of tecovirimat in patients with smallpox or mpox, who were divided into oral tecovirimat and control groups. Patients with mpox enrolled between June 28, 2022, and April 30, 2023, were included. Demographic and clinical details along with blood, urine, pharyngeal swab, and skin lesion samples were gathered for viral analysis. A multivariable Tobit regression model was employed to identify factors influencing prolonged viral detection. ResultsNineteen patients were allocated to the tecovirimat group, and no patients were allocated to the control group. The median age was 38.5 years, and all patients were males. Ten patients (52.6%) were infected with human immunodeficiency virus (HIV). Sixteen patients (84.2%) had severe disease. Nine of the 15 patients (60.0%) (four patients withdrew before day 14) had negative PCR results for skin lesion specimens 14 days after inclusion. The mortality rates were 0% on days 14 and 30. No severe adverse events were reported. HIV status and the number of days from symptom onset to tecovirimat administration were associated with lower Ct values (p = 0.027 and p < 0.001, respectively). The median number of days when PCR testing did not detect the mpox virus in each patient was 19.5 days. ConclusionEarly tecovirimat administration might reduce viral shedding duration, thereby mitigating infection spread. Moreover, patients infected with HIV showed prolonged viral shedding, increasing the transmission risk compared to those without HIV.

Epidemiology of Chlamydia sp. infection in farmed Siamese crocodiles (Crocodylus siamensis) in Thailand

BackgroundAlthough Chlamydia sp. causes widespread disease outbreaks in juvenile crocodiles in Thailand, data regarding the epidemiology, and risk factors of such infections are limited. The aim of this study was to investigate the prevalence and possible risk factors associated with Chlamydia sp. infections on Siamese crocodile (Crocodylus siamensis) farms in Thailand. A cross-sectional study was conducted from July to December 2019. Samples were collected from 40 farms across six regions in Thailand. Conjunctival, pharyngeal, and cloacal swab samples were analyzed for Chlamydiaceae nucleic acids using semi-nested PCR followed by phylogenetic analysis based on the ompA gene fragment. Risk factors of infection were analyzed using chi-square and univariate regression to calculate odds ratios.ResultsThe prevalence of Chlamydia sp. infection across all regions was 65%. The ompA phylogenetic analysis showed that Chlamydia sp. detected in this study was genetically closely related to Chlamydia crocodili and Chlamydia caviae. The risk factors for infection were water source, reusing treated wastewater from the treatment pond, not disposing of leftover food, low frequency of water replacement in the enclosure of juvenile crocodiles, and lack of water replacement after the death of a crocodile.ConclusionThe prevalence of Chlamydia sp. infection in farmed crocodiles in Thailand was 65% during the study period. Cloacal swabs were superior to conjunctival and pharyngeal swabs due to their higher sensitivity in detecting Chlamydia sp., as well as their lower invasiveness. Good management and biosecurity in crocodile farming can reduce the risk of Chlamydia sp. infection.

Acute phase protein concentration in pharyngeal swabs from clinically healthy commercial dairy calves

BackgroundEarly diagnosis of disease in calves is crucial for fast recovery and prudent use of antibiotics. The serum concentration of acute phase proteins (APPs) is up- or downregulated in response to tissue injury and has been studied widely in human medicine. There is growing interest in using APPs as biomarkers for different diseases and as a tool to initiate and monitor treatment in veterinary medicine as well. The concentration of APPs in saliva in healthy calves has not been established and the use of pharyngeal swabs offers a non-invasive alternative to blood sampling. Pharyngeal swabs, tracheal aspirate (TA) and blood samples were collected from 84 clinically healthy commercial dairy calves and analyzed for the APPs serum amyloid A (SAA), haptoglobin (Hp) and lipopolysaccharide binding protein (LBP).ResultsWe found detectable concentrations of SAA, Hp and LBP in pharyngeal swabs from calves, as well as in TA and serum. There were no biologically interesting correlations between the SAA concentrations in serum and TA or pharyngeal swabs. This also applied to Hp and LBP concentrations in serum and TA or pharyngeal swabs.ConclusionsSAA, Hp and LBP can be measured in saliva and TA from calves, but there was no correlation between the specific APP concentration in serum and pharyngeal swab or TA. There was a considerable technical variation in the sampling method for both pharyngeal swab and TA, and further validation of the methods is needed.

Comparison of culture and PCR-DGGE methods to evaluate the airways of cystic fibrosis patients and determination of their antibiotic resistance profile.

Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity. Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing. Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture. Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method.

A High Copy Number from a Pharyngeal Swab Is Not Associated with Different Presenting Features in 100 Children with Acute Adenovirus Infection from a Cluster in Italy.

Human mastadenoviruses, frequently denominated adenoviruses (HAdVs), may cause respiratory tract, gastrointestinal or, less frequently, other involvements. Epidemics of HAdV infections occur globally, in communities, and in closed or crowded settings. In our institution, a cluster of infants and children admitted for HAdV infection was recently observed. The aim of this study was to describe the pattern of their presenting features and investigate the possible correlation between the HAdV copy number and the clinical picture. Two main patterns of clinical presentation were observed: 68 patients had mainly respiratory symptoms (pharyngitis n = 67, cough n = 44; tonsillar exudate n = 17; other respiratory signs n = 4) while 26 patients showed prevalent gastrointestinal involvement (diarrhea n = 26, vomiting n = 8). Patients with respiratory symptoms had a significantly higher count of WBC, PMN, and platelets, while CRP level approached statistical significance (p = 0.07) for higher values in the patients with diarrhea. In order to explore the impact of selected presenting features, the possible association between the level of CRP and the presence of pharyngeal exudate, cough, vomiting, diarrhea, duration of fever, number of neutrophils, and administration of antibiotics was analyzed. Patients falling in the tertile with more elevated CRP values had tonsillar exudate and diarrhea significantly more often, while those in the lower tertile had a 4.4-day duration fever vs. ≥5.0 days in the remaining patients. Antibiotic therapy was administered more frequently to patients with higher values of CRP (p = 0.006). The duration of hospitalization was not associated with the CRP level. The median time from the receipt of a positive HAdV PCR test result to patient discharge was 1 day in 73% of cases. The number of copies of HAdV detected via PCR ranged between 47 million and 15/μL. Falling in the highest tertile of copy number was significantly associated with pharyngitis. The 24 patients with evidence of viral coinfection had no difference in the demographics or presenting features, with the only exception being a significantly higher leukocyte count. The rapid turn-around of the results of the molecular testing of the HAdV genome on a pharyngeal swab allowed us to rapidly diagnose HAdV infection, allowing us to stop antibiotic therapy and immediately discharge the patients, with reduced discomfort for the families and more appropriate use of hospital beds. A high copy number of HAdV from a pharyngeal swab should not be taken as an indicator of worse prognosis, thus allowing for the preferential use of qualitative rather than quantitative assay.

Human Papillomavirus (HPV) Infections Among Participants Undergoing Chlamydia trachomatis Testing in Reunion Island (RUN-SurV-HPV Study): Protocol for a Prevalence Study.

Infection by human papillomavirus (HPV) induces various cancers, mainly cervical cancer but also anal and pharyngeal cancers. Reunion Island is a French department in the Indian Ocean. Due to the history of its settlement, the island's population has a wide variety of origins, and the population's sociodemographic characteristics differ from those of the French mainland. These characteristics make the island's population an original French population in its own right, particularly in terms of health. Cervical cancer incidence and mortality in Reunion Island are 10.4 per 100,000 and 4.4 per 100,000, respectively, both of which are much higher than those in mainland France. There is also a disparity in the prevalence of different HPV types, with types 33 and 52 being overrepresented and type 18 being underrepresented. However, vaccination and screening coverage in Reunion Island is low. It is important to understand the burden of infection and its risk factors in members of the young Reunionese population at risk of HPV infection to promote and evaluate the implementation of future vaccination and screening programs on a larger scale. The RUN-SurV-HPV study will have the following four objectives: (1) to describe the prevalence of HPV genotypes in a population at risk of sexually transmitted infections in Reunion Island; (2) to describe the prevalence of HPV genotypes by anatomical site, gender, and sexuality; (3) to describe the correlates and risk factors for HPV detection; and (4) to examine HPV genotypes between different anatomical sites. Cross-sectional analyses of 1200 routine vaginal, anal, pharyngeal, and urinary samples collected between October 2020 to December 2022 from female and male patients aged 16 to 30 years undergoing Chlamydia trachomatis testing at a sexually transmitted infection (STI) testing center at Reunion Island will be performed. The population included 333 women who all had vaginal and pharyngeal swabs, with 80 of them also having had an anal swab. There are 167 men who have sex with men who have had anal and pharyngeal swabs, and 120 men who have sex with women who have had a urine swab only. Results will be correlated with sociodemographic and clinical data collected routinely during the consultations. HPV detection and genotyping will be performed using the Anyplex II HPV28 detection assay (Seegene). The first polymerase chain reactions should begin in November 2023. The first results should be submitted for publication in 2024. The study will determine HPV prevalence by age, sex, male sexual preference, human immunodeficiency virus status, and STI co-infection. Collecting data from young patients not usually routinely screened for HPV infection will be a simple and reproducible way of better understanding local specificities, encouraging vaccination campaigns in the short-term, and evaluating their effectiveness in the future. DERR1-10.2196/47379.

Design and application of a pharyngeal swab samples collection device

Design and application of a pharyngeal swab samples collection device

Management and control of an outbreak of NDM-producing Klebsiella pneumoniae in a teaching hospital

Abstract Background Outbreaks caused by New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae are a major public health threat. We report an outbreak caused by NDM-producing Klebsiella pneumoniae (KP) in an Italian teaching hospital and describe the composite management approach that led to a successful containment. Methods On August 12 2022, a 39-year old Ukrainian patient with known colonization (rectal swab) by NDM-producing KP was admitted to the Hematology Unit of the University Hospital of Verona, Italy. Six days after, a second patient tested positive for carbapenem-resistant (CR) KP from rectal swab and 2 additional cases (rectal and pharyngeal swab respectively) were identified in the following 2 weeks. The 4 cases were identical strains. Results A multidisciplinary team coordinated the response actions. Isolation measures were ordered for positive patients, including use of dedicated instruments. Screening at admission and every 7 days was placed for all the ward patients. On-site inspections and microbiological screening of ward surfaces and devices were carried out. Infection prevention and control (IPC) measures were strengthened among personnel. Environmental cleaning was implemented by deep treatment of critical points (e.g. toilets) and reinforcement of routine cleaning. The Risk Manager developed an original checklist based on literature to review the implementation of IPC practices for CR Enterobacteriaceae. No new cases were identified from screening in the following weeks and the Unit returned to standard IPC measures. Given that environmental samples were negative and the cases had overlapping personnel, the hypothesis of contact transmission through caregivers was the most plausible. Reinforcement of training on hand hygiene and transmission-based precautions was planned. Conclusions It was possible to contain the hospital outbreak through rapid and diversified reaction capacity. Continuous IPC education is an essential control measure. Key messages • The spread of NDM-producing Enterobacteriaceae in the hospital setting must be countered with enhanced prevention and, in case of outbreak, rapid control. • Effective containment involves a mix of established measures (screening, hygiene, environmental controls) and innovative approaches (e.g. literature-based checklists).

Pooled Pharyngeal, Rectal, and Urine Specimens for the Point-of-Care Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Lay Providers in Key Population-Led Health Services in Thailand.

Routine testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) in people with heightened risk is lacking in Thailand. This study aimed to assess the performance of the Cepheid Xpert CT/NG assay, conducted by key population (KP) lay providers, for CT and NG detection on single-site and pooled specimens from the pharynx, rectum, and urine. Between August and October 2019, 188 men who have sex with men and 11 transgender women were enrolled. Participants collected urine specimens while trained KP lay providers obtained pharyngeal and rectal swabs. Compared to single-site testing with the Abbott RealTime CT/NG assay by medical technologists, the Xpert assay missed one pharyngeal NG infection out of 199 single-site specimens, giving a 93.3% sensitivity for pharyngeal NG and one missed pharyngeal NG infection out of fifty pooled specimens, giving an 88.9% sensitivity for pharyngeal NG. There was no discrepancy between the two assays for CT detection. The Cohen's Kappa coefficient of pooled specimen testing by the Xpert was 0.93 for NG and 1 for CT when compared to single-site testing by Abbott. Implementing pooled specimen testing by KP lay providers can be a cost-saving strategy to enhance the uptake of CT/NG services for populations facing increased risk.

Evaluation of Eazyplex® LAMP test for fast Candida auris direct detection of colonized patients.

Candida auris is a multidrug-resistant pathogen yeast that produces nosocomial outbreaks, due to its ability in colonizing the skin, mucous membranes and surfaces. Rapid diagnosis is essential to control its spread. The aim of this study was to compare the Eazyplex® Candida auris kit (AmplexDiagnostics GmbH) for the rapid identification of patients colonized with C. auris, with the reference method used in our institution (culture and identification by MALDI-TOF). This easy-to-perform test allows obtaining a fast result, in ~30 min. First, we achieved a preliminary study from previously characterized Candida species colonies obtained from 51 clinical samples, with 100% agreement between culture isolation and the Eazyplex® Candida auris LAMP. Second, 152 epidemiological surveillance samples (pharyngeal and axillary-rectal swabs) were tested retrospectively. The sensitivity, specificity, positive and negative predictive values were 91.8%, 98.8%, 98.2% and 94.5%, respectively. Eazyplex® Candida auris showed acceptable results compared with culture in detecting C. auris from surveillance samples with the advantage of single-test and shorter time for handling and result than culture, in addition to its great specificity, positive and negative predictive values.

Self-sampled multi-anatomic site testing for uncovering the community burden of undiagnosed Chlamydia trachomatis and Neisseria gonorrhoeae infection in men who have sex with men.

To detect otherwise undiagnosed asymptomatic sexually transmitted infection (STI), and for estimating prevalence among men who have sex with men (MSM). In this community-based study in Hong Kong, adult MSM were recruited. After completion of an online survey, free multi-anatomic sites self-sampling kits (urine specimens, pharyngeal and rectal swabs) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) tests were delivered to requesting participants. Factors associated with STI positivity were analyzed in logistic regression. From September 2021 to October 2022, 712 MSM were recruited, with 86% aged 18-39, and 16% reported history of chemsex engagement. A majority (81%) had previously undergone HIV testing, 68% had ever tested for STI, and 35% previously diagnosed with STI. Totally 428 (60%) had requested self-sampling kits, and 276 (39%) returned collected samples. Among participants who returned the samples, about half had never been tested in the past and had no history of STI. Overall 21% tested positive for CT and/or NG (CT/NG)-CT positive 16% and NG positive 7%. By anatomic site, 16% of rectal swabs, 7% of pharyngeal swabs, but just 3% of urine specimens were CT/NG positive. The prevalence of CT/NG was not significantly different by history of STI diagnosis and testing. Self-sampled STI testing is a potentially useful means for enhancing uptake of screening in MSM in the community, which could uncover otherwise undiagnosed asymptomatic infections. Internet-based self-sampling for STI testing could complement the current clinic-based STI testing for supporting epidemiologic evaluation of STI control in the community.