Identification of Risk Factors for Nasal Colonization of Methicillin-resistant Staphylococcus aureus and Vancomycin-resistant Staphylococcus aureus in Health Workers at a Tertiary Hospital, Indonesia

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) and Vancomycin-resistant S. aureus (VRSA) frequently cause nosocomial infections yearly. During the COVID-19 pandemic, the potential for excessive use of antibiotics is a global threat to the increasing incidence of multiresistant bacteria. AIM: This study aimed to determine MRSA and VRSA colonization and identify factors associated with the risk of MRSA and VRSA nasal colonization in health workers at Dr. Soemarno Sosroatmodjo General Hospital, Kuala Kapuas, as one of the type C hospitals in Indonesia. METHOD(S): This cross-sectional analytic study at Dr. Soemarno Sosroatmodjo General Hospital, a tertiary hospital in Indonesia. A 128 health workers' subjects had undergone nasal swab screening for MRSA and VRSA colonization examinations. Then, they were asked to complete a questionnaire concerning the risk factors of MRSA and VRSA infections. RESULT(S): Nasal swab results obtained as many as 30 (23.5%) MRSA positive subjects and 6 (4.7%) subjects with positive VRSA. The most common risk factors that led to MRSA colonization included a history of positive MRSA in the previous hospital (60%), a history of ear, nose, and throat infection (41.7%), and did not do hand rub/handwash (36.7%). In comparison, the most risk factors for VRSA colonization were having pigs farm at home (33.3%), a history of positive MRSA in the previous hospital (20%), and a history of hospitalization in the past 6-12 months (16.7%). The results of multivariate analysis showed the most powerful and statistically significant risk factors in influencing nasal MRSA colonization were a history of positive MRSA in the previous hospital (OR 13.69, 95% confidence intervals [CI]: 1.34-140.25, p = 0.028) and did not do hand rub/handwash (OR 2.95, 95% CI: 1.167-7.49, p = 0.023). Meanwhile, marital status (OR 0.160, 95% CI: 0.02-1.06), p = 0.058) and home care service (OR 6.10, 95% CI: 0.79-46.96, p = 0.082) were the strongest risk factors for nasal colonization of VRSA but not statistically significant. CONCLUSION(S): As many as, 23.5% and 4.7% of healthcare workers' subjects were found with nasal colonization of MRSA and VRSA, respectively. Accordingly, strict policies are needed to minimize the transmission of these organisms from the hospital setting to the community.Copyright © 2023 Siti Nur Rohmah, Rizka Humardewayanti Asdie, Ida Yosopa, Daya Daryadijaya.

Screening Strategies in Different Resource Settings

Health care-associated infections/ Hospital-acquired infections (HAIs) have a significant impact on patients' morbidity and mortality. The risk of HAIs in resource-limited settings (RLS) has been reported 2-20 times higher than that in developed countries. Moreover, multi-drug- resistant organisms (MDROs) have emerged and spread throughout the world. In addition, increases in HAIs were observed during the COVID-19 pandemic throughout the world.Thus, screening strategies/surveillance of MDROs were recommended as a core component of infection prevention and control (IPC) measures for the effective HAIs prevention. We review and summarize current critical knowledge on screening strategies in different resource settings, especially on guidelines for the prevention and control of carbapenem- resistant Enterobacteriaceae (CRE), Acinetobacter baumannii (CRAB), and Pseudomonas aeruginosa (CRPsA) in health care facilities. The guidelines (especially WHO) were strongly recommended for surveillance of CRE-CRAB-CRPsA infections and surveillance cultures of asymptomatic CRE colonization. There were conditional recommended on surveillance cultures of the environment for CRE-CRAB-CRPsA colonization/contamination. The surveillance cultures (stool samples or rectal swabs) allowed the early introduction of IPC measures to prevent transmission to other patients and the hospital environment. Given the clinical importance of CRE-CRAB-CRPsA infections, regular ongoing active surveillance of infections were required in all microbiology laboratory settings. In addition, surveillance cultures for asymptomatic CRE colonization should also be performed, guided by local epidemiology and risk assessment. The surveillance cultures of asymptomatic CRE colonization should be considered for patients with previous CRE colonization and patients with a history of recent hospitalization in endemic CRE settings or contacted CRE colonized/ infected patients. In contrast, the evidence available on surveillance cultures for CRAB and CRPsA colonization in asymptomatic patients was not sufficiently relevant for the recommendation. Nowadays, the CRE surveillance strategies have been implemented in various methods from traditional culture- based methods to molecular assays. The limitation of microbiology laboratory capacity for MDROs in RLS was concerning. However, the surveillance data would help with appropriate IPC measure implementation and outbreak investigations. Thus, the proper screening strategies and strengthening microbiology laboratory capacity, especially in RLS are challenge for improving IPC measures and patient outcomes.Copyright © 2023

Helicobacter Pylori and Sars-Cov-2: A Dangerous Pathogenetic Correlation?

Background and aim: The correlation between Covid-19 and nonrespiratory bacteria is mostly unexplored. The following considerations led us to investigate a possible correlation between Hp and SARS-CoV2: both are microbial agents with a very large-scale epidemiology;both can cause GI symptoms;both can persist in the GI tract for long time [Fei Xiao, 2022];patients with pre-existing HP gastric colonization, once infected by SARS-CoV-2, complain more frequently and with greater severity of GI symptoms such as abdominal pain and diarrhea [Balamtekin, 2019];SARS-CoV-2 binds ACE-2 receptors to enter cells, which are widely expressed in the GI tract. In addition, Hp is known to increase the expression of ACE-2 receptors. This study aims to investigate, by C13 Urea BT, the prevalence of Hp infection and the DOB (delta over baseline), in pre-pandemic period (pPP), from Sept. 2017 to Dec. 2019, and during Covid-19 pandemic period (PP), from Jan. 2020 to Apr. 2022, to evaluate whether SARS-CoV-2 and Hp infection association is only due to chance or whether represents a pathogenetic correlation. Material(s) and Method(s): This is a retrospective preliminary study on 1532 randomized patients: 825 and 707 referring respectively to pPP and PP. Result(s): 316 patients underwent C13 Urea BT for the diagnosis of Hp infection: 36 out of 179 (20.11%), and 74 out of 137 (54.01%), respectively in pPP and in PP, tested positive for Hp. The DOB of patients tested during the PP was 40.4+/-17.5, significantly higher when compared to the mean value found in pPP: 17.4+/-16.5 (p=0.0001). [Figure presented] Conclusion(s): Neglecting the search for Hp, also due to difficulties encountered in this period to access BT, represents a risk condition for gastric diseases, especially considering the remarkable elevation of the prevalence and the DOB caused, somehow, by the SARS-CoV-2 virus. Particularly, the higher the DOB, the higher the bacterial load, but, more significantly, the greater the ability of the bacterial strains to produce urease: the strains with the greatest urease-activity are cagA+ strains (those capable of producing the oncogenic protein involved in the process of carcinogenesis) [Moreno-Ochoa, 2020]. Thus, it can be assumed that the higher the DOB, the greater the risk of developing serious gastric problems in the absence of treatment. So, in conclusion, Sars-Cov-2 and HP infection may influence each other. GI morphological and functional alterations due to Sars-Cov-2 infection, which can promote HP colonization and replication, need further investigation.Copyright © 2023. Editrice Gastroenterologica Italiana S.r.l.

Microbiological monitoring of COVID-19 patients in the ICU: a prospective observational study.

Objective. To study spectrum of pathogens and the time to colonization of respiratory samples in patients with severe and critical COVID-19 as well as to analyze incidence of nosocomial infections and structure of prescribed antibacterial drugs. Materials and methods. The prospective observational study included patients aged 18 years and older with confirmed severe and critical COVID-19 from December 2021 to February 2022. During the first 48 hours and then every 2-3 days of hospitalization, a respiratory sample was collected: sputum, tracheal aspirate (if intubated), bronchoalveolar lavage (if bronchoscopy was performed) for microscopy and microbiological examination. Some patients were screened for invasive aspergillosis. Clinical and demographic data, comorbidities, pathogenetic therapy for COVID-19, antibiotic therapy, cases of probable/documented bacterial nosocomial infections, antibiotic-associated diarrhea, and hospital treatment outcomes were recorded. Results. A total of 82 patients were included in this study. Patients with lung parenchyma involvement of more than 50% by computer tomography predominated;most of them (77%) required intubation and mechanical ventilation due to progression of respiratory failure, and 76% of patients had a lethal outcome. During the first 48 hours, a respiratory sample was obtained from 47 patients;the rest of the patients presented with non-productive cough. No growth of microorganisms was detected in 31 (36.8%) cases;clinically significant pathogens were detected in 16 (19.5%) patients. A subsequent analysis included data from 63 patients with a sufficient number of samples for dynamic observation were used. During the first 3 days of ICU stay, the most common bacterial pathogens were Klebsiella pneumoniae without acquired antibiotic resistance and methicillin-susceptible Staphylococcus aureus. From 3rd day and afterwards, an increase in the proportion of Acinetobacter baumannii, other non-fermenting bacteria, and carbapenem-resistant Enterobacterales was noted. Among the pathogens causing lower respiratory tract infections, A. baumannii and carbapenem-resistant K. pneumoniae were predominant pathogens and accounted for 76% of cases. Positive galactomannan test results were obtained in 4 cases. Conclusions. The study confirmed importance of bacterial nosocomial infections in patients with severe and critical COVID-19. In the case of the development of nosocomial lower respiratory tract infections, empirical antimicrobial therapy should take into account the predominance of carbapenem-resistant Enterobacteria and A. baumannii, as well as the possibility of invasive aspergillosis.Copyright © 2022, Interregional Association for Clinical Microbiology and Antimicrobial Chemotherapy. All rights reserved.

Peculiarities of Periodontal Pocket Microbiome in Patients with Generalized Periodontitis in the Post-Covid Period

The oral cavity, like the lungs, is often referred to as the <<ecological niche of commensal, symbiotic, and pathogenic or-ganisms,>> and the emigration and elimination of microbes between them are constant, ensuring a healthy distribution of saprophytic microorganisms that maintains organ, tissue, and immune homeostasis. The prolonged hospital stays due to COVID-19 complications, cross-infection, oxygenation therapy through the mask or incubation, and long-term intravenous infusions limit the patient's ability to care about the oral cavity, regularly clean teeth, floss interdental, etc., which creates extremely favorable conditions for colonization by aerobic and anaerobic pathogens of the oral cavity and periodontal pockets and leads to the rapid progression of chronic generalized periodontitis in this category of patients in the future. The goal of the study was to assess the state of the microbiome of the periodontal pockets of dental patients in the post-covid period. Methods. The object of the study was 140 patients with generalized periodontitis of the I and II stages of development in the chronic course (GP), among which 80 patients had coronavirus disease in the closest past. The patients were randomized by age, sex, and stage of GP development. The diagnosis of periodontal disease was established according to the classification by Danilevskyi. The bacteriological material for aerobic and facultative anaerobic microflora and yeast-like fungi was collected from periodontal pockets with a calibrated bacteriological loop and immediately seeded on blood agar. Results. Significant qualitative and quantitative changes in the nature of the oral microbiocenosis were observed in patients with GP after the recent coronavirus disease, compared with similar patients who did not suffer from COVID-19. We have noticed almost complete disappearance of bacteria that belong to the transient representatives of the oral microflora such as Neisseria, corynebacteria (diphtheria), micrococci, and lac-tobacilli. The main resident representatives of the oral microflora, i.e., alpha-hemolytic Streptococci of the mitis group, were found in all healthy individuals and patients of groups A and C, but in 30.0 +/- 4.58% of patients in group B, alpha-hemolytic streptococci in the contents of periodontal pockets are present in quantities not available for detection by the applied method (<2.7 lg CCU/mL). In terms of species, Streptococcus oralis and Streptococcus salivarius are more characteris-tic in gingival crevicular fluid in healthy individuals (93.8% of selected strains). In 68.4 +/- 3.32% of patients in group A, 64.0 +/- 3.43% of patients in group B, and 67.5 +/- 3.76% of patients in group C, the dominant species were Streptococcus gordonii and Streptococcus sanguinis (p<0.01), which increased pathogenic potential as they produce streptolysin-O, inhibit complement activation, bind to fibronectine, actively form biofilms on the surface of tooth enamel and gum epithelial surface, and can act as an initiator of adhesion of periodontal pathogens. The other representatives of the resident microflora of the oral cavity - Stomatococcus mucilaginosus and Veillonella parvula for the patients of group C are also found in periodontal pockets with a significantly lower index of persistence and minimal population level. In the post-covid period, both the population level and the frequency of colonization of periodontal pockets by Staphylo-cocci and beta-hemolytic Streptococci decreases rapidly. For these patient groups, unlike for those that did not suffer from COVID-19, we did not find any case of colonization with Staphylococcus aureus, as well as beta-hemolytic Streptococci and Epidermal staphylococcus were also absent. The most characteristic in the post-covid period is a decrease in the proportion of alpha-hemolytic Streptococci, an increase in the proportion of yeast-like fungi of Candida species, as well as the appearance of a significant number of gram-negative rod-shaped bacteria (Enterobacteria and Pseudomonads). In periodontal patien s, the microbial count is approximately 2 orders of magnitude lower than in those with GP who did not suffer from COVID-19 (p<0.05). Conclusions. The overpassed coronavirus disease due to intensive antibiotic therapy leads to a marked decrease in the number of viable saprophytic microorganisms in the periodontal pockets of patients with GP. In the post-covid period for the patients with GP, there is a decrease in the level of colonization of periodontal pockets by species of resident oral microflora - alpha-hemolytic Streptococci, reduction of resident micro-organism's species, and almost complete disappearance of transient microflora. On the other hand, the frequency of colonization of periodontal pockets by fungi species, enterobacteria, and pseudomonads significantly increases. There are more expressed disorders in the periodontal pocket's microbiome for the patients with a severe and complicated course of coronavirus disease, such as post-covid pulmonary fibrosis, which requires reconsideration of approaches to therapeutic and pharmacological treatment in this category of patients.Copyright © 2022, Zabolotny Institute of Microbiology and Virology, NAS of Ukraine. All rights reserved.

Intestinal Carriage of Carbapenemase-Producing Enterobacteriaceae Members in Immunocompromised Children During COVID-19 Pandemic

Background: Hospital-acquired infection with carbapenem-resistant Enterobacteriaceae (CRE) is a global concern. The administration of antibiotics among the infected and non-infected immunocompromised children with SARS-CoV-2 is associated with an increased risk of intestinal CRE colonization and bacteremia during hospitalization. Objective(s): The present study aimed to detect the correlation between the intestinal colonization of carbapenemase encoding Enterobacteriaceae with SARS-CoV-2 infection and antibiotic prescription among immunocompromised children admitted to the oncology and Bone Marrow Transplantation (BMT) wards. Method(s): Stool samples were collected from the immunocompromised children, and the members of Enterobacteriaceae were isolated using standard microbiological laboratory methods. Carbapenem resistance isolates were initially characterized by the disc diffusion method according to CLSI 2021 and further confirmed by the PCR assay. SARS-CoV-2 infection was also recorded according to documented real-time PCR results. Result(s): In this study, 102 Enterobacteriaceae isolates were collected from the stool samples. The isolates were from Escherichia spp. (59/102, 57.8%), Klebsiella spp. (34/102, 33.3%), Enterobacter spp. (5/102, 4.9%), Citrobacter spp. (2/102, 1.9%), and Serratia spp. (2/102, 1.9%). The carbapenem resistance phenotype was detected among 42.37%, 73.52%, 40%, 50%, and 100% of Escherichia spp., Klebsiella spp., Enterobacter spp., Citrobacter spp., and Serratia spp., respectively. Moreover, blaOXA-48 (49.1%) and blaNDM-1 (29.4%), as well as blaVIM (19.6%) and blaKPC (17.6%) were common in the CRE isolates. SARS-CoV-2 infection was detected in 50% of the participants;however, it was confirmed in 65.45% (36/55) of the intestinal CRE carriers. The administration of antibiotics, mainly broad-spectrum antibiotics, had a significant correlation with the CRE colonization in both the infected and non-infected children with SARS-CoV-2 infection. Conclusion(s): Regardless of the COVID-19 status, prolonged hospitalization and antibiotic prescription are major risk factors associated with the CRE intestinal colonization in immunocompromised children. Copyright © 2023, Author(s).

Prostate abscesses in patients with COVID-19 treated with genetically engineered biological drugs: IL-6 inhibitors

Introduction: Prostate abscess is a rare complication of acute bacterial prostatitis and accounts for 0.5-2.5% of patients with prostatitis. IL-6 is an immunoregulatory cytokine with multiple biological activities, one of which is urothelial immune defense against bacteria. Prostate abscess clinical presentation in patients with diabetes mellitus and immunodeficiency does not follow the standard criteria. We registered an increased number of prostate abscesses in patients with COVID-19 within a limited time. Method(s): Patients with drainable abscesses according to transrectal ultrasound and pelvic MRI underwent transperineal drainage of the prostate abscess (8 patients of 11). A safety drain was installed into the abscess cavity;trocar cystostomy and antibiotic therapy were performed. Result(s): Within 6 months, 11 cases of prostate abscesses were detected;surgery was performed in 8 cases. However, 9 patients out of 11 had prostate abscesses in the peripheral zone. The average age was 72.8 (43-83) years. All patients received IL-6 inhibitors, followed by glucocorticoid therapy in eight cases. Leukopenia and no CRP elevations in the presence of fever were detected in eight patients. Procalcitonin test showed a bacterial infection only in 5 out of 11 patients. In all eight surgery cases, the aspirate was found in the culture with varying degrees of colonization: Klebsiella pneumonia 105 CFU (in seven patients), 107 CFU (in one patient). The average drainage time was 8 days. Two cases with minor abscesses were fatal. Conclusion(s): Based on the 6-month clinical data, we can estimate an increase in the number of prostate abscesses in patients undergoing COVID-19 therapy and detected a change in their standard localization. The rising number of abscesses within 6 months may be considered as a concomitant risk factor, in particular, due to prolonged urethral catheter-associated bladder drainage, immunosuppressive therapy, and the shutdown of the main local regulatory mechanism of the body's immune response to bacterial infection, mediated by IL-6.

Pediatric Group A Streptococcus (GAS) Pharyngitis Incidence has Decreased During the COVID-19 Pandemic

Background. The COVID-19 pandemic has affected respiratory disease epidemiology. Measures to reduce transmission of SARS-CoV-2 (e.g., masking, social distancing, school closures) have reduced the incidence of common infectious diseases. At least one early report described changes in rates of pediatric GAS pharyngitis. We sought to determine the difference in GAS pharyngitis rates before and after the onset of the pandemic at our children's hospital. Methods. Clinical pharyngeal specimens tested for GAS by rapid antigen tests (RADTs) or LAMP methodology (loop-mediated isothermal amplification of GAS DNA) from January 2019 to March 2022 at our children's hospital were analyzed. Clinician's evaluating patients for GAS pharyngitis perform a RADT, when positive the patient is treated for GAS pharyngitis. When the RADT is negative, a LAMP test is performed. Patients were considered test-positive if either test was positive regardless of clinical symptoms. Annual positivity rates were compared using statistical process control (SPC) charts with both 2019 and 2020 as baseline years (i.e., 2019 vs 2020-3/2022;2020 vs 2021-3/2022). The change in GAS incidence rate (positive patients/ 1000 tested) between years was assessed by chi-square tests. Results. 9,896 patients had throat swabs tested for GAS from January 2019 through March 2022. Using SPC with 2019 as a baseline, there was a 15.1% decrease in mean GAS positivity through 3/2022. With 2020 as baseline, there was a 13.0% decrease in mean GAS positivity through 3/2022. The incidence of positive GAS tests decreased significantly: 2019 vs. 2020-3/2022 (x2 = 84.97, p <=0.00001) and 2020 vs. 2021-3/2022 (x2 = 154.01, p <=0.00001). Figure 1. Conclusion. Using throat swab results, the incidence of pediatric GAS pharyngitis at our hospital has decreased significantly during the COVID-19 pandemic. Implications: Pandemic-related riskmitigationmeasures, such asmasking, social distancing, and school closures, were associated with significantly decreased incidence of GAS pharyngitis. It is likely that GAS colonization and invasive infections were also affected.

Increased Prevalence of Group A Streptococcus (GAS) High Level Macrolide Resistance During the COVID-19 Pandemic

Background. COVID-19 affected the epidemiology ofmany respiratory pathogens including GAS. Assessing genetic heterogeneity (emmtype, antimicrobial resistance, virulence factors) can inform treatment recommendations and targets for potential GAS vaccines. We assessed GAS clinical antibiotic susceptibility and performed whole genome sequencing (WGS) among pediatric pharyngeal isolates from 2020-2022. Methods. From 1/2020-3/2022 we collected throat swabs in pediatric clinics and EDs from children aged 3-18 years in Chicago, IL;Atlanta, GA;Portland, OR;and Phoenix, AZ: 1) with acute GAS pharyngitis and 2) among a convenience sample of asymptomatic children to assess for GAS colonization. Swabs were plated on blood agar. E-tests were used to assess clinical susceptibility to erythromycin (ERY) and ciprofloxacin (CIP). emm type and antimicrobial resistance genes (ERY, Clindamycin (CLI), and fluoroquinolones) were assessed by WGS. Results. 1144 pharyngeal swabs were collected: 359/684 (52%) from children with GAS pharyngitis by rapid test and 20/460 (4.3%) from asymptomatic children yielded GAS on culture. Phenotypic resistance: 55/364 (15%) tested isolates were ERY resistant and 5/364 (1.4%) CIP resistant. The proportion of isolates with ERY resistance increased significantly from 2020 (6%) to 2021-2022 (25%) (chi2 = 23.70, p< .00001) (Figure 1). MICs were high among ERY resistant GAS (Table 1). Genotypic resistance: Of 304 sequenced GAS isolates 40/304 (13%) were ERY resistant, 35/304 (11.5%) were both ERY resistant and CLI (inducible or constitutive) resistant, and 4/304 (1.3%) fluoroquinolone resistant. ermB (62%) was the most common gene for ERY resistance and constitutive CLI resistance, followed by ermTR (23%) and ermT (11%) both conferring inducible CLI resistance. Among the 20 isolates from asymptomatic children no ERY, CLI, or CIP resistance occurred, and no resistance genes were identified. emm types 11, 9, 77, 58 and 94 were associated with ERY and CLI resistance. Conclusion. ERY resistance increased from 2020-2022. The high rate of CLI resistance among ERY resistant GAS was associated with erm genes. These results are important to inform treatment recommendations for GAS pharyngitis and targets for vaccine development that can reduce antimicrobial-resistant GAS disease.

Use of a multiplex PCR assay for detection of respiratory co-infections in COVID-19 hospitalized non-ICU patients: an ace up a clinician's sleeve

Background. Bacterial co-infections in COVID-19 patients represent a significant challenge for clinicians and can impact outcomes. Rapid identification of bacterial co-pathogens improves management, and is crucial to avoid inappropriately administered antimicrobials. We evaluated the use of a multiplex PCR assay in the early detection of respiratory co-infections in COVID-19 hospitalized patients. Methods. The study included non-ICU patients with high clinical suspicion of respiratory co-infection. Lower respiratory tract samples (sputum/bronchial secretions), were analyzed using BIOFIRE FILMARRAY pneumonia panel plus [(bioMerieux, USA), FA]. Specimens were considered as acceptable based on Gram stain. Conventional cultures were also performed. Results. A total of 28 samples from 27 patients (20 males, median age 60 years, IQR 49-71) were analyzed. 8/27 patients were intubated, 5 were treated with high flow nasal canula oxygenation and 11 with high or low oxygen mask. 18 patients received dexamethasone. Co-infection was detected in 17/27 patients (62.9%). 11 specimens were collected in less than 48 hours from admission and no target was identified in 6/11. Detected pathogens and AMR genes, per sample tested, are presented in the table. Bacterial pathogens and any AMR genes were detected in 15 and 4 samples, respectively, leading to modifications of antimicrobial treatment. The semi-quantitative results along with patients' clinical presentation assisted with differentiation of bacterial colonization versus infection, especially in cases where multiple targets were identified. De-escalation was implemented for 12 patients, for whom no co-infection or a viral co-pathogen (n=2) was detected. One patient was co-infected with another Coronavirus;further analysis, using the FA respiratory panel, detected Human coronavirus HKU-1 along with SARS-CoV-2. Median time until discharge or death was 13.5 days (IQR 9-24). Overall mortality was 33.3%. Detected pathogens, microbial load and AMR genes, per sample tested. Conclusion. Implementation of FA assay proved effective for the rapid detection of respiratory co-infections in COVID-19 non-ICU patients. Molecular panel-based assays can contribute to timely adaptation of antimicrobial treatment, benefiting patient management and antibiotic stewardship strategies.

Targeted therapeutic agent for Streptococcus pneumoniae stereotype 3 infection

Streptococcus pneumoniae (Spn) is a Gram-positive bacterial pathogen, which has been a major threat to human health. Spn is the causal agent to the invasive pneumococcal diseases (IPD) and according to CDC, IPD causes 150,000 hospitalizations every year in the United States alone. Additionally, pneumococcal co-infections are a driving force behind the mortality associated with other infectious diseases, such as flu and more recent pandemic outbreak COVID-19. Importantly recent report from WHO confirmed that, Spn is an antimicrobial resistance (AMR) bacterial pathogen, and it is becoming resistant to antibiotic therapies which are widely used to treat Spn infections. Among more than hundred different Spn strains, serotype 3 (Spn3) has unique biological and physical structural challenges such as thick capsular polysaccharide (CPS), high viscosity and mucoid nature, which help Spn3 to escape from host immune responses. The CPS of Spn3 also renders it a highly unresponsive stereotype to the multivalent conjugate vaccine developed against Spn, and thus incidence rates of serotype 3 continue to raise. Because of the unresponsiveness to available pneumococcal conjugate vaccines (PCV) and antibiotics resistance, a novel therapeutic agent is necessary to control the invasive pneumococcal serotype 3 infection. We have identified and cloned the Pn3Pase gene expressed by a Paenibacillus strain. The purified Pn3Pase enzyme degrades the CPS of the Spn3, rendering the bacterium immune-susceptible. We confirmed that recombinantly purified Pn3Pase can degrade the capsule of living Spn3;the unencapsulated Spn3 are not infectious. Also, Spn3 that is unencapsulated by Pn3Pase is efficiently targeted by phagocytosis which also limits the nasopharyngeal colonization in a mouse colonization model. We have also observed that Pn3Pase protects the mice from lethal challenge with Spn3. Pn3Pase is not toxic and repeated administration in mice does not stimulate significant host immune responses against the enzyme. Our results indicate that Pn3Pase serves as an alternative to antibiotics and could effectively make up for vaccine shortcomings, therefore a promising therapeutic agent against Spn3 infections.

Bacterial colonization of the upper airways of children positive and negative for SARS-CoV-2 during the COVID-19 pandemic.

BACKGROUND: Our understanding of the influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bacterial colonization in the children's upper nasopharyngeal tract during the coronavirus infectious disease (COVID-19) pandemic is limited. This study aimed to determine whether there were any differences in bacterial colonization between asymptomatic children with or without a positive SARS-CoV-2 quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) results in the community setting. METHODS: A cross-sectional community-based exploratory study was conducted from March to May 2021 in Semarang, Central Java Province, Indonesia. Using stored nasopharyngeal swabs collected from children under 18 years as a contact tracing program, we performed a real-time quantitative (qPCR) for the most important bacterial colonizing pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Klebsiella pneumoniae. RESULTS: Swabs from a total of 440 children were included in this study, of which 228 (51.8%) were RT-qPCR-confirmed SARS-CoV-2 positive. In the 440 children, colonization rates were highest for H. influenzae (61.4%), followed by S. pneumoniae (17.5%), S. aureus (12.0%), and K. pneumoniae (1.8%). The co-occurrence of both S. pneumoniae and H. influenzae in the upper respiratory tract was significantly associated with a SARS-CoV-2 negative RT-qPCR. In contrast, colonization with only S. aureus was more common in SARS-CoV-2-positive children. CONCLUSION: Overall, this exploratory study concludes that there is a significant difference in the bacterial nasopharyngeal colonization pattern between SARS-CoV-2 positive and negative in asymptomatic children in the community in Indonesia.

GBS antenatal screening and recto-vaginal colonization rates before and during the COVID-19 pandemic

Background: The SARS-CoV-2 pandemic has resulted in the implementation of recommendations to reduce interpersonal contact. From March 2020, rules were applied also in Italian Obstetrics units. Recent data report reduced rates of nosocomial and surgical site infections during the pandemic period. We wonder whether measures for containment of SARS-CoV-2 transmission would affect Group B streptococcus (GBS) maternal recto-vaginal colonization rates, usually screened at 36-37 weeks' gestation. The primary endpoint of this study was to evaluate the rate of maternal GBS colonization at antenatal screening. Method(s): This is a retrospective observational study (carried out in district of Modena), comparing maternal GBS colonization rates in the pre-COVID-19 (2018-2019) and during the pandemic period (2020-2021). Rates of rectovaginal colonization were retrieved from the laboratory database. The total number of deliveries was collected. Data were analyzed by using the Chi-Squared test, also evaluating the adherence to the GBS screening. A p-value < 0.05 was considered significant. Result(s): A total of 10968 and 10802 deliveries occurred in the pre-COVID-19 and the Pandemic period respectively (overall reduction in deliveries of 1.5%). The adherence to the antenatal GBS screening declined from 96.6% (pre-COVID-19 era) to 91.6% (pandemic era, p<0.001). Notably, the proportion of positive GBS screening remained stable (18.3% in 2018-2019 and 18.2% in 2020-2021, p=0.80). Conclusion(s): During the SARS-CoV-2 pandemic, we reported a reduced adherence to antenatal GBS screening. SARS-CoV-2 containment measures adopted by both the population and hospital professionals did not affect GBS colonization rates.

Group B Strep in Pregnancy and Babies Conference

The proceedings contain 9 papers. The topics discussed include: phospholipid vesicles for detection of Group B Streptococcus;naturally acquired serotype-specific anti-GBS CPS IgG concentrations: a pilot UK prospective cohort study;rates of lumbar puncture after antibiotics in infants with sepsis: an Italian multicenter study;Invasive Group-B Streptococcus disease in the neonatal period and risk of epilepsy - a population-based cohort study;incidence of maternal Group B Streptococcus (GBS) bacteremia and clinical impact on mother and baby in a maternity unit in North West London;the US centers for disease control and prevention-led study to establish immunologic endpoints associated with protection against infant invasive group B streptococcal disease: methodology and updates;GBS antenatal screening and recto-vaginal colonization rates before and during the COVID-19 pandemic;group B Streptococcus surveillance among pregnant women in Rio de Janeiro, Brazil over a period of 14 years (2008-2021);and brain lesions complicating Group B Streptococcus early and late-onset disease.

Stent Encrustation and Indwelling Stent Times

Introduction: A pathways streamlining stone management identified four rate-limiting processes causing delay and affecting outcome. Key performance indicators (KPI) with set targets were created to address them. These are: 1) Time to CT with report (< 24hrs). 2) Time to operative care (< 48hrs). 3) Time to discussion at stone MDT ≤2 weeks. 4) Indwelling stent time (IDST) ≤12 weeks Ureteric-stents cause morbidity if left in-situ long-term. This includes bacterial colonization and encrustation. Methods: Aim: a) identify IDST during pre-COVID and COVID periods, b) review encrusted-stents removed within the study timeframe and c) root-cause for delayed stent removal and encrustation. Stent register reviewed between Jan-2019 and Mar-2021. Mean IDST pre- and post-COVID calculated. Information on indication, insertion date and removal retrieved from register and clinical-notes. Root-cause analysis to identify factors influencing delayed removal and encrustation. Results: 841 stents inserted within study timeline;436 pre-COVID and 405 during COVID. Identical stent-times for both periods, 86% cases pre-COVID and 85% during COVID having IDST <12 weeks. Average IDST of 6 weeks and 5 weeks in pre-COVID and COVID periods respectively. 11 encrusted-stents removed (7 pre-COVID, and 4 COVID), with average encrusted-stent duration of 29 weeks pre-COVID and 16 weeks during COVID. Factors involved in encrustation and delayed removal include systems and patient-related factors, failed initial removal, complex surgical planning, ESWL and dissolution therapy. Discussion & Conclusions: No difference in IDST during pre-COVID and COVID periods. A lowered encrusted IDST during COVID, likely attributed to departmental prioritisation of stone-pathway, stent register, and use of a green-listed operative site.

LIKELIHOOD OF ENDOSCOPY CANCELLATION BASED ON VANCOMYCINRESISTANT ENTEROCOCCI (VRE) COLONIZATION STATUS AND INFECTION CONTROL PRACTICES

Background: “Terminal cleaning” is a practice of rigorous cleaning of endoscopy suite following endoscopies for patients colonized with vancomycin-resistant enterocci (VRE) with the intention of reducing VRE transmission. Such practice entails double-wiping all surfaces including the floor with disinfectants before a non-VRE patient can use the endoscopy room. While intuitive, such time-consuming practice is not supported by evidence and may have unintended negative impact on patient access to timely endoscopic evaluation. Aims: To determine whether terminal cleaning of endoscopy suite for VRE-colonized patients has any negative impact on inpatient access to timely endoscopic evaluation. Methods: As part of a quality improvement study, inpatient endoscopy data was gathered over a 3-month period between February 2021 and April 2021 at a tertiary centre. EUS, ERCP, and travel cases outside of the endoscopy suite were excluded. The cancellation rates were compared between VRE-colonized patients and non-VRE patients using the Fisher's exact test. P value of <0.05 was considered statistically significant. Results: A total of 262 inpatient endoscopic procedures were scheduled and included in the study. Sixty-six (25.2%) of inpatient procedures were cancelled during this period (Table 1). A total of 24 procedures were scheduled for VRE patients, 9 of which were cancelled because of insufficient operating time and two due to concurrent carbapenamase-producing organism carriage and poor bowel preparation. In the non-VRE group, 55 (23.3%) procedures were cancelled for various reasons (Table 1). In subgroup analysis where cancellations related to COVID-19 (n=14) were omitted, VRE patients had a significantly higher rate of procedure cancellations compared to non-VRE patients (42.3% vs. 18.5%;p<0.01). Conclusions: The overall endoscopy cancellation rate for VRE-colonized patients was higher than those who were non-VRE-colonized. We propose that this is likely secondary to the delays from unnecessary terminal cleans imposed for VRE-colonized patients and await for postintervention data. (Table Presented).

RESISTANCE FACTORS OF KLEBSIELLA PNEUMONIAE BACTERIA DURING COVID-19 PANDEMIC

Multidrug-resistant K. pneumoniae bacterial strains producing extended range of beta-lactamases or carbapenemases are of serious clinical concern. The aim of the study was to determine the resistance factors of K. pneumoniae strains isolated from the lower respiratory tract of patients diagnosed with community-acquired pneumonia during the COVID-19 pandemic. Materials and methods. The study of resistance to antimicrobial drugs included 138 strains of K. pneumoniae isolated from the sputum of patients treated in infectious diseases monohospitals in the city of Tyumen and the Tyumen region within the period from May 2020 to June 2021. Among the strains examined, 51.4% of them were isolated from SARS-CoV-2 positive patients. The presence of resistance genes was determined by PCR in 71 strains of K. pneumoniae (34 strains from COVID-19-positive and 37 strains from COVID-19-negative patients). Identification of isolated bacterial strains was carried out according to the protein spectra by using a desktop time-of-flight mass spectrometer with matrix laser desorption MALDI-TOF MS (Bruker, Germany). The belonging of the strains to the hypermucoid phenotype was determined using the string test. Sensitivity to antimicrobial drugs was assessed in the disk diffusion method on Muller-Hinton medium. The sensitivity of culture strains to bacteriophage preparations was determined by the drop method (spot-test). In the study, we used “Polyvalent Sextaphage Pyobacteriophage” and “Purified Polyvalent Klebsiella Bacteriophage”, JSC NPO Microgen, Russia. Detection of resistance genes to beta-lactam antibiotics by real-time PCR was carried out using the BakRezista kit (OOO DNA-technology, Russia). The results of the study evidence that K. pneumoniae bacteria isolated from COVID-19-positive and COVID-19-negative patients diagnosed with community-acquired pneumonia displayed a high resistance to antimicrobial drugs and commercial phage-containing drugs. Resistance of K. pneumoniae strains was recorded from 50% (to aminoglycosides and carbapenems) to 90% (to inhibitor-protected penicillins). Sensitivity to bacteriophages was noted on average in no more than 20% of strains. It is important to emphasize that strains isolated from COVID-19-positive patients more often showed a hypermucoid phenotype, suggesting a high bacterial virulence, and also showed greater resistance to all groups of antibacterial drugs examined in the study, which is confirmed by the presence of resistance genes of the ESBL group and carbapenemase. The results of the study suggest that the high level of resistance of K. pneumoniae strains isolated from COVID-19-positive patients is associated with immunosuppression provoked by the SARS-CoV-2 virus, which contributes to their colonization by more virulent strains.

SHOULD WE BE TESTING FOR SPIROCHETOSIS IN COVID PATIENTS PRESENTING WITH PERSISTENT DIARRHEA? A CASE STUDY

Purpose/Background: In the US, intestinal spirochetosis (IS) as a cause of infectious colitis has mainly been described in the HIV positive population. This case describes IS in an HIV negative, COVID positive patient suggesting the need for a broader differential of chronic diarrhea in the COVID era. Hypothesis/Aim: To increase awareness of the need for a potentially broader differential of chronic diarrhea in the COVID era. Methods/Interventions: This is a case study describing an association between COVID and intestinal spirochetosis. Results/Outcome(s): Spirochetes, gram negative spiral-shaped flagellated bacteria, are best known for their ability to cause systemic disease in the form of Syphilis and Lyme Disease, but the genus Brachyspiraceae (Brachyspira aalborgi, Brachyspira pilosicoli) has also been described as both a commensal organism and an invasive pathogen causing intestinal spirochetosis (IS). IS in the US has largely been described in the MSM HIV population as a colitis presenting with abdominal pain and persistent diarrhea secondary to epithelial invasion with destruction of the intestinal brush border leading to malabsorption. IS remains an important part of the work up of infectious colitis in this population. In this case study, IS was diagnosed in an HIV negative, COVID positive patient whose COVID diagnosis coincided with the symptomatic presentation of IS suggesting that it is important to include IS in the differential diagnosis of chronic diarrhea in the COVID population regardless of HIV status. In this study, a 60 yo HIV negative MSM presented with abdominal pain x 3 weeks followed by persistent watery diarrhea refractory to imodium. No history of recent travel. No known infectious contacts. Prior colonoscopy 9 years prior to presentation WNL. After one episode of hematochezia, CT abd/pelvis was performed demonstrating colitis and COVID-related changes to the lung bases. Testing confirmed COVID infection, which was self-limited. Initial work up for infectious colitis was negative for gonorrhea, chlamydia, HIV, HSV, O+P, and C. Difficile. Colonoscopy was performed revealing no evidence of gross colitis. Histopathology demonstrated microscopic colitis w/ spirochete colonization of the intestinal epithelium (image 1). A course of metronidazole led to resolution of symptoms. Limitations: This is a descriptive study describing an association, but it does not imply causation. Conclusions/Discussion: Intestinal spirochetosis has been described as a cause of abdominal pain and refractory diarrhea in the US mainly in an immunosuppressed, HIV positive population. This case describes symptomatic intestinal spirochetosis in an HIV negative, COVID positive patient who hitherto COVID diagnosis had no risk factors for immunosuppression suggesting a link between COVID and IS. Further review is necessary to establish a true association, but this case suggests that IS should be considered during the work up of chronic diarrhea in COVID positive patients. (Figure Presented).

Basophil activation test: current applications and future perspectives

The basophil activation test (BAT) is a flow cytometric assay that evaluates the percentage of activation or degranulation of peripheral blood basophils, after “in vitro” exposure to specific allergens. In sensitized patients, the stimulation of peripheral blood basophils with a specific allergen induces or up-regulates the expression of molecules, such as CD63 and CD203c, which represent, markers of degranulation and activation of basophils, respectively. The validity of the BAT requires a negative control (sterile saline) and a positive control (anti-IgE molecules). Several studies have demonstrated the role of the BAT in supporting the diagnosis of drug, food and hymenoptera venom allergy. The BAT has shown a low sensitivity but good specificity in diagnosing allergy to drugs such as NSAIDs, beta-lactam antibiotics, quinolones and muscle relaxants. In food allergy, the sensitivity and specificity of the BAT depends on the food;in the case of peanut allergy the sensitivity reaches 96% while the specificity the 100%. In addition, the BAT is an useful tool to monitor the natural resolution of allergies and the clinical effects induced by either immunotherapy or anti-IgE treatment. Finally, the BAT has been utilized to study the pathogenetic mechanisms underlying several IgE-mediated diseases. For example, in patients affected by severe bronchial asthma, the BAT has demonstrated the ability of Staphylococcus aureus enterotoxins to induce the activation of basophils supporting the role of these enterotoxins as “triggers” of the inflammatory cascade in bronchial asthma. In patients with cystic fibrosis the BAT can be used to dis-criminate allergic bronchopulmonary aspergillosis from Aspergillus colonization. More recently, the BAT has been demonstrated as a potential diagnostic tool to evaluate allergy to the polyethylene glycol (PEG) present in the anti-SARS-CoV-2 BNT162b2 mRNA vaccine.

Low Rates of Bacterial Co-infection in Hospitalized Patients with COVID-19

Background. The rate of bacterial co-infection in inpatients with COVID-19 is unknown, however, patients who are hospitalized with COVID-19 often receive antibiotics for community-acquired bacterial pneumonia (CABP). Reducing unnecessary antibiotic usage in this population is important to prevent adverse effects and slow the development of antimicrobial resistance. Methods. We performed a retrospective chart review on patients admitted to our health system between March and May 2020 with confirmed COVID-19 by nasopharyngeal PCR. We reviewed patients with positive cultures from urine, blood, sputum, and sterile sites. Positive cultures were reviewed to determine if they represented a true infection versus a contaminant or colonization. Patients with true infections were categorized as having a co-infection (CI) if the positive culture was collected within 48 hours of initial positive SARS-CoV-2 PCR test. Additional data was collected on patient demographics, types of infections, organisms grown, and antibiotic usage. Results. 902 patients were admitted with positive SARS-CoV-2 tests during the study period. Of these, 47 patients (5.2%) had a bacterial CI. Some patients had more than one CI, with 53 total CIs identified. The median age of patients with CI was 66 years old (39 - 90). Tables 1 and 2 describe patient characteristics and infections. A subgroup analysis on types of bacteria was done on the 20 patients with a respiratory CI, who accounted for 2.2% of all COVID-positive patients admitted during the study period. In these infections, Staphylococcus aureus, Streptococcus species, and Haemophilus influenzae were the most common organisms, accounting for 60%, 15%, and 10% infections, respectively. Conclusion. The overall rate of CIs in patients admitted with COVID-19 was low. Some of these CIs may represent an "incidentally positive" COVID-19 test if a patient presented with one infection and had asymptomatic carriage of SARS-CoV-2 when community prevalence was high. Further analysis is needed to evaluate specific risk factors for co-infection.