Infectious Microorganisms Research Articles

Investigating the changing taxonomy and antimicrobial resistance of bacteria isolated from door handles in a new infectious disease ward pre- and post-patient admittance.

Healthcare-associated infections (HAIs) are a significant burden to health systems, conferring increased morbidity, mortality, and financial costs to hospital admission. Antimicrobial resistance (AMR) further compounds the issue as viable treatment options are constrained. Previous studies have shown that environmental cleaning interventions reduced HAIs. To ensure the effectiveness of these, it is important to analyze the hospital environment at a microbial level, particularly high-touch surfaces which see frequent human interaction. In addition to identifying infectious microorganisms, it is also beneficial to assess typically non-infectious organisms, as traits including AMR can be transferred between the two. Our study identified that there were high levels of antibiotic resistance in typically non-infectious organisms found on high touch surfaces on a hospital ward. However, the organisms identified suggested that the cleaning protocols in place were sufficient, with their presence being due to repeated recolonization events through human interaction after cleaning had taken place.

A natural killer cell mimic against intracellular pathogen infections.

In the competition between the pathogen infection and the host defense, infectious microorganisms may enter the host cells by evading host defense mechanisms and use the intracellular biomolecules as replication nutrient. Among them, intracellular Staphylococcus aureus relies on the host cells to protect itself from the attacks by antibiotics or immune system to achieve long-term colonization in the host, and the consequent clinical therapeutic failures and relapses after antibiotic treatment. Here, we demonstrate that intracellular S. aureus surviving well even in the presence of vancomycin can be effectively eliminated using an emerging cell-mimicking therapeutic strategy. These cell mimics with natural killer cell-like activity (NKMs) are composed of a redox-responsive degradable carrier, and perforin and granzyme B within the carrier. NKMs perform far more effectivly than clinical antibiotics in treating intracellular bacterial infections, providing a direct evidence of the NK cell-mimicking immune mechanism in the treatment of intracellular S. aureus.

Are SNPs Linked to Somatic Cell Score Suitable Markers for the Susceptibility to Specific Mastitis Pathogens in Holstein Cows?

Mastitis in cattle is often caused by microorganism infections in the udder. The three most common pathogens are esculin-positive streptococci (SC+), coagulase-negative staphylococci (CNS), and Escherichia coli (E. coli). In a previous study, 10 SNPs were associated with somatic cell score and mastitis in diverse Holstein populations. We tested these SNPs for their effects on individual pathogen presence. Milk and pathogen samples of 3076 Holstein cows were collected from four farms. Samples were excluded if multiple pathogens were present at the same time. Records of the same pathogen within 14 days of each other were counted as one infection. This resulted in 1129 pathogen-positive samples. Cases and controls were in ratios of 20:80 for SC+, 8:92 for CNS, and 11:89 for E. coli. The lasso, backward, and forward methods were used to narrow down SNPs associated with pathogen presence. The suitability of the SNPs to separate the samples into cases or controls for each pathogen was indicated using ROC curves. The Cochran-Armitage (CAT) and the Jonckheere-Terpstra (JTT) tests evaluated the influence of the SNPs on pathogen presence. Finally, a generalised linear mixed model (GLMM) including fixed environmental effects and a random sire effect was fitted to the binary trait of pathogen presence to test for association. In total, six out of the 10 investigated SNPs showed associations with pathogen presence based on the forward method: Two SNPs each for SC+ (rs41588957, rs41257403) and CNS (rs109934030, rs109441194), and three for E. coli (rs109934030, rs41634110, rs41636878). The CAT and GTT tests linked four SNPs (rs41588957, rs41634110, rs109441194, rs41636878) to pathogen presence, two of which were confirmed with the GLMM (rs41634110, rs109441194), with effects on CNS and E. coli. The SNPs linked to CNS and those linked to E. coli explained 13.2% and 13.8% of the variance, compared to 19% and 18.4%, respectively, of the full model with all 10 SNPs. Half of the SNP genotypes previously linked to lower SCS also decreased the probability for pathogen presence and might therefore be targets not just for lower SCS but for a better pathogen resistance. Trial Registration: Not applicable, no new data were collected for this study.

Comparison of the activity of two elastin-like recombinant carriers fused to the antimicrobial peptide indolicidin.

Recombinant fusion biotechnology is a powerful tool for producing antimicrobial peptides (AMPs), which can contribute to limiting the number of potentially infectious microorganisms. AMPs are often expressed in fusion with a carrier protein, a strategy that prevents toxic effects on host bacterial cells and protects them from proteolytic degradation. Among the many fusion carriers available, elastin-like polypeptides offer several valuable advantages related to their unique thermo-responsive behavior. The Human Elastin-like Polypeptide was successfully employed to produce a model fusion construct with the indolicidin domain. Recently, an elastin-based variant of this polypeptide was developed, modulating the sequence of the hydrophobic domains, thus enhancing the phase transition properties. Here, a new carrier based on this sequence that was produced, physicochemically characterized, and employed as a fusion partner for the indolicidin is described. This work aims to compare two different elastin-based carriers and their indolicidin fusion derivatives, as well as to determine, based on their properties, which may be the most advantageous carrier for producing antimicrobial domains. This study was focused on the elastin-like polypeptides as a tunable expression platform particularly suitable for producing AMPs and for their integration in biomimetic interfaces that acquire the capacity to inhibit bacterial growth.

A Novel PCR-Free Ultrasensitive GQD-Based Label-Free Electrochemical DNA Sensor for Sensitive and Rapid Detection of Francisella tularensis

Biological warfare agents are infectious microorganisms or toxins capable of harming or killing humans. Francisella tularensis is a potential bioterrorism agent that is highly infectious, even at very low doses. Biosensors for biological warfare agents are simple yet reliable point-of-care analytical tools. Developing highly sensitive, reliable, and cost-effective label-free DNA biosensors poses significant challenges, particularly when utilizing traditional techniques such as fluorescence, electrochemical methods, and others. These challenges arise primarily due to the need for labeling, enzymes, or complex modifications, which can complicate the design and implementation of biosensors. In this study, we fabricated Graphene Quantum dot (GQD)-functionalized biosensors for highly sensitive label-free DNA detection. GQDs were immobilized on the surface of screen-printed gold electrodes via mercaptoacetic acid with a thiol group. The single-stranded DNA (ssDNA) probe was also immobilized on GQDs through strong π−π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, leading to a decrease in the effect of GQD but a positive shift associated with the increase in DNA concentration. The specificity of the developed system was observed with different microorganism target DNAs and up to three-base mismatches in the target DNA, effectively distinguishing the target DNA. The response time for the target DNA molecule is approximately 1010 s (17 min). Experimental steps were monitored using UV/Vis spectroscopy, Atomic Force Microscopy (AFM), and electrochemical techniques to confirm the successful fabrication of the biosensor. The detection limit can reach 0.1 nM, which is two–five orders of magnitude lower than previously reported methods. The biosensor also exhibits a good linear range from 105 to 0.01 nM and has good specificity. The biosensor’s detection limit (LOD) was evaluated as 0.1 nM from the standard calibration curve, with a correlation coefficient of R2 = 0.9712, showing a good linear range and specificity. Here, we demonstrate a cost-effective, GQD-based SPGE/F. tularensis DNA test suitable for portable electrochemical devices. This application provides good perspectives for point-of-care portable electrochemical devices that integrate sample processing and detection into a single cartridge without requiring a PCR before detection. Based on these results, it can be concluded that this is the first enzyme-free electrochemical DNA biosensor developed for the rapid and sensitive detection of F. tularensis, leveraging the nanoenzyme and catalytic properties of GQDs.

Type 1 diabetes and parasite infection: An exploratory study in NOD mice.

Microorganisms have long been suspected to influence the outcome of immune-related syndromes, particularly autoimmune diseases. Type 1 diabetes (T1D) results from the autoimmune destruction of the insulin-producing beta cells of pancreatic islets, causing high glycemia levels. Genetics is part of its aetiology, but environmental factors, particularly infectious microorganisms, also play a role. Bacteria, viruses, and parasites influence the outcome of T1D in mice and humans. We used nonobese diabetic (NOD) mice, which spontaneously develop T1D, to investigate the influence of a parasitic infection, leishmaniasis. Leishmania amazonensis is an intracellular eukaryotic parasite that replicates predominantly in macrophages and is responsible for cutaneous leishmaniasis. The implication of Th1 immune responses in T1D and leishmaniasis led us to study this parasite in the NOD mouse model. We previously constructed osteopontin knockout mice with a NOD genetic background and demonstrated that this protein plays a role in the T1D phenotype. In addition, osteopontin (OPN) has been found to play a role in the immune response to various infectious microorganisms and to be implicated in other autoimmune conditions, such as multiple sclerosis in humans and experimental autoimmune encephalomyelitis (EAE) in mice. We present herein data demonstrating the role of OPN in the response to Leishmania in NOD mice and the influence of this parasitic infection on T1D. This exploratory study aimed to investigate the environmental infectious component of the autoimmune response, including Th1 immunity, which is common to both T1D and leishmaniasis.

Immunoregulatory protein B7-H3 upregulated in bacterial and viral infection and its diagnostic potential in clinical settings.

Bacterial and viral infections cause a huge burden to healthcare settings worldwide, and mortality rates associated with infectious microorganisms have remained high in recent decades. Despite tremendous efforts and resources worldwide to explore diagnostic biomarkers, rapid and easily assayed indicators for the diagnosis of bacterial and viral infections remain a challenge. B7 homolog 3 (B7-H3), a member of the B7 family of immunoregulatory proteins, is overexpressed in patients with septicemia, meningitis, pneumonia, and hepatitis. Therefore, B7-H3 could be used as a potential clinical indicator and therapeutic target for bacterial and viral infections caused by H. pylori, S. pneumoniae, M. pneumoniae, hepatitis B virus (HBV), viral hemorrhagic septicemia virus (VHSV), respiratory syncytial virus (RSV), and human immunodeficiency virus (HIV). Moreover, the interplay between infectious microorganisms and B7-H3 and exploration of the functional roles of the B7-H3 molecule could aid in the development of novel strategies for disease diagnosis and immunotherapy.

A Novel Deep Learning Framework Enhanced by Hybrid Optimization Using Dung Beetle and Fick’s Law for Superior Pneumonia Detection

Pneumonia is an inflammation of lung tissue caused by various infectious microorganisms and noninfectious factors. It affects people of all ages, but vulnerable age groups are more susceptible. Imaging techniques, such as chest X-rays (CXRs), are crucial in early detection and prompt action. CXRs for this condition are characterized by radiopaque appearances or sometimes a consolidation in the affected part of the lung caused by inflammatory secretions that replace the air in the infected alveoli. Accurate early detection of pneumonia is essential to avoid its potentially fatal consequences, particularly in children and the elderly. This paper proposes an enhanced framework based on convolutional neural network (CNN) architecture, specifically utilizing a transfer-learning-based architecture (MobileNet V1), which has outperformed recent models. The proposed framework is improved using a hybrid method combining the operation of two optimization algorithms: the dung beetle optimizer (DBO), which enhances exploration by mimicking dung beetles’ navigational strategies, and Fick’s law algorithm (FLA), which improves exploitation by guiding solutions toward optimal areas. This hybrid optimization effectively balances exploration and exploitation, significantly enhancing model performance. The model was trained on 7750 chest X-ray images. The framework can distinguish between healthy and pneumonia, achieving an accuracy of 98.19 ± 0.94% and a sensitivity of 98 ± 0.99%. The results are promising, indicating that this new framework could be used for the early detection of pneumonia with a low cost and high accuracy, especially in remote areas that lack expertise in radiology, thus reducing the mortality rate caused by pneumonia.

B-229 Extraction-free Nucleic Acid Sample Preparation from Inhibitor Rich Samples via Hyperbaric Heating

Abstract Background Extraction-based nucleic acid sample preparation for PCR is limited by long processing times, liquid transfers, cost, and storage requirements. Extraction-free approaches enable streamlined sample prep but are severely impacted by inhibitors present in biological sample matrices. We previously reported the use of Hyperbaric Heating (HBH) for effective organism lysis and demonstrate here its effectiveness to prepare nucleic acids for PCR from various inhibitor-rich sample matrix types. Methods HBH exposes the sample to high temperature/high pressure environment for a short duration. This process effectively lyses organisms and denatures inhibitors within seconds. Samples are sealed within a pressure-tight metallic vessel, then rapidly heated using magnetic induction. Within the sealed metallic vessel, vaporization of the aqueous sample raises the internal pressure, enabling an internal temperature higher than 100°C. Proprietary sample processing beads containing chelating agents and other proteins protect nucleic acids from fragmentation during heating. Results The efficacy of HBH for PCR amplification was tested against commercial kits and extraction-free methods. HBH treatment of nasal swab samples spiked with inactivated SARS-CoV-2 elicited detection down to 125 viral copies/mL. Viruses such as RSV and Influenza spiked in nasal swab samples demonstrated comparable PCR results as extraction prepped samples. HBH treatment of microbe samples, including Candida albicans spiked in urine and Bacillus subtilis spiked in serum, had comparable PCR threshold cycles as microbe specific DNA extraction methods (Table 1). Conclusions HBH is a generalizable extraction-free nucleic acid sample prep technology affording detection capabilities comparable to commercial sample prep methods. We demonstrated the use of HBH sample prep for detection of several infectious microorganisms in common biological matrices (nasal swab, serum, urine) without additional sample purification. With its ease of use, speed, and lower cost, HBH will be a key tool in applications where nucleic acid amplification is pivotal for diagnostic and research use.

Multimodal surveillance of Care-related infections by Alert microorganisms in Ospedali Riuniti di Vittoria e Comiso ASP Ragusa

Background: monitoring the incidence and surveillance of alert microorganism infections detected in inpatients of the Ospedali Riuniti di Vittoria and Comiso in 2023. Objectives: early identification and implementation of shared pathways aimed at prevention and control of care-related infections. the spread of colonization and infections; promotion and implementation of effective risk assessment programs. Methods: a multicenter study was conducted on 79 patients with infections with Alert microorganisms, in ordinary hospitalization, day service, and day hospital, of the "R. Guzzardi" hospitals of Vittoria and "R. Margherita" of Comiso. Sample stratification was performed according to gender, females 51.9% and males 48%, and the four age groups: 18-40 (4.8%), 41-60 (9.5%), 61-80 (45.2%), >80 (40.5%), x̄ 51.90. The calculated mortality rate was n.16 (20.25%). The types, number and frequency of use of invasive devices were described (n.68, 86%, including 64.5% urinary bladder catheter). Results: the operating unit in which there is significant positivity to Alert infections is the UOC of Internal Medicine (40.5%), followed by RSA (16.46%) and ICU (8.86%), table1. The most representative Alert is Acinetobacter baumannii (24.05%), other microorganisms isolated are Klebsiella P. (22.78%), Escherichia c. (21.52%), and Staphylococcus A. (18.99%). In addition, a significant correlation between microorganisms and sample type is confirmed (p=0.019). Inpatient days are proportional to the care complexity index (p=0.0021). In addition, there is no correlation between inpatient days and microorganism type. Conclusions: the reduction of inpatient time and the move toward territorial continuity of care will promote the community spread of selected antibiotic-resistant bacteria in the hospital. Surveillance measures include early identification of patients positive to Alerts, active follow-up of colonized patients, isolation of colonized/infected patients, and adoption of contact precautions in the management of such patients.

Distribution and antimicrobial susceptibility of pathogenic micro-organisms in pediatric urinary tract infections

Distribution and antimicrobial susceptibility of pathogenic micro-organisms in pediatric urinary tract infections

Effect of onion skin powder on color, lipid, and protein oxidative stability of premade beef patty during cold storage

The impact of premade beef patty (BBP) with red onion skin powder (OSP) at 0, 1, 2, and 3% levels on color, lipid, and protein oxidative stability, and infection degree of microorganisms during cold storage was investigated. The objective was to determine the effect of color by L*, a*, b*, and the content of MetMb. The inhibitory effect of OSP on the oxidation of lipid and protein was studied based on TBARS and the carbonyl content of protein in samples at different storage times. TVB-N content was used to characterize the degree of infection of microorganisms and their effect on meat quality. The results showed that the addition of OSP reduced the pH, L *, a*, and b * values of BBP, and improved the hardness, springiness, gumminess, and cohesiveness of BBP, but had no significant effect on the chewiness of BBP (p > 0.05). After 12 days of storage, the carbonyl group and TBARS content in the BBP supplemented with 3%OSP was significantly lower than that in the control group (p < 0.05). Furthermore, the addition of OSP significantly inhibited the TVB-N increase during beef patty storage. These results indicated that OSP has a good research prospect as a natural antioxidant or preservative.

Cytologic diagnosis and differential diagnosis of histiocytic signet ring cells in effusion specimens.

Benign histiocytic proliferation in effusion specimens can be found in a variety of diseases such as rheumatoid arthritis, systemic lupus erythematosus, microorganism infections, trauma, reactive eosinophilic pleuritis, and others. In addition, nodular histiocytic/mesothelial hyperplasia is another well-recognized rare cause. The previous studies have shown that proliferative histiocytes have raisinoid nuclei and abundant eosinophilic granular cytoplasm and can be confused with malignant lesions, especially metastatic carcinomas. In this study, we evaluated the cytomorphology of benign histiocytes, discussed the diagnosis and differential diagnosis, and the clinical significance of histiocytic signet ring cells in effusion cytology. Seven hundred and fifty-five benign effusion cases (433 pleural effusions and 322 abdominal fluids) were found over 1 year. Among benign cases, 35 cases (28 pleural effusions and seven abdominal fluids) were included with findings of dominantly histiocytic signet ring cell morphology as well as immunohistochemical (IHC) stains. The clinical findings were also correlated. In contrast to the well-documented cytomorphology of raisinoid nuclei and eosinophilic cytoplasm of proliferative histiocytes in previous studies, we find that these cells predominately presented as signet ring cell morphology with clear cytoplasm. The most characteristic findings of benign histiocytes in pleural effusions are: (1) cells are arranged in sheets and/or scattered individual cells, but no two- or three-dimensional cell clusters; (2) cells are intermediate in size and with normal N/C ratio; (3) cells have eccentric located nuclei and abundant clear cytoplasm, giving signet ring cell appearance; (4) nuclei have fine granular chromatin pattern, no hyperchromia or coarse chromatin pattern, no nuclear atypia; and (5) immunohistochemical (IHC) stains demonstrate a strongly positivity for macrophage-histiocyte lineage marker CD68, but negativity for epithelial markers and mesothelial markers. Clinically, these patients do not demonstrate nodularity or lesions in the mesothelial lining of serous cavities. Our study provides a detailed characterization of benign histiocytic signet ring cells in effusion cytology. The differential diagnosis of histiocytic signet ring cells is broad. The most important differential diagnoses are metastatic adenocarcinoma and epithelioid signet ring cell mesothelioma. The accurate diagnosis is critical for the appropriate clinical management of the patient. Cytopathologists should be aware of the diagnostic pitfalls of benign histiocytic signet ring cells in effusion samples in daily practice.

Unraveling the treasure trove of phytochemicals in mitigating the Salmonella enterica infection.

Foodborne diseases triggered by various infectious micro-organisms are contributing significantly to the global disease burden as well as to increasing mortality rates. Salmonella enterica belongs to the most prevalent form of bacteria accountable for significant burden of foodborne illness across the globe. The conventional therapeutic approach to cater to Salmonella enterica-based infections relies on antibiotic therapy, but the rapid emergence of the antibiotic resistance strains of Salmonella sp. necessitates the development of alternative treatment and prevention strategies. In light of this growing concern, the scientific community is rigorously exploring novel phytochemicals harnessed from medicinally important plants as a promising approach to curb Salmonella enterica infections. A variety of phytochemicals belonging to alkaloids, phenols, flavonoid, and terpene classes are reported to exhibit their inhibitory activity against bacterial cell communication, membrane proteins, efflux pumps, and biofilm formation among drug resistant Salmonella strains. The present review article delves to discuss the emergence of antibiotic resistance among Salmonella enterica strains, various plant sources, identification of phytochemicals, and the current state of research on the use of phytochemicals as antimicrobial agents against Salmonella enterica, shedding light on the promising potential of phytochemicals in the fight against this pathogen.

A multiple method for sensitively detecting 17 highly infectious bacteria and viruses with distinguished melting peaks

BackgroundMultiple fluorescence PCR was used to facilitate the low cost detection of such infectious pathogens. The melting curve combined with the fluorescence PCR method was used to detect more targets. The characteristic melting peaks of the melting curve formed by the melting probe were complementary to the fluorescent probes and more targets could be identified by the different melting peaks in one fluorescence channel. ResultsThe most optimal conditions were confirmed by optimizing the experimental conditions, such as the concentration of fluorescent probes and the melting probe, which is crucial for forming the characteristic melting peaks. LOD, multiplex performance and sample detection performance were evaluated separately. According to the results, the LOD of all targets was as low as five or ten copies/tube, excepting for Zaire type Ebola virus, whose LOD is 25 copies/tube. The method could simultaneously detected more targets, even up to eight bacteria or nine viruses and the result was accurate. In 173 clinical or real-world samples, the result was in keeping with the expected or clinical results, excepting for one case of the soil sample, and the consistency rate of the detection results reached 99.42%. SignificanceWe achieved a novel method for multiple detection of up to 17 highly infectious pathogenic microorganisms and performed well in real sample detection, and the results were consistent with the expected or clinical results. We provided a new detection tool for disease prevention, control centers and clinical practice.

Robust and low-cost open-source device for detecting infectious microorganisms by loop-mediated isothermal amplification

Loop-Mediated Isothermal Amplification (LAMP) is a useful technique for detecting infectious microorganisms in human fluids since it performs similarly to conventional PCR, the results are obtained faster and no thermocyclers or complex devices are required. Since only two isothermal blocks (95 °C to lyse cells and 65 °C for DNA amplification) are needed, LAMP is particularly suited for applications in Low- and Middle-Income Countries (LMICs). To validate such assumption, we first designed and tested Arduino-controlled LAMP thermoblocks to process a considerable number of samples simultaneously with a low-energy consumption to enable routine use under worst-case conditions (no main power source and low ambient temperatures).The thermoblocks were tested when battery-powered at temperature down to 5 °C, showing high stability in well temperatures (<0.8 °C). The charge required for both thermoblocks to simultaneously achieve the target temperatures after switching on and to keep their working temperatures were 4.1 A·h and 2.4 A·h/h, respectively. Second, we implemented a low-cost viewer with LEDs and filters to detect the fluorescent LAMP reaction. All the components required for the instrument are for general purpose and readily available by e-commerce. Thus, the LAMP device allows for considerable autonomy by using a typical car battery in rural and itinerant healthcare or field hospitals in LMICs, even under difficult environmental conditions.

Detection of rare microorganisms in bone and joint infections by metagenomic next-generation sequencing.

This aim of this study was to analyze the detection rate of rare pathogens in bone and joint infections (BJIs) using metagenomic next-generation sequencing (mNGS), and the impact of mNGS on clinical diagnosis and treatment. A retrospective analysis was conducted on 235 patients with BJIs who were treated at our hospital between January 2015 and December 2021. Patients were divided into the no-mNGS group (microbial culture only) and the mNGS group (mNGS testing and microbial culture) based on whether mNGS testing was used or not. A total of 147 patients were included in the no-mNGS group and 88 in the mNGS group. The mNGS group had a higher detection rate of rare pathogens than the no-mNGS group (21.6% vs 10.2%, p = 0.016). However, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and higher infection control rates compared with the no-mNGS group (p = 0.017, p = 0.003, and p = 0.028, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.957). In culture-negative cases, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and a higher infection control rate than the no-mNGS group (p = 0.036, p = 0.033, p = 0.022, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.748). mNGS improves detection of rare pathogens in BJIs. mNGS testing reduces antibiotic-related complications, shortens hospital stay and antibiotic use duration, and improves treatment success rate, benefits which are particularly evident in culture-negative cases.

Infections after musculoskeletal injuries in earthquake survivors.

This study aimed to investigate the infections following musculoskeletal injuries in earthquake survivors, offering a future clinical point of reference for the handling of musculoskeletal injuries resulting from earthquakes. In this single-center retrospective observational study, 225 earthquake survivors (120 females, 105 males; median: 39 years; range, 18 to 94 years) admitted between February 2023 and April 2023 were evaluated. Patients with musculoskeletal injuries and patients who had at least one month of follow-up data were included in the study. Diagnosis of healthcare-associated infections was verified by an infection control physician in accordance with the Centers for Disease Control and Prevention. Among all cultures, the most isolated pathogen was Acinetobacter baumannii (49.4%), followed by enterococci (28.6%). Colistin sensitivity of A. baumannii was 36 (94.7%). However, sensitivity rate was 5.3% for ciprofloxacin, 10.5% for piperacillin-tazobactam, and 26.4% for carbapenems, which are frequently used for skin and soft tissue infections. Among all, 76% of the microorganisms isolated from wound culture and 58% of the microorganisms isolated from deep tissue culture were found to be multidrug-resistant pathogens. During the follow-up, 12 (5.3%) patients had hospital-acquired urinary tract infections, 13 (5.7%) patients had hospitalacquired bloodstream infections, one (0.4%) patient had hospital-acquired pneumonia, and 74 (32.8%) patients had surgical site infections. Eighty (35.6%) of the patients were followed up in the intensive care unit, and the overall mortality rate was 2.7%. While gram-positive microorganisms are frequently the causative microorganisms in infections after traumatic injuries, this study revealed that gram-negative microorganisms could be observed more frequently in postearthquake traumatic injuries. Most causative microorganisms are resistant to commonly prescribed antibiotics in clinical settings, which makes them more challenging to treat.

Antibiotics Utilization Pattern in a Children’s Medical Center in North of Iran

Background: The development of a system for rational use of antimicrobials seems mandatory. Furthermore, since hospitals do not share the same bacterial flora and have different patterns of antibiotic therapy the purpose of the present study is to perform a Drug Utilization Evaluation (DUE) on the pattern of antibiotic administration in patients hospitalized in 17 Shahrivar Pediatric Hospital, RASHT, Iran. Methods: In this descriptive cross-sectional study that was conducted in a one-year period (2021-2022), 560 patients were randomly selected and their medication data were collected based on the gender and age as well as the type, dose, duration of antibiotic therapy and the results of bacterial cultures and also susceptibility of the infectious microorganisms. Results: The average age of patients was 53.56 months with 46.9% of them being less than 24 months old. The highest rate of antibiotics administration belonged to the infectious diseases ward (30%) and 33% of antibiotics were prescribed by pediatric infectious diseases specialists. The result of most of the cultures was reported as negative (98.38%), the most prevalent microorganism was Escherichia Coli from urine cultures (2.38%) and Staphylococcus Aureus from sputum cultures (14.28%). The highest prescribed antibiotics were ceftriaxone (51.2%) and vancomycin (45.6%). It was determined the antibiotic stipend was 15.6% of the whole budget for purchasing medicine. Conclusions: It is necessary to develop a guideline regarding the prescription of antibiotics in children's departments, which reduces empiric treatment and the requirement to adjust the drug after a negative culture.

Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia.

Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce. We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia. Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing. This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.