Microbiological Tests Research Articles

Lowering the Acquisition of Multi-drug Resistant Organism (MDROs) with Pulsed-xenon (LAMP) Study: a cluster randomized controlled, double-blinded, interventional crossover trial.

Environmental disinfection is essential for reducing spread of healthcare associated infections (HAIs). Previous studies report conflicting results regarding the effects of ultraviolet light (UV) in reducing infections. This trial evaluated the impact of adding pulsed xenon UV (PX-UV) to standard terminal cleaning in reducing environmentally-implicated HAIs (eiHAIs). The LAMP trial was conducted in 2 hospitals (15 inpatient wards) utilizing a cluster randomized controlled, double-blinded, interventional crossover trial comparing standard terminal cleaning followed by either pulsed xenon ultraviolet (PX-UV) disinfection (intervention arm) or sham disinfection (control arm). The primary outcome was incidence of eiHAIs from clinical microbiology tests on the 4th day of stay or later or within 3 days after discharge from the study unit. EiHAIs included clinical cultures positive for vancomycin-resistant enterococci (VRE), extended spectrum beta-lactamase-producing Escherichia coli or Klebsiella pneumonia, methicillin-resistant Staphylococcus aureus (MRSA), and Acinetobacter baumannii, and stool PCR positive for Clostridiodes difficile. Between May 18, 2017 to Jan 7, 2020, 25,732 patients were included, with an incidence of 601 eiHAI and 180,954 patient days. There was no difference in the rate of eiHAIs in the intervention and sham arms (3.49 vs 3.17 infections/1000 patient days respectively, RR 1.10 CI (0.94, 1.29, p= 0.23)). Study results were similar when stratified by eiHAI type, hospital, and unit type. The LAMP study failed to demonstrate an effect of the addition of UV light disinfection following terminal cleaning on reductions in rates of eiHAIs. Further investigations targeting hospital environmental surfaces and the role of no touch technology to reduce HAIs are needed.

Infectious etiologies of persistent and chronic diarrhea in Asian developing countries: A systematic review and meta-analysis.

Infectious causes of diarrhea contribute significantly to morbidity in Asia. We conducted a systematic review and meta-analysis of the prevalence of infectious etiologies of persistent and chronic diarrhea in Asian adults. Searches were performed on PubMed and Scopus for studies from January 1, 1970, to May 30, 2023. Sixteen studies were identified and included. The meta-analysis was conducted with the random-effects method, estimating the pooled prevalence of groups of infectious pathogens as causes of persistent and chronic diarrhea among Asian adults. The findings were highly heterogeneous and indicative of publication bias. The majority of studies were conducted on persons living with human immunodeficiency virus infection (PLHIV). The studies were predominantly from low-income and middle-income Asian countries. The most common cause was parasitic, with a pooled prevalence of 0.52 (95% confidence interval 0.28-0.65, I2=99%, Cochran's Q=1027.44, P<0.01), followed by bacterial, fungal, and viral causes, which were substantially rarer. Negative microbiological testing was also common, with a pooled prevalence for a negative test being 0.37 (95% confidence interval 0.17-0.52, I2=99%, Cochran's Q=1027.44, P<0.01). Subgroup analyses of studies conducted among PLHIV, from year 2000 and among those conducted in Southeast Asia showed a similar prevalence of parasitic causes of diarrhea. In conclusion, inAsian adults with persistent and chronic diarrhea, parasitic causes were most prevalent. However, the estimate of true prevalence is limited by significant heterogeneity among the available studies. More study in this field is required, especially examining PLHIV in the post-antiretroviral therapy era and from high-income countries.

Immunoadsorption as a method of antibody donation during the COVID-19 pandemic.

Initial therapeutic efforts to treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) included the use of plasma from convalescent donors containing anti-SARS-CoV-2 antibodies. High-neutralizing antibody titres are required for therapeutic efficacy. This study aims to show that immunoadsorption followed by tangential flow filtration can be used to obtain antibody concentrates with high-neutralizing capacities. Eligible donors (n = 10, five males and three females) underwent immunoadsorption using adsorber columns specific for human antibodies. Glycine-washed out eluates of 1.5 L volume were further concentrated by tangential flow filtration using 30 kDa ultrafiltration membranes. The same membranes were applied for diafiltrations to exchange residual glycine for 0.9% normal saline. Antibody concentrates were obtained within 8 h from the start of donation and had, 4.58 ± 1.95, 3.28 ± 1.28 and 2.02 ± 0.92 times higher total IgG, IgA and IgM concentrations, 3.29 ± 1.62 and 3.74 ± 0.6 times higher SARS-CoV-2 N and S antibody concentrations and 3.85 ± 1.71 times higher SARS-CoV-2 S-specific IgG concentrations compared to the donors' peripheral blood. The specific SARS-CoV-2 virus neutralization capacities increased in all but one concentrate. All antibody concentrates (50-70 mL final volume) passed microbiological tests, were free of hazardous glycine levels and could be stored at -80°C and 4°C for 1 year with 20 ± 3% antibody loss. Immunoadsorption followed by tangential flow filtration is a feasible procedure to collect IgG, IgA and IgM as well as SARS-CoV-2 N- and S-specific antibody concentrates of low volume, free of albumin and coagulation factors. Whether these concentrates can be used as passive immunisation in infected patients remains to be elucidated.

TA-Cloning for Diabetes Treatment: Expressing Corynebacterium Malic Enzyme Gene in E. coli.

Diabetes mellitus represents a persistent metabolic condition marked by heightened levels of blood glucose, presenting a considerable worldwide health concern, and finding targeted treatment for it is a crucial priority for global health. Gram-positive aerobic bacteria, predominantly inhabiting water and soil, are known carriers of various enzyme-encoding genetic material, which includes the malic enzyme gene that plays a role in insulin secretion. Corynebacterium glutamicum bacteria (ATCC 21799) were acquired from the Pasteur Institute and confirmed using microbiological and molecular tests, including DNA extraction. After identification, gene purification and cloning of the maeB gene were performed using the TA Cloning method. Additionally, the enhancement of enzyme expression was assessed using the expression vector pET-28a, and validation of simulation results was monitored through a real-time PCR analysis. Based on previous studies, the malic enzyme plays a pivotal role in maintaining glucose homeostasis, and increased expression of this enzyme has been associated with enhanced insulin sensitivity. However, the production of malic enzyme has encountered numerous challenges and difficulties. This study successfully isolated the malic enzyme genes via Corynebacterium glutamicum and introduced them into Escherichia coli for high-yield production. According to the results, the optimum temperature for the activity of enzymes has been identified as 39°C.

Observational and cross-sectional study on clinical profile of nontuberculous mycobacterial (NTM) disease in patients at tertiary care hospital of central India

Background Nontuberculous Mycobacterial (NTM) diseases present unique clinical challenges and are increasingly recognised as significant contributors to respiratory and extrapulmonary morbidity. This study protocol outlines an observational and cross-sectional investigation aiming to comprehensively understand the clinical profile of NTM disease, including its prevalence, risk factors, and clinical features, in patients at a tertiary care hospital in central India. Methods Over two years, from July 2022 to June 2024, a convenience sample size will be recruited from TB suspects meeting inclusion criteria. Comprehensive data collection will be conducted, including demographic information, clinical history, radiological findings, microbiological test results, and risk factor assessments. Statistical methods will be applied to the collected data, including descriptive statistics, comparative analysis, risk factor assessments, and multivariate analyses. Expected Results The study aims to provide valuable insights into the prevalence and clinical manifestations of NTM disease, shedding light on the risk factors contributing to its occurrence. The statistical analyses will identify key factors associated with NTM disease and characterise its clinical and radiological features.

A metagenomics-based workflow for the detection and genomic characterization of GBS in raw freshwater fish.

The need for a rapid and accurate food microbiological testing method is apparent for a timely and effective foodborne outbreak response. This is particularly relevant for emerging foodborne pathogens such as Group B Streptococcus (GBS) whose associated food safety risk might be undercharacterized. By using GBS in raw freshwater fish as a case example, this study describes the development of a metagenomics-based workflow for rapid food microbiological safety testing and surveillance. This study can inform as a working model for various foodborne pathogens in other complex food matrices, paving the way for future methodological development of metagenomics for food microbiological safety testing.

Formulation and Evaluation of Multipurpose Herbal Cream

The remedies used to improve a person's look are called herbal cosmetics. The current study set out to create a herbal cream with antifungal, antibacterial, anti-acne properties, as well as moisturizing, nourishing, lightening, and treating a range of skin conditions. Various unrefined medications were consumed, including Curcuma longa (turmeric rhizomes), Nirgundi (Vitex negundo Linn), Azadirachta Indica (neem leaves). The cream is prepared by slab Technique. Final samples underwent accelerated stability testing in an environmental chamber with a temperature of 25 ± 100C and a humidity of 60 ± 10% RH. It was discovered that every product was stable, showing no evidence of phase separation or color change. Additionally, a patch test was performed for sensitivity testing, and there was no indication of any allergic reactions or skin irritation. This work primarily it focuses on evaluating the microbiological quality of prepared cosmetics. To everyone's amazement, both formulations passed the microbiological limit tests according to international standards. It has been established that the formulation of herbal cosmetics is safe for use and can be applied as a barrier to protect skin.

Polyherbal Soap - Unveiling Formulation Techniques and Quality Assessment Methods

Polyherbal soaps, a fusion of diverse botanicals, epitomize natural skincare. This article delves into their creation and meticulous quality assessments, spotlighting their relevance in modern skincare. The formulation process unveils a symphony of botanical contributions, like neem, turmeric, and aloe vera, enriching these soaps. Crafting these soaps involves artful techniques, from precision in the cold process to strategic additives amplifying their skin-nurturing effects. Evaluations ensure sensory allure and safety, employing chromatography to reveal skin-enhancing compounds and rigorous microbiological tests affirming efficacy against harmful agents. These soaps excel in acne care, hydration, and soothing effects. Challenges in consistency and compliance persist, yet the future promises ongoing innovation, bolstering their significance in skincare. This exploration invites all to discover polyherbal soaps, where nature meets scientific scrutiny for a holistic skincare journey.

Metrisor: A novel diagnostic method for metritis detection in cattle based on machine learning and sensors

The Metrisor device has been developed using gas sensors for rapid, highly accurate and effective diagnosis of metritis. 513 cattle uteri were collected from abattoirs and swabs were taken for microbiological testing. The Metrisor device was used to measure intrauterine gases. The results showed a bacterial growth rate of 75.75 % in uteri with clinical metritis. In uteri positive for clinical metritis, the most commonly isolated and identified bacteria were Trueperella pyogenes, Fusobacterium necrophorum and Escherichia coli. Measurements taken with Metrisor to determine the presence of metritis in the uterus yielded the most successful results in evaluations of relevant machine learning algorithms. The ICO (Iterative Classifier Optimizer) algorithm achieved 71.22 % accuracy, 64.40 % precision and 71.20 % recall. Experiments were conducted to examine bacterial growth in the uterus and the random forest algorithm produced the most successful results with accuracy, precision and recall values of 78.16 %, 75.30 % and 78.20 % respectively. ICO also showed high performance in experiments to determine bacterial growth in metritis-positive uteri, with accuracy, precision and recall values of 78.97 %, 77.20 % and 79.00 %, respectively. In conclusion, the Metrisor device demonstrated high accuracy in detecting metritis and bacterial growth in uteri and could identify bacteria such as E. coli, S. aureus, coagulase-negative staphylococci, T. pyogenes, Bacillus spp., Clostridium spp. and F. necrophorum with rates up to 80 %. It provides a reliable, rapid and effective means of detecting metritis in animals in the field without the need for laboratory facilities.

Implementation of ISO 16140-3:2021 for Enumeration of Enterobacteriaceae in Food Products

Method verification is one of the steps required to ensure that all methods used meet the standards required for data reliability and accuracy in a laboratory that implements Good Laboratory Practices (GLP). In accordance with ISO 16140-3:2021, the method verification for microbiology testing implemented by calculating the Intralaboratory Reproducibility Standard Deviation (SIR) for implementation verification and eBias value for food item verification. Method verification for enumeration of Enterobacteriaceae in food products using ISO 16140-3 has never been carried out at the Indonesian Food and Drug Authority (FDA) laboratories. Therefore, verification of this method needs to be performed. This study aimed to verify the ISO 21528-2:2017 as reference method for enumeration of Enterobacteriaceae in food products by colony count technique. The selected food item for implementation verification was pasteurized milk while for food item verification, the selected food items were yogurt, traditional preserved egg (telur pindang), sweet and hard candy, seasoning dry powder, worcester sauce and cassava chips. All of selected foods were artificially contaminated with Escherichia coli WDCM 00012. The SIR value obtained was 0.12 ≤ 2× 0,18 (lowest mean value of SR from ISO 21528-2:2017), indicating that the acceptability limit for the implementation verification was met. While the eBias value for all selected food item were less than 0,5 log10, thus the verification study in the National Quality Contol Laboratory of Drug and Food (NQCLDF), Indonesian FDA, meets the acceptance criteria defined in the standard ISO 16140-3:2021.

РОЛЬ МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКИХ МЕТОДОВ ИССЛЕДОВАНИЙ В ЭТИОПАТОГЕНЕЗЕ ОСТЕОМИЕЛИТА ЧЕЛЮСТЕЙ

The subject of the study is the importance of molecular genetic research methods in the study of the etiopathogenesis of osteomyelitis of the jaws. The purpose of the work is to provide up-to-date information to researchers, dental surgeons, and maxillofacial surgeons on the possibilities of molecular genetic research in identifying bacterial pathogens in osteomyelitis of the jaws, as well as to reflect genetic markers of pathogenicity factors for a number of the main causative agents of the disease. Methodology. International scientific databases PubMed, ScienceDirect, Scopus, Cochrane Collaboration, Elsevier, as well as electronic catalogs eLIBRARY.RU and CyberLeninka.ru were used. Results. A review of publications demonstrated that S. aureus and S. Epidermidis dominate the etiological spectrum of causative agents of bone tissue infections. The participation of these microorganisms is determined by a whole range of pathogenicity factors. Toxins and Panton-Valentine leukocidin (PVL) genes play a major role in the pathogenesis of osteomyelitis and disease progression. It has been shown that the pathogenic bacteria Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans are capable of inducing differentiated production of cytokines. The most attention has been attracted to E. faecium, which exhibits multidrug resistance to a wide range of antibiotics. The proportion of infections mediated by S. epidermidis and S. Saprophyticus is, on average, about 25% of cases. The proportion of representatives of gram-negative flora Escherichia, Klebsiella, Enterobacter, Citrobacter, Proteus, Providencia, Serratia reaches 23% of cases. Pathogenic nosocomial strains of P. aeruginosa are also involved in the formation of chronic inflammation in osteomyelitis. According to the results of published studies, more than a third of cases of chronic osteomyelitis are mediated by microbial associations, which are dominated by S. aureus, S. epidermidis and, less commonly, E. faecalis. Conclusions. The use of PCR analysis to identify the causative agents of osteomyelitis and gene amplification using specific primers has a huge advantage over routine microbiological tests, being an informative method for studying the pathogenicity factors of the main pathogens. The high importance of molecular genetic methods in the study of the etiopathogenesis of osteomyelitis of the jaws requires their widespread use in the clinic of surgical dentistry and maxillofacial surgery to successfully solve complex problems in the rehabilitation of patients with this disease.

Quantum-chemical calculation, antibiotic potentiating activity, evaluation of efflux pump inhibition against S. aureus multi-resistant strains and molecular docking of the drugs isoniazid and hydralazine

In recent years, due to the uncontrolled use of antibiotics and natural evolution, many pathogenic microorganisms have acquired resistance to currently available drugs. Consequently, the number of infections caused by these microorganisms, considered multi-resistant to antimicrobial drugs, has increased, becoming a serious global public health problem. In the search for alternative therapies, drug repositioning represents a promising way to introduce new medicines. Hydralazine exhibits antihypertensive and peripheral vasodilatory action and isoniazid is a prodrug used as the first choice for the chemotherapy treatment of tuberculosis. In this work, microbiological tests were performed to investigate the modulator potential and efflux pump inhibition on S. aureus multi-resistant strains of the drugs isoniazid and hydralazine. In addition, the Density Functional Theory was used to determine the electronic and reactivity properties. Association of Ciprofloxacin with hydralazine on the K2068 strain proved to be better than the association of Norfloxacin with this antihypertensive on the 1199B strain of S. aureus. Association of isoniazid with ciprofloxacin in the K2068 strain was irrelevant and may have generated antagonism. The opposite effect was observed when associated with Norfloxacin in strain 1199B, where a significant reduction in the MIC of Norfloxacin was observed when associated with isoniazid. Regarding the association of hydralazine and isoniazid with EtBr, the results of this study showed that only hydralazine was able to positively modify the MIC of bromide on strains 1199B and K2068, presenting better results with this last strain, while in tests with to isoniazid. Molecular docking was used to verify the feasibility of forming receptor-ligand complexes and the replicability of the results. The molecular docking study against MepA indicated a possible synergistic effect between hydralazine and the antibiotic ciprofloxacin. Regarding NorA, the data indicated that hydralazine could act through competitive inhibition with the control norfloxacin, since it interacts in the same region of the antibiotic binding site through interactions in common with residues Glu-222, Tyr-225 and Val -302.

Development of an expert system for assessing failures in oil and gas pipelines due to microbiologically influenced corrosion (MIC)

This study highlights the modeling of an expert system for the classification of internal microbiologically influenced corrosion (MIC) failures related to pipelines in the upstream oil and gas industry. The model is based on artificial neural networks (ANNs) and involves the participation of 15 MIC experts. Each expert evaluated a number of model case studies ranging from MIC- to non-MIC-driven upstream pipeline failures. The model accounts for variations in microbiological testing methods, microbiological sample types, and degradation morphology, among other variables. It also accounts for missing datasets, which is commonly the case in actual failure assessments. The outcome is an expert system model whose outputs are classes (classification ANN) which comprises MIC potential and data confidence. The performances of two approaches are contrasted in this study. One classifies the output in 5 classes, a 5-output classification (5OC) model; the other in 3 classes, a 3-output classification (3OC) model. The 5OC model had an accuracy of 62.0% while the simpler 3OC model had a better accuracy of 74.8%. This modelling exercise has demonstrated that knowledge from experts can be captured in a reasonably effective model to screen for possible MIC failures. It is hoped that this study not only may contribute to a better understanding of the prevalence of MIC in the oil and gas sector, but also may highlight the key areas necessary to improve the diagnosis of MIC failures in the future.

Review: Policy strategy of nano cosmetic testing in Indonesia

The implementation of nanotechnology in the cosmetic industry has developed promptly in recent decades. Among them are sunscreen, skincare, decorative makeup, and hair colorant. The cosmetics industry is a significant user of nanoscale raw materials in its manufacturing procedures. However, the supervision regarding the safety and quality of cosmetic products containing nanomaterials (NMs) in Indonesia conducted by the Indonesian FDA remains not fully optimized. This poses a challenge for the Indonesian FDA, particularly concerning the significance of employing appropriate characterization methods and the necessity for systematic evaluation. Hazard identification, exposure evaluation, microbiological testing, and NM characterization are some methods that can be conducted for monitoring nano cosmetics. Procuring instruments for nano-analysis will be a significant investment for the purpose of monitoring cosmetic products marketed in Indonesia.

Engineered lecithin-based proniosomes for enhanced trans-tympanic permeation: In vitro, microbiological, ex vivo and invivo evaluation

Otitismedia is an acute illness that specifically targets the middle ear. It affects around one-third of the pediatric population in the US. This study aimed to develop lecithin-based proniosomes to enhance the trans-tympanic permeation of the antimicrobial drug ofloxacin (OFX) and boost its antibacterial properties. Proniosomes were fabricated by the coacervation technique using a Box-Behnken design. The investigated factors were cholesterol amount (A), surfactant-to-drug ratio (B), and Brij percentage (C). The numerical optimization feature of Design-Expert® software was implemented to choose the optimum formula. The criteria for selection involved decreasing the polydispersity index (PDI) and particle size (PS) while maximizing the absolute value of zeta potential (ZP) and the percentage of entrapment efficacy (EE%). The formula with the highest desirability value (0.748), an EE% of 73.38 %, a PS of 625.35 nm, and a ZP of −44.20 mV was selected as the optimum formula. Additional investigations were conducted to illustrate the morphological appearance, release rate, stability, activity, and tolerability of the selected formula, such as invitro,ex vivo, microbiological, and invivo tests. Results demonstrated that, compared to the OFX solution (2118.72 μg/cm2), the optimum formula was found to have better otic tolerance, augmented trans-tympanic permeation (3701.01 μg/cm2), and improved antibacterial activity. The aforementioned outcomes highlighted the capability of the OFX-loaded lecithin-based proniosomes to be used as a promising non-invasive delivery system for the treatment of otitismedia.

Novel 3D printed polysaccharide-based materials with prebiotic activity for potential treatment of diaper rash

Diaper rash, mainly occurring as erythema and itching in the diaper area, causes considerable distress to infants and toddlers. Increasing evidence suggests that an unequal distribution of microorganisms on the skin contributes to the development of diaper dermatitis. Probiotic bacteria, like Staphylococcus epidermidis, are crucial for maintaining a healthy balance in the skin's microbiome, among others, through their fermentative metabolites, such as short-chain fatty acids. Using a defined prebiotic as a carbon source (e.g., as part of the diaper formulation) can selectively trigger the fermentation of probiotic bacteria. A proper material choice can reduce diaper rash incidence by diminishing the skin exposure to wetness and faeces. Using 3D printing, we fabricated carbon-rich materials for the top sheet layer of baby diapers that enhance the probiotic activity of S. epidermidis. The developed materials' printability, chemical composition, swelling ability, and degradation rate were analysed. In addition, microbiological tests evaluated their potential as a source of in situ short-chain fatty acid production. Finally, biocompatibility testing with skin cells evaluated their safety for potential use as part of diapers. The results demonstrate a cost-effective approach for producing novel materials that can tailor the ecological balance of the skin microflora and help treat diaper rash.

Exploring the Pathogen Diagnosis and Prognostic Factors of Severe COVID-19 Using Metagenomic Next-Generation Sequencing: A Retrospective Study

Background: This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology. Methods: We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information. Results: In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P&lt;0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P&lt;0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924. Conclusion: The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.

Molecular characterization of carbapenemase and extended spectrum beta-lactamase producing Acinetobacter baumannii isolates causing surgical site infections in Ethiopia

BackgroundAcinetobacter baumannii is an opportunistic pathogen that can cause a variety of nosocomial infections in humans. This study aimed to molecularly characterize extended-spectrum beta-lactamase (ESBL) producing and carbapenem-resistant Acinetobacter species isolated from surgical site infections (SSI).MethodsA multicentre cross-sectional study was performed among SSI patients at four hospitals located in Northern, Southern, Southwest, and Central parts of Ethiopia. The isolates were identified by microbiological methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility was determined using disk diffusion. The presence of phenotypic ESBL and carbapenemase production was detected by employing standard microbiological tests, including combined disk diffusion (CDT). ESBL and carbapenem resistance determinants genes were studied by polymerase chain reaction (PCR) and sequencing.ResultsA total of 8.7% Acinetobacter species were identified from 493 culture-positive isolates out of 752 SSI wounds. The species identified by MALDI-TOF MS were 88.4% A. baumannii, 4.7% Acinetobacter pittii, 4.7% Acinetobacter soli, and 2.3% Acinetobacter lactucae. Of all isolates 93% were positive for ESBL enzymes according to the CDT. Using whole genome sequencing 62.8% of the A. baumannii harbored one or more beta-lactamase genes, and 46.5% harbored one or more carbapenemase producing genes. The distribution of beta-lactamases among Acinetobacter species by hospitals was 53.8%, 64.3%, 75%, and 75% at JUSH, TASH, DTCSH, and HUCSH respectively. Among ESBL genes, blaCTX−M alleles were detected in 21.4% of isolates; of these 83.3% were blaCTX−M−15. The predominant carbapenemase gene of blaOXA type was detected in 24 carbapenem-resistant A. baumannii followed by blaNDM alleles carried in 12 A. baumannii with blaNDM−1 as the most common.ConclusionsThe frequency of Acinetobacter species that produce metallobetalactamases (MBLs) and ESBLs that were found in this study is extremely scary and calls for strict infection prevention and control procedures in health facilities helps to set effective antibiotics stewardship.

Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections.

The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.

Correlation of CD4+ count and viral load with urinary tract infection and antimicrobial resistance pattern of bacterial uropathogens among HIV patients in Wolaita Sodo, South Ethiopia.

The permanence of HIV patients in healthcare provision centers exposes their weak immunity to various nosocomial microorganisms that migrate into and out of the hospital environment. The incidence of bacterial infections, including urinary tract infection, was inversely correlated with CD4+ T cells. Urinary tract infection (UTI) is one of the clinical problems among HIV patients. There was scarcity of published data on the relationship between viral load, CD4+ level, and UTI. This study aimed to assess the relationship between viral load and CD4 with bacterial UTI among HIV patients. The cross-sectional study was conducted in the Wolaita Sodo Town Health Center ART clinic. The socio-demographic data were collected using a pre-designed questionnaire. Patients' charts were reviewed to collect the current CD4 and viral load. Urine specimens were inoculated on blood agar, cysteine lactose electrolyte deficient (CLED) agar, and MacConkey agar, and bacterial species were finally identified using various biochemical methods. Antimicrobial sensitivity testing was conducted using standard microbiological tests. Bivariate and multivariate analyses were employed to describe the association between pairs of variables and to examine the relationship between independent variables and dependent variables. In this study, the overall prevalence of urinary tract infection (UTI) was 13.7%. Escherichia coli, Staphylococcus aureus, Pseudomonas aeroginosa, Staphylococcus saprophyticus, Proteus mirabilis, and Klebsiella pneumoniae were bacterial uropathogens detected in this study. E.coli (45.7%) was the predominant isolate followed by S. aureus (14.3%). Positive correlation between CD4+ count and urinary tract infection was detected and found statistically significant (r = 0.288 p > 0.01), whereas the viral load and urinary tract infection negatively correlated and showed statistically significant association (p < 0.01). The resistance rate of E.coli was 94%, 75%, and 69% to ciprofloxacin, norfloxacin, and cefepime, respectively. This study revealed that E.coli exhibited 94% and 75% resistance to amoxicillin-clavulanic acid and tetracycline, respectively. K. pneumoniae demonstrated complete resistance (100%) to amoxicillin-clavulanic acid, tetracycline, and trimethoprim-sulfamethoxazole, while showing 100% susceptibility to ciprofloxacin and nitrofurantoin. In the present study, the magnitude of the multi-drug resistance (MDR) was found to be 80%. CD4+ count, combination of antiretroviral therapy (ART) drugs, and a history of hospitalization were risk factors for urinary tract infection. In the current study, urinary tract infection emerged as a significant health concern among people living with HIV following their ART. The occurrence of urinary tract infection among HIV patients could be influenced by multifactorial factors that require further study. The CD4+ count was positively correlated with the prevalence of UTI, whereas the viral load was negatively correlated. The CD4+ count, combination of ART, and history of hospitalization were independent risk factors for UTI. The prevalence of MDR bacterial pathogens were notably high. Therefore, the treatment of UTI in HIV patients should be prescribed based on antibacterial susceptibility testing results.