Microbiology Laboratory Research Articles

Challenging diagnosis of parasitic infection and practical guidance to clinical microbiology laboratories in Korea

Challenging diagnosis of parasitic infection and practical guidance to clinical microbiology laboratories in Korea

Impact of COVID-19 Restrictions on Incidence of Enteropathogenic Bacteria, Virus, and Parasites in Denmark: A National, Register-Based Study.

Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of enteropathogenic microorganisms may have been reduced in Denmark during the COVID-19 pandemic. All Departments of Clinical Microbiology in Denmark provided data on the monthly incidence of Salmonella spp., Escherichia coli, Campylobacter spp., Clostridioides difficile, Norovirus GI+GII, Giardia duodenalis, and Cryptosporidium from March 2018 to February 2021. The data were divided into three periods as follows: Control Period 1 (March 2018 to February 2019); Control Period 2 (March 2019 to February 2020); and the Restriction (pandemic) Period (March 2020 to February 2021). The incidences of pathogenic Salmonella spp.-, Escherichia coli-, and Campylobacter spp.-positive samples decreased by 57.3%, 48.1%, and 32.9%, respectively, during the restriction period. No decrease in C. difficile was observed. Norovirus GI+GII-positive samples decreased by 85.6%. Giardia duodenalis-positive samples decreased by 66.2%. Cryptosporidium species decreased by 59.6%. This study demonstrates a clear decrease in the incidence of enteropathogenic bacteria (except for C. difficile), viruses, and parasites during the SARS-CoV-2 restriction period in Denmark.

Multidrug Resistance And Susceptibility Profile of Outpatient Escherichia Coli Clinical Isolates

Background: To gain better understanding about the impact of antibiotic selection pressure on antimicrobial resistance (AMR) in Nigeria, it is important to conduct and review from time to time the susceptibility profile of clinically important bacteria including Escherichia coli. This study investigated the susceptibility and multidrug resistance profile of E. coli isolates from urine samples of patients who received outpatient’s medical services in Abakaliki. Methods: A total of 50 non-duplicate clinical isolates of E. coli from the microbiology laboratory section of a tertiary hospital in Abakaliki, Nigeria was recruited for this study. Susceptibility studies were determined using amoxicillin (20 µg), ceftazidime (30 µg), ciprofloxacin (5 µg), gentamicin (10 µg), nitrofurantoin (300 µg) and erythromycin acid (15 µg) by the modified Kirby–Bauer disk diffusion method. All susceptibility studies were carried out as per the guidelines of the Clinical Laboratory Standard Institute (CLSI). Multidrug resistance was evaluated by the multiple antibiotic resistance index (MARI) calculation. Results: The E. coli isolates showed reduced susceptibility to gentamicin (75%), ciprofloxacin (85%), nitrofurantoin (95%), amoxicillin (100%), erythromycin (100%) and ceftazidime (95%). A total of 12 E. coli isolates were multidrug resistant to clinically important antibiotics in the classes: cephalosporins, macrolides, aminoglycosides, fluoroquinolones, penicillins and nitrofurantoin. Conclusion: We report a high rate of antibiotic resistance of outpatients E. coli isolates which concurrently showed multidrug resistance to important antibiotic classes. These findings have clinical significance and provide a benchmark for future studies on the susceptibility pattern of clinical isolates in Nigeria. This preliminary study reiterates the need to reinvigorate antibiotic stewardship in our local hospitals so as to preserve the clinical efficacy of available antibiotics since it takes years for a new antibiotic to be developed.

Biphasic Medium Using Nicotinamide for Detection of Pyrazinamide Resistance in Mycobacterium tuberculosis.

Reliable drug susceptibility testing of pyrazinamide (PZA) is technically difficult, since PZA activity is pH sensitive. The aim of this study was to evaluate a biphasic medium assay (BMA) for the reliable detection of PZA resistance in Mycobacterium tuberculosis (MTB) using nicotinamide (NIC) as a surrogate for PZA and identifying the appropriate cut-off value for the assay. The PZA susceptibility of 122 multidrug-resistant tuberculosis (MDR-TB) isolates and 39 drug-susceptible tuberculosis (DS-TB) isolates was examined using the BMA with NIC at four different concentrations (250, 500, 1000, and 2000 mg/L) and comparing the results with results from the BACTEC MGIT 960 reference method. Out of 122 MDR-TB isolates, 40 were identified as resistant by the BACTEC MGIT 960 system, of which 92.5% contained mutations within their pncA gene plus promoter region. A minimum inhibitory concentration of NIC ≥ 1000 mg/L was used as the cut-off concentration to define resistance in correlation with the MGIT 960 outcomes. NIC-BMA had a sensitivity of 90.91%, a specificity of 100%, and an accuracy of 97.52% compared with the MGIT 960 method. NIC-BMA is a promising assay to screen PZA resistance in microbiological laboratories without automation or advanced molecular instruments.

Points to consider when establishing an equipment calibration programme in a conventional food microbiology laboratory for ISO/IEC 17025:2017 accreditation purpose

Points to consider when establishing an equipment calibration programme in a conventional food microbiology laboratory for ISO/IEC 17025:2017 accreditation purpose

Identification of Bacteria from Public Toilets of Modern Market (Goico) in Musanze Town, Rwanda

Background: Bacteria are present on all surfaces, to which they were carried by many direct and indirect methods of transmission. A toilet is simply a receptacle into which both solid and liquid waste of human origin, in the form of urine and excreta are discharged. In public toilets, complete strangers mix and use the same sanitary facilities, with all the related risks of bodily fluid exchange, contamination and organism transmission. Unhygienic use of the toilet’s facilities may cause urine and fecal residues after use to serve as a major reservoir or source of human pathogen, which may in turn bring about disease outbreak. Aim: This study aimed at Identification of Bacteria from Public Toilets of Modern Market (Goico) In Musanze Town, Rwanda Method: This cross-sectional study was conducted to identify bacteria from GOICO market toilets. About 40 samples; 20 from male and 20 from female toilets were collected and transported to INES-clinical microbiology laboratory for microbiological analysis. Laboratory techniques including culture, gram stain, biochemical tests and antibiogram were performed. Results: The most predominant bacteria isolated was S. aureus (31.43%), followed by S. typhi (20%), Streptococcus(15.71%), E. coli(12.86%), P. aeuriginosa(10%), P. mirabilis(7.14%), C. freundi(1.43%), S. epidermidis (1.43%). It was noted that female toilets were more contaminated (51.43%) than male toilets (48.57%). All gram positive and gram-negative bacteria were sensitive to Gentamicin. Almost all bacteria except P. mirabilis were sensitive to Norfloxacin, gram negative showed a resistance to Vancomycin and Novobiocin. Conclusion: These results should alert public toilets users that extreme caution must be executed while using these toilets, as they may be a source of pathogenic bacteria. The best way to keep a toilet and its seat free of bacteria is to clean it with bleach. Otherwise, keep the bacteria at bay by washing your hands, and if you just don't trust that toilet seat, wipe it down with a disinfectant or antibacterial wipe before you sit. Keywords: Bacteria, Public toilets, E. coli, S. typhi, Urinary tract

Bacteriological profile in patients with cesarean infection at Ruhengeri level two teaching Hospital

Background: A cesarean infection is a referral hospital acquired bacterial infection that occurs after deliver by cesarean section which could be emergency or elective. As highlighted by the various researchers that the infections following a cesarean delivery, which some people call a C-section, are common. The wound coming into contact with bacteria or other harmful microbes is a common cause of these infections. The main objective of this study was the assessment of bacteria isolated from cesarean infection patients attending Ruhengeri level two teaching hospital. Methodology: A cross-sectional study was conducted and total of 30 wound swabs of cesarean were collected from inpatient of Ruhengeri level two teaching hospital.Data were analyzed using SPSS statistical software (version 20). Results: The results showed that the most predominant bacteria isolated from patients with cesarean infection was S. aureus (28.1%) followed by S. pyogenes (18.8%), K. pneumoniae (18.8%), P. aeruginosa (12.5%), S.epidermidis (9.4%), E. coli (6.3%) and P. mirabilis(6.3%). Antibiotics sensitivity test was performed, so this study showed the predominant antibiotic which were sensitively to different bacteria were Chloramphenicol, Gentamycin and Norfloxacin and most bacteria were resistance to Rifampicin and Vancomycin. Conclusion: This study has shown that there are many bacteria that may be isolated in cesarean infection. It has also shown that some of the isolated bacteria were sensitive and other were resistant to Rifampicin and Vancomycin. The study recommends that Rwandan government should create more clinical microbiological laboratory, in Rwanda, in order to minimize the antibiotic resistance and also on the side of health care providers, especially at Ruhengeri level two teaching hospital, they should use the experienced workers in order to minimise the risks of getting caesarean infection and also to recommend the patients taking care their wound. Keywords: Cesarean infection, Bacteria, Antibiotics, Bacteriological profile

Isolation and Identification of Bacteria from Electronic devices used by Students and Staffs in Ines Ruhengeri

Background: Electronic devices have become one of the most essential accessories being used in daily lives including schools. Those devices increase the communication and using them makes learning much easier. Microbial contamination of electronic devices and inanimate surface of electronic equipment at INES-Ruhengeri can have a significant role for transmission of pathogenic bacteria. Aim: The aim of this study was to isolate and identify bacteria from electronic devices used by students and staffs at INES-Ruhengeri University. Methodology: This cross-sectional study was done on 40 electronic devices such as computers, microscopes, global positioning system (GPS) and total stations A random sampling method was applied from sterile swab soaked in peptone water solution by the technique of bearing on the surface of the entire devices and then placed in a transport medium. Collected samples were then taken in INES-Ruhengeri Microbiology laboratory for further experiments. Results: All 40 electronic devices were contaminated with bacteria. The most predominant bacteria isolated from electronic devices was S.aureus (25.9%) followed by Bacillus spp(24.1%), K.pneumonia(12.9%), S.epidermis(12.9%), Micrococcus spp(7.4%), P.aeruginosa(5.5%), E.coli(3.3%), Salmonella spp(3.3%) and Shigella spp(3.3%). Antimicrobial susceptibility pattern of selected antibiotics was performed. Norfloxin was the most sensitive antibiotic on all isolated bacteria. Chloramphenicol antibiotic shown no activity over any of the isolated bacteria, to imply that all bacteria had resistance on it. Conclusion: This study shown that there is bacterial contamination to all devices and antibiotic susceptibility test shown that some antibiotics were sensitive and resistant to the isolated bacteria.

Epidemiology and antimicrobial resistance of Mycobacterium spp. in the United Arab Emirates: a retrospective analysis of 12 years of national antimicrobial resistance surveillance data.

The Eastern Mediterranean Regional Office (EMRO) region accounts for almost 8% of all global Mycobacterium tuberculosis (TB) cases, with TB incidence rates ranging from 1 per 100,000 per year in the United Arab Emirates (UAE) to 204 per 100,000 in Djibouti. The national surveillance data from the Middle East and North Africa (MENA) region on the epidemiology and antimicrobial resistance trends of TB, including MDR-TB remains scarce. A retrospective 12-year analysis of N = 8,086 non-duplicate diagnostic Mycobacterium tuberculosis complex (MTB complex) isolates from the UAE was conducted. Data were generated through routine patient care during the 2010-2021 years, collected by trained personnel and reported by participating surveillance sites to the UAE National Antimicrobial Resistance (AMR) Surveillance program. Data analysis was conducted with WHONET, a windows-based microbiology laboratory database management software developed by the World Health Organization Collaborating Center for Surveillance of Antimicrobial Resistance, Boston, United States (https://whonet.org/). A total of 8,086 MTB-complex isolates were analyzed. MTB-complex was primarily isolated from respiratory samples (sputum 80.1%, broncho-alveolar lavage 4.6%, pleural fluid 4.1%). Inpatients accounted for 63.2%, including 1.3% from ICU. Nationality was known for 84.3% of patients, including 3.8% Emiratis. Of UAE non-nationals, 80.5% were from 110 countries, most of which were Asian countries. India accounted for 20.8%, Pakistan 13.6%, Philippines 12.7%, and Bangladesh 7.8%. Rifampicin-resistant MTB-complex isolates (RR-TB) were found in 2.8% of the isolates, resistance to isoniazid, streptomycin, pyrazinamide, and ethambutol, was 8.9, 6.9, 3.4 and 0.4%, respectively. A slightly increasing trend of resistance among MTB-complex was observed for rifampicin from 2.5% (2010) to 2.8% (2021). Infections due to MTB-complex are relatively uncommon in the United Arab Emirates compared to other countries in the MENA region. Most TB patients in the UAE are of Asian origin, mainly from countries with a high prevalence of TB. Resistance to first line anti-tuberculous drugs is generally low, however increasing trends for MDR-TB mainly rifampicin linked resistance is a major concern. MDR-TB was not associated with a higher mortality, admission to ICU, or increased length of hospitalization as compared to non-MDR-TB.

Investigation of SCCmec types using the real time PCR method in cefoxitin-resistant Staphylococcus aureus isolates

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that can cause many community and hospital-acquired infections. This study was conducted to investigate the SCCmec gene types responsible for methicillin resistance in MRSA isolates isolated from hospitalised patients. Material and methodsMRSA isolates isolated from samples sent from various clinics to Gaziantep University Hospital Microbiology Laboratory between March 2021–January 2022 were included in the study. Bacteria were identified using by VITEK 2 automated system. Cefoxitin (FOX) resistance was determined by the disc diffusion method according to EUCAST standards. Cefoxitin resistance was confirmed by the Penicillin Binding Protein 2′ latex agglutination test. Types of mecA, mecC, coa, nuc, Panton Valentin Leukocidin (PVL), ccrC2, class A mec, SCCmec types in isolates detected as MRSA were investigated by real-time PCR. ResultsIn this study, 116 isolates meeting the study criteria were examined. By detecting the nuc and coa genes in all isolates by PCR, the phenotypic identification of S.aureus was confirmed. While the mecA gene was detected in all MRSA isolates, no mecC gene was detected in any isolates. Detected SCCmec types were as follows; SCCmec Type 1 (2.6%), Type II (28.4%), Type III (12.9%), Type IVa (11.2%), Type IVb (3.4%), Type IVc (3.4%), Type IVg (12.1%), Type V (0.9%), Type VII (4.3%), Type VIII (18.1%), Type IX (0.9%), Type XII (1.7%). On the other hand, SCCmec Type VI, X, XI and XIII were not found in any isolate. It was determined that four of the MRSA isolates (3.4%) carried the PVL gene that two (50%) of these were found in SCCmec Type VIII. ConclusionMonitoring of FOX resistance is an effective and safe method for determination of MRSA isolates. The change in the mec gene causes resistance, which should be monitored regularly with molecular methods. Our study is the first study in Turkey.

Healthcare-associated Diarrhea due to Clostridioides difficile in Patients Attending a Tertiary Care Teaching Hospital of North India.

Healthcare-associated diarrhea (HCAD) is diarrhea that develops at least after 3 days of hospitalization, with the most common infectious cause being Clostridioides difficile. Over the last decade, there has been a remarkable growth in the frequency and severity of C. difficile infection (CDI), making it one of the most prevalent healthcare-associated infections. This study aimed to analyze the prevalence and risk factors associated with CDI. A total of 107 patients with clinical suspicion of having HCAD were included in this study. Enzyme-linked fluorescent assay (ELFA) technique-based glutamate dehydrogenase (GDH) and toxin A/B assay were used as per the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) for diagnosing CDI. The details about associated comorbidities were retrieved from the hospital information system records. The presence of risk factors was noted. Risk factors associated with CDI were looked for. Out of the 107 stool samples received in the microbiology laboratory from patients with suspected HCAD eight (7.6%) samples were positive for CDI. The most frequent comorbidity observed in these patients was renal illness (acute or chronic kidney disease). In this study, a total of 7/8 cases were on multiple antibiotics most common being carbapenem. The 6-year prevalence of CDI observed in this study was found to be 7.6% risk factors, associated with CDI were kidney disease, diabetes mellitus, malignancy, and exposure to broad-spectrum antibiotics. Raj N, Agarwal J, Singh V, et al. Healthcare-associated Diarrhea due to Clostridioides difficile in Patients Attending a Tertiary Care Teaching Hospital of North India. Euroasian J Hepato-Gastroenterol 2024;14(1):60-64.

Application of ISO 16140-3:2021 standard to verify compact dry BC method in a single food microbiology laboratory

Application of ISO 16140-3:2021 standard to verify compact dry BC method in a single food microbiology laboratory

Exploring Prescription Practices: Insights from an Antimicrobial Stewardship Program at a Tertiary Healthcare Facility, Rwanda.

Antimicrobial resistance (AMR) is a major public health threat linked to increased morbidity and mortality. It has the potential to return us to the pre-antibiotic era. Antimicrobial stewardship (AMS) programs are recognized as a key intervention to improve antimicrobial use and combat AMR. However, implementation of AMS remains limited in Africa, particularly in Rwanda. This study aimed to assess prescription practices, identify areas for improvement, and promote adherence to AMS principles. Conducted at King Faisal Hospital in Rwanda, this qualitative study used semi-structured interviews with eight participants until saturation was reached. The interviews were recorded, transcribed, and thematically analyzed, revealing four emerging themes. The first theme was on AMS activities that were working well based on availability of microbiology laboratory results and prescription guidelines as factors influencing antibiotic prescription adjustments. The second theme was related to challenges during the implementation of the AMS program, including the prescription of broad-spectrum antibiotics, limited local data on AMR patterns, and stock-outs of essential antibiotics. The third theme was on the importance of adhering to AMR management guidelines at KFH. The last emerged on recommendations from participants centered on regular training for healthcare workers, widespread dissemination of AMR findings across departments, and the enforcement of antibiotic restriction policies. These actions can improve prescription behaviors, upholding the highest standards of patient care, and strengthening the nascent AMS program.

CLINICAL AND LABORATORY PROFILE OF ADMITTED PATIENTS PRESENTING WITH FEBRILE ILLNESS DUE TO DENGUE AND SCRUB TYPHUS COINFECTION FROM A TERTIARY CARE HOSPITAL IN SOUTH RAJASTHAN, INDIA

Objective: The present study aims at describing the clinical features, laboratory diagnosis, and complications in patients presenting with febrile illness due to scrub typhus and dengue coinfection from Southern Rajasthan, India. Method: This present prospective, observational, and hospital-based study conducted in the Department of Microbiology of AIMS & RC, Rajsamand, located in Southern Rajasthan, from January 2021 to December 2021. Scrub typhus was diagnosed in the microbiology laboratory by performing SD Bioline, one-step scrub typhus for the detection of IgM antibody, and dengue fever using J.mitra and Co. Pvt. Ltd., rapid card test for the detection of NS1 antigen and IgM antibody. Result: Out of 500 patients suspected of AUFI, 25 (5%) patients diagnosed of having dengue and scrub typhus coinfection. Fever was present in all 25 (100%) patients and 13 (52%) of patients had arthralgia, nausea, and vomiting. The most common sign noticed in our study was pallor and icterus in 10 (40%) patients each followed by shock/hypotension in 8 (32%) and hepatosplenomegaly in 5 (20%). The most predominant laboratory finding was thrombocytopenia (<1.0 × 106/cumm) in 23 (92%) patients, while elevated bilirubin (>2 mg/dl) in 22 (88%) and elevated transaminase and prolonged aPTT in 21 (84%) patients each. The majority of patients 23 (92%) had hepatic dysfunction, i.e., in followed by multi-organ dysfunction (MODS) in 15 (60%). Conclusion: In developing countries like India, particularly in tropical areas, dengue, and scrub typhus coinfection is under-recognized entity. Additional investigation should be carried out in cases of AUFI patients with features such as hypotension, leukocytosis, early drop in platelet counts, and hypoalbuminemia.

Antagonism and mycoparasitism mechanism of T. harzianum against pathogenic fungus species of F. oxysporum and Capnodium sp.

The purpose of this study was to test the ability of T. harzianum to inhibit the growth of pathogenic mold species and to determine the effectiveness of T. harzianum mold species in inhibiting the growth of pathogenic molds, as well as investigate how T. harzianum and pathogenic molds interact with each other. The Microbiology Laboratory of the Department of Biology, Faculty of Mathematics and Natural Sciences, State University of Malang, is where this research was conducted. The dual culture method was used for this test by using Czapek Agar (CA) medium. The isolated molds were then incubated for 4x24 hours at 25O–27OC. After that, the antagonism power was calculated. The results of macroscopic and microscopic observations were used to assess the mechanism of T. harzianum mold antagonism against pathogenic molds. The results showed that Trichoderma mold species were more resistant to the pathogenic mold Fusarium oxysporum than the pathogenic mold Capnodium. The antagonistic power of T. harzianum was 80%, with the antagonistic power of Capnodium sp. at 66.7%. The mechanism of mycoparasitism occurs when the hyphae of T. harzianum attach or entangle the hyphae of pathogenic molds, causing damage to the hyphal structure and inhibiting the growth of pathogenic molds.

Performance Evaluation of a Commercial Automated Library Preparation System for Clinical Microbial Whole-Genome Sequencing Assays

Next-generation sequencing (NGS) has proven clinical utility on disease management and serves as an important tool for genomic surveillance. Currently, hurdles surrounding its implementation, namely the complex and demanding analytical workflows, have impeded its widespread use in many laboratories. To address this challenge, the UCLA Molecular Microbiology and Pathogen Genomics Laboratory evaluated the performance of the Tecan MagicPrep NGS system, a commercial automated solution for library preparation for clinical whole-genome sequencing assays, against the Illumina Nextera DNA Flex Library Prep. Using 35 unique organisms (28 bacteria and 7 fungi) for various clinical applications, including microbial identification and genomic characterization, we compared the quantity and quality of the prepared libraries and the resulting sequences, and concordance of the overall results. We also assessed the impact of its implementation on laboratory workflow. The MagicPrep NGS produced higher library concentrations with smaller sizes, and correspondingly, higher molarity. Quality metrics of the sequences, however, demonstrated no significant impact on the overall results, producing 100% concordance with the reference method. Importantly, workflow analysis showed 5 hours less hands-on time per run with more flexibility. This evaluation study indicates that performance of the MagicPrep NGS is comparable to the Nextera DNA Flex with the added benefit of improving workflow efficiency and reducing labor for performing routine clinical microbial whole-genome sequencing tests.

Assay the effect of antimicrobial activity of some medicinal plant extracts against some Bacteria may Causing Urinary Tract Infection

Over population are using herbal medicines, Plant medicines may be beneficial, but are not completely harmless. This study was conducted in microbiology labs. Of art and science faculty - al-marj - university of Benghazi. The purpose of this study was to assay the effect of antimicrobial activity of warm Aqueous and ethanol solvent of Thymus vulgaris, Globularia alypium, Phagnalon rupestre L. and Peganum harmala Extracts against different microbial isolates of pathogenic bacteria gram negative (Escherichia coli and Klebsiella penomniae), and gram positive Staphylococcus aureus that may Causing Urinary tract Infection. All isolates were identified at educational El marj Hospital. The results obtained showed a significant inhibiting effect of the ethanolic and warm Aqueous extracts against both gram negative and gram positive bacteria were studied. The results were shown that the effect of Thymus vulgaris, Globularia alypium, and Phagnalonrupestre L., and Peganum harmala of water and ethanol extract tested with various concentrations appeared stimulations effect on the growth rate of bacteria tested.

Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era

BackgroundThe concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting.MethodsTwo time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2.ResultsThe results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022.ConclusionThe results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.

A 3-D interactive microbiology laboratory via virtual reality for enhancing practical skills

Virtual Reality (VR) laboratories are a new pedagogical approach to support psychomotor skills development in undergraduate programmes to achieve practical competency. VR laboratories are successfully used to carry out virtual experiments in science courses and for clinical skills training in professional courses. This paper describes the development and evaluation of a VR-based microbiology laboratory on Head-Mounted Display (HMD) for undergraduate students. Student and faculty perceptions and expectations were collected to incorporate into the laboratory design. An interactive 3-dimensional VR laboratory with a 360° view was developed simulating our physical laboratory setup. The laboratory environment was created using Unity with the (created) necessary assets and 3D models. The virtual laboratory was designed to replicate the physical laboratory environment as suggested by the students and faculty. In this VR laboratory, six microbiology experiments on Gram staining, bacterial streaking, bacterial motility, catalase test, oxidase test and biochemical tests were placed on the virtual platform. First-year biomedical science students were recruited to evaluate the VR laboratory. Students’ perception of the virtual laboratory was positive and encouraging. About 70% of the students expressed they felt safe using the VR laboratory and that it was engaging. They felt that the VR laboratory provided an immersive learning experience. They appreciated that they could repeat each experiment multiple times without worrying about mistakes or mishaps. They could personalise their learning by concentrating on the specific experiments. Our in-house VR-based microbiology laboratory was later extended to other health professions programmes teaching microbiology.

Phenotypic Screening and Antibiogram of Infectious Ulcerative Keratitis Cases in Tripoli Eye Hospital, Libya

Aims: This study to investigate the most prevalent pathogens that cause corneal ulcer in Tripoli-Libya, and to recognize the antibiogram of the isolated pathogens Study Design: This study was a prospective study performed in eye hospital (Zawyet-Aldahmany eye hospital). Place and Duration of Study: It was conducted at the microbiology laboratory of the hospital over a year from December 2018 to January 2020, The overall size of the sample enrolled in this study was 50 inpatients in the admission department, which was taken according to the incidence of the corneal ulceration cases admitted to the hospital. Methodology: The corneal scrapings and swabs were collected and subjected to microbiological examination. Demographic data and risk factors were collected for each patient. The antibiotic susceptibility of the bacterial microorganisms was determined by the Kirby-Bauer disk diffusion method, to identify the most appropriate antibiotic for each bacterial isolate. Results: 60% of the patients were males, the mean age of the patients was 46.5 years, unilateral right eye keratitis was involved in (54%) of cases, trauma was the major risk factor (24%), followed by systemic disease (14%). Concerning the seasonal distribution of the cases between months, our study revealed that summer and winter seasons in Libya (January, July, August, and September) involved most of the cases, and interestingly, fungal keratitis (Aspergillus) was higher in (July, August), which is the summer season in Libya. The culture positive rate was (80%), of which (36%) were bacterial, and (22%) were fungal pathogens, and the other (22%) were mixed fungal and bacterial cultures. The most common bacterial isolate was (26%) P.aeruginosa and (16%) staphylococcus aureus, while Aspergillus (40%) was the most common fungal isolate, followed by Penicillium and fusarium species. Our results showed that P.aeruginosa was the responsible microorganism for rapid keratitis progression in three cases who were using cosmetic lenses promptly. Concerning antibiotic sensitivity, all gram-negative bacteria and positive isolates were susceptible to old-generation fluoroquinolones such as ciprofloxacin and levofloxacin, while ceftazidime showed resistance to penicillins. Conclusion: In conclusion, with early suspicion and microbiological diagnostic procedures, appropriate therapy can only reduce the incidence of this threatening ocular case.