Types Of Clinical Specimens Research Articles

Comparison of SARS-CoV-2 RNA detection in different types of clinical specimens among suspected COVID-19 patients in Addis Ababa, Ethiopia

Comparison of SARS-CoV-2 RNA detection in different types of clinical specimens among suspected COVID-19 patients in Addis Ababa, Ethiopia

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

Applying improved ddPCR to reliable quantification of MPXV in clinical settings.

The ddPCR technique proved to be a sensitive and valuable tool for accurately quantifying MPXV viral loads in various clinical specimen types. The findings provided valuable insights into the necessary pre-treatment protocols for MPXV diagnosis in ddPCR detection and the potentially suitable sample types for collection. Therefore, such results can aid in comprehending the potential characteristics of MPXV infection and the usage of ddPCR in clinical settings.

Performance Characteristics of a Real-Time PCR Assay for Direct Detection of Streptococcus pneumoniae in Clinical Specimens

Community-acquired pneumonia and complications, such as bacteremia and meningitis due to Streptococcus pneumoniae infection, still occur in at-risk populations, despite the availability of effective vaccines. Laboratory confirmation of S. pneumoniae remains challenging despite advances in blood culture techniques and the availability of nucleic acid amplification tests. The goal of this study was to determine the performance characteristics of a molecular assay designed as a diagnostic test using primary clinical specimens for invasive pneumococcal disease. The molecular assay adapted for the Luminex ARIES (Austin, Texas, USA) instrument targets an S. pneumoniae specific gene (autolysin, lytA) in clinical specimens. Using real-time PCR Multicode technology, four different clinical specimen types were evaluated. Specimen types included bronchoalveolar lavage, whole blood, cerebrospinal fluid, and urine to cover the various presentations and appropriate specimen types for invasive pneumococcal infections. The limit of detection for urine was 10 cfu/mL, while bronchoalveolar lavage, cerebrospinal fluid and whole blood were 100 cfu/mL. Accuracy and specificity were both 100%, and all specimen types were stable for 8 days at 4ºC. Finally, 38 clinical specimens were tested to further evaluate the assay. The performance characteristics met CLIA standards for a clinical diagnostic assay and offers a sensitive and specific real-time PCR test for direct detection of S. pneumoniae in relevant clinical specimens.

Abstract 7287: High-grade serous ovarian carcinoma detected with TP53 mutation panel and SiMSen-Seq

Abstract Background: Ovarian carcinoma (OC) has the highest mortality among gynecologic malignancies due to absent or unspecific symptoms. The high-grade serous ovarian carcinoma (HGSC) accounts for over 60% of the OC associated deaths. The most frequent genetic aberrations in HGSC are mutations in the TP53 gene, detected in approximately 96% of the tumors. Previous studies have proposed potential diagnostic utility of detecting mutations in circulating tumor DNA (ctDNA) from OC patients. However, the need for diagnostic methods capable of detecting asymptomatic HGSC is unmet. Objectives: The primary aims of this study were to design a screening tool for identification of HGSC and to evaluate the suitability of various clinical specimen types for diagnostic applications. Methods: In this study, we designed a highly sensitive and robust screening tool using the simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing (SiMSen-Seq) technique for identification of HGSC (n=11) by TP53 mutation profile in various clinical specimen for diagnostic applications. Specimens sampled included primary tumors, ascites, plasma, vaginal samples, and both liquid and solid samples from cyst-, endocervical-, and endometrial origin (n=94). Results: The in-house designed panel amplified 17 regions, encompassing 619 nucleotide positions within the TP53 gene. Pathogenic variants were identified in 10/11 of the primary tumors, with a VAF ≥ 9% (range: 9-91). Preliminary data indicated that all (100%) paired samples obtained corresponding somatic mutations between two or more of the different compartments from the same patient. In total 10/10 ascites-, 16/16 cyst-, 8/8 plasma-, 5/8 vaginal-, 17/22 endocervical-, and 14/19 endometrial samples showed somatic variants at a consensus read depth of 3 and a minimum VAF ≥ 0.1%. Conclusion: The present study suggests that the TP53 mutation panel can identify somatic variants in a variety of non-invasive liquid biopsies. Additionally, the assessment of the TP53 mutation panel exhibits potential for forthcoming clinical utilization as a diagnostic tool. Citation Format: Amanda Olsson Widjaja, Peter Micallef, Benjamin Ulfenborg, Maria Lycke, Ulf Gyllensten, Therese Carlsson, Tobias Österlund, Anders Ståhlberg, Anna Linder, Karin Sundfeldt. High-grade serous ovarian carcinoma detected with TP53 mutation panel and SiMSen-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7287.

SURVEY OF ANTIBIOTIC RESISTANCE OF ISOLATED BACTERIAL STRAINS AT NINH THUAN PROVINCE GENERAL HOSPITAL IN 2023

Objectives: Distribution of the proportion of bacterial isolates and their antibiotic resistance rate at Ninh Thuan Provincial General Hospital (NTPGH).Subjects and methods: All bacterial isolates from various types of clinical specimens from a departments of NTPGH from October 1, 2022 to September 30, 2023.Methods: Cross-sectional description.Results and conclusions: Of the 993 samples designated for culture, 988 cultured samples contained pathogenic bacteria, accounting for 99.5%. Pus specimens account for the highest rate of 32.1%; Gramnegative bacteria account for 76% while Escherichia coli was found in 324 samples, accounting for 32.8%, the highest proportion. Escherichia coli resists ampicillin, bactrim, and tetracycline at 95.4%, 90.5%, and 75.8%, respectively. Staphylococcus aureus resists penicillin, azithromycin, erythromycin, clindamycin, oxacillin, and bactrim at 96.5%, 93.5%, 93.2%, 93.2%, 81.9%, and 75.0 %, correspondingly. Acinetobacter spp. resists cefotaxime at 100%, ceftriaxone (100%), bactrim (92.3%), ceftazidime (90.9%), cefepime (87.8%), tetracycline (84.7%), gentamycin (81 .4%), ciprofloxacin (80.0%), levofloxacin (78.9%), and piperacillin-tazobactam (76.9%). Klebsiella spp. resists ampicillin, and bactrim at 99.1%, and (86.7%),respectively. Enterococcus spp. resists tetracycline at 85.7%. Proteus spp. resists tetracycline, bactrim, and ampicillin at 94.9%, (86.8%), and (78.3%), correspondingly. Pseudomonas aeruginosae resists ampicillinsulbactam, and ceftriaxone at 100%, and 75%, respectively.

Antimicrobial resistance profiles of bacterial isolates from clinical specimens referred to Ethiopian Public Health Institute: analysis of 5-year data

BackgroundAntimicrobial resistance is one of the common global public health problems. The emergence of antimicrobial resistance is multifactorial, and tackling its development is challenging. Consequently, infections caused by resistant bacteria are unresponsive to conventional drugs, resulting in prolonged and severe illnesses, higher mortality rates, and considerable healthcare costs. Therefore, understanding the antimicrobial resistance profiles of bacterial pathogens is essential to optimize treatments and reduce the risks associated with infections. This study aimed to determine the antimicrobial resistance patterns of bacterial isolates from different clinical specimens at the Ethiopian Public Health Institute (EPHI).Materials and methodsThe retrospective cross-sectional study was conducted on the bacterial culture and antibiotic susceptibility reports of different clinical specimens referred to the Bacteriology Laboratory of EPHI from September 2015 to August 2019. Standard bacteriological techniques were used for the isolation and identification of the bacteria. Data were extracted from 840 patients’ records, which included the type of clinical sample cultured, the name of the bacteria, the representations of the antibiotics used for susceptibility testing, and the susceptibility results. Descriptive statistics were used to describe the bacterial isolates and the antimicrobial resistance profiles.ResultsEight types of clinical specimens were analyzed for bacterial isolates and urine specimens were the most analyzed. Ten different genera of bacteria were identified by culture. Almost all the isolates were gram-negative bacteria, while only one species of gram-positive (Staphylococcus aureus) was reported. Antibiotic sensitivity patterns were tested on 840 culture isolates. Escherichia coli strains revealed more than 57% resistance to seventeen antibiotics. Klebsiella pneumoniae showed nearly 70% or greater resistance rates for 17 of the antibiotics used. The overall detected multidrug resistance (MDR) was 64.29%. The highest MDR was reported in Acinetobacter strains (84%) followed by K. pneumoniae (80%).ConclusionsThe multidrug resistance rates found in this study were alarming. Strengthening antimicrobial resistance surveillance at the national level is mandatory, and antimicrobial sensitivity testing should be accessible at local diagnostic centers.

Molecular Detection and Typing of Treponema pallidum in Non-Ocular Samples from Patients with Ocular Syphilis

ABSTRACT Introduction Ocular syphilis is a rare but potentially sight-threatening manifestation of infection with the spirochete Treponema pallidum subspecies pallidum. Molecular strain typing of clinical specimens obtained from patients with syphilis can provide useful epidemiological and clinical information. In this study, we assess the utility of non-ocular clinical samples in strain typing for patients with diagnosed ocular syphilis. Methods We collected samples of excess blood, serum, and cerebrospinal fluid (CSF) from 6 patients with ocular syphilis treated in 2013–2016. DNA was extracted, purified, and then analyzed using an enhanced molecular typing method including sequence analysis of tp0548, number of repeats in the arp gene, and restriction fragment length polymorphism of the tpr gene. Results Molecular strain typing based on tp0548 gene sequence analysis revealed two cases of type F and two cases of type G in 3 of 6 (50%) cases with CSF samples, 1 of which was obtained after starting antibiotics. In a patient with 2 distinct episodes, the same tp0548 type (type G) was identified in both episodes using different sample types (CSF, whole blood). Serum samples were available in 6 cases, but none were successfully typed with any of the methods. Amplification of the tpr and arp genes was unsuccessful in all cases. Overall, strain types were identified in 4 of the 7 episodes. Conclusion Treponema pallidum strain types F and G were detected in CSF or whole blood in 4 of 7 episodes in this series. We demonstrate moderate sensitivity of strain typing in ocular syphilis using non-ocular clinical specimens.

Changing Pattern of Antifungal Drug Resistance in a Tertiary Health-care Facility – A Cross-sectional Study

Background: Fungal infections remain a major source of morbidity and mortality, but treatment choices are restricted due to limited classes of antifungal agents. The emergence of antifungal drug resistance (AFDR) is a major concern. Understanding trend in the development of AFDR will facilitate the use of therapeutic strategies to overcome and prevent antifungal resistance. The primary objective of the present study was to find out the pattern of AFDR in laboratory-confirmed mycological culture isolates. Methodology: The record-based cross-sectional study was carried out to analyze all the mycological culture sensitivity reports during a period of 3 years. The data set included clinicodemographic parameters such as age, gender, provisional diagnosis, type of culture specimens, identified fungal isolate, and susceptibility pattern. The association between the selected parameters and the pattern of AFDR was found out by Pearson's Chi-squared test. Results: AFDR among the isolates was 22 (75.86%), 8 (61.54%), 25 (100%), and 7 (70%) during the period from 2019 to 2022. The rate of AFDR was 33.87% during the study period. Antifungal susceptibility testing showed a rising trend in fluconazole resistance from 2019 (27.2%) to 2022 (57.1%). AFDR was highest in the age group of 41–60 years (48.3%), in males (72.5%), in skin scrapings (40.3%), and in cases with a provisional diagnosis of deep mycosis (51.6% in deep mycosis vs. 46.7% in superficial mycosis). The association between age, type of clinical specimen, type of mycosis, and occurrence of AFDR was statistically significant (P ≤ 0.05). The most common fungal specimen isolated was Candida albicans whereas the highest prevalence of AFDR was observed among Candida glabrata. Conclusion: In all the clinical conditions (superficial and deep mycosis), resistance to fluconazole was the predominant type of AFDR. There was a rising trend in the resistance pattern to fluconazole which is one of the most commonly used antifungal agents.

Active Surveillance of Antimicrobial Resistance and Carbapenemase-Encoding Genes According to Sites of Care and Age Groups in Mexico: Results from the INVIFAR Network.

We analyzed the antimicrobial resistance (AMR) data of 6519 clinical isolates of Escherichia coli (n = 3985), Klebsiella pneumoniae (n = 775), Acinetobacter baumannii (n = 163), Pseudomonas aeruginosa (n = 781), Enterococcus faecium (n = 124), and Staphylococcus aureus (n = 691) from 43 centers in Mexico. AMR assays were performed using commercial microdilution systems (37/43) and the disk diffusion susceptibility method (6/43). The presence of carbapenemase-encoding genes was assessed using PCR. Data from centers regarding site of care, patient age, and clinical specimen were collected. According to the site of care, the highest AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from ICU patients. In contrast, in A. baumannii, higher AMR was observed in isolates from hospitalized non-ICU patients. According to age group, the highest AMR was observed in the ≥60 years age group for E. coli, E. faecium, and S. aureus, and in the 19-59 years age group for A. baumannii and P. aeruginosa. According to clinical specimen type, a higher AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from blood specimens. The most frequently detected carbapenemase-encoding gene in E. coli was blaNDM (84%).

COVIDpro: Database for Mining Protein Dysregulation in Patients with COVID-19.

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 still has limited treatment options. Our understanding of the molecular dysregulations that occur in response to infection remains incomplete. We developed a web application COVIDpro (https://www.guomics.com/covidPro/) that includes proteomics data obtained from 41 original studies conducted in 32 hospitals worldwide, involving 3077 patients and covering 19 types of clinical specimens, predominantly plasma and serum. The data set encompasses 53 protein expression matrices, comprising a total of 5434 samples and 14,403 unique proteins. We identified a panel of proteins that exhibit significant dysregulation, enabling the classification of COVID-19 patients into severe and non-severe disease categories. The proteomic signatures achieved promising results in distinguishing severe cases, with a mean area under the curve of 0.87 and accuracy of 0.80 across five independent test sets. COVIDpro serves as a valuable resource for testing hypotheses and exploring potential targets for novel treatments in COVID-19 patients.

Evaluation of In Vitro Activity of Ceftolozane/Tazobactam and Ceftazidime/Avibactam Against Carbapenem-Resistant Pseudomonas aeruginosa Strains and Mechanisms of Carbapenem Resistance: Data from Tertiary Care Hospital

Background: Carbapenem-resistant Pseudomonas aeruginosa is an endemic problem in several countries, notably Turkey. Objectives: This study aimed to investigate the underlying mechanisms contributing to the carbapenem resistance phenotype and enhance the in-vitro activity of ceftolozane-tazobactam (C/T) and ceftazidime-avibactam (C/A) against carbapenem-resistant P. aeruginosa strains. Methods: A total of 114 carbapenem-resistant P. aeruginosa strains were isolated from different types of clinical specimens. The tested antibiotics were evaluated using the antibiotic disk diffusion method. Additionally, C/T and C/A were tested using the gradient test method. The efficacy of phenylalanine-arginine-β-naphthylamide (PAβN) as efflux pump inhibitors was assessed to determine their ability to reduce meropenem minimum inhibitory concentrations. Polymerase chain reaction (PCR) assays were conducted to identify blaIMP, blaVIM, and blaNDM-1. Results: Among 114 strains of carbapenem-resistant P. aeruginosa, overall resistance rates for C/T and C/A were 10.7% and 8.8%, respectively. Efflux pump inhibitor-based antibiotic susceptibility testing indicated that 35.08% of strains showed resistance modulated by PAβN. Among the strains, 27 (24.5%) were found to produce metallo-beta-lactamase (MBL), with blaVIM (17 strains, 14.91%) being the most common, followed by blaIMP (12 strains, 10.53%). Conclusions: Emerging carbapenem resistance in P. aeruginosa strains is a serious therapeutic challenge for clinicians. Carbapenem resistance can be influenced by various factors, some of which were not assessed in our study. Nonetheless, our results revealed that the main mechanism associated with carbapenem-resistant P. aeruginosa strains is a PAβN-sensitive efflux pump. Among acquired MBLs, VIM-type enzymes were found to be the most prevalent.

Antibiotic resistance and Virulence Genes of Pseudomonas aeruginosa isolates in southwest, Nigeria

Pseudomonas aeruginosa is a ubiquitous bacterium that causes various hospital- acquired and community-acquired infections. It has been reported that the clinical isolates of P. aeruginosa are difficult to treat because of their virulence factors and antibiotics resistances. The aim of present study was to screen the antibiotic resistance patterns and the prevalence of virulence factor genes in a set of Pseudomonas aeruginosa isolated from Ogbomoso, and to determine whether a correlation exists between the prevalence of virulence factors and antibiotic resistance of P. aeruginosa. A total of 100 P. aeruginosa isolates were collected from various types of clinical specimens. Antimicrobial susceptibility testing was performed using the Kirby-bauer method. In addition, PCR assays were used for screening four virulence encoding genes (OPRL, LasB, PLCH and ToxA). The results showed that OPRL (79%) and LasB (62%) were the most frequent virulence genes in P. aeruginosa strains, followed by PLCH (41%) and ToxA (35%). The highest resistance was detected towards Piperacillin (42%) and Tetracycline (42%). Moderate rate of resistance (12-39%) were detected towards the other antibiotics. The virulent factors identified in this study provide valuable information regarding the prevalence of resistance genes of P. aeruginosa isolates in Ogbomoso, Nigeria and their potential impact on treatments that exploit the unique physiology of the pathogen. This will be useful for the health workers to improve infection control measures and to establish a surveillance system. Keywords: antibiotic resistance, virulence genes, Pseudomonas Aeruginosa

Genotype Distribution and Antibiotic Susceptibility Pattern of Clinical Isolates of Group B Streptococcus in a Tertiary Care Hospital in Puducherry, South India.

Streptococcus agalactiae apart from being a colonizer in the genital region is also associated with several other invasive infections in all age groups. With the varied distribution of serotypes across different regions of the world, universal vaccination is also unattainable. However, in India, the knowledge of group B Streptococcus (GBS) genotype distribution is deficient. Thus, this study was initiated to add data on this aspect. Methodology. A cross-sectional study was conducted using isolates of group B Streptococcus from all clinical specimens. Along with that, the clinical specimen type and the antibiotic resistance profile of the isolates were correlated with the genotypes recognized through a multiplex PCR assay. Among the 86 isolates subjected to multiplex PCR for genotype identification, five genotypes were identified with genotype Ib as the predominant one (34.9%), followed by III (20.9%), II (16.3%), Ia (12.7%), and V (11.6%). The results demonstrated a correlation of types Ib and III with vaginal colonization and type II with urine specimens in the current study. This preliminary study exhibited the distribution of common genotypes and their antibiotic resistance profiles in various GBS isolates. However, multiple studies across the country with larger sample sizes are needed to validate these findings.

Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study.

The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests. We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient. The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001). PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.

Genotypic Diversity, Antibiotic Resistance, and Virulence Phenotypes of Stenotrophomonas maltophilia Clinical Isolates from a Thai University Hospital Setting.

Stenotrophomonas maltophilia is a multidrug-resistant organism that is emerging as an important opportunistic pathogen. Despite this, information on the epidemiology and characteristics of this bacterium, especially in Thailand, is rarely found. This study aimed to determine the demographic, genotypic, and phenotypic characteristics of S. maltophilia isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand. A total of 200 S. maltophilia isolates were collected from four types of clinical specimens from 2015 to 2016 and most of the isolates were from sputum. In terms of clinical characteristics, male and aged patients were more susceptible to an S. maltophilia infection. The majority of included patients had underlying diseases and were hospitalized with associated invasive procedures. The antimicrobial resistance profiles of S. maltophilia isolates showed the highest frequency of resistance to ceftazidime and the lower frequency of resistance to chloramphenicol, levofloxacin, trimethoprim/sulfamethoxazole (TMP/SMX), and no resistance to minocycline. The predominant antibiotic resistance genes among the 200 isolates were the smeF gene (91.5%), followed by blaL1 and blaL2 genes (43% and 10%), respectively. Other antibiotic resistance genes detected were floR (8.5%), intI1 (7%), sul1 (6%), mfsA (4%) and sul2 (2%). Most S. maltophilia isolates could produce biofilm and could swim in a semisolid medium, however, none of the isolates could swarm. All isolates were positive for hemolysin production, whereas 91.5% and 22.5% of isolates could release protease and lipase enzymes, respectively. In MLST analysis, a high degree of genetic diversity was observed among the 200 S. maltophilia isolates. One hundred and forty-one sequence types (STs), including 130 novel STs, were identified and categorized into six different clonal complex groups. The differences in drug resistance patterns and genetic profiles exhibited various phenotypes of biofilm formation, motility, toxin, and enzymes production which support this bacterium in its virulence and pathogenicity. This study reviewed the characteristics of genotypes and phenotypes of S. maltophilia from Thailand which is necessary for the control and prevention of S. maltophilia local spreading.

Diagnostic Value of Whole-Blood and Plasma Samples in Epstein-Barr Virus Infections.

Epstein-Barr virus (EBV) is an oncogenic virus classified by the World Health Organization as a class 1 carcinogen. Post-transplant lymphoproliferative disorders are believed to be strongly related to an EBV infection. Monitoring of EBV DNAemia is recommended to assess the risk of reactivation of latent infection and to assess the effectiveness of therapy. Currently, various types of clinical specimens are used for this purpose. The aim of the study was to assess a reliable method of EBV viral load investigation depending on the clinical material used: whole blood or plasma samples. We found that of 134 EBV-DNA-positive whole-blood samples derived from 51 patients (mostly hemato-oncology or post-transplantation), only 43 (32.1%) were plasma-positive. Of these, 37 (86.0%) had lower plasma DNAemia compared to the corresponding whole-blood samples. We conclude that whole-blood samples have a higher sensitivity than plasma samples in EBV DNA detection. The clinical utility of the tests is unclear, but our results suggest that either whole blood or plasma should be used consistently for EBV viral load monitoring.

PREVALENCE OF VIRULENCE GENES IN CLINICAL ISOLATES OF PSEUDOMONAS AND ITS ASSOCIATION WITH ANTIBIOTIC SUSCEPTIBILITY

Pseudomonas aeruginosa is a gram negative rod shaped and opportunistic bacterium that causes Opportunistic infections with help of potential virulence factors in immunosuppressed patients. Exotoxin A and exoenzyme S, catalyze the transfer of ADP-ribose moiety of NAD to plasma proteins in eukaryotic host cells. Exotoxin A has major role in Pseudomonas aeruginosa that causes toxicity by inhibition of protein synthesis while Exo S is involved in invasion, colonization and dissemination of infections. The main objective of this study was to investigate the association between virulence genes of Pseudomonas (exotoxin A and exoenzyme S) with antibiotic resistance patterns. This research was done in Microbiology Laboratory of Shaikh Zayed Hospital, Lahore, during October to December, 2021. Total 11,187 clinical samples were processed at culture and sensitivity bench in this tenure and 100 isolates of Pseudomonas aeruginosa were isolated on basis of morphological characters and standard biochemical procedures in microbiology laboratory. Disk diffusion method (Kirby-Bauer) was used for testing Antibiotic Susceptibility. The toxA and exoS genes were detected in 100 clinical isolates by PCR technique. The correlation was used for finding the association between detected genes and antibiotic susceptibility patterns of Pseudomonas aeruginosa. In antibiotic susceptibility pattern Gentamicin was most common resistant drug and Polymixin B and Colistin were most effective drugs with 100% sensitivity. Prevalence of toxA+ and exoS+ strains was 95% and 87%, respectively. Correlation was used to find association between genes and drug resistance pattern and there was no significant association P value &lt;0.5. High frequency of toxA+ and exoS+ strains isolated from all type of clinical specimens suggest these genes are also possible cause of resistance of drugs but negative association between them highlights that there are some other factors other than these genes which need to be focused in future studies to come over drug resistivity of Pseudomonas aeruginosa.

Antibiogram Analysis of Salmonella paratyphi A Isolated from Gall Bladder Patients in District Peshawar, Pakistan

Salmonella paratyphi A harbors gall bladder in the human body. It serves as a site of persistence for Salmonella paratyphi A. It is an enteric pathogen which has become resistant to many drugs. Therefore, the current study was designed for the identification and antibiogram analysis of S. paratyphi A, isolated from the gall bladder patients undergone cholecystectomy. It included 250 samples of bile, stone, and tissue of patients. The sampleswere cultured on blood, macConkey, and Salmonella Shigella media. Further identification was carried out by morphological oxidase test and Analytical Profile Index (API) strips, followed by antibiogram analysis of the isolates. In the current study, twenty-eight (11.2%) paratyphi A were isolated including 10 (10%) from male patients and 18 (12%) from female patients. Furthermore, 96 samples were found to be positive formiscellaneous growth including 53 with S. typhi (21.2%), 13 with Escherichia coli (5.2%), 09 with Klebsiella (3.6%), 07 with Providencia (2.8%), 05 with Pseudomonas (2%), 03 with Proteus (1.2%), and 06 with Staphylococcus aureus (2.4%). The distribution and susceptibility pattern of S. paratyphi A isolates was checked in different types of clinical specimens including bile, stones, tissue, bile/stones, bile/tissue, stones/tissue, and bile/stone/tissue. S. paratyphi A was distributed as follows: bile (11), stones (5), tissue (3), bile/ stones (4), stones/ tissue (1), bile/tissue (1), and bile/stones/tissue (3). The results of the antibiogram analysisfound that the isolates of Paratyphi A were resistant to sulfamethoxazole 23 (82.14%), cefixime 23 (82.14%),ceftriaxone (rocephin) 20 (71.42%), augmentin 19 (67.85%), and azithromycin 18 (64.28%). The increased susceptibility of these isolates was towards meronem 28 (100%), imipenem 28 (100%), cefoperazon + sulbactam (sulzone) 25 (89.28%), and amikacin 23 (82.14%). The current study signifies the use of the Antibiogram Analysis of Salmonella paratyphi A most susceptible and effective antibiotic options for gall bladder diseases complicated by S. paratyphi A, which showed resistance to ceftriaxone (rocephin), cefixime, sulfamethoxazole, azithromycin, and augmentin, while sensitivity to meropenem, imipenem, cefoperazone + sulbactam (sulzone), and amikacin. It makes the latter a better choice for treatment against the gall stone disease complicated with S. paratyphi A infection.

P158 Epidemiology of aspergillosis in Kuwait: a nationwide study

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PMObjectives Aspergillus is the most common filamentous fungi involved in human infections. It is characterized by causing various forms of clinical presentations, ie, invasive, chronic, and allergic forms. It is associated with considerable morbidity and mortality. In spite of this, the epidemiology of Aspergillus infections is scarce in Kuwait. This study aims to describe the epidemiology of aspergillosis in Kuwait on a national scale.MethodsThis is a 2-year retrospective observational study designed to analyze the demographic and mycological data on all Aspergillus isolates derived from clinical samples processed or submitted to the Mycology reference laboratory (MRL) by all government microbiology laboratories in Kuwait. Using the Mycology reference laboratory surveillance system, the required data was collected. It covers patients’ age, gender, type of clinical samples, care settings (outpatient, wards, or ICU), the name of the Aspergillus species, and antifungal susceptibility for Aspergillus fumigatus. Species-level identification of Aspergillus was mostly based on morphological characteristics, except in a few cases where MALDI-TOF or PCR-sequencing of rDNA were performed. Antifungal susceptibility testing was done using Etest method according to manufacturer instructions. EUCAST clinical breakpoints were followed for the interpretation of antifungal susceptibility results for A. fumigatus species.ResultsIn total, 327 Aspergillus isolates from 277 patients were found. A total of 34/277 patients had 2 or more samples yielding either the same Aspergillus spp. (n = 17) or a different species (n = 17). The most prevalent type of clinical specimens was respiratory sample (n = 196, 60%), followed by ear swabs (n = 64, 19.6%), and nails (n = 24, 7.3%). A. niger (n = 147) was the most isolated species, involving 45% of aspergillosis cases followed by four other species including A. fumigatus (n = 64), A. flavus (n = 55), A. terreus (n = 38), and A. nidulans (n = 13). A total of 10 cases were caused by rare Aspergillus spp. All A. fumigatus isolates were susceptible to voriconazole. Itraconazole also exhibited excellent in vitro activity against nearly all A. fumigatus except 4 isolates that were resistant.ConclusionsThis study reveals the epidemiology of aspergillosis from several perspectives. It gives some insights on the burden of Aspergillosis in Kuwait, especially during the COVID-19 pandemic. Respiratory samples were the predominant positive samples suggesting high rates of pulmonary aspergillosis. A. niger, not A. fumigatus or A. flavus, is the most prevalent agent of aspergillosis in Kuwait. Azole resistance is rare among A. fumigatus. Further studies are needed to explore the spectrum of clinical presentations with special emphasis on pulmonary aspergillosis.