Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance.

BACKGROUND: Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers. METHODS: A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens. RESULTS: Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons. CONCLUSIONS: The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

Influenza A (H1N1) 2009 pandemia. The experience of a tertiary care center in Beirut.

INTRODUCTION: In March 2009, a new influenza virus strain emerged, currently known as the 2009 pandemic H1N1 virus. The virus first appeared in Mexico and rapidly spread globally to reach a pandemic level in June of the same year. We describe here the experience of one major referral center in Beirut, Lebanon. MATERIALS AND METHODS: The laboratory department at St. George Hospital University Medical Center received respiratory specimens from hospital wards, the emergency department, in addition to a considerable proportion collected directly from "outpatients" in the lab. We used the real time RT-PCR as our main diagnostic test. We collected data about the patients from the laboratory information system and from the hospital medical records department. RESULTS: From mid-August 2009 till the end of January 2010, a total of 1771 specimens were analyzed, with 948 (53.5%) returning positive for influenza A (H1N1) by RT-PCR. Only 79 patients with H1N1 infection required hospitalization. Most of H1N1 confirmed patients were children and adolescents aged 5 to 17 years and young adults between 25 and 44 years. The most common symptoms at presentation were: fever, cough, shortness of breath, chills, rhinorrhea or nasal congestion, as well as gastrointestinal symptoms. Twenty-three patients required ICU care and eight patients died. The vast majority had an uncomplicated course of illness and was managed in an outpatient setting. CONCLUSION: The percentage of positive tests during the pandemia was significantly elevated, although few patients experienced drastic clinical outcomes.

A case study exploring the impact of JCI standards implementation on staff productivity and motivation at the laboratory and blood bank.

BACKGROUND AND AIMS: Quality of care has transformed to become an essential element of healthcare service delivery, which caused decision makers in Health Care Organisations (HCOs) to seek methods to evaluate the level of care provided. The field of accreditation is under massive development, especially in healthcare organizations. Joint Commission International (JCI) accreditation is one of the accreditation bodies that require a lot of documentation and quality improvement to guarantee proper standard application. The process of accreditation is known to be demanding and requires staff involvement to guarantee successful implementation. METHODS: This study focuses on the impact of JCI standards implementation on staff productivity and motivation in a 350-bed hospital. An interpretive approach was used to collect empirical data by interpreting the population's behavior, which is represented in this study by the questionnaire. The study is considered an emergent study that identified, explained, illustrated, and developed a model of staff motivation. In this type of study, the process of inquiry, supporting arguments, and questions of interest is developed after the launching of the study and during the process of data collection. Thus, the researcher relied on the social constructive paradigm, whereby the grounded theory (GT) is used to build the research model of staff motivation during the process of accreditation. RESULTS: By studying the Turn Around Time (TAT) performance indicator, the study showed that TAT of tests decreased by 3% after JCI standards implementation, which was reflected at two different laboratory sections. The trainings conducted throughout the process of standards implementation also resulted in enhancing the quality of samples, which was demonstrated by the decrease in the percentage of rejected samples. CONCLUSION: Staff productivity increases when JCI standards are implemented. However, staff motivation is dependent on their involvement with management decisions and the smooth transition through change management, which ensures staff retention and therefore increase productivity.

Prevalence of CYP2C19 polymorphisms in the Lebanese population.

Clopidogrel is one of the most commonly prescribed drugs, as its combination with low-dose aspirin is the recommended oral anti-platelet therapy, to prevent ischaemic events following coronary syndromes or stent placement. Numerous recent studies have shown that polymorphisms in the gene encoding the cytochrome P450 (CYP450) 2C19 enzyme (CYP2C19) contribute to variability in response to clopidogrel; patients with certain common genetic variants of CYP2C19 (2, 3) have a reduced metabolism of clopidogrel and have a higher rate of cardiovascular events or stent thrombosis compared to patients with the CYP2C19 (1) allele. CYP2C19 2 is most common in Caucasians, Africans and Asians while CYP2C19 3 has been found mostly in Asians. Since the prevalence of these variants in the Lebanese population has not yet been reported, our aim was to determine the genotypes of CYP2C19 in our population. CYP2C19 (1/2/3) variants were assessed by Polymerase Chain Reaction-Restriction Length Polymorphism (PCR-RFLP) assays in a representative sample of 161 unrelated healthy Lebanese volunteers. The allele frequencies of CYP2C19 2 and 3 were 0.13 and 0.03. Carriers of the CYP2C19 2 or 3 represented 24.2% of the subjects. Our data show no significant difference in the frequency of CYP2C19 allelic variants when compared to Caucasian populations and demonstrate that the application of the recent FDA recommendations would also be beneficial in Lebanon, allowing physicians to identify patients at high risk for atherothrombotic events, and eventually advising them to consider other antiplatelet medications or alternative dosing strategies in poor metabolizers.

Histomolecular characterization of intracranial meningiomas developed in patients exposed to high-dose cyproterone acetate: an antiandrogen treatment.

BACKGROUND: Meningiomas are the most common primary intracranial tumors in adults. The relationship between meningiomas and exogenous sex hormones such as cyproterone acetate (CPA) is well documented, yet the underlying mechanisms remain unknown. Defining the histomolecular status of meningiomas developed on CPA would help us to better understand the oncogenesis of these tumors. METHODS: We identified 30 patients operated for a meningioma after long-term high-dose CPA therapy and with a history of CPA discontinuation before establishing the indication for surgical intervention. We used array-comparative genomic hybridization (to characterize copy number changes in those 30 meningiomas and subsequently performed next-generation sequencing with the National Institute of Cancer (INCa) solid tumor panel, which is a targeted panel of clinically actionable genes. We also examined grade, type, and clinical features. RESULTS: We identified AKT1 mutations or PIK3CA mutations in 33.3% of CPA meningiomas. AKT1 and PIK3CA mutations were mutually exclusive. Enrichment in oncogenic PIK3CA mutations in the CPA cohort was detected. CPA meningiomas showed chromosomal stability and were located mainly in the skull base. Ninety percent of CPA meningiomas were low-grade meningiomas and 63.4% were meningotheliomas. Half of our CPA cohort had microcystic components. CONCLUSION: Our study shows that low-grade meningothelial meningiomas of the skull base are predominant in CPA meningiomas. We identified PIK3CA/AKT1 pathway as a hypothetical actor in onco-pharmacological interaction between meningiomas and CPA. This signaling pathway could be an interesting target for precision medicine trials in meningioma patients who have been subjected to CPA. Our results could invite the scientific community to review the current classification of meningiomas and to evolve toward more specific histomolecular classification.

Association of structural and numerical anomalies of chromosome 22 in a patient with syndromic intellectual disability.

Array comparative genomic hybridization (aCGH) is now widely adopted as a first-tier clinical diagnostic test for patients with developmental delay (DD)/intellectual disability (ID), autism spectrum disorders, and multiple congenital anomalies. Nevertheless, classic karyotyping still has its impact in diagnosing genetic diseases, particularly mosaic cases. We report on a 30 year old patient with syndromic intellectual disability, a 22q13.2 microdeletion and mosaic trisomy 22. The patient had the following clinical features: intrauterine growth retardation at birth, hypotonia, cryptorchidism, facial asymmetry, enophthalmus, mild prognathism, bifid uvula, hypoplastic upper limb phalanges, DD including speech delay, and ID. Whole genome aCGH showed a de novo 1 Mb interstitial heterozygous deletion in 22q13.2, confirmed by fluorescence in situ hybridization in all cells examined. Moreover, 18% cells had an extra chromosome 22 suggesting a trisomy 22 mosaicism. Almost all 22q13 deletions published so far have been terminal deletions with variable sizes (100 kb to over 9 Mb). Very few cases of interstitial 22q13.2 deletions were reported. In its mosaic form, trisomy 22 is compatible with life, and there are about 20 reports in the literature. It has a variable clinical presentation: growth restriction, dysmorphic features, cardiovascular abnormalities, hemihyperplasia, genitourinary tract anomalies and ID. Neurodevelopmental outcome ranges from normal to severe DD. The patient presents clinical features that are common to both the interstitial 22q13 deletion and the mosaic trisomy 22; characteristics related to the interstitial deletion alone and others explained solely by the mosaic trisomy. Our case points out the role of conventional cytogenetic tools in mosaic cases that could be missed by microarray technology. We therefore suggest the combination of both conventional and molecular karyotyping in the investigation of certain genetic diseases.

Pharmacogenetics of coumarin dosing: prevalence of CYP2C9 and VKORC1 polymorphisms in the Lebanese population.

BACKGROUND: Polymorphisms in the genes encoding the cytochrome P450 2C9 enzyme (CYP2C9) and the vitamin K epoxide reductase (VKORC1) are known to contribute to variability in sensitivity to coumarins. Patients with certain common genetic variants of CYP2C9 (*2 & *3) or a VKORC1 polymorphism (-1639A Allele) require a lower dose of coumarin and are also at higher risk for over-anticoagulation and serious bleeding. In August 2007, the FDA label for warfarin was updated to highlight the benefit of genetic testing to predict warfarin response. AIM: Since the prevalence of these variants in the Lebanese population has not yet been reported, our aim was to determine the genotypes of CYP2C9 and VKORC1 in our population and to compare allele frequencies with previous findings from other ethnic groups. MATERIALS AND METHODS: CYP2C9 (*1/*2/*3) and VKORC1 (*A/*G) allelic variants were assessed by polymerase chain reaction-restriction fragment length polymorphism assays in a diversified sample of 161 unrelated healthy Lebanese volunteers. RESULTS: The allele frequencies of CYP2C9 *2 and *3 were 0.112 and 0.096 respectively, whereas VKORC1-1639A was 0.528. Carriers of the CYP2C9 *2 or *3 represented 34.2% of the subjects, whereas those of the VKORC1-1639A represented 73.9%. CONCLUSION: Our data show no significant difference in the frequency of CYP2C9 allelic variants when compared to the Caucasian population, whereas the allelic frequency of VKORC1-1639A was very high. Over 50% of the Lebanese population seem to be carrying more than two independent risk alleles, and is therefore potentially at high risk of over-anticoagulation.