Detection of Methicillin-Resistant Staphylococcus aureus (MRSA) Using Loop Mediated Isothermal Amplification (LAMP)

Staphylococcus aureus is one of the most common pathogens that cause a wide range of infections ranging from skin and soft tissue infections to invasive, life threatening infections. The emergence of methicillin-resistant Staphylococcus aureus (MRSA) substantially increased healthcare burdens associated with Staphylococcal infections because of high morbidity and mortality and increasing the need for efficient and cost-effective screening methods, for high-risk patients. The objective of this study is to develop two molecular methods, real-time PCR and loop-mediated isothermal amplification (LAMP), and validate them following Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP) standards. The real time PCR assay was developed targeting mecA, mecC, nuc, and coa to detect S. aureus and methicillin-resistance. The assay had high precision, a linear range of 104-108 CFU/ml, and 95% accuracy. The assay detects MRSA, MSSA, MR-CoNS, and MS CoNS. The LAMP assay was developed targeting the same genes; however, its lower limit of detection was 106 CFU/ml, which was much higher than that of the real-time PCR assay. Additional studies are required to optimize the performance characteristics of the LAMP assay further. Nevertheless, the real-time PCR assay developed in this study will be useful for the detection of MRSA in a cost-effective manner

Microbiome engineering to combat antimicrobial resistance and upsurge productivity of food animals: a systematic review

Extensive antimicrobial usage in animal farming plays a prominent role in the antimicrobial resistance (AMR) crisis and is repeatedly highlighted as an area needing development under the ‘One Health’ approach. Alternative therapies such as microbiome products can be used as prophylaxis to help avoid infectious disease. However, a limited number of studies have focused on AMR-targeted microbiome products. We conducted this systematic review by using PRISMA guidelines to screen for literature that have evaluated food animals’ health when administrated with microbiome products targeting antimicrobial resistance (AMR) or antibiotic-resistant genes (ARGs). We searched and examined studies from SCOPUS, Web of Science, Embase, and Science direct databases for studies published up to November 2021, restricted to the English language. The findings of this review showed that microbiome products have a promising capability to tackle specific AMR/ARGs coupled with animal’s health and productivity improvement. Furthermore, our study showed that probiotics were the most favorable tested microbiome products, with the most targeted resistance being to tetracycline, macrolides, and beta-lactams. While microbiome products are promising alternatives to antibiotic prophylactics, there is a dearth of studies investigating their efficacy in targeting AMR. Thus, it is highly recommended to further investigate, develop, and improve the microbiome, to better understand its utility and circumvent its limitations.The authors thank Barzan holdings for the financial support

The Current Status of Cytomegalovirus (CMV) Prevalence in the MENA region: a systematic review

Human cytomegalovirus (CMV) is a highly prevalent herpesvirus worldwide. According to the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO), CMV infects people of all ages, and by the age of five, approximately one-third of children in the United States are infected. Although the infection is generally asymptomatic, it can cause severe disease in immunocompromised patients, transplant and transfusion recipients, as well as newborn neonates. The objective of this study is to systematically review published literature on CMV in the MENA region to estimate its incidence in the region and describe its epidemiological and clinical significance. The literature was searched through four scientific databases: PubMed, Scopus, Science Direct, and Web of Science. A total of 72 studies from 11 countries satisfied the inclusion criteria, covering a period from 1988–2019. The CMV IgG seroprevalence ranged from 8.7–99.2% (SD = 38.95%). CMV incidence in these countries ranged between 1.22% and 77% in transplant and transfusion recipients, with an increase in incidence with advanced age. However, the incidence rate was unclear for congenital CMV due to the variability of the reporting. This review highlights the need for more robust and well-designed studies to better estimate CMV incidence in the MENA region, standardize diagnostic criteria, and consider prophylactic and pre-emptive treatments to limit the morbidity and mortality of the disease

Retail Chicken Carcasses as a Reservoir of Multidrug-Resistant .

is a major cause of foodborne disease outbreaks worldwide, mainly through poultry. Recently, there has been an increase in multidrug-resistant (MDR) infections globally. The increased drug resistance results in increased costs and poorer health outcomes due to unavailability or delayed treatment. This study aims to determine the prevalence of in retail raw chicken meat and identify their antimicrobial resistance profiles. A total of 270 retail raw chicken carcasses (local and imported) were collected from three hypermarket chains in Qatar between November 2017 and April 2018. Thirty carcasses were contaminated with (11.11%). The prevalence of in locally produced chicken was higher than in imported chicken (OR = 2.56, 95% CI: 1.18-5.53,  = 0.016). No significant differences were found between the prevalence and storage temperature or hypermarket chain. The highest resistance rates in the isolates were reported to tetracycline (73.7%) followed by nitrofurantoin (53.3%), ampicillin (50%), amoxicillin-clavulanic acid, ceftriaxone (26.7%), and ciprofloxacin (23.3%). Eight isolates were potential extended-spectrum β-lactamase-producers, all in imported frozen chicken ( < 0.0001). Additionally, 43.3% of the isolates were MDR and associated with frozen chicken (OR = 16.88, 95% CI: 2.55-111.47,  = 0.002). The findings indicate that while the prevalence of in retail chicken in Qatar is moderate, a large proportion of them are MDR.This research was funded by, Biomedical Research Centre, Qatar University, grant number “BRC-2018-ID-01 to Nahla O. Eltai.

Plasmid-mediated colistin resistance encoded by mcr-1 gene in Escherichia coli co-carrying blaCTX-M-15 and blaNDM-1 genes in pediatric patients in Qatar

Plasmid-mediated colistin resistance encoded by mcr-1 gene in Escherichia coli co-carrying blaCTX-M-15 and blaNDM-1 genes in pediatric patients in Qata

An efficient machine learning model based on improved features selections for early and accurate heart disease predication

Coronary heart disease has an intense impact on human life. Medical history-based diagnosis of heart disease has been practiced but deemed unreliable. Machine learning algorithms are more reliable and efficient in classifying, e.g., with or without cardiac disease. Heart disease detection must be precise and accurate to prevent human loss. However, previous research studies have several shortcomings, for example, take enough time to compute while other techniques are quick but not accurate. This research study is conducted to address the existing problem and to construct an accurate machine learning model for predicting heart disease. Our model is evaluated based on five feature selection algorithms and performance assessment matrix such as accuracy, precision, recall, F1-score, MCC, and time complexity parameters. The proposed work has been tested on all of the dataset's features as well as a subset of them. The reduction of features has an impact on the performance of classifiers in terms of the evaluation matrix and execution time. Experimental results of the support vector machine, K-nearest neighbor, and logistic regression are 97.5%,95 %, and 93% (accuracy) with reduced computation times of 4.4, 7.3, and 8seconds respectively

Fecal Carriage and Molecular Characterization of Carbapenemase-Producing Enterobacterales in the Pediatric Population in Qatar

Whole-genome sequencing was used to characterize carbapenemase-producing Enterobacterales (CPE) strains recovered from rectal screening swab samples obtained from children at a tertiary-care pediatric hospital in Qatar during a 3-year period. A total of 72 CPE isolates recovered from 61 fecal carriers were characterized. Escherichia coli (47 isolates [65.3%]) and Klebsiella pneumoniae (22 isolates [30.6%]) were the most common species identified. High levels of genetic diversity were observed for both species. These 72 isolates produced 78 carbapenemases, characterized as either NDM-type (41 enzymes [52.6%]) or OXA-48-type (37 enzymes [47.4%]). NDM-5 (24 enzymes [30.8%]), NDM-1 (15 enzymes [19.2%]), and OXA-181 (15 enzymes [19.2%]) were the most common variants detected within each type. Twenty-three NDM producers exhibited difficult-to-treat resistance, compared with only 2 of the OXA-48 producers. Multiple comorbidities were identified in 88.5% of the patients, whereas recent travel history to countries in which CPE are endemic was documented for 57.4% of the patients. All 9 blaOXA-48-type-gene-containing E. coli sequence type 38 (ST38) strains were isolated from patients without international travel history. The mean quarterly incidence of fecal carriage decreased more than 6-fold after the implementation of coronavirus disease 2019 (COVID-19)-related international travel restrictions in Qatar in mid-March 2020. Our data suggest that NDM-type and OXA-48type carbapenemases expressed by a large diversity of E. coli and K. pneumoniae genotypes are largely dominant in the pediatric population of Qatar. Although our data indicate successful local expansion of E. coli ST38 strains harboring blaOXA-244 genes, at least within health care settings, blaOXA-48-type and blaNDM-type genes appear to have been mainly introduced sporadically by asymptomatic carriers who visited or received health care in some nearby countries in which the genes are endemic. IMPORTANCE To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.Sidra Internal Research Funding grant (project SIRF_200040)

Identification of mcr-8 in Clinical Isolates From Qatar and Evaluation of Their Antimicrobial Profiles

This study was performed to investigate the genotypic causes of colistin resistance in 18 colistin-resistant Klebsiella pneumoniae (n = 13), Escherichia coli (n = 3) and Pseudomonas aeruginosa (n = 2) isolates from patients at the Hamad General Hospital, Qatar. MIC testing for colistin was performed using Phoenix (BD Biosciences, Heidelberg, Germany) and then verified with SensiTest Colistin (Liofilchem, Zona Ind. le, Italy). Strains determined to be resistant (MIC > 4-16 μg/mL) were then whole-genome sequenced (MiSeq, Illumina, Inc.). Sequences were processed and analysed using BacPipe v1.2.6, a bacterial whole genome sequencing analysis pipeline. Known chromosomal modifications were determined using CLC Genomics Workbench v.9.5.3 (CLCbio, Denmark). Two K. pneumoniae isolates (KPN-15 and KPN-19) harboured mcr-8.1 on the IncFII(K) plasmids, pqKPN-15 and pqKPN-19, and belonged to ST383 and ST716, respectively. One E. coli isolate harboured mcr-1.1 on the IncI2 plasmid pEC-12. The other 15 isolates harboured known chromosomal mutations linked to colistin resistance in the PhoPQ two-component system. Also, three K. pneumoniae strains (KPN-9, KPN-10 and KPN-15) showed disruptions due to IS elements in mgrB. To our knowledge, this marks the first description of mcr-8.1 in K. pneumoniae of human origin in Qatar. Currently, more research is necessary to trace the source of mcr-8.1 and its variants in humans in this region.Hamad Medical Corporatio

Assessment of Indoor Air Quality of Four Primary Health Care Centers in Qatar.

Airborne bacteria pose a potential risk to human health upon inhalation in the indoor environments of health care facilities. Airborne bacteria may originate from various sources, including patients, workers, and daily visitors. Hence, this study investigates the quantity, size, and identification of airborne bacteria indoors and outdoors of four Primary Health Care Centers (PHCC) in Doha, Qatar. Air samples were collected from the lobby, triage room, and outside environment of the centers, including, Qatar University (QU-HC), Al-Rayyan (AR-HC), Umm-Ghuwailina (UG-HC), and Old Airport (OA-HC) between August 2020 and March 2021, throughout both the hot and the cold seasons. Samples were collected using an Anderson six-stage cascade impactor. The mean of the total colony-forming units was calculated per cubic meter of air (CFU/m). QU-HC had the lowest mean of total bacterial count compared with other centers in the indoor and outdoor areas with 100.4 and 99.6 CFU/m, respectively. In contrast, AR-HC had the highest level, with 459 CFU/m indoors, while OA-HC recorded the highest bacterial concentration of the outdoor areas with a total mean 377 CFU/m. In addition, 16S rRNA sequencing was performed for genera identification. , , , and were the four most frequently identified bacterial genera in this study. The abundance of airborne bacteria in the four health centers was higher in the cold season. About 46% of the total airborne bacterial count for three PHCC centers exceeded 300 CFU/m, making them uncompliant with the World Health Organization's (WHO) recommendation for indoor settings. Consequently, an IAQ standards should be shaped to establish a baseline for measuring air pollution in Qatar. Additionally, it is crucial to understand seasonal fluctuations better so that hospitals can avoid rising and spreading infection peaks.This research was funded partially by Primary Health Care Corporation, grant number PHCC/RC/18/06/002

Non-invasive diagnostic tests for Helicobacter pylori infection

BACKGROUND: Helicobacter pylori (H pylori) infection has been implicated in a number of malignancies and non-malignant conditions including peptic ulcers, non-ulcer dyspepsia, recurrent peptic ulcer bleeding, unexplained iron deficiency anaemia, idiopathic thrombocytopaenia purpura, and colorectal adenomas. The confirmatory diagnosis of H pylori is by endoscopic biopsy, followed by histopathological examination using haemotoxylin and eosin (H & E) stain or special stains such as Giemsa stain and Warthin-Starry stain. Special stains are more accurate than H & E stain. There is significant uncertainty about the diagnostic accuracy of non-invasive tests for diagnosis of H pylori. OBJECTIVES: To compare the diagnostic accuracy of urea breath test, serology, and stool antigen test, used alone or in combination, for diagnosis of H pylori infection in symptomatic and asymptomatic people, so that eradication therapy for H pylori can be started. SEARCH METHODS: We searched MEDLINE, Embase, the Science Citation Index and the National Institute for Health Research Health Technology Assessment Database on 4 March 2016. We screened references in the included studies to identify additional studies. We also conducted citation searches of relevant studies, most recently on 4 December 2016. We did not restrict studies by language or publication status, or whether data were collected prospectively or retrospectively. SELECTION CRITERIA: We included diagnostic accuracy studies that evaluated at least one of the index tests (urea breath test using isotopes such as13C or14C, serology and stool antigen test) against the reference standard (histopathological examination using H & E stain, special stains or immunohistochemical stain) in people suspected of having H pylori infection. DATA COLLECTION AND ANALYSIS: Two review authors independently screened the references to identify relevant studies and independently extracted data. We assessed the methodological quality of studies using the QUADAS-2 tool. We performed meta-analysis by using the hierarchical summary receiver operating characteristic (HSROC) model to estimate and compare SROC curves. Where appropriate, we used bivariate or univariate logistic regression models to estimate summary sensitivities and specificities. MAIN RESULTS: We included 101 studies involving 11,003 participants, of which 5839 participants (53.1%) had H pylori infection. The prevalence of H pylori infection in the studies ranged from 15.2% to 94.7%, with a median prevalence of 53.7% (interquartile range 42.0% to 66.5%). Most of the studies (57%) included participants with dyspepsia and 53 studies excluded participants who recently had proton pump inhibitors or antibiotics.There was at least an unclear risk of bias or unclear applicability concern for each study.Of the 101 studies, 15 compared the accuracy of two index tests and two studies compared the accuracy of three index tests. Thirty-four studies (4242 participants) evaluated serology; 29 studies (2988 participants) evaluated stool antigen test; 34 studies (3139 participants) evaluated urea breath test-13C; 21 studies (1810 participants) evaluated urea breath test-14C; and two studies (127 participants) evaluated urea breath test but did not report the isotope used. The thresholds used to define test positivity and the staining techniques used for histopathological examination (reference standard) varied between studies. Due to sparse data for each threshold reported, it was not possible to identify the best threshold for each test.Using data from 99 studies in an indirect test comparison, there was statistical evidence of a difference in diagnostic accuracy between urea breath test-13C, urea breath test-14C, serology and stool antigen test (P = 0.024). The diagnostic odds ratios for urea breath test-13C, urea breath test-14C, serology, and stool antigen test were 153 (95% confidence interval (CI) 73.7 to 316), 105 (95% CI 74.0 to 150), 47.4 (95% CI 25.5 to 88.1) and 45.1 (95% CI 24.2 to 84.1). The sensitivity (95% CI) estimated at a fixed specificity of 0.90 (median from studies across the four tests), was 0.94 (95% CI 0.89 to 0.97) for urea breath test-13C, 0.92 (95% CI 0.89 to 0.94) for urea breath test-14C, 0.84 (95% CI 0.74 to 0.91) for serology, and 0.83 (95% CI 0.73 to 0.90) for stool antigen test. This implies that on average, given a specificity of 0.90 and prevalence of 53.7% (median specificity and prevalence in the studies), out of 1000 people tested for H pylori infection, there will be 46 false positives (people without H pylori infection who will be diagnosed as having H pylori infection). In this hypothetical cohort, urea breath test-13C, urea breath test-14C, serology, and stool antigen test will give 30 (95% CI 15 to 58), 42 (95% CI 30 to 58), 86 (95% CI 50 to 140), and 89 (95% CI 52 to 146) false negatives respectively (people with H pylori infection for whom the diagnosis of H pylori will be missed).Direct comparisons were based on few head-to-head studies. The ratios of diagnostic odds ratios (DORs) were 0.68 (95% CI 0.12 to 3.70; P = 0.56) for urea breath test-13C versus serology (seven studies), and 0.88 (95% CI 0.14 to 5.56; P = 0.84) for urea breath test-13C versus stool antigen test (seven studies). The 95% CIs of these estimates overlap with those of the ratios of DORs from the indirect comparison. Data were limited or unavailable for meta-analysis of other direct comparisons. AUTHORS' CONCLUSIONS: In people without a history of gastrectomy and those who have not recently had antibiotics or proton ,pump inhibitors, urea breath tests had high diagnostic accuracy while serology and stool antigen tests were less accurate for diagnosis of Helicobacter pylori infection.This is based on an indirect test comparison (with potential for bias due to confounding), as evidence from direct comparisons was limited or unavailable. The thresholds used for these tests were highly variable and we were unable to identify specific thresholds that might be useful in clinical practice.We need further comparative studies of high methodological quality to obtain more reliable evidence of relative accuracy between the tests. Such studies should be conducted prospectively in a representative spectrum of participants and clearly reported to ensure low risk of bias. Most importantly, studies should prespecify and clearly report thresholds used, and should avoid inappropriate exclusions