Validation of GeneXpert testing for SARS-CoV-2 RNA in eight hospital laboratories in Oman

In response to the current COVID-19 pandemic, numerous commercial assays have been developed for the detection of SARS-CoV-2 for use in the clinical diagnostic laboratories. To date, there is limited comparison of testing methods performed in different hospital laboratory sites. The aims of the study were to evaluate the analytical performance of Cepheid Xpert Xpress SARS-CoV-2 when compared to RT-PCR. This is a cross-sectional study. A total of 155 nasopharyngeal swabs were taken in duplicate from patients presenting with suspected COVID-19 to 8 hospitals in Oman. One swab was tested by the hospital laboratory and the duplicate swab was sent to the national Central Public Health Laboratory (CPHL) for testing. We compared the analytical performance of the commercially available point of care Cepheid Xpert Xpress SARS-CoV-2 assay which was used in the 8 different hospitals with assays including Liferiver, Sansure, TIB MOL BIOL, Kingfisher and COBAS 6800 by Roche which were performed at the CPHL. Testing of the duplicate swabs revealed excellent agreement of results with the viral loads of Ct values ranging from 16-43 for the E gene, 18-44 for the N gene and 17-44 for the ORF gene using the Liferiver assay. The overall sample sensitivity and specificity of the Cepheid Xpert Xpress SARS-CoV-2 assay were both 100% and there was 100% agreement across specimens. We conclude that the rapid GeneXpert and RT-PCR kits assessed in this study may be used for routine diagnostic testing of COVID-19 patients by experienced clinical microbiology diagnostic laboratories. Our results highlight the importance of rapid molecular testing at different sites within a country in a public health emergency

Recurrent Infective Endocarditis in an Adolescent due to Streptococcus agalactiae: A Rare Presentation of a Common Pathogen

Streptococcus agalactiae is known to cause invasive infections in risk groups such as pregnant women, newborns, and immunosuppressed patients but it is uncommon in older children. We describe a case of recurrent infective endocarditis due to S. agalactiae in an 11-year-old boy with Loeys-Dietz syndrome who was successfully treated with long-term antimicrobial therapy for one year

Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity

Background The Sultanate of Oman is country a low TB-incidence, with less than seven cases per 105 population detected in 2020. Recent years have witnessed a persistence in TB cases, with sustained incidence rate among expatriates and limited reduction among Omanis. This pattern suggests transmission from the migrant population. The present study examined the genetic profile and drug resistance-conferring mutations in Mycobacterium tuberculosis collected from Omanis and expatriates to recognise possible causes of disease transmission. Methods We examined M. tuberculosis cultured positive samples, collected from Omanis (n = 1,344) and expatriates (n = 1,203) between 2009 and 2018. These isolates had a known in vitro susceptibility profile to first line anti-TB, Streptomycin (SM), Isoniazid (INH), Rifampicin (RIF), Ethambutol (EMB) and Pyrazinamide (PZA). The diversity of the isolates was assessed by spacer oligo-typing (spoligotyping). Drug resistance-conferring mutations resulted from full-length sequence of nine genes (katG, inhA, ahpc, rpoB, rpsL, rrs, embB, embC, pncA) and their phenotypic relationship were analysed. Results In total, 341/2192 (13.4%), M. tuberculosis strains showed resistance to any drug, comprising mono-resistance (MR) (242, 71%), poly-resistance (PR) (40, 11.7%) and multi-drug resistance (MDR) (59, 17.3%). The overall rate of resistance among Omanis and expatriates was similar; however, MDR and PZAR were significantly higher among Omanis, while INHR was greater among expatriates. Mutations rpsL K43R and rpoB S450L were linked to Streptomycin (SMR) and Rifampicin resistance (RIFR) respectively. Whereas, katG S315T and inhA –C15T/G–17T were associated with Isoniazid resistance (INHR). The resistance patterns (mono-resistant, poly-resistant and MDR) and drug resistance-conferring mutations were found in different spoligo-lineages. rpsL K43R, katG S315T and rpoB S450L mutations were significantly higher in Beijing strains. Conclusions Diverse drug resistant M. tuberculosis strains exist in Oman, with drug resistance-conferring mutations widespread in multiple spoligo-lineages, indicative of a large resistance reservoir. Beijing’s M. tuberculosis lineage was associated with MDR, and multiple drug resistance-conferring mutations, favouring the hypothesis of migration as a possible source of resistant lineages in Oman

Clinical and molecular epidemiology of Crimean-Congo hemorrhagic fever in Oman

BackgroundCrimean-Congo hemorrhagic fever (CCHF) is a serious disease with a high fatality rate reported in many countries. The first case of CCHF in Oman was detected in 1995 and serosurveys have suggested widespread infection of humans and livestock throughout the country.MethodologyCases of CCHF reported to the Ministry of Health (MoH) of Oman between 1995 and 2017 were retrospectively reviewed. Diagnosis was confirmed by serology and/or molecular tests in Oman. Stored RNA from recent cases was studied by sequencing the complete open reading frame (ORF) of the viral S segment at Public Health England, enabling phylogenetic comparisons to be made with other S segments of strains obtained from the region.FindingsOf 88 cases of CCHF, 4 were sporadic in 1995 and 1996, then none were detected until 2011. From 2011-2017, incidence has steadily increased and 19 (23.8%) of 80 cases clustered around Eid Al Adha. The median (range) age was 33 (15-68) years and 79 (90%) were male. The major risk for infection was contact with animals and/or butchering in 73/88 (83%) and only one case was related to tick bites alone. Severe cases were over-represented: 64 (72.7%) had a platelet count ConclusionsCCHF is well-established throughout Oman, with a single strain of virus present for at least 20 years. Most patients are men involved in animal husbandry and butchery. The high mortality suggests that there is substantial under-diagnosis of milder cases. Preventive measures have been introduced to reduce risks of transmission to animal handlers and butchers and to maintain safety in healthcare settings

Dynamics of Mycobacterium tuberculosis Lineages in Oman, 2009 to 2018

Study aim. Effective Tuberculosis (TB) control measures in Oman have reduced the annual incidence of tuberculosis cases by 92% between 1981 and 2016. However, the current incidence remains above the program control target of <1 TB case per 100,000 population. This has been partly attributed to a high influx of migrants from countries with high TB burdens. The present study aimed to elucidate Mycobacterium tuberculosis infection dynamics among nationals and foreigners over a period of 10 years. Methods. The study examined TB cases reported between 2009 and 2018 and examined the spatial heterogeneity of TB cases and the distribution of M. tuberculosis genotypes defined by spoligotypes and MIRU-VNTR among Omanis and foreigners. Results. A total of 484 spoligoprofiles were detected among the examined isolates (n = 1295). These include 943 (72.8%) clustered and 352 (27.2%) unique isolates. Diverse M. tuberculosis lineages exist in all provinces in Oman, with most lineages shared between Omanis and foreigners. The most frequent spoligotypes were found to belong to EAI (318, 30.9%), CAS (310, 30.1%), T (154, 14.9%), and Beijing (88, 8.5%) lineages. However, the frequencies of these lineages differed between Omanis and foreigners. Of the clustered strains, 192 MTB isolates were further analysed via MIRU-VNTR. Each isolate exhibited a unique MIRU-VNTR profile, indicative of absence of ongoing transmission. Conclusions. TB incidence exhibits spatial heterogeneity across Oman, with high levels of diversity of M. tuberculosis lineages among Omanis and foreigners and sub-lineages shared between the two groups. However, MIRU-VNTR analysis ruled out ongoing transmission

PulseNet International survey on the implementation of whole genome sequencing in low and middle-income countries for foodborne disease surveillance

PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.Cooperative Agreement number NU60OE000104, funded by the Centers for Disease Control and Prevention.https://home.liebertpub.com/publications/foodborne-pathogens-and-disease/108hj2023Medical Microbiolog

Prolonged Excretion of Poliovirus among Individuals with Primary Immunodeficiency Disorder: An Analysis of the World Health Organization Registry

Individuals with primary immunodeficiency disorder may excrete poliovirus for extended periods and will constitute the only remaining reservoir of virus after eradication and withdrawal of oral poliovirus vaccine. Here, we analyzed the epidemiology of prolonged and chronic immunodeficiency-related vaccine-derived poliovirus cases in a registry maintained by the World Health Organization, to identify risk factors and determine the length of excretion. Between 1962 and 2016, there were 101 cases, with 94/101 (93%) prolonged excretors and 7/101 (7%) chronic excretors. We documented an increase in incidence in recent decades, with a shift toward middle-income countries, and a predominance of poliovirus type 2 in 73/101 (72%) cases. The median length of excretion was 1.3 years (95% confidence interval: 1.0, 1.4) and 90% of individuals stopped excreting after 3.7 years. Common variable immunodeficiency syndrome and residence in high-income countries were risk factors for long-term excretion. The changing epidemiology of cases, manifested by the greater incidence in recent decades and a shift to from high- to middle-income countries, highlights the expanding risk of poliovirus transmission after oral poliovirus vaccine cessation. To better quantify and reduce this risk, more sensitive surveillance and effective antiviral therapies are needed

case report Oman Medical Journal [2017], Vol. 32, No. 1: 62–65 Imported Case of Melioidosis in Oman: Case Report

Melioidosis is an infectious disease caused by the bacterium Burkholderia pseudomallei. It is most commonly described in Southeast Asia and Northern Australia and some imported cases in non-endemic areas. We describe the case of a 55-year-old Omani man with fulminant sepsis who worked in Laos, Cambodia. B. pseudomallei was isolated from the patient’s blood and was identified by means of microbiological and biochemical tests. We highlight the importance of careful attention to non-fermentative gram-negative rods in a septic patients who have worked or travelled to Southeast Asia

Hospitalised patients with Influenza A (H1N1) in the Royal Hospital, Oman: Experience of a tertiary care hospital, July–December 2009

Objectives: The aim of this study was to describe the clinical characteristics, risk factors, laboratory investigations and outcome of hospitalised patients with positive Influenza A (H1N1) at the Royal Hospital in Oman. Methods: We extracted data from the retrospective medical charts, radiological and laboratory findings of 131 patients who were confirmed as positive for Influenza A (H1N1) by real-time reverse-transcriptasepolymerase-chain-reaction from 21 July to 23 December 2009. Results: The median age was 24 years with 34.4% in the paediatric age group. Most (63%) of hospitalised patients were female. Symptoms at presentation included mainly fever (93.9%) and respiratory symptoms (89.3%). 83% of the patients had at least one risk factor and pregnancy was the most common associated condition (22.9%). Most of the patients had reduced lymphocytic count (57.3%) and high levels of serum C-reactive protein, aspartate transaminase and lactate dehydrogenase (75.7%, 75% and 70.8% respectively). The majority of the patients (64.5%) had evidence of pneumonia and radiological findings constituted mainly bi-lateral infiltrates (60.6%). Antiviral therapy was administered to 95.4% of the patients who mostly received it 48 hours after disease onset. Death occurred in 6.9% of patients. Out of these, 88.9% required Intensive Care Unit (ICU) care and mechanical ventilation. Conclusion: Influenza A (H1N1) infection mainly affected those of younger age and females. Associated medical conditions were common, with pregnancy being interestingly the commonest risk factor. The infection caused severe illness that required ICU admission and led to death in 6.9% of patients.

The epidemiology and outcomes of infective endocarditis in a tertiary care hospital in Oman

Objectives We undertook this study to describe the epidemiological and clinical features of infective endocarditis (IE) and to study the complications and management of IE in a tertiary care hospital in Oman. Methods This is a retrospective study of 58 adult patients (>13 years of age) admitted to the Royal Hospital with IE from June 2006 to June 2011. Results Of the 58 patients, 40 (69%) were males, and 18 (31%) were females (ratio 2.2). The median age was 43.6 years (range: 14–85). Forty-eight cases (82.7%) had native valves, nine patients (15.6%) had prosthetic valves, and one case (1.7%) had a pacemaker. The most commonly involved valves were mitral (33, 56.9%) and aortic (23, 39.7%). The blood cultures were positive in 47 (81%) patients, and the most commonly isolated organisms were Streptococci spp., which were found in 20 (34.5%) patients, and Staphylococci spp., which were found in 19 (32.8%) patients. The complication rate was 21%. A total of 15 (25.9%) patients underwent surgical intervention, and the in-hospital mortality rate was 27.6%. Conclusions Native-valve IE is the predominant type of endocarditis and is more of an acute disease. The prevalence of Staphylococci spp. IE is similar to that of Streptococci spp. IE, and its associated mortality remains high