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

Characteristics, Risk Factors, and Survival Analysis of Candida auris Cases: Results of One-Year National Surveillance Data from Oman

Background: Candida auris (C. auris) is an emerging healthcare-associated pathogen resulting in significant morbidity and mortality. The aim of this study is to report data from the national C. auris surveillance system for 2019 and conduct a survival analysis of the reported cohort. Methods: a retrospective analysis was conducted for all C. auris cases reported nationally to the Oman Antimicrobial Surveillance System (OMASS) in 2019, and isolates were sent to the Central Public Health Laboratories (CPHL). Clinical and demographic data were obtained through the E-Surveillance reporting system and the Electronic System (NEHR Al-Shifa) at CPHL. Statistical analysis was done using Kaplan–Meier analysis and Cox proportional hazard models. Results: One hundred and twenty-nine isolates of C. auris were grown from 108 inpatients; 87% were isolated from clinical samples, of which blood was the most common (38.9%). Forty (37%) were ≥65 years of age, 72 (66.7%) were males, and 85 (78.7%) were Omani nationals. Of the total isolates, 43.5% were considered as colonization; 56.5% were considered infection, of which 61.8% of them were candidemia. At least one risk factor was present in 98.1% of patients. The mean time from admission to infection was 1.7 months (SD = 2.8), and the mean length of hospital stay was 3.5 months (SD = 4). Totals of 94.8% and 96.1% of the isolates were non-susceptible to fluconazole and amphotericin, respectively. The variables found to be significantly associated with longer survival post C. auris diagnosis (p < 0.05) were age < 65 years, absence of comorbidities, length of stay < 3 months, colonization, and absence of candidemia. The infection fatality rate was 52.5%. Conclusion: Including C. auris in an ongoing antimicrobial surveillance program provides important data for the comprehensive management of this growing public health threat. The current study shows health care outbreaks of C. auris are ongoing, with 52.5% infection fatality, although our isolates remained sensitive to Echinocandins in vitro

The First Confirmed Pediatric Chronic Osteomyelitis due to Coxiella Burnetii in Oman

We describe here the first confirmed case in Oman of chronic osteomyelitis due to Coxiella burnetii, in a previously healthy four-year-old Omani girl. After laboratory confirmation of C. burnetii infection using molecular and qualitative and quantitative serological assays, the case was successfully managed with a combination of oral ciprofloxacin and cotrimoxazole and thereafter followed up for a long period without remission.</jats:p

Assessment of Phenotypic Tools for Detection of OXA-48, KPC, and NDM in Klebsiella pneumoniae in Oman

Background: The alarming increase in carbapenemase-producing Enterobacterales is a matter of grave public health concern. The most ubiquitous carbapenemases, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-&beta;-lactamase (NDM)-, and oxacillinase (OXA-48)-like enzymes, belong to the Ambler molecular classes A, B, and D, respectively. KPC- and OXA-48-like enzymes have a serine-based hydrolytic mechanism, while NDMs are metallo-&beta;-lactamases that contain zinc in the active site. For the judicious use of reserve drugs and promoting antimicrobial stewardship, timely detection of carbapenemases is essential. While molecular tools are the gold standard for the detection of these enzymes, many laboratories have limited access to them. This study focused on evaluating in-house tools and commercial phenotypic tests for the detection of OXA-48-, KPC-, and NDM-like enzymes in K. pneumoniae, the predominant extremely drug-resistant pathogen in Oman. Methods: In total, 80 GeneXpert/PCR-confirmed (40 OXA-48 and 20 KPC and NDM each) and 37 whole-genome-sequenced (25 OXA-232 and 6 KPC-2, plus NDM-1 and NDM-5) K. pneumoniae were subjected to screening by temocillin (30 &mu;g disk) (MAST Diagnostica, Germany) and D71C (MASTDISCS&reg;). Isolates resistant to temocillin (&lt;11 mm) and D71C were subjected to four tests: an in-house tool (OXA-48 disk test) and three commercial phenotypic tests: (i) the MASTDISCS&reg; Combi (D72C) (MAST Group Ltd., Bootle, UK); (ii) the MASTDISCS&reg; Combi (D73C) (MAST Group Ltd., UK); and (iii) an immunochromatographic assay (ICT), which is the KPC/IMP/NDM/VIM/OXA-48 Combo test kit (Medomics, China), for the detection of OXA-48-, KPC-, and NDM-like carbapenemases. Results: Temocillin exhibited good sensitivity and specificity (100% and 97.50%) compared to D71C (70% and 100%). Among the confirmatory tests, the in-house OXA-48 disk test had 92.50% sensitivity and 100% specificity, while the commercial MAST DISC tests D72C, D73C, and ICT had 97.50%, 95.00%, and 100% sensitivity and 100%, 91.67%, and 95% specificity, respectively. Conclusions: The temocillin disk test is a good screening tool. With high sensitivity and specificity, ease of performance, short turnaround time, and low cost, we recommend the ICT format for routine diagnostic use. In resource-constrained centers, the OXA-48 disk test is an excellent alternative with high sensitivity and specificity

Characteristics, Risk Factors, and Survival Analysis of Candida auris Cases: Results of One-Year National Surveillance Data from Oman

Background: Candida auris (C. auris) is an emerging healthcare-associated pathogen resulting in significant morbidity and mortality. The aim of this study is to report data from the national C. auris surveillance system for 2019 and conduct a survival analysis of the reported cohort. Methods: a retrospective analysis was conducted for all C. auris cases reported nationally to the Oman Antimicrobial Surveillance System (OMASS) in 2019, and isolates were sent to the Central Public Health Laboratories (CPHL). Clinical and demographic data were obtained through the E-Surveillance reporting system and the Electronic System (NEHR Al-Shifa) at CPHL. Statistical analysis was done using Kaplan–Meier analysis and Cox proportional hazard models. Results: One hundred and twenty-nine isolates of C. auris were grown from 108 inpatients; 87% were isolated from clinical samples, of which blood was the most common (38.9%). Forty (37%) were ≥65 years of age, 72 (66.7%) were males, and 85 (78.7%) were Omani nationals. Of the total isolates, 43.5% were considered as colonization; 56.5% were considered infection, of which 61.8% of them were candidemia. At least one risk factor was present in 98.1% of patients. The mean time from admission to infection was 1.7 months (SD = 2.8), and the mean length of hospital stay was 3.5 months (SD = 4). Totals of 94.8% and 96.1% of the isolates were non-susceptible to fluconazole and amphotericin, respectively. The variables found to be significantly associated with longer survival post C. auris diagnosis (p &lt; 0.05) were age &lt; 65 years, absence of comorbidities, length of stay &lt; 3 months, colonization, and absence of candidemia. The infection fatality rate was 52.5%. Conclusion: Including C. auris in an ongoing antimicrobial surveillance program provides important data for the comprehensive management of this growing public health threat. The current study shows health care outbreaks of C. auris are ongoing, with 52.5% infection fatality, although our isolates remained sensitive to Echinocandins in vitro.</jats:p