Candida auris has emerged in the past decade as a multi-drug resistant public health threat causing health care outbreaks. Here we report epidemiological, clinical, and microbiological investigations of a C. auris outbreak in a regional Omani hospital between April 2018 and April 2019. The outbreak started in the intensive care areas (intensive care unit (ICU), coronary care unit (CCU), and high dependency unit) but cases were subsequently diagnosed in other medical and surgical units. In addition to the patients’ clinical and screening samples, environmental swabs from high touch areas and from the hands of 35 staff were collected. All the positive samples from patients and environmental screening were confirmed using MALDI-TOF, and additional ITS-rDNA sequencing was done for ten clinical and two environmental isolates. There were 32 patients positive for C. auris of which 14 (43.8%) had urinary tract infection, 11 (34.4%) had candidemia, and 7 (21.8%) had asymptomatic skin colonization. The median age was 64 years (14–88) with 17 (53.1%) male and 15 (46.9%) female patients. Prior to diagnosis, 21 (65.6%) had been admitted to the intensive care unit, and 11 (34.4%) had been nursed in medical or surgical wards. The crude mortality rate in our patient’s cohort was 53.1. Two swabs collected from a ventilator in two different beds in the ICU were positive for C. auris. None of the health care worker samples were positive. Molecular typing showed that clinical and environmental isolates were genetically similar and all belonged to the South Asian C. auris clade I. Most isolates had non-susceptible fluconazole (100%) and amphotericin B (33%) minimal inhibitory concentrations (MICs), but had low echinocandin and voriconazole MICs. Despite multimodal infection prevention and control measures, new cases continued to appear, challenging all the containment efforts.

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.

Hypervirulent Klebsiella pneumoniae (hvKp) is a variant that has been increasingly linked to severe, life-threatening infections including pyogenic liver abscess and bloodstream infections. HvKps belonging to the capsular serotypes K1 and K2 have been reported worldwide, however, very scarce studies are available on their genomics and virulence. In the current study, we report four hypermucoviscous extended-spectrum β-lactamase-producing hvKp clinical strains of capsular serotype K1 and K2 isolated from pus and urine of critically ill patients in tertiary care hospitals in Oman. These strains belong to diverse sequence types (STs), namely ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2). To study their virulence, a Galleria mellonella model and resistance to human serum killing were used. The G. mellonella model revealed that the K1/ST-23 isolate was the most virulent, as 50% of the larvae died in the first day, followed by isolate K2/ST-231 and K2/ST-14, for which 75% and 50% of the larvae died in the second day, respectively. Resistance to human serum killing showed there was complete inhibition of bacterial growth of all four isolates by the end of the first hour and up to the third hour. Whole genome sequencing (WGS) revealed that hvKp strains display a unique genetic arrangement of k-loci. Whole-genome single-nucleotide polymorphism-based phylogenetic analysis revealed that these hvKp isolates were phylogenetically distinct, belonging to diverse clades, and belonged to different STs in comparison to global isolates. For ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2), there was a gradual decrease in the number of colonies up to the second to third hour, which indicates neutralization of bacterial cells by the serum components. However, this was followed by a sudden increase of bacterial growth, indicating possible resistance of bacteria against human serum bactericidal activity. This is the first report from Oman detailing the WGS of hvKp clinical isolates and assessing their resistance and virulence genomics, which reinforce our understanding of their epidemiology and dissemination in clinical settings.

In December 2018, routine surveillance identified an autochthonous outbreak of dengue fever in Muscat Governorate, Oman, a region previously free of dengue fever. Routine surveillance confirmed locally acquired cases in the second week of December, leading to a rapid public health response including case management guidance and epidemiological investigations. The main activity was the vector survey using systematic sampling to assess extent of previously unreported Aedes aegypti presence followed by a campaign aimed to eliminate breeding sites of A. aegypti". During a 5-month period, 343 suspected cases were reported from Muscat Governorate with 122 from the outbreak affected area. Out of 207 probable cases eligible for laboratory testing as per guidelines issued, 59 cases were confirmed. The vector elimination campaign started on January 8, 2019 after a media advocacy using television and social media and concluded on January 23. By the end of campaign, the case load had decreased significantly in the affected area with no reports of locally acquired cases from adjoining areas of Muscat Governorate, indicating no further spread. Rapid notification and early community-wide, extensive vector control activities effectively contained the autochthonous dengue fever virus outbreak.

This study was undertaken to determine the serotype distribution and drug susceptibility patterns in pneumococcal isolates recovered from patients with invasive pneumococcal disease (IPD). All invasive pneumococcal isolates received between June 2014 and June 2016 were included in the study as part of a national laboratory-based IPD surveillance program. Isolates recovered from clinical specimens of normally sterile body sites were included. A total of 41 different serotypes were identified among the 132 pneumococcal isolates included in this study. The most prevalent serotypes/serogroups were 12 (8.3%), 15 (8.3%), 19F (7.6%), 3 (6.1%), and 19A (6.1%);. It was observed that overall vaccine coverage rates for pneumococcal conjugate vaccines (PCV), PCV7, PCV10 and PCV13 were 15.9%, 24.2% and 37.1% respectively. 56.8% (n=75) of the isolates were non-susceptible to at least one antibiotic and 40.9% (n=54) of the isolates were resistant to PEN (M). 18.9% (n=25) of the isolates were multi-drug resistant (MDR).The case fatality rate was 15.9%. Our study results call for broader vaccine coverage, emphasizes the need to introduce the conjugate pneumococcal vaccine for the high risk adult population and stress the importance of continuous surveillance of serotypes and antimicrobial resistance to guide vaccine development and antimicrobial stewardship activities.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Oman’s robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.