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Objectives To highlight the importance of molecular testing on characterizing extensively drug-resistant (XDR) Salmonella Typhi (S. Typhi) and link it to the current outbreak in Sindh, Pakistan. Methods We report three travel-related typhoid fever cases caused by XDR S. Typhi that presented between January 2019 and August 2019. Antimicrobial susceptibility and genotyping with pulse-field gel electrophoresis (PFGE) were performed. Whole genome sequencing (WGS) was performed to characterise the genomic clonality in relation to the emerging outbreak of S. Typhi in Sindh, Pakistan and to study the molecular resistance profiles. Results Laboratory testing revealed resistance to all first-line antibiotics (i.e ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole), as well as to quinolones and third-generation cephalosporins, leading the patients’ therapy to be changed to use carbapenems. Classical MLST (cMLST) revealed that the strains were of sequence type 1 (ST1) and the core genome sequence (cgWGS) analysis closely clustered our strains with internationally reported strains from Pakistan, India, and the UK. The strains were found to carry a blaCTX-15 gene-harbouring IncY plasmid, which encodes resistance to ceftriaxone. Conclusions This report alerts clinicians to the use of appropriate empirical treatments in such scenarios and highlights the significance of the global spread of XDR Salmonella Typhi.

Background In Oman, many extended families tend to live in one household. Some families can include 20–30 individuals with the majority of them being children. This study investigates the role of children in spreading SARS-CoV-2 causing COVID-19 within family clusters in Oman. Methods This retrospective study includes data of 1026 SARS-CoV-2 positive children (≤18 years) collected from the national surveillance database for COVID-19 between 1 February 2020 and 30 May 2020. Results We included 1026 patients. Most, 842 were Omani (82%), 52% male, and 28.5% asymptomatic. Close to the half of symptomatic 419 (40%), patients presented with fever associated with other respiratory symptoms. Fifty pediatric patients were index cases who transmitted the virus to 107 patients in total (86 adults and 21 children) with a mode of 1. There is no statistical significance of all studied risk factors in the transmission of the SARS-CoV-2 virus including age, gender, and cycle threshold (CT) value. Conclusions According to this study, children are not to be considered a significant driver of transmission of SARS-CoV-2 in Oman.

Highlights • 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%). • The study revealed a good agreement between genetic and epidemiological data. • Oman’s robust surveillance system was very efficient to guide the outbreak investigation processes in the country, • The study illustrates the future importance of molecular epidemiology to lead the national response to outbreaks and pandemics., Background 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. Methods 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. Findings 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. Interpretation 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.

HIV prevalence in Oman is low (5 %). HIV screening is performed at regional public health laboratories as part of a medical fitness programme for residency applicants. We conducted a retrospective evaluation of indeterminate serology results from 11 females of African origin, aged 21–43 years. Serology testing for HIV was conducted according to the national Oman algorithm: fourth-generation immunoassays (Bio-Rad GS HIV Combo Ag/Ab EIA, Siemens Enzygnost HIV Integral 4, Abbott ARCHITECT HIV Ag/Ab Combo, Roche Elecsys HIV Combi PT, bioMérieux VIDAS HIV DUO QUICK), confirmatory assays (Geenius HIV 1/2 Confirmatory, INNO-LIA HIV I/II Score) and PCR testing. Confirmatory testing to resolve indeterminate results was conducted with available samples for five patients using a combination of immunoassays, confirmatory assays, PCR/PERT and pro-viral DNA levels, at three external laboratories; Roche Diagnostics (Germany), Swiss National Laboratory (Switzerland) and Barts Health NHS Trust (UK). Nineteen serum, 15 plasma and two whole-blood samples were analysed. Nine of ten patients analysed on Bio-Rad and Siemens immunoassays were highly reactive; seven were highly reactive on the Abbott assay. Eight of nine patients tested with the Roche assay were negative. Three of four patients tested on the bioMérieux assay were negative. Five patients underwent confirmatory testing at external laboratories; all were negative by HIV-RNA or pro-viral DNA testing. In conclusion, HIV-RNA and pro-viral DNA testing is recommended for HIV screening of individuals from high-prevalence regions coming to low-prevalence regions.

Following the detection of the first human case of avian influenza A subtype H9N2 in 1998, more than 40 cases were diagnosed worldwide. However, the spread of the virus has been more remarkable and significant in global poultry populations, causing notable economic losses despite its low pathogenicity. Many surveillance studies and activities conducted in several countries have shown the predominance of this virus subtype. We present the case of a 14-month-old female in Oman with an A(H9N2) virus infection. This is the first human case of A(H9N2) reported from Oman and the Gulf Cooperation Countries, and Oman is the second country outside of southern and eastern Asia to report a case (cases have also been detected in Egypt). The patient had bronchial asthma and presented with a high-grade temperature and symptoms of lower respiratory tract infection that necessitated admission to a high dependency unit in a tertiary care hospital. It is of urgency that a multisector One Health approach be established to combat the threat of avian influenza at the animal–human interface. In addition to enhancements of surveillance and control in poultry, there is a need to develop screening and preventive programs for high-risk occupations. Keywords: Avian influenza A, One Health, A(H9N2), Virus infection, Oman

Background: Non-pharmaceutical interventions (NPIs), particularly mobility restrictions, are mainstay measures for the COVID-19 pandemic worldwide. We evaluated the effects of Oman’s mobility restriction strategies to highlight their efficacy in controlling the pandemic. Methods: Accessible national data of daily admissions and deaths were collected from 1 April 2020 to 22 May 2021. Google Community Mobility Report (CMR) data were downloaded for the same period. Among six CMR categories, three were used and reduced to one index—the community mobility index (CMI). We used a generalised linear model with a negative binomial distribution combined with a non-linear distributed lag model to investigate the short-term effects of CMI on the number of admitted PCR-confirmed COVID-19 cases and deaths, controlling for public holidays, day of the week, and Eid/Ramadan days. Results: We demonstrated the feasibility of using CMRs in the evaluation and monitoring of different NPIs, particularly those related to movement restriction. The best movement restriction strategy was a curfew from 7 p.m. to 5 a.m. (level 3 of CMI = 8), which had a total reduction of 35% (95% confidence interval (CI), 25–44%) in new COVID-19 admissions in the following two weeks, and a fatality reduction in the following four weeks by 52% (95% CI, 11–75%). Conclusion: Evening lockdown significantly affected the course of the pandemic in Oman which lines up with similar studies throughout the world.

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.

We describe the case of a 47 years old Sri Lankan man living in Oman with melioidosis and the resultant occupational risk of exposure to 5 laboratory staff members to the causative agent, Burkholderia pseudomallei. Widely reported as an endemic disease in tropical and subtropical areas, B. pseudomallei was imported to Oman by our patient who had risk factors of diabetes mellitus and alcoholic cirrhotic liver disease. Microbiological and biochemical tests identified the gram negative bacillus, B. pseudomallei, in the patient’s blood sample. Five laboratory workers had occupational exposure to Burkholderia pseudomallei and received post-exposure prophylaxis. Our report highlights the importance of early suspicion of the infection and managing the patient with the correct international protocols for melioidosis especially for patients with severe sepsis and septic shock in the Intensive Care Unit (ICU). Furthermore, the importance of increased awareness among laboratory personnel and the need for good laboratory practices is reported. Furthermore, improved surveillance is essential to guide early diagnosis and prompt treatment.

Objective: This study was undertaken to determine the serotype distribution and drug susceptibility patterns in pneumococcal isolates recovered from patients with invasive pneumococcal disease (IPD). Methods: 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. Results: 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%), 19 F (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%. Conclusion: 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. Keywords: Streptococcus pneumoniae, IPD, Serotype, Antibiotic resistance, Oman, Vaccination

OBJECTIVE: To determine the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare workers (HCWs) based on risk of exposure to COVID-19 patients. METHOD: This was a SARS-CoV-2 seroprevalence cross-sectional study in risk-stratified HCWs randomly selected from three main district hospitals in Oman. RESULTS: 1078 HCWs were included, with an overall SARS-CoV-2 seroprevalence of 21%. The seropositivity rates in low-, variable-, and high-risk groups were 29%, 18%, and 17%, respectively (p-value < 0.001). The study found higher positivity in males (crude odds ratio [COR] 1.71, 95% confidence interval [CI] 1.28-2.3), and workers residing in high-prevalence areas (COR 2.09, 95% CI 1.42-3.07). Compared with doctors, workers from supporting services, administration staff, and nurses were more likely to test positive for SARS-CoV-2 antibodies (COR 9.81, 95% CI 5.26-18.27; 2.37, 95% CI 1.23-4.58; 2.08 95% CI 1.14-3.81). The overall rate of previously undetected infection was 12%, with higher values in low-risk HCWs. High district prevalence was a driving factor for seropositivity in the low-risk group (adjusted odds ratio [AOR] 2.36, 95% CI 1.0-5.59). CONCLUSION: Low-risk supporting services workers can drive SARS-CoV-2 transmission in hospitals. More attention and innovation within this area will enhance the safety of health care during epidemics/pandemics.

Highlights • There is 15 % excess mortality in ‘all-cause mortality’ in Oman during the study period, mainly in the >60-year-old age group. • 66 % of the excess death during the study period was attributed to COVID-19. • Excess mortality was found in the respiratory, infectious and unclassified diseases. • This excess mortality re-enforces the importance of a holistic approach in managing the syndemic effects of COVID-19., Background Mortality surveillance provides a crucial method for monitoring disease activity. Coronavirus disease 2019 (COVID-19) can cause excess mortality both directly and indirectly by increasing deaths from other diseases. The aim of this study was to investigate the effects of COVID-19 on mortality in Oman. Methods A cross-sectional retrospective analysis of mortality data from 1 January 2015 to 16 August 2020 was undertaken. Baseline mortality estimated using the Farrington flexible model and excess mortality were calculated for the pandemic period (16 March–16 August 2020) according to cause of death, place of death and age group. Results During the pandemic period, there was a 15% [95% confidence interval (CI) 14–17] increase in all-cause mortality from baseline. When classifying by cause, there was a 9% (95% CI 5–12) increase in deaths due to respiratory diseases, a 2% (95% CI 1–4) increase in deaths due to infectious diseases and a 9% (95% CI 8–11) increase in unclassified deaths. In terms of place of death, 12% (95% CI 11–14) of excess mortality occurred in hospitals and 7% (95% CI 5–8) occurred in homes during the pandemic period. Patients aged >60 years recorded a 15% (95% CI 13–16) increase in all-cause mortality during this period. Conclusion The COVID-19 pandemic has resulted in a 15% increase in all-cause mortality in Oman, mainly as a result of deaths from COVID-19. However, unclassified deaths, deaths due to respiratory diseases and deaths due to infectious diseases have also increased, enforcing the need for a holistic approach and appropriate coordination of health services during such health crises.

In this paper, we present a multicentre record-based descriptive study used to estimate the incidence and characterize the spectrum of confirmed bacille Calmette–Guérin (BCG) vaccine-related disease among children in Oman. This study included all children (age ≤ 14 years) who had culture and/or polymerase chain reaction (PCR)-confirmed BCG disease from January 2006 to December 2018, as identified from Central Public Health Laboratory data and International Classification of Diseases coding of an electronic patient information system. In total, 88 children confirmed to have BCG disease were included in the study, making an average incidence of 9.2 cases per 100,000 vaccinated neonates. The males comprised 65.9%, Omanis 93.2%, and the median age of presentation was 4 months in children with BCG disease. The most common type of disease was BCG abscesses (72.4%). Children with immunodeficiency and those presenting within 6 months were found to have a more severe and disseminated disease. In total, 28 children had immunodeficiency. The age of presentation and type of BCG disease was significantly associated with immunodeficiency status. The majority of cases required therapy (both medical and surgical) and recovered well. The incidence of laboratory-confirmed BCG vaccine-related disease was low in Oman supporting continuing the use of the BCG vaccination practice at birth.

Highlights • Rt can be used to closely monitor the non-pharmaceutical interventions (NPI) of COVID-19 epidemic. • Generally, the activity of the epidemic in Oman. • Other factors, like the return of overseas students, have increased the epidemic activity. • Responses to NPI is different between migrants and natives., Background COVID-19’s emergence carries with it many uncertainties and challenges, one of which is epidemic management strategies. Oman has implemented non-pharmaceutical interventions (NPIs) to mitigate the impact of COVID-19. However, responses to NPIs may be different across different populations in a country with a large number of migrants like Oman. This study investigates the different responses to NPIs assessing the use of time-varying reproduction number (Rt) to monitor it. Methods Polymerase chain reaction (PCR) laboratory-confirmed COVID-19 data from Oman was used from February 24th to June 3rd, 2020 and included demographic and epidemiological information. Data were arranged into pairs of infector–infectee, and two main libraries of R software were used to estimate reproductive number (Rt). Rt was calculated for both Omanis and non-Omanis. Findings A total of 13,538 cases were included, 44·9% of which were Omanis. Among all, we identified 2769 infector–infectee pairs to calculate Rt. There was a sharp drop in Rt from 3·7, (95% confidence interval [CI] 2·8-4·6) mid-March to 1·4 (95% CI 1·2–1·7) in late March in response to NPIs. Then Rt decreased to 1·2 (95% CI 1·1–1·3) late April when it rose, corresponding to the easing up of NPIs. Comparing the two groups, the response to major public health controls was more evident in Omanis in reducing the Rt to 1·09 (95% CI 0·84–1·3) at the end of March. Interpretation Use of real-time estimation of Rt has allowed us to follow the effect of NPIs. The migrant population responds differently than the Omani population.

Objectives: The aim of the current study was to describe COVID-19’s epidemiological characteristics in Oman during the initial stages of the outbreak and compare findings with other countries’ reports. Methods: Data were drawn from a descriptive, records-based review of reported cases of COVID-19 collected through the national COVID-19 Surveillance System from February to April 2020. Results: A total of 2,443 confirmed cases were reported during the study period. The overall first-time testing rate for this period was 851.7 per 100,000, the positivity rate was 53.1 (confidence intervals [CI]: 51.0–55.2) and the death rate was 0.32 (CI: 0.20–0.54) per 100,000 population, respectively. The overall national positive ratio was 5.7% and ranged from 2.2–7.1% across various governorates. Muscat Governorate had the highest positive ratio (12.5%). People in the 51–60 year old age group (RR = 1.97), males (RR = 1.24), non-Omanis (RR = 2.33) and those living in Muscat (RR = 2.14) emerged as categories with significant demographic risk for COVID-19 cases when compared to the national average. The mean age was 35.6 ± 13.4. Asymptomatic cases accounted for nearly 16%. Conclusion: The overall rate of COVID-19 cases and deaths were low in Oman compared to the rest of the world during the study period. Keywords: Coronavirus; COVID-19; SARS-CoV2; Epidemiology; Pandemic; Oman.

The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.

Aim: The purpose of this viewpoint is to summarize the advantages and constraints of the tools and strategies available for reducing the annual incidence of tuberculosis (TB) by implementing the World Health Organization (WHO) End TB Strategy and the linked WHO TB Elimination Framework, with special reference to Oman. Methods: The case-study was built based on the presentations and discussions at an international workshop on TB elimination in low incidence countries organized by the Ministry of Health, Oman, which took place from September 5 to September 7, 2019, and supported by the WHO and European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Results: Existing tools were reviewed, including the screening of migrants for latent TB infection (LTBI) with interferon-gamma release assays, clinical examination for active pulmonary TB (APTB) including chest X-rays, organization of laboratory services, and the existing centres for mandatory health examination of pre-arrival or arriving migrants, including examination for APTB. The need for public-private partnerships to handle the burden of screening arriving migrants for active TB was discussed at length and different models for financing were reviewed. Conclusions: In a country with a high proportion of migrants from high endemic countries, screening for LTBI is of high priority. Molecular typing and the development of public-private partnerships are needed. (C) 2020 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. Funding Agencies|WHOWorld Health Organization; ESCMID; Qiagen; Cepheid; Advanced Healthcare Solutions; PfizerPfizer; MSD; QIAGEN Sciences Inc.

To fulfil the World Health Organization (WHO) End TB strategy, screening for tuberculosis (TB) in immigrants is an important component of the strategy to reduce the TB burden in low-incidence countries. Oman has an annual TB incidence rate of 5.7 per 100000 and transmission from migrants with activated latent TB infection (LTBI) to nationals is a concern. The aim of this study was to determine the proportion of migrants to the Sultanate of Oman with LTBI. The study used an interferon-gamma release assay (IGRA) to assess previous exposure to TB, defining LTBI and a positive IGRA with a normal chest X-ray. 1049 subjects were surveyed. Six participants were excluded from the analysis as they had been recently vaccinated and 1 had an indeterminate result, thus 1042 subjects were included. The overall IGRA-positive rate was 22.4% (234/1042), 30.9% and 21.2% of African and Asian migrants, respectively, were IGRA-positive. Fifty-eight of the participants had a strong IGRA reactivity defined as more than 4 IU/ml. The study shows the proportion of migrants from Asia and Africa with LTBI and 24.7% (58/234) of IGRA-positive migrants had an IGRA of >4 IU/ml, defining a subpopulation with a high risk of developing active TB in the first two years of arrival to the country.

Background Influenza is a serious vaccine-preventable disease with high incidence, hospitalization, and mortality in high-risk groups. The epidemiology, seasonality, and risk factors for influenza are well defined in most of the temperate countries, but estimating influenza burden in the World Health Organization (WHO) Region for the Eastern Mediterranean is scarce. In Oman, despite the advancements in influenza surveillance, the clinical burden and seasonality of influenza remain not fully understood. Objectives To estimate the incidence of influenza-associated hospitalizations and in-hospital death in Oman. Patients and methods Influenza-associated hospitalizations and in-hospital deaths were estimated using hospital discharge records based on ICD-10 codes (J09-J18), results of virological analysis and population census for the period between 2012 and 2015. Results During 2012 and 2015, we identified a total of 19 405 influenza-associated hospitalization and 847 deaths. Influenza positivity percentage ranged from 6.4% in 2013 to 20.6% in 2015. Influenza-associated hospitalization incidence rate was 7.3 (95% CI: 6.4-8.1) per 100 000 in 2013 and 27.5 (95% CI: 25.9-29.1) per 100 000 in 2015 with an overall rate of 20.6 (95% CI: 19.9-21.3) per 100 000. The highest incidence of influenza-associated death was among those aged ≥65 years and ranged between 39.5 (95% CI: 27.3-51.8) per 100 000 in 2014 and 11.3 (95% CI: 7.5-15.1) in 2015. Conclusions Influenza causes a substantial number of hospitalizations and deaths in Oman. Hospitalization rates were highest among children, and adults ≥65 years showed the highest death rate. The potential value of using seasonal influenza vaccine in these groups should be considered.

Background: Immunological cross-reactivity between common cold coronaviruses (CCC) and SARS-CoV-2 might account for the reduced incidence of COVID-19 in children. Evidence to support speculation includes in vitro evidence for humoral and cellular cross-reactivity with SARS-CoV-2 in specimens obtained before the pandemic started. Method: We used retrospective health insurance enrollment records, claims, and laboratory results to assemble a cohort of 869,236 insured individuals who had a PCR test for SARS-CoV-2. We estimated the effects of having clinical encounters for various diagnostic categories in the year preceding the study period on the risk of a positive test result. Findings: After adjusting for age, gender and care seeking behavior, we identified that individuals with diagnoses for common cold symptoms, including acute sinusitis, bronchitis, or pharyngitis in the preceding year had a lower risk of testing positive for SARS-CoV-2 (OR=0.76, 95%CI=0.75, 0.77). No reduction in the odds of a positive test for SARS-CoV-2 was seen in individuals under 18 years. The reduction in odds in adults remained stable for four years but was strongest in those with recent common cold symptoms. Interpretation: While this study cannot attribute this association to cross-immunity resulting from a prior CCC infection, it is one potential explanation. Regardless of the cause, the reduction in the odds of being infected by SARS-CoV-2 among those with a recent diagnosis of common cold symptoms may have a role in shifting future COVD-19 infection patterns from endemic to episodic.

Objectives: Considering the increasing, significant burden that coronavirus disease 2019 (COVID-19) imposes on the healthcare system, the need for simple, rapid, and affordable diagnostic tests to support the existing costly and demanding polymerase chain reaction (PCR) assay becomes required. This prospective diagnostic test accuracy study aims to evaluate the performance of four different COVID-19 rapid antigen tests compared to real-time reverse transcription PCR (rRT-PCR) between June and July 2020 to determine the feasibility of integrating these tests into the diagnostic algorithm in clinical settings. Methods: Swabs were collected from 306 patients and analyzed using rRT-PCR and antigen tests from four different providers. Results: The antigen tests’ sensitivities were 65.8%, 69.8%, 64.0%, and 64.3% for the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid fluorescent immunoassay (FIA) test, BIOCREDIT COVID-19 Ag test, and Sofia SARS-CoV-2 antigen FIA test, respectively. Specificity was 94.1% for PCL COVID-19 Ag Rapid test and 100% for the other three assays. All assays showed a significant negative correlation between the reference rRT-PCR Ct values and Ag test results. Besides, sensitivities of the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid FIA test, and BIOCREDIT COVID-19 Ag test improved to ≥ 85% after exclusion of samples with PCR Ct values > 30. Conclusions: The high specificity of the rapid antigen tests and other parameters like simplicity, rapidity, and affordability suggest that antigen tests are likely to be helpful if integrated and interpreted appropriately in stepwise diagnostic algorithms. Given the low sensitivity of 64.0–69.8% of the antigen tests, we recommend that clinically relevant negative results undergo further testing Ag to confirm or exclude a COVID-19 diagnosis.

Objectives: Previously, web-based tools for cross-sectional antimicrobial point prevalence surveys (PPSs) have been used in adults to develop indicators of quality improvement. We aimed to determine the feasibility of developing similar quality indicators of improved antimicrobial prescribing focusing specifically on hospitalized neonates and children worldwide. Methods: A standardized antimicrobial PPS method was employed. Included were all inpatient children and neonates receiving an antimicrobial at 8:00 am on the day of the PPS. Denominators included the total number of inpatients. A web-based application was used for data entry, validation and reporting. We analysed 2012 data from 226 hospitals (H) in 41 countries (C) from Europe (174H; 24C), Africa (6H; 4C), Asia (25H; 8C), Australia (6H), Latin America (11H; 3C) and North America (4H). Results: Of 17693 admissions, 6499 (36.7%) inpatients received at least one antimicrobial, but this varied considerably between wards and regions. Potential indicators included very high broad-spectrum antibiotic prescribing in children of mainly ceftriaxone (ranked first in Eastern Europe, 31.3%; Asia, 13.0%; Southern Europe, 9.8%), cefepime (ranked third in North America, 7.8%) and meropenem (ranked first in Latin America, 13.1%). The survey identified worryingly high use of critically important antibiotics for hospital-acquired infections in neonates (34.9%; range from 14.2% in Africa to 68.0% in Latin America) compared with children (28.3%; range from 14.5% in Africa to 48.9% in Latin America). Parenteral administration was very common among children in Asia (88%), Latin America (81%) and Europe (67%). Documentation of the reasons for antibiotic prescribing was lowest in Latin America (52%). Prolonged surgical prophylaxis rates ranged from 78% (Europe) to 84% (Latin America). Conclusions: Simple web-based PPS tools provide a feasible method to identify areas for improvement of antibiotic use, to set benchmarks and to monitor future interventions in hospitalized neonates and children. To our knowledge, this study has derived the first global quality indicators for antibiotic use in hospitalized neonates and children., peer-reviewed

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.

Background Colistin is a polypeptide antibiotic drug that targets lipopolysaccharides in the outer membrane of Gram-negative bacteria. Inactivation of the mgrB-gene is a common mechanism behind colistin-resistance in Klebsiella pneumoniae (Kpn). Since colistin is a cyclic polypeptide, it may exhibit cross-resistance with the antimicrobial peptide LL-37, and with other innate effector mechanisms, but previous results are inconclusive. Objective To study potential cross-resistance between colistin and LL-37, as well as with other innate effector mechanisms, and to compare virulence of colistin-resistant and susceptible Kpn strains. Materials/methods Carbapenemase-producing Kpn from Oman (n = 17) were subjected to antimicrobial susceptibility testing and whole genome sequencing. Susceptibility to colistin and LL-37 was studied. The surface charge was determined by zeta-potential measurements and the morphology of treated bacteria was analyzed with electron microscopy. Bacterial survival was assessed in human whole blood and serum, as well as in a zebrafish infection-model. Results Genome-analysis revealed insertion-sequences in the mgrB gene, as a cause of colistin resistance in 8/17 isolates. Colistin-resistant (Col-R) isolates were found to be more resistant to LL-37 compared to colistin-susceptible (Col-S) isolates, but only at concentrations ≥50 μg/ml. There was no significant difference in surface charge between the isolates. The morphological changes were similar in both Col-R and Col-S isolates after exposure to LL-37. Finally, no survival difference between the Col-R and Col-S isolates was observed in whole blood or serum, or in zebrafish embryos. Conclusion Cross-resistance between colistin and LL-37 was observed at elevated concentrations of LL-37. However, Col-R and Col-S isolates exhibited similar survival in serum and whole blood, and in a zebrafish infection-model, suggesting that cross-resistance most likely play a limited role during physiological conditions. However, it cannot be ruled out that the observed cross-resistance could be relevant in conditions where LL-37 levels reach high concentrations, such as during infection or inflammation.

Background: In December 2018, routine surveillance identified an autochthonous outbreak of dengue fever in Muscat Governorate, Oman, a region previously free of dengue fever. Methods: 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”. Results: 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. Conclusions: Rapid notification and early community-wide, extensive vector control activities effectively contained the autochthonous dengue fever virus outbreak. Keywords: Dengue fever, Autochthonous outbreak, Oman, Aedes aegypti, Vector-borne illness, Disease surveillance

Background Crimean-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. Methodology Cases 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. Findings Of 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 < 50 x 109/L and 32 (36.4%) died. There was no intrafamilial spread or healthcare-associated infection. The viral S segments from 11 patients presenting in 2013 and 2014 were all grouped in Asia 1 (IV) lineage. Conclusions CCHF 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., Author summary Crimean-Congo hemorrhagic fever, an often fatal tick-borne viral disease, has made an impact in the Sultanate of Oman—affecting nationals and expatriates alike—for the past 20 years. In this retrospective review of the epidemiology and outcomes of cases in Oman from 1995 to 2017, we identified 4 sporadic cases in 1995 and 1996, then none until 2011, followed by a steady increase until 2017. The mortality rate of 32 of 88 cases (36.4%) is high in comparison to studies from other countries and this could be explained by under-diagnoses of milder cases in the Sultanate. Transmission is commonly associated with animal husbandry and butchering and 88% cases were infected by contact with animals, whereas transmission by tick bite is more commonly recorded in some countries. A proportion of cases (23.8%) were clustered around the Eid-Al-Ahda festival which has, from 2011–2017, occurred in the summer months, which have a higher risk of transmission. This additional risk has been noted and preventive measures have been introduced to reduce the risk of transmission to animal handlers and butchers.

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&rsquo, 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&ndash, 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&rsquo, 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: This study was conducted to assess the variation in prescription practices for systemic antimicrobial agents used for prophylaxis among pediatric patients hospitalized in 41 countries worldwide.Methods: Using the standardized Antibiotic Resistance and Prescribing in European Children Point Prevalence Survey protocol, a cross-sectional point-prevalence survey was conducted at 226 pediatric hospitals in 41 countries from October 1 to November 30, 2012.Results: Overall, 17693 pediatric patients were surveyed and 36.7% of them received antibiotics (n = 6499). Of 6818 inpatient children, 2242 (32.9%) received at least 1 antimicrobial for prophylactic use. Of 11899 prescriptions for antimicrobials, 3400 (28.6%) were provided for prophylactic use. Prophylaxis for medical diseases was the indication in 73.4% of cases (2495 of 3400), whereas 26.6% of prescriptions were for surgical diseases (905 of 3400). In approximately half the cases (48.7% [1656 of 3400]), a combination of 2 or more antimicrobials was prescribed. The use of broad-spectrum antibiotics (BSAs), which included tetracyclines, macrolides, lincosamides, and sulfonamides/trimethoprim, was high (51.8% [1761 of 3400]). Broad-spectrum antibiotic use for medical prophylaxis was more common in Asia (risk ratio [RR], 1.322; 95% confidence interval [CI], 1.202-1.653) and more restricted in Australia (RR, 0.619; 95% CI, 0.521-0.736). Prescription of BSA for surgical prophylaxis also varied according to United Nations region. Finally, a high percentage of surgical patients (79.7% [721 of 905]) received their prophylaxis for longer than 1 day.Conclusions: A high proportion of hospitalized children received prophylactic BSAs. This represents a clear target for quality improvement. Collectively speaking, it is critical to reduce total prophylactic prescribing, BSA use, and prolonged prescription.

Background Crimean-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. Methodology Cases 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. Findings Of 88 cases of CCHF, 4 were sporadic in 1995 and 1996, then none occurred 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 < 50 x 109/L and 32 (36.4%) died. There was no intrafamilial spread or healthcare-associated infection. The viral S segments from 11 patients presenting in 2013 and 2014 were all grouped in Asia 1 (IV) lineage. Conclusions CCHF 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.

Objectives: This study aimed to understand the epidemiology of meningitis cases admitted to hospitals in Oman and to identify any changing microbial patterns from the introduction of the new vaccines. Methods: A retrospective analysis of all cases of meningitis reported through a national surveillance system. Meningitis is a notifiable disease. Results: Of a total of 581 cases of meningitis from the period between January 1, 2005 and December 31, 2013, 15% (88) were confirmed to be bacterial in origin and 7.2% (42/581) viral. In 50.9% (296) of patients with suspected pyogenic meningitis, no specific bacterial pathogen were identified, and in 26% of cases (151) a cerebrospinal fluid study could not be undertaken. Among 88 cases with confirmed bacterial pathogens the organisms identified were Streptococcus pneumoniae (65.9%), Neisseria meningitides (18.2%), Haemophilus influenzae (6.8%), and other organisms (9.1%). The peak incidence was in children

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&ndash, 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 &ge, 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.

Objectives: To investigate the course of a community gastroenteritis outbreak by Salmonella and implement interventional activities and roles to prevent occurring such an outbreak in the future. Methods: From August 27 to 2 September 2015, 101 individuals were reported among a local community. All affected individuals had a history of food consumption at a local restaurant. A rapid response team conducted active surveillance and interview with the affected individuals and workers of the restaurant. Food items and stools from food handlers and affected individuals were cultured and sent for genotyping. An environmental audit of the restaurant had been conducted. Results: The total majority of the affected individuals were male and more than 70% belonged to the young age group from 15 to 45 years. Out of the total, 97% had diarrhea, 70% fever, 56% abdominal cramps and 49% vomiting. All those affected were managed symptomatically except for 14 cases admitted for intravenous rehydration. Breakdown of food safety and basic personal hygiene were detected in the environment of the restaurant and among the workers. There are 39 out of 49 stool cultures of cases, six out of 18 food handlers, and five food samples were positive for Salmonella spp. The identical DNA fingerprinting pattern among S. Weltevreden strains originating from human cases and food was detected. Conclusion: This is the first reported community foodborne of S. Weltevreden outbreak in Oman. The importance of food safety and rigors environmental safety is emphasized. Basic personal hygiene and training of food handlers in restaurants are recommended with public health measurements.

The objective of this study was to compare central line-associated bloodstream infection (CLABSI) rates in Gulf Cooperation Council (GCC) states with those of the U.S. National Healthcare Safety Network (NHSN) and International Nosocomial Infection Control Consortium (INICC) using pooled data from 6 hospitals in 3 GCC countries. The overall CLABSI rate was 3.1 per 1,000 central line days. After adjusting for differences in intensive care unit types, the risk of CLABSI in GCC hospitals was 146% higher than NHSN hospitals but 33% lower than INICC hospitals.

Q fever endocarditis is the most common presentation of chronic infection of Coxiella burnetii, but it rarely occurs in the pediatric age group. We report the first case of Q fever endocarditis in an Omani child. The affected 11-year-old female lives in the Al Batinah governorate in the north of Oman and was known to have congenital heart disease. She presented with features of chronic blood culture-negative endocarditis. The C. burnetii infection was confirmed with the indirect immunofluorescence assay. The patient responded well to a combination of doxycycline and hydroxychloroquine therapy.

Purpose. The molecular epidemiology and resistance mechanisms of carbapenem-resistant Pseudomonas aeruginosa (CRPA) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, the United Arab Emirates, Oman, Qatar, Bahrain and Kuwait. Methodology. Isolates were screened for common carbapenem-resistance genes by PCR. Relatedness between isolates was assessed using previously described genotyping methods: an informative-single nucleotide polymorphism MassARRAY iPLEX assay (iPLEX20SNP) and the enterobacterial repetitive intergenic consensus (ERIC)-PCR assay, with selected isolates being subjected to multilocus sequence typing (MLST). Ninety-five non-repetitive isolates that were found to be resistant to carbapenems were subjected to further investigation. Results/Key findings. The most prevalent carbapenemase-encoding gene, bla VIM-type, was found in 37/95 (39 %) isolates, while only 1 isolate (from UAE) was found to have bla IMP-type. None of the CRPA were found to have bla NDM-type or bla KPC-type. We found a total of 14 sequence type (ST) clusters, with 4 of these clusters being observed in more than 1 country. Several clusters belonged to the previously recognized internationally disseminated high-risk clones ST357, ST235, ST111, ST233 and ST654. We also found the less predominant ST316, ST308 and ST823 clones, and novel MLST types (ST2010, ST2011, ST2012 and ST2013), in our collection. Conclusion. Overall our data show that ‘high-risk’ CRPA clones are now detected in the region and highlight the need for strategies to limit further spread of such organisms, including enhanced surveillance, infection control precautions and further promotion of antibiotic stewardship programmes.