Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways.

Tuberculosis (TB) originating from expatriates that hail from high TB-burden countries is hypothesized to play a role in continued TB transmission in Oman. Here, we used whole-genome sequencing (WGS) to assess national TB transmission dynamics. The annual incidence per 100,000 population per year was calculated for nationals and expatriates. A convenience sample of Mycobacterium tuberculosis (MTB) isolates from 2018 to 2019 was sequenced and analyzed with publicly available TB sequences from Bangladesh, Tanzania, the Philippines, India, and Pakistan. Relatedness was assessed by generating core-genome single nucleotide polymorphism (SNP) distances. The incidence of TB was five cases per 100,000 persons in 2018 and seven cases per 100,000 persons in 2020 (R2 = 0.34, P = 0.60). Incidence among nationals was 3.9 per 100,000 persons in 2018 and 3.5 per 100,000 persons in 2020 (R2 = 0.20, P = 0.70), and incidence among expatriates was 7.2 per 100,000 persons in 2018 and 12.7 per 100,000 persons in 2020 (R2 = 0.74, P = 0.34). Sixty-eight local MTB isolates were sequenced and analyzed with 393 global isolates. Isolates belonged to nine distinct spoligotypes. Two isolates, originating from an expatriate and an Omani national, were grouped into a WGS-based cluster (SNP distance < 12), which was corroborated by an epidemiological investigation. Relatedness of local and global isolates (SNP distance < 100) was also seen. The relatedness between MTB strains in Oman and those in expatriate countries of origin can aid inform TB control policy. Our results provide evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman. IMPORTANCE Tuberculosis (TB) incidence in Oman remains above national program control targets. TB transmission originating from expatriates from high TB-burden countries has been hypothesized to play a role. We used whole-genome sequencing (WGS) to assess TB transmission dynamics between expatriates and Omani nationals to inform TB control efforts. Available Mycobacterium tuberculosis isolates from 2018 to 2019 underwent WGS and analysis with publicly available TB sequences from Bangladesh, the Philippines, India, and Pakistan to assess for genetic relatedness. Our analysis revealed evidence of previously unrecognized transmission between an expatriate and an Omani national, which was corroborated by epidemiological investigation. Analysis of local and global isolates revealed evidence of distant relatedness between local and global isolates. Our results provide evidence that WGS can complement classic public health surveillance to inform targeted interventions to achieve the End TB strategy goal in Oman.

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.

Clinical Characteristics of COVID-19 from the Otorhinolaryngologist's Perspective: First Report from Oman, Middle East.

To study the otorhinolaryngological clinical characteristics of COVID-19 positive patients. A prospective cross sectional study on sixty five patients who were SARS-CoV-2 PCR positive, and completed 14 days of isolation period were surveyed with a questionnaire. The responses were evaluated and assessed. Sixty five SARS-Cov-2 PCR positive cases were included in the study. There were 57 (87.6%) males and 8 (12.3%) females. Thirty five (53.8%) were in home isolation, whereas, 30 (46.2%) were under institutional care. Forty five patients (72.6%) presented with mild symptoms, and 4 (6.4%) developed moderate symptoms. Thirteen (21%) were asymptomatic. Overall, 46 patients (70.7%) presented with upper airway symptoms with or without general symptoms. More than half of the patients experienced pharyngodynia or sorethroat, smell and taste dysfunction as common symptoms (66.7%, 61.4% and 50.7% respectively). Severe headache was noticed by eighteen (27.7%) patients. Other respiratory symptoms such as nasal congestion, rhinorrhoea, sneezing, facial pain, etc. were present with less frequency. In more than half of the patients (61.5%), all the symptoms recovered within 5 days, in 12 (18.5%) between 5 and 8 days, and in 9 (13.8%), between 9 and14 days. However, in four patients, symptoms lasted for 28-30 days. In seven patients (10.7%), symptoms recurred after the period of isolation, however, the retest was negative. Fever, cough and or shortness of breath are the commonly reported prominent symptoms of COVID-19, however, there is a changing trend of clinical presentation towards variable otorhinolaryngologic manifestations. Pharyngodynia, taste and smell dysfunctions are common in patients with COVID-19, and could represent potential characters.

HIV and Pregnancy: A Retrospective Descriptive Cross-sectional Study of Prevalence, Maternal, Obstetrical, and Neonatal Outcome at a Tertiary Care Hospital in Oman.

OBJECTIVES: We sought to investigate the prevalence of HIV in pregnant women and the maternal, obstetrical, and neonatal outcomes over 13 years (2005-2017) at Sultan Qaboos University Hospital, a tertiary hospital in Muscat, Oman. METHODS: Our study design was a retrospective descriptive cross-sectional study of HIV-positive women in the department of obstetrics and gynecology. We had an unlimited sample size due to the rarity of the disease. We aimed to include all pregnant Omani women who tested positive for HIV in their antenatal screening from 1 January 2005 to 31 December 2017. The patient records were reviewed using the hospital information system service. RESULTS: There were a total of 13 688 women with 104 281 pregnancies over the study period. The prevalence of Omani pregnant women with HIV was 0.1% (1:1000) with 0.03% of seropositive pregnancies (3:10 000). Of these seropositive pregnancies, 78.6% were known HIV carriers, while 21.4% were newly diagnosed cases. The live birth rate was 90.3%, with 9.7% resulting in miscarriage. All the miscarriages were to known HIV-positive mothers who were managed in accordance with international guidelines. Of the live births, 10.7% were unknown HIV-positive mothers with a mean gestational age of 39.67 weeks and a mean birth weight of 3.2 kg. The rate of mother-to-child transmission (MTCT) of HIV in this group was 33.3%. In contrast, 89.3% of the live births to known HIV-positive mothers delivered neonates with a mean gestational age of 37.4 weeks and a mean birth weight of 2.6 kg with 0.0% MTCT. Modes of delivery, antepartum, intrapartum and postpartum complications as well as long-term neonatal outcomes were analyzed according to the status of the mother at first presentation. CONCLUSIONS: Strategies have been placed by programs in Oman to focus on the wellbeing of pregnant women and the protection of newborns against HIV infection. Strict implementations on preventing MTCT allowed preventing HIV in children possible. Antiretroviral therapy significantly reduces vertical transmission of HIV, in addition to abstinence of breastfeeding. More importantly, all HIV-positive pregnant women should follow the prevention of MTCT programs set out by the Ministry of Health.

Pattern of Viral Infections among Infants and Children Admitted to the Paediatric Intensive Care Unit at Sultan Qaboos University Hospital, Oman.

OBJECTIVES: The aim of this study was to describe the pattern of viral infections in infants and children admitted to the Paediatric Intensive Care Unit (PICU) at Sultan Qaboos University Hospital (SQUH) in Muscat, Oman. METHODS: A retrospective review of patient records was carried out on all patients admitted to the PICU between January 2011 and December 2012. In order to detect viruses, polymerase chain reaction (PCR) technology was used to detect viruses in nasopharyngeal aspirates, tracheal aspirates, plasma, stool and urine samples. All infants and children below 13 years old, who were admitted to the PICU at SQUH during the study period and with confirmed viral infections, were included in the study. RESULTS: A total of 373 infants and children were admitted to the PICU during the study period. Viruses were detected in 34 patients. The most frequently detected viruses were cytomegalovirus (CMV) in 29.4%; this virus was noted predominantly in immuncompromised patients (80%, P = 0.023) and was associated with increased mortality (50%, P = 0.031) and prolonged PICU stay (70%, P = 0.045). Fatalities before discharge were recorded in 23.5% of the patients. The most frequent risk factors for viral infections were an age of <12 months old (47.1%), assisted ventilation/intubation (52.9%) and a prolonged PICU stay (55.9%). CONCLUSION: The results of this study found that CMV was the most common viral infection among infants and children admitted to the PICU in SQUH. CMV was also the leading cause of mortality.

Complicated subacute bacterial endocarditis in a patient with ventricular septal defect.

Infective endocarditis (IE) is an uncommon but life-threatening infection. Despite advances in management, it still causes high morbidity and mortality. We report the case of an 8-year-old girl who presented with a prolonged fever of 2.5 months duration and a history of a small perimembranous ventricular septal defect. She was diagnosed with subacute bacterial endocarditis secondary to Streptococcus mutans. The patient developed a septic pulmonary embolism; however, with the use of appropriate antimicrobial therapy, she made an uneventful recovery. Clinicians should have a high index of suspicion for IE as the possible cause of a prolonged fever, especially in the presence of congenital heart disease (CHD). Currently, IE prophylaxis is not indicated for unrepaired acyanotic CHD. Nevertheless, with the new changes in the guidelines, more prospective studies are needed to investigate the incidence of IE in such lesions, before long-term conclusions can be drawn.

Spectrum of AIDS Defining Opportunistic Infections in a Series of 77 Hospitalised HIV-infected Omani Patients.

OBJECTIVES: Most of the morbidity and mortality in human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) result from opportunistic infections (OIs). Although the spectrum of OIs in HIV infected patients from developing countries has been reported, there is a paucity of data on the natural history, pattern of disease, and survival of hospitalised patients with HIV/AIDS, particularly in Arab countries. The aim of this study was to study retrospectively the spectrum and frequency of various OIs in a cohort of hospitalised HIV-infected Omani patients. METHODS: Included in the study were 77 HIV-infected Omani patients admitted to a tertiary care teaching hospital in Muscat, Oman, between January 1999 and December 2008. They were diagnosed on their first admission and hence were not on highly active antiretroviral therapy (HAART) at presentation. The frequency of various clinical and laboratory findings and individual OIs were analysed. RESULTS: In total, 45 patients (58%) had one or more AIDS-defining OIs. Pneumocystis jiroveci pneumonia (PCP) was commonest (25%), followed by cryptococcal meningitis (22%), cytomegalovirus (CMV), retinitis (17%), disseminated tuberculosis (15%), and cerebral toxoplasmosis (12.5%). Only one patient with Mycobacterium avium-intracellulare (MAI) was identified and one patient had disseminated visceral leishmaniasis. The majority of patients (77%) had CD4+ counts <200 cells/µL. Ten patients (22%) died during hospital stays, with five deaths (50%) being caused by disseminated CMV infection. CONCLUSION: A wide spectrum of OIs is seen in hospitalised HIV-infected patients in Oman. P. jiroveci pneumonia and cryptococcal meningitis were the commonest OIs, while disseminated CMV was the commonest cause of death. We hope these results will advance the knowledge of specialists treating HIV in Oman and the Gulf region.

The importance of HIV antenatal screening programs for pregnant women.

OBJECTIVE: To investigate retrospectively the prevalence of human immunodeficiency virus (HIV)-1 and 2 among pregnant women during a 10-year period. METHODS: The total number of pregnant women attending the Sultan Qaboos University Hospital (SQUH), Muscat, Oman between January 1995 and December 2005 was 11553 women. Their age range was 16-45 years (average of 28.67.6 years). The women were tested for HIV-1 and 2 using the standard enzyme-linked immunosorbent assay (ELISA). Positive samples were further tested by Western Blot. The data were statistically analyzed using the Statistical Package for Social Sciences Version 10.0. RESULTS: By ELISA testing, 21 women were positive for HIV-1 (prevalence rate: 0.2%) and 3 women were weakly positive for HIV-1 (24 women; 0.2% prevalence rate). However, 15 women were confirmed HIV-1 positive using the Western Blot method (prevalence rate: 0.13%) with an average of 1.5 positive women per year. None of the women were found positive for HIV-2. CONCLUSION: This relatively high prevalence of HIV-1 among pregnant women attending SQUH, highlights the need for screening all pregnant women attending different hospitals and antenatal clinics in Oman. This is essential for preventing the transmission of HIV-1 and 2 to the infants and to the community, and for the appropriate medical treatment and counseling of affected women.