Hanan H. Balkhy

Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study

Summary Background Middle East respiratory syndrome (MERS) is a new human disease caused by a novel coronavirus (CoV). Clinical data on MERS-CoV infections are scarce. We report epidemiological, demographic, clinical, and laboratory characteristics of 47 cases of MERS-CoV infections, identify knowledge gaps, and define research priorities. Methods We abstracted and analysed epidemiological, demographic, clinical, and laboratory data from confirmed cases of sporadic, household, community, and health-care-associated MERS-CoV infections reported from Saudi Arabia between Sept 1, 2012, and June 15, 2013. Cases were confirmed as having MERS-CoV by real-time RT-PCR. Findings 47 individuals (46 adults, one child) with laboratory-confirmed MERS-CoV disease were identified; 36 (77%) were male (male:female ratio 3·3:1). 28 patients died, a 60% case-fatality rate. The case-fatality rate rose with increasing age. Only two of the 47 cases were previously healthy; most patients (45 [96%]) had underlying comorbid medical disorders, including diabetes (32 [68%]), hypertension (16 [34%]), chronic cardiac disease (13 [28%]), and chronic renal disease (23 [49%]). Common symptoms at presentation were fever (46 [98%]), fever with chills or rigors (41 [87%]), cough (39 [83%]), shortness of breath (34 [72%]), and myalgia (15 [32%]). Gastrointestinal symptoms were also frequent, including diarrhoea (12 [26%]), vomiting (ten [21%]), and abdominal pain (eight [17%]). All patients had abnormal findings on chest radiography, ranging from subtle to extensive unilateral and bilateral abnormalities. Laboratory analyses showed raised concentrations of lactate dehydrogenase (23 [49%]) and aspartate aminotransferase (seven [15%]) and thrombocytopenia (17 [36%]) and lymphopenia (16 [34%]). Interpretation Disease caused by MERS-CoV presents with a wide range of clinical manifestations and is associated with substantial mortality in admitted patients who have medical comorbidities. Major gaps in our knowledge of the epidemiology, community prevalence, and clinical spectrum of infection and disease need urgent definition. Funding None.

Rift Valley fever: an uninvited zoonosis in the Arabian peninsula

Rift Valley fever (RVF) is an acute viral disease, affecting mainly livestock but also humans. The virus is transmitted to humans through mosquito bites or by exposure to blood and bodily fluids. Drinking raw, unpasteurized milk from infected animals can also transmit RVF. Routine vaccination of livestock in Africa has been prohibitively expensive, leading to endemicity of RVF in most African countries. Reports in September 2000 first documented RVF occurring outside of Africa in the Kingdom of Saudi Arabia and Yemen. Prior to this outbreak, the potential for RVF spread into the Arabian Peninsula had already been exemplified by a 1977 Egyptian epidemic. This appearance of RVF outside the African Continent might be related to importation of infected animals from Africa. In the most recent outbreak patients presented with a febrile haemorrhagic syndrome accompanied by liver and renal dysfunction. By the end of the outbreak, April 2001 statistics from the Saudi Ministry of Health documented a total of 882 confirmed cases with 124 deaths. Both the severity of disease and the relatively high 14% death rate might be a consequence of underreporting of less severe disease. Travellers to endemic areas may be at risk of acquiring the disease if exposed to animals or their body fluids directly or through mosquito bites. Special education regarding both modes of transmission and the geographical distribution of this disease needs to be given to travellers at risk.

Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study

Summary Background Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. Methods Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85–95%, and four 30–50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. Findings Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. Interpretation We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. Funding Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.

Clinical Course and Outcomes of Critically Ill Patients With Middle East Respiratory Syndrome Coronavirus Infection

In a study of patients hospitalized with suspected Middle East respiratory syndrome coronavirus infection, those with confirmed disease had preexisting comorbid conditions and required mechanical v...

Brucellosis and International Travel

Brucellosis is a zoonotic disease of worldwide distribution that mainly affects persons working with domestic animals and animal products. Despite being controlled in many developed countries, the disease remains endemic in many parts of the world, including Latin America, the Middle East, Spain, parts of Africa, and western Asia. The disease is mainly transmitted to humans through the ingestion of raw milk or non-pasteurized cheese contaminated with one of the four Brucella species pathogenic to humans. The clinical presentation can vary from asymptomatic infection with seroconversion to a full-blown clinical picture of fever, night sweats and joint manifestations; rarely, there is hepatic, cardiac, ocular or central nervous system involvement. Since travelers may be affected, travel health physicians need to know the clinical presentation of patients with brucellosis and preventive strategies.

Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus

ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R0) for the virus that is less than 1. IMPORTANCE MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus. MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus.

Influenza a common viral infection among Hajj pilgrims: time for routine surveillance and vaccination.

BACKGROUND The annual Hajj pilgrimage to Mecca, Saudi Arabia brings over two million people to a small confined area. Respiratory tract infection is the most common disease transmitted during this period. For most of the etiologic agents of upper respiratory tract infections, no vaccine or prophylaxis is available, except for influenza. Yearly influenza vaccination of high-risk groups is recommended, but no special recommendations are available for those performing the Hajj or other similar large congregational activities. Viral surveillance studies are being carried out through more than 100 centers around the world to identify newly emerging viruses. Saudi Arabia is not one of those centers and no routine surveillance takes place. METHODS Five hundred Hajj pilgrims presenting with upper respiratory tract symptoms from different parts of the world were screened by way of a throat swab for viral culture, including influenza A and B, parainfluenza, respiratory syncytial virus (RSV), adenovirus, herpes simplex virus (HSV), and enteroviruses. Information was collected on age, sex, nationality, smoking habits and upper respiratory tract symptoms. Vaccination status for influenza and meningococcus was obtained by self-declaration, since most pilgrims did not have their vaccination cards with them. Only those with symptoms including at least fever, reported by the patient to be >38.3 degrees C, and/or sore throat were included. Pilgrims with any other symptoms, especially myalgia and fatigue alone, were excluded, since many of the physical chores during the pilgrimage may contribute to such symptoms. RESULTS Fifty-four patients (10.8%) had positive viral throat cultures. Of these, 27 (50%) were influenza B, 13 (24.1%) were HSV, 7 (12.9%) were RSV, 4 (7.4%) were parainfluenza, and 3 (5.6%) were influenza A. No enteroviruses or adenoviruses were detected, and no multiple infections were detected. Only 22 (4.7%) pilgrims received the influenza vaccine. When the results are applied to the total number of pilgrims in 2003, an estimate of 24,000 cases of influenza is obtained. CONCLUSION The findings from this study suggest a high incidence of influenza as a cause of upper respiratory tract infection among pilgrims, estimated to be 24,000 cases per Hajj season, excluding those becoming ill from contact with Hajj pilgrims returning home. They also indicate a very low vaccination rate for the influenza vaccine; as well as poor knowledge of its existence. Continued surveillance during the Hajj pilgrimage is necessary. The influenza vaccine should be a priority for those attending the Hajj pilgrimage, and should also be considered for antiviral prophylaxis.

Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study

Abstract The Saudi Arabian Ministry of Health implemented a pro-active surveillance programme for Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV). We report MERS-CoV data from 5065 Kingdom of Saudi Arabia individuals who were screened for MERS-CoV over a 12-month period. From 1 October 2012 to 30 September 2013, demographic and clinical data were prospectively collected from all laboratory forms received at the Saudi Arabian Virology reference laboratory. Data were analysed by referral type, age, gender, and MERS-CoV real-time PCR test results. Five thousand and 65 individuals were screened for MER-CoV: hospitalized patients with suspected MERS-CoV infection (n = 2908, 57.4%), healthcare worker (HCW) contacts (n = 1695; 33.5%), and family contacts of laboratory-confirmed MERS cases (n = 462; 9.1%). Eleven per cent of persons tested were children (<17 years of age). There were 108 cases (99 adults and nine children) of MERS-CoV infection detected during the 12-month period (108/5065, 2% case detection rate). Of 108 cases, 45 were females (six children and 39 adults) and 63 were males (three children and 60 adults). Of the 99 adults with MERS-CoV infection, 70 were hospitalized patients, 19 were HCW contacts, and ten were family contacts. There were no significant increases in MERS-CoV detection rates over the 12-month period: 2.6% (19/731) in July 2013, 1.7% (19/1100) in August 2013, and 1.69% (21/1238) in September 2013. Male patients had a significantly higher MERS-CoV infection rate (63/2318, 2.7%) than females (45/2747, 1.6%) (p 0.013). MERS-CoV rates remain at low levels, with no significant increase over time. Pro-active surveillance for MERS-CoV in newly diagnosed patients and their contacts will continue.

Ventilator-associated pneumonia in a pediatric intensive care unit in Saudi Arabia: A 30-month prospective surveillance

OBJECTIVE To describe the rate, risk factors, and outcome of ventilator-associated pneumonia (VAP) in pediatric patients. METHODS This prospective surveillance study of VAP among all patients receiving mechanical ventilation for 48 hours or more admitted to a pediatric intensive care unit (PICU) in Saudi Arabia from May 2000 to November 2002 used National Nosocomial Infections Surveillance (NNIS) System definitions. RESULTS Three hundred sixty-one eligible patients were enrolled. Most were Saudi with a mean age of 28.6 months. Thirty-seven developed VAP. The mean VAP rate was 8.87 per 1,000 ventilation-days with a ventilation utilization rate of 47%. The mean duration of mechanical ventilation was 21 days for VAP patients and 10 days for non-VAP patients. The mean PICU stay was 34 days for VAP patients and 15 days for non-VAP patients. Among VAP patients, Pseudomonas aeruginosa was the most common organism, followed by Staphylococcus aureus. Other gram-negative organisms were also encountered. There was no significant difference between VAP and non-VAP patients regarding mortality rate. Witnessed aspiration, reintubation, prior antibiotic therapy, continuous enteral feeding, and bronchoscopy were associated with VAP. On multiple logistic regression analysis, only prior antibiotic therapy, continuous enteral feeding, and bronchoscopy were independent predictors of VAP. CONCLUSIONS The mean VAP rate in this hospital was higher than that reported by NNIS System surveillance of PICUs. This study has established a benchmark for future studies of VAP in the pediatric intensive care population in Saudi Arabia. Additional studies from the region are necessary for comparison and development of preventive measures.

β-Lactamase Production in Key Gram-Negative Pathogen Isolates from the Arabian Peninsula

SUMMARY Infections due to Gram-negative bacilli (GNB) are a leading cause of morbidity and mortality worldwide. The extent of antibiotic resistance in GNB in countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Kuwait, Qatar, Oman, and Bahrain, has not been previously reviewed. These countries share a high prevalence of extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing GNB, most of which are associated with nosocomial infections. Well-known and widespread β-lactamases genes (such as those for CTX-M-15, OXA-48, and NDM-1) have found their way into isolates from the GCC states. However, less common and unique enzymes have also been identified. These include PER-7, GES-11, and PME-1. Several potential risk factors unique to the GCC states may have contributed to the emergence and spread of β-lactamases, including the unnecessary use of antibiotics and the large population of migrant workers, particularly from the Indian subcontinent. It is clear that active surveillance of antimicrobial resistance in the GCC states is urgently needed to address regional interventions that can contain the antimicrobial resistance issue.