Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.

The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole-genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the emergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth, and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (MRSA). Our study demonstrates the importance of whole-genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally, resulting in small-scale community and health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. This study demonstrates the importance of whole-genome sequencing for the surveillance of highly antibiotic-resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.

Molecular Typing of ST239-MRSA-III From Diverse Geographic Locations and the Evolution of the SCCmec III Element During Its Intercontinental Spread.

ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in geographically defined clades. In the present study, a collection of 184 ST239-MRSA-III isolates, mainly from countries not covered by the previous studies were characterized using two DNA microarrays (i) targeting an extensive range of typing markers, virulence and resistance genes and (ii) a SCCmec subtyping array. Thirty additional isolates underwent whole-genome sequencing (WGS) and, together with published WGS data for 215 ST239-MRSA-III isolates, were analyzed using in-silico analysis for comparison with the microarray data and with special regard to variation within SCCmec elements. This permitted the assignment of isolates and sequences to 39 different SCCmec III subtypes, and to three major and several minor clades. One clade, characterized by the integration of a transposon into nsaB and by the loss of fnbB and splE was detected among isolates from Turkey, Romania and other Eastern European countries, Russia, Pakistan, and (mainly Northern) China. Another clade, harboring sasX/sesI is widespread in South-East Asia including China/Hong Kong, and surprisingly also in Trinidad & Tobago. A third, related, but sasX/sesI-negative clade occurs not only in Latin America but also in Russia and in the Middle East from where it apparently originated and from where it also was transferred to Ireland. Minor clades exist or existed in Western Europe and Greece, in Portugal, in Australia and New Zealand as well as in the Middle East. Isolates from countries where this strain is not epidemic (such as Germany) frequently are associated with foreign travel and/or hospitalization abroad. The wide dissemination of this strain and the fact that it was able to cause a hospital-borne pandemic that lasted nearly 50 years emphasizes the need for stringent infection prevention and control and admission screening.

Acute viral respiratory infections among children in MERS-endemic Riyadh, Saudi Arabia, 2012-2013.

The emergence of the Middle East Respiratory Syndrome (MERS) in Saudi Arabia has intensified focus on Acute Respiratory Infections [ARIs]. This study sought to identify respiratory viruses (RVs) associated with ARIs in children presenting at a tertiary hospital. Children (aged ≤13) presenting with ARI between January 2012 and December 2013 tested for 15 RVs using the SeeplexR RV15 kit were retrospectively included. Epidemiological data was retrieved from patient records. Of the 2235 children tested, 61.5% were ≤1 year with a male: female ratio of 3:2. Viruses were detected in 1364 (61.02%) children, 233 (10.4%) having dual infections: these viruses include respiratory syncytial virus (RSV) (24%), human rhinovirus (hRV) (19.7%), adenovirus (5.7%), influenza virus (5.3%), and parainfluenzavirus-3 (4.6%). Children, aged 9-11 months, were most infected (60.9%). Lower respiratory tract infections (55.4%) were significantly more than upper respiratory tract infection (45.3%) (P < 0.001). Seasonal variation of RV was directly and inversely proportional to relative humidity and temperature, respectively, for non MERS coronaviruses (NL63, 229E, and OC43). The study confirms community-acquired RV associated with ARI in children and suggests modulating roles for abiotic factors in RV epidemiology. However, community-based studies are needed to elucidate how these factors locally influence RV epidemiology. J. Med. Virol. 89:195-201, 2017. © 2016 Wiley Periodicals, Inc.

A Comparative Study of Clinical Presentation and Risk Factors for Adverse Outcome in Patients Hospitalised with Acute Respiratory Disease Due to MERS Coronavirus or Other Causes.

Middle East Respiratory syndrome (MERS) first emerged in Saudi Arabia in 2012 and remains a global health concern. The objective of this study was to compare the clinical features and risk factors for adverse outcome in patients with RT-PCR confirmed MERS and in those with acute respiratory disease who were MERS-CoV negative, presenting to the King Fahad Medical City (KFMC) in Riyadh between October 2012 and May 2014. The demographics, clinical and laboratory characteristics and clinical outcomes of patients with RT-PCR confirmed MERS-CoV infection was compared with those testing negative MERS-CoV PCR. Health care workers (HCW) with MERS were compared with MERS patients who were not health care workers. One hundred and fifty nine patients were eligible for inclusion. Forty eight tested positive for MERS CoV, 44 (92%) being hospital acquired infections and 23 were HCW. There were 111 MERS-CoV negative patients with acute respiratory illnesses included in this study as "negative controls". Patient with confirmed MERS-CoV infection were not clinically distinguishable from those with negative MERS-CoV RT-PCR results although diarrhoea was commoner in MERS patients. A high level of suspicion in initiating laboratory tests for MERS-CoV is therefore indicated. Variables associated with adverse outcome were older age and diabetes as a co-morbid illness. Interestingly, co-morbid illnesses other than diabetes were not significantly associated with poor outcome. Health care workers with MERS had a markedly better clinical outcome compared to non HCW MERS patients.

Diversity of methicillin-resistant Staphylococcus aureus CC22-MRSA-IV from Saudi Arabia and the Gulf region.

OBJECTIVES: CC22-MRSA-IV, UK-EMRSA-15/Barnim EMRSA, is a common and pandemic strain of methicillin-resistant Staphylococcus aureus (MRSA) that has been found mainly in Western Europe, but also in other parts of the world including some Gulf countries. One suspected case of an infection with this strain in a patient who was admitted to the surgical unit in Riyadh, Kingdom of Saudi Arabia (KSA) was investigated in order to check whether this strain has reached KSA. METHODS: Besides the index isolate, 46 additional isolates of CC22-MRSA-IV from patients from KSA, Abu Dhabi, Kuwait, and Germany (patients with a history of travel in the Middle East), were characterized by microarray hybridization. RESULTS: The study revealed a regional presence of as many as six distinct 'strains' of CC22-MRSA-IV that could be distinguished based on carriage of SCCmec IV subtypes and virulence factors. No true UK-EMRSA-15/Barnim EMRSA was identified in Riyadh; all suspected isolates from Riyadh were assigned to other, albeit related strains. However, this strain was identified in Abu Dhabi and Kuwait. CONCLUSIONS: CC22-MRSA-IV from KSA could be linked to other epidemic strains from the Middle East and possibly India, rather than to the Western European UK-EMRSA-15/Barnim EMRSA. High-resolution typing methods, including SCCmec subtyping, might help to differentiate related epidemic strains and to monitor routes of transmission.

Molecular Epidemiology of Hospital Outbreak of Middle East Respiratory Syndrome, Riyadh, Saudi Arabia, 2014.

We investigated an outbreak of Middle East respiratory syndrome (MERS) at King Fahad Medical City (KFMC), Riyadh, Saudi Arabia, during March 29-May 21, 2014. This outbreak involved 45 patients: 8 infected outside KFMC, 13 long-term patients at KFMC, 23 health care workers, and 1 who had an indeterminate source of infection. Sequences of full-length MERS coronavirus (MERS-CoV) from 10 patients and a partial sequence of MERS-CoV from another patient, when compared with other MERS-CoV sequences, demonstrated that this outbreak was part of a larger outbreak that affected multiple health care facilities in Riyadh and possibly arose from a single zoonotic transmission event that occurred in December 2013 (95% highest posterior density interval November 8, 2013-February 10, 2014). This finding suggested continued health care-associated transmission for 5 months. Molecular epidemiology documented multiple external introductions in a seemingly contiguous outbreak and helped support or refute transmission pathways suspected through epidemiologic investigation.

Acute Middle East Respiratory Syndrome Coronavirus: Temporal Lung Changes Observed on the Chest Radiographs of 55 Patients.

OBJECTIVE: The objective of our study was to describe lung changes on serial chest radiographs from patients infected with the acute Middle East respiratory syndrome corona-virus (MERS-CoV) and to compare the chest radiographic findings and final outcomes with those of health care workers (HCWs) infected with the same virus. Chest radiographic scores and comorbidities were also examined as indicators of a fatal outcome to determine their potential prognostic value. MATERIALS AND METHODS: Chest radiographs of 33 patients and 22 HCWs infected with MERS-CoV were examined for radiologic features indicative of disease and for evidence of radiographic deterioration and progression. Chest radiographic scores were estimated after dividing each lung into three zones. The scores (1 [mild] to 4 [severe]) for all six zones per chest radiographic examination were summed to provide a cumulative chest radiographic score (range, 0-24). Serial radiographs were also examined to assess for radiographic deterioration and progression from type 1 (mild) to type 4 (severe) disease. Multivariate logistic regression analysis, Kaplan-Meier survival curve analysis, and the Mann-Whitney U test were used to compare data of deceased patients with those of individuals who recovered to identify prognostic radiographic features. RESULTS: Ground-glass opacity was the most common abnormality (66%) followed by consolidation (18%). Overall mortality was 35% (19/55). Mortality was higher in the patient group (55%, 18/33) than in the HCW group (5%, 1/22). The mean chest radiographic score for deceased patients was significantly higher than that for those who recovered (13 ± 2.6 [SD] vs 5.8 ± 5.6, respectively; p = 0.001); in addition, higher rates of pneumothorax (deceased patients vs patients who recovered, 47% vs 0%; p = 0.001), pleural effusion (63% vs 14%; p = 0.001), and type 4 radiographic progression (63% vs 6%; p = 0.001) were seen in the deceased patients compared with those who recovered. Univariate and logistic regression analyses identified the chest radiographic score as an independent predictor of mortality (odds ratio [OR], 1.38; 95% CI, 1.07-1.77; p = 0.01). The number of comorbidities in the patient group (n = 33) was significantly higher than that in the HCW group (n = 22) (mean number of comorbidities, 1.90 ± 1.27 vs 0.17 ± 0.65, respectively; p = 0.001). The Kaplan-Meier analysis revealed a median survival time of 15 days (95% CI, 4-26 days). CONCLUSION: Ground-glass opacity in a peripheral location was the most common abnormality noted on chest radiographs. A higher chest radiographic score coupled with a high number of medical comorbidities was associated with a poor prognosis and higher mortality in those infected with MERS-CoV. Younger HCWs with few or no comorbidities had a higher survival rate.

Rapid detection of Panton-Valentine leukocidin in Staphylococcus aureus cultures by use of a lateral flow assay based on monoclonal antibodies.

Panton-Valentine leukocidin (PVL) is a virulence factor of Staphylococcus aureus, which is associated with skin and soft-tissue infections and necrotizing pneumonia. To develop a rapid phenotypic assay, recombinant PVL F component was used to generate monoclonal antibodies by phage display. These antibodies were spotted on protein microarrays and screened using different lukF-PV preparations and detection antibodies. This led to the identification of the optimal antibody combination that was then used to establish a lateral flow assay. This test was used to detect PVL in S. aureus cultures. The detection limit of the assay with purified native and recombinant antigens was determined to be around 1 ng/ml. Overnight cultures from various solid and liquid media proved suitable for PVL detection. Six hundred strains and clinical isolates from patients from America, Europe, Australia, Africa, and the Middle East were tested. Isolates were genotyped in parallel by DNA microarray hybridization for confirmation of PVL status and assignment to clonal complexes. The sensitivity, specificity, and positive and negative predictive values of the assay in this trial were 99.7, 98.3, 98.4, and 99.7%, respectively. A total of 302 clinical isolates and reference strains were PVL positive and were assigned to 21 different clonal complexes. In summary, the lateral flow test allows rapid and economical detection of PVL in a routine bacteriology laboratory. As the test utilizes cultures from standard media and does not require sophisticated equipment, it can be easily integrated into a laboratory's workflow and might contribute to timely therapy of PVL-associated infections.

Characterisation of MRSA strains isolated from patients in a hospital in Riyadh, Kingdom of Saudi Arabia.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is spreading worldwide and poses a serious public health problem, being present in hospital settings and communities. However, from the Middle East and the Arabian Peninsula few molecular typing data on MRSA strains are currently available. In order to obtain data on the population structure of MRSA in Riyadh, Saudi Arabia, 107 clinical and environmental MRSA isolates were genotyped using a microarray-based assay. RESULTS: Five major MRSA strains from four clonal complexes were identified CC8/ST239-III (20.75%), PVL-positive as well as -negative CC22-IV (18.87% and 9.43%, respectively), PVL-positive CC30-IV (12.26%) and PVL-positive CC80-IV (17.92%). Minor strains, which accounted for less than 3% each, included CC1-IV/SCCfus, PVL-positive CC1/ST772-V, PVL-positive as well as- negative CC5-IV, CC5-IV/SCCfus, CC5-V, CC6-IV, CC45-IV, PVL-negative CC80-IV, PVL-positive CC88-IV, CC97-V and a CC9/ST834-MRSA strain. CONCLUSIONS: Typing of MRSA strains from Riyadh revealed a high diversity of clonal complexes. The prevalence of the genes encoding the Panton-Valentine leukocidin was surprisingly high (54.21%), and a significant rate of resistance markers was detected also in strains considered as community-associated.

The role of the laboratory in the diagnosis and management of chronic hepatitis C patients.

Clinical diagnosis of chronic hepatitis C infections is a difficult task. This is due to the insidious nature of the infection and the subclinical and symptomless presentation in the majority of cases. The laboratory plays a principal role not only in the specific diagnosis of the infection but also in assessing the severity and evolution of the liver disease, selection of patients for therapeutic intervention, monitoring treatment and determining the outcome of treatment. To attain these goals, improvements in sensitivity and specificity of various techniques, including molecular diagnostic assays, have been introduced. Most importantly, patients may be excluded if they have conditions that are contra-indicated for treatment as determined by laboratory parameters. In cases of adverse events the drugs may be reduced or withdrawn based on clinical and laboratory results. The improvement over the last decade of laboratory assays has paralleled the success in the sustained response rates reported for hepatitis C virus treatment. A good laboratory provides the tools for diagnosis and treatment essential for good management. This is a multidisciplinary approach involving all branches of pathology.

Hepatitis C virus seroprevalence rate among Saudis.

OBJECTIVE: The aim of the study is to determine the seroprevalence of hepatitis C virus (HCV) in blood donors, children, pregnant women, hemodialysis patients and drug addicts in Saudi Arabia. METHODS: Using third generation enzyme immunoassay kits, we have screened Saudi cohorts of all ages and sexes, namely infants, pre-school, school children, young adults and adults (blood donors and antenatals) for antibodies to HCV. We have also reviewed HCV seroprevalence data among high risk groups from 1998 to 2002. RESULTS: An overall 1.1% (6313 out of 557813) seroprevalence rate was determined among Saudi blood donors; 0.1% (5 out of 3854) in Saudi children; and 0.7% (22 out of 3127) among pregnant women. Hemodialysis patients remain at highest risk of infection at 55.7% whereas intravenous drug addicts have 14% exposure rate. CONCLUSION: We conclude that the present public health schemes have been effective in reducing hepatitis C infection in the general community in the Kingdom of Saudi Arabia but the infection among high risk groups remain a major problem that needs to be actively addressed.

Hepatitis C genotypes/subtypes among chronic hepatitis patients in Saudi Arabia.

OBJECTIVE: The object of this study is to determine the molecular epidemiology of hepatitis C virus (HCV) in the Kingdom of Saudi Arabia (KSA). METHODS: Four hundred and ninety-two histological proven chronic HCV patients prospectively recruited from all regions of KSA, between November 1999 and March 2002, were genotyped and subtyped using amplified products of specific primers from the 5-UTR region in a reverse transcription polymerase chain reaction (Roche Diagnostics, Switzerland) followed by a reverse hybridization technique (Innolipa HCV II [Innogenetics, Belgium]). RESULTS: Sixty-two percent of Saudis were found to be genotype 4. Other genotypes were 1 (24.1%); 2 (7.4%); 3 (5.9%); 5 (0.3%); and 10 (0.3%). There were no differences in distribution patterns between sexes and ages. All regions showed similar distribution except the Eastern region where subtype 2a/c seem to have emerged. Diabetic patients and those with a history of blood transfusion had the same pattern as those with community acquired HCV. Among the non-Saudis (mostly Egyptians), genotype 4 predominated (88%). CONCLUSION: We conclude that 86% of Saudi chronic hepatitis C cases are due to genotypes 1 and 4. Since these are considered "difficult to treat" an aggressive approach to management using combination therapy of pegylated interferon plus ribavirin for 48 weeks should be considered for all cases of chronic hepatitis C until genotyping proves otherwise.