Evaluation of Quantitative Hepatitis C Virus Core Antigen Testing as a Tool for Screening and Confirmation of HCV Infection.

BACKGROUND: Hepatitis C is a common viral infection worldwide. Finding the most effective diagnostic methods with low cost is always needed for laboratory improvement. In this study, we evaluated the performance of a quantitative chemiluminescent hepatitis C virus core antigen (HCV cAg) test by comparing it with the HCV confirmatory antibody line immunoblot assay (HCV Ab-LIA) test as well as the HCV quantitate reverse transcription-polymerase chain reaction (qRT-PCR) test. METHODS: A total of 394 samples were enrolled in the retrospective study. Of these, 225 samples were tested using HCV Ab screening and confirmatory Ab-LIA along with chemiluminescent HCV core Ag testing, while 169 samples were tested using qRT-PCR for HCV RNA and chemiluminescent HCV core Ag testing. RESULTS: Out of these, 225 positive samples tested by HCV Ab screening test were analyzed using the confirmatory Ab LIA and HCV cAg assays, a total of 183 samples (81.3 %) were confirmed to be Ab-positive, and among those, 77 samples (42.1%) were also positive for HCV cAg. Thirty-eight samples (20.76%) were HCV Ab indeterminate, and all of them were HCV cAg negative. Four samples (1.8%) were HCV Ab LIA-negative and negative for HCV cAg. Moreover, 169 samples were measured for qRT-PCR HCV viral load and quantitative HCV cAg test. One hundred and three samples were positive for HCV RNA, while 66 were negative. Among the positives, 96/103 samples were HCV cAg positive and 7/103 samples were negative. Out of the negatives, 4/66 samples were HCV cAg positive but 62/66 samples were negative. The HCV cAg results were concordant with the qRT-PCR results in 158 samples (93.5%); however, 11 samples (6.5%) were found to be discrepant. The sensitivity, specificity, positive predictive value, and negative predictive value of the quantitative HCV cAg were found to be 93%, 94%, 96%, and 90%, respectively. The overall coefficient of correlation between the HCV RNA levels and HCV cAg data was determined to be r2 = 0.9. CONCLUSIONS: The HCV cAg test showed a high correlation with the HCV RNA levels and may potentially be used as a more cost-effective alternative to the HCV RNA qRT-PCR test.

The Prevalence of the Virulence Genes of Staphylococcus aureus in Sickle Cell Disease Patients at KSUMC, Riyadh, Saudi Arabia.

Staphylococcus aureus in the blood of sickle cell disease (SCD) patients may result in a significant increase in morbidity and mortality. S. aureus strains contain various virulence characteristics, including the ability to create a variety of toxins and develop drug resistance. The current study sought to assess the prevalence of S. aureus in SCD patients and to identify the pathogen's virulence characteristics. Between 2017 and 2021, blood samples and data were collected at King Saud University Medical City (KSUMC) in Riyadh, Saudi Arabia. The Vitek system PCR and gene sequencing methods were used for identification, antibiotic resistance patterns, and genetic analysis. During the study period, 47 S. aureus blood isolates (methicillin-resistant S. aureus (MRSA) 41.6% and non-MRSA 58.4%) were isolated from 2406 SCD patients. The prevalence percentages of virulence genes (finbB, sdrC, sdrD, icaA, coa, nuc, hlg, hla, finbA, clfA, efb, pvl, agr, spa, seb, sea, sec, tst, and sed) among all the isolates from the SCD patients compared with non-SCD patients (control group) were as follows: (100% vs. 100%), (100% vs. 100%), (100% vs. 100%), (100% vs. 87.5%), (100% vs. 81.3%), (100% vs. 100%), (100% vs. 100%), (100% vs. 100%), (97.9% vs. 81.3%), (97.9% vs. 100%), (97.9% vs. 87.5%), (54.3% vs. 56.3%), (46.8% vs. 75%), (42.6% vs. 43.8%), (27.7% vs. 0%), (25.5% vs. 12.5%), (12.8% vs. 6.3%), (4.3% vs. 12.5%), and (4.3% vs. 0%). Regarding the resistance genes (plaZ, mecA, ermA, ermC, tetK, tetM, and ermB) of the S. aureus strains isolated from the SCD patients compared with non-SCD patients (control group), the prevalence percentages were as follows: (100% vs. 100%), (100% vs. 56.3%), (0% vs. 31.3%), (31.9% vs. 18.8%), (40.4% vs. 25%), (0% vs. 0%), and (0% vs. 0%). As for the antibiotic (ampicillin, penicillin, amoxicillin, cefazolin, imipenem, oxacillin, erythromycin, tetracycline, azithromycin, ciprofloxacin, moxifloxacin, and levofloxacin) resistance of the S. aureus strains isolated from the SCD patients compared with non-SCD patients (control group), the prevalence percentages were as follows: (100% vs. 100%), (97.9% vs. 100%), (72.3% vs. 25%), (68.1% vs. 37.5%), (68.1% vs. 25%), (66% vs. 25%), (36.2% vs. 18.8%), (23.4% vs. 12.5%), (19.1% vs. 12.5%), (17% vs. 12.5%), (14.9% vs. 25%), and (10.6% vs. 18.7%). This study concluded that several virulence genes were present in the S. aureus strains recovered from the SCD patients at KSUMC, with all the isolates containing the finbB, sdrC, sdrD, icaA, coa, nuc, hlg, and hla genes.

Chemokine Levels among Patients with Middle East Respiratory Syndrome Coronavirus Infection.

Middle East respiratory syndrome coronavirus (MERS-CoV) is associated with significant morbidity and mortality due to intense pulmonary inflammation. Enhanced chemokine-mediated leukocyte infiltration in lungs has been linked with unfavorable outcomes with respect to the disease. This cross-sectional study assessed the levels of chemokines among 46 MERS-CoV-infected patients (19 asymptomatic and 27 symptomatic) and 52 healthy controls using a customized Luminex human chemokine magnetic multiplex panel. The plasma levels of interferon-inducible protein (IP)-10 (568.5 ± 114.7 vs. 55.19 ± 5.85 pg/mL; p < 0.0001), macrophage inflammatory protein (MIP)-1 alpha (MIP-1A) (30.78 ± 2.81 vs. 18.16 ± 0.91 pg/mL; p < 0.0001), MIP-1B (36.63 ± 4.25 vs. 25.26 ± 1.51 pg/mL; p < 0.003), monocyte chemoattractant protein (MCP)-1 (1267 ± 309.5 vs. 390.0 ± 35.51 pg/mL; p < 0.0002), and monokine-induced gamma interferon (MIG) (28.96 ± 3.93 vs. 16.29 ± 1.69 pg/mL; p < 0.001), interleukin (IL)-8 (147.9 ± 21.57 vs. 84.63 ± 10.62 pg/mL; p < 0.004) were significantly higher in symptomatic patients than healthy controls. Likewise, the levels of IP-10 (247.6 ± 80.09 vs. 55.19 ± 5.85 pg/mL; p < 0.0002) and MCP-1 (650.7 ± 149 pg/mL vs. 390 ± 35.51 pg/mL; p < 0.02) were also significantly higher in asymptomatic patients compared to healthy controls. However, no differences were observed in the plasma levels of MIP-1A, MIP-1B, MIG, and IL-8 between asymptomatic patients and uninfected controls. Conversely, the mean plasma levels of regulated on activation normal T cell expressed and secreted (RANTES) (3039 ± 301.0 vs. 4390 ± 223 pg/mL; p < 0.001) and eotaxin (176.9 ± 30.20 vs. 296.2 ± 28.11 pg/mL; p < 0.01) were significantly lower in symptomatic MERS-CoV-infected patients compared to healthy controls. Likewise, the levels of eotaxin (162.7 ± 21.60 vs. 296.2 ± 28.11 pg/mL; p < 0.01) were also significantly lower in asymptomatic patients. Interestingly, the level of MCP-1 (2139 ± 548.2 vs. 776.5 ± 165.3 pg/mL; p < 0.004) was significantly higher in deceased symptomatic patients compared to recovered symptomatic patients. MCP-1 was the only chemokine associated with a higher risk of mortality. Symptomatic MERS-CoV-infected patients had a significant elevation of plasma chemokines and elevated MCP-1 levels were found to be associated with fatal outcomes.

The Attributable Factors That Increase the Likelihood of Central Line Associated Blood Stream Infection Related In-Hospital 30-Day Mortality.

OBJECTIVE: The objective is to investigate the attributable factors associated with an increase in hospital 30-day mortality of central line bloodstream infection (CLABSI). METHODS: A retrospective cohort study was conducted at King Saud University Medical City (KSUMC). The sample included adult patients who developed CLABSI between March 2016 and February 2018 after having a central line inserted at KSUMC in Riyadh, Saudi Arabia. RESULTS: A total of 283 patients were involved in the study. The 30-day mortality rate was 18.8%. Patients were more likely to die if they were in the intensive care unit (ICU) or required ICU admission after infection (p<0.001). This was also observed in patients who required inotropes or intubation before or after culture (p<0.001). There was a statistically significant difference of 6.60±5.62 in the mean score on the Acute Physiologic Assessment and Chronic Health Evaluation (APACHE) II between before and after culture (p<0.001). The likelihood of death was significantly higher among patients with higher APACHE II scores before and after culture (p<0.001). The presence of CLABSI-related sequelae was not associated with increased mortality (p<0.595). CONCLUSIONS: The clinical characteristics of CLABSI patients are variable and can increase the risk of mortality or complicate the treatment course. Physicians should be aware of the significance of these factors as potential causes of increased mortality.

Genetic Diversity and Evolutionary Kinetics of Influenza A Virus H3N2 Subtypes Circulating in Riyadh, Saudi Arabia.

Presence of a large foreign workforce and the annual gathering of people for pilgrimage from around the globe have significantly contributed to the emergence and diversity of respiratory viruses in Saudi Arabia. Here, we report the sequence and phylogenetic analysis of the H3N2 subtype of influenza A virus (IAV) in clinical samples collected from Riyadh, Saudi Arabia. Based on RT-PCR, IAV was found in 88 (28.3%) of the 311 samples screened. Of the 88-IAV positive samples, 43 (48.8%) were H1N1 subtype while the remaining 45 (51.2%) were found to be of the H3N2 subtype. Complete sequencing of HA and NA genes of H3N2 revealed, twelve and nine amino acid (AA) substitutions respectively, and importantly, these variations are absent in the current vaccine strains. Based on the phylogenetic analysis, the majority of H3N2 strains were grouped in the same clades as the vaccine strains. Importantly, the N-glycosylation sites at AA 135(NSS) were found to be unique to 6 strains in the investigated HA1 protein and were absent in the current vaccine strains. These data may have significant clinical implications in designing novel and population-based vaccines for IAV and underscore the need for regular monitoring of efficacy of vaccines due to emerging variants.

Assessment of Proinflammatory Cytokines Among Patients with Middle East Respiratory Syndrome Coronavirus Infection.

Middle East respiratory syndrome coronavirus (MERS-CoV) is associated with significant morbidity and mortality. This study was performed to assess the proinflammatory cytokines profile among MERS-CoV patients. A total of 46 MERS-CoV-infected patients (27 symptomatic and 19 asymptomatic) were assessed and compared with 52 normal healthy controls for plasma levels of interleukin (IL)-1ß, tumor necrosis factor (TNF)-α, IL-17, IL-7, IL-6, interferon (IFN)-α, and IL-15 using a customized luminex kit. Whereas asymptomatic MERS-CoV patients and controls were no different; the mean plasma levels among MERS-CoV symptomatic patients were significantly higher than the normal controls: IL-1ß (16.89 ± 1.23 vs. 12.80 ± 0.59 pg/mL; p < 0.001), TNF-α (14.04 ± 0.93 vs. 10.35 ± 0.29 pg/mL; p < 0.0001), IL-17 (14.3 ± 0.89 vs. 11.47 ± 0.61 pg/mL; p < 0.001), IL-7 (21.56 ± 1.00 vs. 16.31 ± 0.30 pg/mL; p < 0.0001), IL-6 (156.5 ± 37.90 vs. 18.60 ± 1.59 pg/mL; p < 0.0001), and IFN-α (68.73 ± 13.06 vs. 23.57 ± 1.05 pg/mL; p < 0.0001). The mean plasma levels of IL-7 (24.81 ± 1.63 vs. 19.79 ± 0.94 pg/mL; p < 0.01), IL-6 (312.7 ± 94.67 vs. 101.2 ± 25.67 pg/mL; p < 0.01), and IFN-α (89.00 ± 18.97 vs. 51.05 ± 8.68 pg/mL; p < 0.05) were significantly elevated among MERS-CoV symptomatic patients with fatal outcome compared with MERS-CoV symptomatic patients who survived. Only IL-7 was found to have a higher risk ratio of mortality (4.76, 95% confidence interval: 1.5-14.94; p < 0.01). No differences were observed in IL-15 levels among the groups. Significantly elevated proinflammatory cytokines among symptomatic MERS-CoV-infected patients may contribute to manifestations of cytokine storm frequently observed among critically ill MERS-CoV patients and IL-7 may serve as a marker for disease activity.

Microbial surveillance of Hajj tents: Bioaerosol sampling coupled with real-time multiplex PCR.

BACKGROUND: Respiratory tract infections are common among pilgrims attending annual Hajj in Mecca, Saudi Arabia. Pilgrims typically spend most of the Hajj period inside ventilated tents, where microorganisms may be transmitted through bioaerosols and droplets. OBJECTIVE: To perform microorganism surveillance inside Hajj tents and assess the similarities between microorganisms isolated from tent bioaerosol samples and nasopharyngeal swabs (NP) of tent occupants. METHODS: Respiratory microorganisms in bioaerosols collected from Hajj tents over a 4-day period were compared with NP of tent occupants using real-time multiplex polymerase chain reaction analysis. RESULTS: A total of 152 samples were collected: 120 tent bioaerosol samples collected on days 9, 10, 11, and 12 of Dhu al-Hijjah, and 32 NP collected on day 12 of Dhu al-Hijjah (corresponding to 23/08/2018). Eighty-three (69.2%) bioaerosol samples tested positive for at least 1 microorganism, with the number of pathogens increasing over the 4 days of sampling. Twenty-seven (84.38%) NP swabs from tent occupants also tested positive. Microorganisms identified in pilgrim nasal carriage and tent bioaerosol samples were similar, and included K. pneumonia, S. aureus, S. pneumonia, human adenovirus, Moraxella, influenza A, and H. influenza. CONCLUSIONS: The data suggest that the Hajj tent environment may contribute to the spread of airborne infections during Hajj. This can have important ramifications for novel pathogens with pandemic potential.

Practice guidelines for the management of Helicobacter pylori infection: The Saudi H. pylori Working Group recommendations.

The eradication rates for Helicobacter pylori globally are decreasing with a dramatic increase in the prevalence of antibiotic resistant bacteria all over the world, including Saudi Arabia. There is no current consensus on the management of H. pylori in Saudi Arabia. The Saudi Gastroenterology Association developed these practice guidelines after reviewing the local and regional studies on the management of H. pylori. The aim was to establish recommendations to guide healthcare providers in managing H. pylori in Saudi Arabia. Experts in the areas of H. pylori management and microbiology were invited to write these guidelines. A literature search was performed, and all authors participated in writing and reviewing the guidelines. In addition, international guidelines and consensus reports were reviewed to bridge the gap in knowledge when local and regional data were unavailable. There is limited local data on treatment of H. pylori. The rate of clarithromycin and metronidazole resistance is high; therefore, standard triple therapy for 10-14 days is no longer recommended in the treatment of H. pylori unless antimicrobial susceptibility testing was performed. Based on the available data, bismuth quadruple therapy for 10-14 days is considered the best first-line and second-line therapy. Culture and antimicrobial susceptibility testing should be considered following two treatment failures. These recommendations are intended to provide the most relevant evidence-based guidelines for the management of H. pylori infection in Saudi Arabia. The working group recommends further studies to explore more therapeutic options to eradicate H. pylori.

ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia.

Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.

Differential expression of carcinoembryonic antigen-related cell adhesion molecule-5 (CEACAM5) and dipeptidyl peptidase-4 (DPP4) with detection of Middle East respiratory syndrome-coronavirus in peripheral blood.

BACKGROUND: Middle East respiratory syndrome-coronavirus (MERS-CoV) utilizes CD26 (dipeptidyl peptidase-4) and CD66e or CEACAM5 (carcinoembryonic antigen-related cell adhesion molecule 5) receptors for cell infection. Peripheral blood mononuclear cells (PBMCs) play a critical role in mounting adaptive immune response against the virus. This study was performed to assess the expression of CD26 and CD66e on PBMCs and their susceptibility to MERS-CoV infection. METHODS: Surface expression of CD26 and CD66e receptors on PBMCs from MERS-CoV patients (n = 20) and healthy controls (n = 20) was assessed by flow cytometry and the soluble forms were determined by enzyme-linked immunosorbent assay (ELISA). MERS-CoV UpE and Orf1a genes in PBMCs were detected by using Altona diagnostics reverse transcription polymerase chain reaction (RT-PCR) kit. RESULTS: Mean fluorescent intensity (MFI) of CD66e was significantly higher on CD4 + lymphocytes (462.4 ± 64.35 vs 325.1 ± 19.69; p < 0.05) and CD8 + lymphocytes (533.8 ± 55.32 vs 392.4 ± 37.73; p < 0.04) from patients with MERS-CoV infection compared to the normal controls. No difference in MFI for CD66e was observed on monocytes (381.8 ± 40.34 vs 266.8 ± 20.6; p = 0.3) between the patients and controls. Soluble form of CD66e among MERS-CoV patients was also higher than the normal controls (mean= 338.7 ± 58.75 vs 160.7 ± 29.49 ng/mL; p < 0.01). Surface expression of CD26 on PBMCs and its soluble form were no different between the groups. MERS-CoV was detected by RT-PCR in 16/20 (80%) patients from whole blood, among them 8 patients were tested in PBMCs, 4/8 (50%) patients were positive. CONCLUSION: Increased expression levels of CD66e (CEACAM5) may contribute to increased susceptibility of PBMCs to MERS-CoV infection and disease progression.

Possible vertical transmission of corona virus disease 19 (COVID-19) from infected pregnant mothers to neonates: a multicenter study.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious with various possible routes of transmission, resulting in high mortality globally. Controversy exists regarding the vertical transmission of the SARS-CoV-2 infection to fetuses of COVID-19-infected women. The aim of this study was to investigate the possibility of the vertical transmission of SARS-CoV-2 from COVID-19-infected mothers to their neonates. MATERIALS AND METHODS: We prospectively collected demographical and clinical characteristics of 31 COVID-19 positive pregnant women and their neonates. All mothers and neonates were tested for SARS-CoV-2 infection using the real-time polymerase chain reaction on nasopharyngeal swabs and breast milk samples. Antenatal and placental abnormalities were ultrasonically and histopathologically examined. In cord blood samples, the immunoglobins (Ig) M and IgG were estimated qualitatively. RESULTS: The women's mean age and gestational age were 31 years and 38 weeks, respectively, with 58% undergoing an elective cesarean section. Gestational diabetes was reported in 29% of cases, 64.5% of women were medically free and only 16.12% were symptomatic. A normal antenatal ultrasound was observed in 77.42% of cases. Nine cord blood samples were positive for IgG. Villous infarction (24%), villous agglutination, and chorangiosis (51%), accelerated villous maturation (21%) and reduced and hypercoiling were reported for 6.97% of the umbilical cords. Three newborns had possible vertical transmission of SARS-CoV-2 infection, of which, two were preterm and IUFD. The third neonate was born full-term, admitted to NICU and later discharged in good health. CONCLUSION: Our findings support the possibility of the direct vertical transmission of the SARS-CoV-2 infection to neonates from infected mothers. Further studies with a larger sample size are required to validate the current findings.

The antimicrobial activity of ceftobiprole against Methicillin-resistant Staphylococcus aureus and multi-drug resistant Pseudomonas aeruginosa: A large tertiary care university hospital experience in Riyadh, Saudi Arabia.

OBJECTIVES: To assess the antibacterial activity of ceftobiprole against Methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (P. aeruginosa) from various body specimen types and different patterns of resistance. METHODS: A retrospective cohort study with a total of 49 MRSA and 99 P. aeruginosa isolated in the Microbiology Laboratory at King Saud University Medical City, Riyadh, Saudi Arabia, between 2018-2019, were used. Isolates were randomly selected from various specimen types. The minimum inhibition concentration (MIC) of ceftobiprole was determined by E-test. Breakpoints carried out by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) were used to assess antibiotic susceptibility. RESULTS: Approximately 100% of the MRSA isolates were susceptible with MIC50/90 value of 1/1.5 mg/L while 69.8% of multi-drug resistant (MDR) P. aeruginosa isolates were resistant with MIC50/90 value of 16/32 mg/L. CONCLUSION: The excellent activity of ceftobiprole against MRSA would have major implications in management of the patients with serious infections, as an empirical treatment or alternative to vancomycin. Ceftobiprole has a very low activity against MDR P. aeruginosa, and its susceptibility should be tested prior to use for treatment.

Initial Fluid Balance Associated Outcomes in Children With Severe Sepsis and Septic Shock.

INTRODUCTION: Net fluid balance and its role in sepsis-related mortality is not clear; studies suggest that aggressive fluid resuscitation can help in treatment, whereas others consider it is associated with poor outcomes. This study aimed to clarify the possible association of initial 24 hours' fluid balance with poor outcomes in pediatric patients with sepsis. METHODS: Retrospective data analysis included pediatric patients admitted with suspected or proven sepsis or septic shock to pediatric intensive care unit (PICU) of a tertiary care teaching hospital in Saudi Arabia. RESULTS: The study included 47 patients; 13 (28%) died, and mortality rate was significant in children with neurologic failure (P < 0.02), mechanical ventilation within 24 hours of admission (P < 0.03), leukopenia (P < 0.02), abnormal international normalized ratio (P < 0.02), initial blood lactate levels higher than 5 mmol/L (P < 0.02), or positive fluid balance at 24 hours of admission to the PICU (P < 0.001). CONCLUSION: Among children with sepsis and/or septic shock, there is significant association between mortality and initial high blood lactate levels and positive fluid balance at 24 hours from admission to the PICU.

The Laboratory Diagnosis of Clostridioides difficile Infection: An update of current laboratory practice.

Clostridioides difficile can cause colitis and is associated with hospital acquired infections. The C. difficile infection (CDI) is due to production of toxins A and B which bind to epithelial cell surface receptors and triggers signaling pathways, leading to loss of epithelial barrier function, apoptosis, and inflammation, culminating in diarrheal disease. In early days, laboratory diagnosis of CDI was based on cell culture, identification of toxins, and their cytopathic effects. These assays were replaced by enzyme immunoassays for the detection of C. difficile toxins and the GDH house-keeping gene for improved specificity. Later, molecular assays with higher sensitivity were introduced which are becoming easier to incorporate into the test algorithm. The diagnosis of CDI and significance of laboratory results can be challenging with asymptomatic colonization of C. difficile in some patients. Test result interpretation is even more challenging due to multiple guidelines, emerging resistant C. difficile ribotypes, as well as differences in disease prevalence. An accurate test result for diagnosis of CDI depends on selecting patients with high pre-test probability, collecting an acceptable stool specimen, and a thorough understanding of current test methods.

Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia.

BACKGROUND: Streptococcus anginosus is an emergence opportunistic pathogen that colonize the human upper respiratory tract (URT), S. anginosus alongside with S. intermedius and S. constellatus, members of S. anginosus group, are implicated in several human infections. However, our understanding this bacterium to the genotype level with determining the genes associated with pathogenicity and antimicrobial resistance (AMR) is scarce. S. anginosus 47S1 strain was isolated from sore throat infection, the whole genome was characterized and the virulence & AMR genes contributing in pathogenicity were investigated. METHODOLOGY: The whole genome of 47S1 was sequenced by Illumina sequencing technology. Strain 47S1 genome was de novo assembled with different strategies and annotated via PGAP, PROKKA and RAST pipelines. Identifying the CRISPR-Cass system and prophages sequences was performed using CRISPRloci and PhiSpy tools respectively. Prediction the virulence genes were performed with the VFDB database. AMR genes were detected in silico using NCBI AMRFinderPlus pipeline and CARD database and compared with in vitro AST findings. RESULTS: ß-hemolytic strain 47S1 was identified with conventional microbiology techniques and confirmed by the sequences of 16S rRNA gene. Genome of 47S1 comprised of 1981512 bp. Type I-C CRISPR-Cas system and 4 prophages were detected among the genome of 47S1. Several virulence genes were predicted, most of these genes are found in other pathogenic streptococci, mainly lmb, pavA, htrA/degP, eno, sagA, psaA and cpsI which play a significant role in colonizing, invading host tissues and evade form immune system. In silico AMR findings showed that 47S1 gnome harbors (tetA, tetB &tet32), (aac(6')-I, aadK &aph(3')-IVa), fusC, and PmrA genes that mediated-resistance to tetracyclines, aminoglycosides, fusidic acid, and fluoroquinolone respectively which corresponds with in vitro AST obtained results. In conclusion, WGS is a key approach to predict the virulence and AMR genes, results obtained in this study may contribute for a better understanding of the opportunistic S. anginosus pathogenicity.

Isolation and molecular characterization of multidrug-resistant Salmonella enterica serovars.

BACKGROUND: Salmonellosis is a foodborne zoonosis leaving gastrointestinal illness and drug-resistant genes to the consumers. To prevent Salmonella contamination associated health issues in the chicken meat sold in Riyadh city in Saudi Arabia. The evaluation of the Salmonella isolates from the meat sample needs to be screened for the composition of Salmonella serotypes and antimicrobial resistance pattern at the molecular level. METHODS AND RESULTS: Using specific growth media for Salmonella spp., swabs taken from the whole-body surfaces of 200 chilled broiler chickens from different vendors in the city of Riyadh, were screened for Salmonella contamination. Biochemical and molecular characterization of the isolates showed the presence of the serovars, Salmonella enterica, Salmonella Enteritidis, S. Typhimurium, S. Kentucky, and S. Tennessee. The isolated serovars exhibited multidrug resistance [MDR] resistance to antibiotics. Molecular characterization of the different serovars shows the presence of sixteen drug-resistant genes. The drug resistance mechanism at the molecular level varied with serotypes according to the nature of the antibiotics they encountered. A comparative study of the nature of the drug-resistant gene and the common antibiotics used in poultry farming in that province matches much, indicating adaptive variation in S. enterica serotypes to survive in the host's gut biome. The resistance genes from the chicken meat have every chance to get into the human system. The native microbes in consumers may acquire drug-resistant genes from S. entericus serovars. Such conditions may lead to treatment complications in the hosts. CONCLUSIONS: The results indicated that Salmonella infections constituted a potential risk to consumers through chicken flocks and noted that the genotypic resistance pattern to antibiotics draws attention in terms of both human and animal health. Also, promote other options for poultry farming, avoiding antibiotics supplementation.

The bacterial colonization of healthcare workers' mobile phones in a large tertiary care teaching hospital in Saudi Arabia.

INTRODUCTION: The use of mobile phones by healthcare workers is a risk factor for microorganism transmission in healthcare settings. Pathogenic bacteria such as methicillin-resistant Staphylococcus aureus and gram-negative bacteria like Escherichia coli that are known to cause nosocomial infection have been isolated from mobile phones. In this cross-sectional study, we assess the burden and related risk factors of the bacterial colonization of healthcare workers' mobile phones. METHODOLOGY: We collected samples from the mobile phones of 130 healthcare workers' in a Saudi Arabian teaching hospital, using moistened cotton swabs. The isolated organisms were identified using an automated identification and susceptibility system. Multiple logistic regression analysis was used to test the data. RESULTS: Of 130 swabs collected, 45 (34.6%) grew one species and 48 (36.9%) grew two or more. Staphylococcus epidermidis was the most commonly isolated bacteria (52.3%), followed by Micrococcus and related species (25.4%), Staphylococcus hominis (13.8%), and Bacillus species (6.9%). Clinically significant microorganisms such as S. aureus and Pseudomonas sp. were identified in 2 (1.5%) samples, respectively. The odds of mobile phone colonization were 8.5 times higher (95% CI = 3.2-23.1) in the laboratory, neonatal intensive care unit, and medicine departments. Mobile phones owned for more than one year were more likely to be culture positive (OR = 2.9, 95% CI = 1.1-7.6). CONCLUSIONS: In our study, the prevalence of bacterial colonization among healthcare workers' mobile phones was high. Our findings suggest that high-risk groups for mobile phone colonization-such as laboratory, neonatal intensive care unit, and medicine department staff-should be a priority for preventative measures, to improve infection control.

COVID-19 Critical Care Simulations: An International Cross-Sectional Survey.

Objective: To describe the utility and patterns of COVID-19 simulation scenarios across different international healthcare centers. Methods: This is a cross-sectional, international survey for multiple simulation centers team members, including team-leaders and healthcare workers (HCWs), based on each center's debriefing reports from 30 countries in all WHO regions. The main outcome measures were the COVID-19 simulations characteristics, facilitators, obstacles, and challenges encountered during the simulation sessions. Results: Invitation was sent to 343 simulation team leaders and multidisciplinary HCWs who responded; 121 completed the survey. The frequency of simulation sessions was monthly (27.1%), weekly (24.8%), twice weekly (19.8%), or daily (21.5%). Regarding the themes of the simulation sessions, they were COVID-19 patient arrival to ER (69.4%), COVID-19 patient intubation due to respiratory failure (66.1%), COVID-19 patient requiring CPR (53.7%), COVID-19 transport inside the hospital (53.7%), COVID-19 elective intubation in OR (37.2%), or Delivery of COVID-19 mother and neonatal care (19%). Among participants, 55.6% reported the team's full engagement in the simulation sessions. The average session length was 30-60 min. The debriefing process was conducted by the ICU facilitator in (51%) of the sessions followed by simulation staff in 41% of the sessions. A total of 80% reported significant improvement in clinical preparedness after simulation sessions, and 70% were satisfied with the COVID-19 sessions. Most perceived issues reported were related to infection control measures, followed by team dynamics, logistics, and patient transport issues. Conclusion: Simulation centers team leaders and HCWs reported positive feedback on COVID-19 simulation sessions with multidisciplinary personnel involvement. These drills are a valuable tool for rehearsing safe dynamics on the frontline of COVID-19. More research on COVID-19 simulation outcomes is warranted; to explore variable factors for each country and healthcare system.

COVID-19 vaccine uptake among healthcare workers in the fourth country to authorize BNT162b2 during the first month of rollout.

BACKGROUND: The Kingdom of Saudi Arabia (KSA) was the fourth country in the world to authorize the BNT162b2 coronavirus disease 2019 (COVID-19) vaccine, which it rolled out on December 17, 2020 and first targeted at healthcare workers (HCWs). This study assesses vaccine uptake among this group during the first month of its availability. METHODS: A national cross-sectional, pilot-validated, self-administered survey was conducted among HCWs in the KSA between December 27, 2020 and January 3, 2021. The survey included sociodemographic details, previous contact with COVID-19 patients, previous infection with COVID-19, receiving (or registering with the Ministry of Health website to receive) the COVID-19 vaccine, sources of HCWs' information on vaccines, awareness of emerging variants of concern, and anxiety level using the 7-item Generalized Anxiety Disorder assessment. A descriptive bivariate analysis and multivariate logistic binary regression analysis were performed. The primary evaluated outcome was vaccine uptake. RESULTS: Of the 1058 participants who completed the survey, 704 (66.5%) were female, and 626 (59.2%) were nurses. Of all the respondents, 352 (33.27%) were enrolled to receive or had already received the vaccine, while 706 (66.73%) had not enrolled. In a bivariate analysis, not enrolling for vaccination was more likely in females than males (78.5% vs. 21.5%, P < 0.001), HCWs between the ages of 20 and 40 years than those >40 years (70.4% vs. 29.6%, P = 0.005), Saudi HCWs than expatriates (78% vs 22%, P < 0.001), and among HCWs who used social media as a source of information than those who did not (69.8% vs. 38.6%, P < 0.001). In a multivariate analysis, independent factors associated with uptake were being a Saudi national (aOR = 1.918, 95 %CI = 1.363-2.698, P < 0.001), working in an intensive care unit (aOR = 1.495, 95 %CI = 1.083-2.063, P = 0.014), and working at a university hospital (aOR = 1.867, 95 %CI = 1.380-2.525, P < 0.001). CONCLUSIONS: A low level of vaccine uptake was observed especially in female HCWs, those younger than 40 years old, and those who used social media as their source of vaccine information. This survey provides important information for public health authorities in order to scale up vaccination campaigns targeting these HCWs to increase vaccine enrollment and uptake.

Antimicrobial resistance trends of non-fermenter Gram negative bacteria in Saudi Arabia: A six-year national study.

BACKGROUND: Antimicrobial resistance (AMR) of non-fermenting Gram-negative bacteria (NFGNB) is increasingly recognized as urgent healthcare threat. Trend data on AMR of NFGNB in Saudi Arabia are either old or limited. The objective was to estimate the prevalence and resistance trends of isolated NFGNB in Saudi Arabia. METHODS: A retrospective multicenter study involving seven tertiary care hospitals in Saudi Arabia was conducted between 2011 and 2016. Susceptibility testing for non-duplicate isolates was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines in College of American Pathologists accredited diagnostic microbiology laboratories in the participating hospitals. RESULTS: Out of 461,274 isolates, 100,132 (21.7%) were NFGNB which represented 30% of gram-negative pathogens. Pseudomonas aeruginosa was the most common (73.6%), followed by Acinetobacter baumannii (21.0%) and Stenotrophomonas maltophilia (5.3%). Resistance trends of P. aeruginosa were increasing for aztreonam (absolute increase during the study was 17.3%), imipenem (12.3%), and meropenem (11.6%). A. baumannii was fully resistant to several beta lactam drugs, and resistance trends were increasing for potential treatments such as tigecycline (25.1%) and tobramycin (15.5%). S. maltophilia was >90% resistant to trimethoprim/ sulfamethoxazole and ciprofloxacin by the end of the study. CONCLUSION: We are reporting high and/or increasing resistance of NFGNB to common treatment options. The current findings call for urgent actions to combat the increasing resistance of NFGNB. Large scale sharing of AMR data collected at different hospitals with the Saudi AMR committee would be critical to set priorities and monitor progress.