Binding selectivity analysis of new delhi metallo-beta-lactamase-1 inhibitors using molecular dynamics simulations: Exploring possibilities for decoding antimicrobial drug resistance.

BACKGROUND: New Delhi metallo-beta-lactamase-1 (NDM1) confers resistance to several bacterial species against a broad range of beta-lactam antibiotics and turning them into superbugs that pose a significant threat to healthcare systems worldwide. As such, it is a potentially relevant biological target for counteracting bacterial infections. Given the lack of effective treatment options against NDM1 producing bacteria, finding a reliable inhibitor for the NDM1 enzyme is crucial. METHODS: Using molecular dynamics simulations, the binding selectivities and affinities of three ligands, viz. PNK, 3S0, and N1G were investigated against NDM1. RESULTS: The results indicate that N1G binds with more affinity to NDM1 than PNK and 3S0. The binding energy decomposition analysis revealed that residues I35, W93, H189, K211, and N220 showed significant binding energies with PNK, 3S0, and N1G, and hence are crucially involved in the binding of the ligands to NDM1. Molecular dynamics trajectory analysis further elicited that the ligands influence dynamic flexibility of NDM1 morphology, which contributes to the partial selectivities of PNK, 3S0, and N1G. CONCLUSIONS: This in silico study offers a vital information for developing potential NDM1 inhibitors with high selectivity. Nevertheless, in vitro and in vivo experimental validation is mandated to extend the possible applications of these ligands as NDM1 inhibitors that succor in combating antimicrobial resistance.

Isolation and Detection of Drug-Resistant Bacterial Pathogens in Postoperative Wound Infections at a Tertiary Care Hospital in Saudi Arabia.

Background: Surgical site infections (SSIs), especially when caused by multidrug-resistant (MDR) bacteria, are a major healthcare concern worldwide. For optimal treatment and prevention of antimicrobial resistance, it is important for clinicians to be aware of local drug-resistant bacterial pathogens that cause SSIs. Objective: To determine the frequency patterns of drug-resistant bacterial strains causing SSIs at a tertiary care hospital in Saudi Arabia. Methods: This retrospective study was conducted at the Microbiology laboratory of Al-Noor Specialist Hospital, Makkah, Saudi Arabia, and included wound swab samples from all cases of SSI between January 01, 2017, and December 31, 2021. The swabs were processed for the identification of bacterial strains and their resistance pattern to antibiotics according to the Clinical and Laboratory Standards Institute. Results: A total of 5409 wound swabs were analyzed, of which 3604 samples (66.6%) were from male. Most samples were from the Department of Surgery (43.3%). A total of 14 bacterial strains were isolated, of which 9 were Gram-negative bacteria. The most common isolates were Klebsiella pneumoniae, followed by Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and vancomycin-resistant S. aureus (VRSA). In terms of MDR in 2021, the highest rate of carbapenem-resistance was in A. baumannii (97%). MDR was as follows: A. baumannii, 97%; K. pneumoniae, 81%; E. coli, 71%; MRSA, 60%; P. aeruginosa, 33%; VRE, 22%; and VRSA, 2%. Conclusion: This study showed that in the city of Makkah, Saudi Arabia, the rates of MDR bacteria are high, with the majority being Gram-negative.

Prevalence and Antibiogram Pattern of Klebsiella pneumoniae in a Tertiary Care Hospital in Makkah, Saudi Arabia: An 11-Year Experience.

Infectious disease is one of the greatest causes of morbidity and mortality worldwide, and with the emergence of antimicrobial resistance, the situation is worsening. In order to prevent this crisis, antimicrobial resistance needs to be monitored carefully to control the spread of multidrug-resistant bacteria. Therefore, in this study, we aimed to determine the prevalence of infection caused by Klebsiella pneumoniae and investigate the antimicrobial profile pattern of K. pneumoniae in the last eleven years. This retrospective study was conducted in a tertiary hospital in Makkah, Saudi Arabia. Data were collected from January 2011 to December 2021. From 2011 to 2021, a total of 61,027 bacterial isolates were collected from clinical samples, among which 14.7% (n = 9014) were K. pneumoniae. The antibiotic susceptibility pattern of K. pneumoniae revealed a significant increase in the resistance rate in most tested antibiotics during the study period. A marked jump in the resistance rate was seen in amoxicillin/clavulanate and piperacillin/tazobactam, from 33.6% and 13.6% in 2011 to 71.4% and 84.9% in 2021, respectively. Ceftazidime, cefotaxime, and cefepime resistance rates increased from 29.9%, 26.2%, and 53.9%, respectively, in 2011 to become 84.9%, 85.1%, and 85.8% in 2021. Moreover, a significant increase in the resistance rate was seen in both imipenem and amikacin, with an average resistance rate rise from 6.6% for imipenem and 11.9% for amikacin in 2011 to 59.9% and 62.2% in 2021, respectively. The present study showed that the prevalence and drug resistance of K. pneumoniae increased over the study period. Thus, preventing hospital-acquired infection and the reasonable use of antibiotics must be implemented to control and reduce antimicrobial resistance.

Virological surveillance, molecular phylogeny, and evolutionary dynamics of hepatitis C virus subtypes 1a and 4a isolates in patients from Saudi Arabia.

Hepatitis C virus (HCV) subtypes are pre-requisite to predict endemicity, epidemiology, clinical pathogenesis, diagnosis, and treatment of chronic hepatitis C infection. HCV genotypes 4 and 1 are the most prevalent in Saudi Arabia, however; less consensus data exist on circulating HCV subtypes in infected individuals. This study was aimed to demonstrate the virological surveillance, phylogenetic analysis, and evolutionary relationship of HCV genotypes 4 and 1 subtypes in the Saudi population with the rest of the world. Fifty-five clinical specimens from different parts of the country were analyzed based on 5' untranslated region (5' UTR) amplification, direct sequencing, and for molecular evolutionary genetic analysis. Pair-wise comparison and multiple sequence alignment were performed to determine the nucleotide conservation, nucleotide variation, and positional mutations within the sequenced isolates. The evolutionary relationship of sequenced HCV isolates with referenced HCV strains from the rest of the world was established by computing pairwise genetic distances and generating phylogenetic trees. Twelve new sequences were submitted to GenBank, NCBI database. The results revealed that HCV subtype 4a is more prevalent preceded by 1a in the Saudi population. Molecular phylogeny predicts the descendants' relationship of subtype 4a isolates very close to Egyptian prototype HCV strains, while 1a isolates were homogeneous and clustering to the European and North American genetic lineages. The implications of this study highlight the importance of HCV subtyping as an indispensable tool to monitor the distribution of viral strains, to determine the risk factors of infection prevalence, and to investigate clinical differences of treatment outcomes among intergenotypic and intragenotypic isolates in the treated population.

Consensus small interfering RNA targeted to stem-loops II and III of IRES structure of 5' UTR effectively inhibits virus replication and translation of HCV sub-genotype 4a isolates from Saudi Arabia.

Being the most conserved region of all hepatitis C virus (HCV) genotypes and sub-genotypes, the 5' untranslated region (5' UTR) of HCV genome signifies it's importance as a potential target for anti-mRNA based treatment strategies like RNA interference. The advent and approval of first small interference RNA (siRNA) -based treatment of hereditary transthyretin-mediated amyloidosis for clinical use has raised the hopes to test this approach against highly susceptible viruses like HCV. We investigated the antiviral potential of consensus siRNAs targeted to stem-loops (SLs) II and III nucleotide motifs of internal ribosome entry site (IRES) structure within 5' UTR of HCV sub-genotype 4a isolates from the Saudi population. siRNA inhibitory effects on viral replication and translation of full-length HCV genome were determined in a competent, persistent, and reproducible Huh-7 cell culture system maintained for one month. Maximal inhibition of RNA transcript levels of HCV-IRES clones and silencing of viral replication and translation of full-length virus genome was demonstrated by siRNAs targeted to SL-III nucleotide motifs of IRES in Huh-7 cells. siRNA Usi-169 decreased 5' UTR RNA transcript levels of HCV-IRES clones up to 75% (P < 0.001) at 24 h post-transfection and 80% (P < 0.001) at 48 h treatment in Huh-7 cells. 5' UTR-tagged GFP protein expression was significantly decreased from 70 to 80% in Huh-7 cells co-transfected with constructed vectors (i.e. pCR3.1/GFP/5' UTR) and siRNA Usi-169 at 24 h and 48 h time-span. Viral replication was inhibited by more than 90% (P < 0.001) and HCV core (C) and hypervariable envelope glycoproteins (E1 and E2) expression was also significantly degraded by intracytoplasmic siRNA Usi-169 activity in persistent Huh-7 cell culture system. The findings unveil that siRNAs targeted to 5' UTR-IRES of HCV sub-genotype 4a Saudi isolates show potent silencing of HCV replication and blocking of viral translation in a persistent in-vitro Huh-7 tissue culture system. Furthermore, we also elucidated that siRNA silencing of viral mRNA not only inhibits viral replication but also blocks viral translation. The results suggest that siRNA potent antiviral activity should be considered as an effective anti-mRNA based treatment strategies for further in-vivo investigations against less studied and harder-to-treat HCV sub-genotype 4a isolates in Saudi Arabia.

Prevalence of Human Parvovirus B19 in Neurological Patients: Findings from Region of Western Saudi Arabia.

Human parvovirus (B19) infection causes Erythema infectiosum in persons with other hematological disorders like aplastic anemia and complications such as hydrops fetalis, spontaneous abortions. This study aimed to determine the prevalence of IgG and IgM antibodies in B19 infected neurological patients and to assess possible transmission related risk factors. This cross-sectional descriptive study comprised 140 neurological patients. Blood samples were screened for both IgG and IgM against B19 by ELISA and nested PCR. IgG and IgM accounted 6.4% and 3.5% prevalence in neurological patients. Both IgG and IgM revealed prevalence of 3.5% simultaneously in different age groups. IgG and IGM Nested PCR displayed 6.42% B19 viral DNA prevalence among samples analyzed. Among B19 risk associated factors, only history of blood transfusion (Odds Ratio=1.9:1, P=0.04) was significantly associated with B19 infection among neurological patients. Neurological patients showed very less prevalence of B19 infection and hence disclose no significant association on risk factors associated with its transmission.

Molecular characterisation in tongue squamous cell carcinoma reveals key variants potentially linked to clinical outcomes.

BACKGROUND: Oral tongue squamous cell carcinoma (OTSCC) is a highly aggressive malignancy characterized by frequent recurrence, poor survival with relatively few therapeutic options due to the late diagnosis in many cases. OBJECTIVES: Understanding the molecular pathways underlying OTSCC tumourigenesis and the discovery of diagnostic and/or prognostic biomarkers. METHODS: We performed high-throughput mutational analysis of 44 OTSCC formalin-fixed paraffin-embedded (FFPE) cases using the Cancer Hotspots Panel (CHP) v2 on the Ion Torrent™platform. We determined the frequency of human papilloma virus (HPV) using PCR and Epstein bar virus (EBV) positivity using immunohistochemistry. As a control for EBV infection we screened matched non-tumourous tissues. RESULTS: Sequencing analysis identified missense, nonsense and frameshift mutations in TP53 (66%), PIK3CA (27%), CDKN2A (25%), EGFR (18%), and PTEN (14%). Interestingly, no significant associations were found between damaging mutations and clinicopathological data. A total of 10/44 of the OTSCC samples (23%) tested was positive for HPV18 DNA. OTSCC patients with positive HPV infection had worse overall survival compared to HPV-negative cases as determined by Kaplan-Meier survival (p= 0.023). Furthermore, EBNA1 expression showed a strong tumour-enriched expression pattern in 20 out of 21 samples (95%) in the epithelial compartments of the tissues analysed. CONCLUSIONS: Taken together, this study highlights that the two most common events in OTSCC are TP53 mutations and EBV positivity. Helping to understand the contribution of TP53 mutations and EBV infection events could serve as useful biomarkers for OTSCC.

A review of phenolic compounds in oil-bearing plants: Distribution, identification and occurrence of phenolic compounds.

Over the last two decades, separation, identification and measurement of the total and individual content of phenolic compounds has been widely investigated. Recently, the presence of a wide range of phenolic compounds in oil-bearing plants has been shown to contribute to their therapeutic properties, including anti-cancer, anti-viral, anti-oxidant, hypoglycemic, hypo-lipidemic, and anti-inflammatory activities. Phenolics in oil-bearing plants are now recognized as important minor food components due to several organoleptic and health properties, and they are used as food or sources of food ingredients. Variations in the content of phenolics in oil-bearing plants have largely been attributed to several factors, including the cultivation, time of harvest and soil types. A number of authors have suggested that the presence phenolics in extracted proteins, carbohydrates and oils may contribute to objectionable off flavors The objective of this study was to review the distribution, identification and occurrence of free and bound phenolic compounds in oil-bearing plants.

Antimicrobial susceptibility of bacterial and fungal infections among infected diabetic patients.

Objective: To determine the antimicrobial susceptibility of the most common bacterial and fungal infections among infected diabetic patients. Methods: This study was conducted at the Umm Al-Qura University, Makkah, Saudi Arabia, from June 2011 to June 2012, and comprised specimens collected from diabetics. Antibiotic susceptibility test using disc diffusion method was performed for bacterial isolates, and antifungal susceptibility test using colorimetric method for candida isolates. Results: Of the 138 specimens, antibacterial susceptibility test was performed for 129(93.5%) bacterial isolates while antifungal resistance test was performed for 9(6.5%) candida isolates. Of the bacterial isolates, 27(20.9%) were escherichia coli, 26(20.1%) staphylococcus aureus and 15(11.6%) were pseudomonas aeruginosa isolates. All Escherichia coli and staphylococcus aureus were susceptible to amikacin and vancomycin (100% each). Moreover, all candida species were susceptible to amphotericin B, econazole, fluconazole, ketoconazole and nystatin (100% each). CONCLUSIONS: The most effective antibiotics for bacterial infections among diabetic patients were vancomycin for gram-positive bacteria, amikacin for gram-negative bacteria and for bacteria isolated from diabetic patients with foot infections.

Seroprevalence of erythrovirus B19 in Saudi pregnant women.

BACKGROUND: Erythrovirus B19 infection is associated with clinical symptoms that range from mild to severe. The common clinical presentation of B19 virus (B19V) infection is erythema infectiosum, arthropathy, aplastic crisis, and fetal infection. Infection in seronegative pregnant women can lead to fetal hydrops. OBJECTIVES: To determine the seroprevalence of immunoglobulin G (IgG) to erythrovirus B19 in Saudi pregnant women in the cities of Makkah and Jeddah in Saudi Arabia. MATERIALS AND METHODS: A total of 364 blood (serum) samples were tested for erythrovirus B19-specific-IgG antibody in Saudi pregnant women in the cities of Makkah and Jeddah in Saudi Arabia. RESULTS: Erythrovirus B19-specific-IgG antibodies were detected in 182/364 (50%) of Saudi pregnant women of different age groups. CONCLUSION: This study indicated that B19V is clearly circulating in the community in a way that is similar to what is found in most nontemperate countries.

Investigation of natural lipid-phenolic interactions on biological properties of virgin olive oil.

There is limited knowledge regarding the impact of naturally occurring lipid-phenolic interactions on the biological properties of phenolics in virgin olive oil. Free and bound phenolics were isolated via sequential methanolic extraction at 30 and 60 °C, and were identified and quantified using reversed phase high performance liquid chromatography, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and gas chromatography. Decreased oleic acid concentrations and increased concentrations of palmitoleic acid, stearic, linoleic, and linolenic acids were observed in virgin olive oil after removal of free and bound lipid phenolic compounds. The presence of p-hydroxybenzoic acid and tyrosol bound to glycerides was determined via LC-MS/MS, which indicates natural lipid-phenolic interactions in virgin olive oil. Both free and lipid bound phenolic extracts exerted antiproliferative activities against the CRC1 and CRC5 colorectal cancer cell lines. The present work indicates that naturally occurring lipid-phenolic interactions can affect the biological properties of phenolics in virgin olive oil.

Demographic distribution and transmission potential of influenza A and 2009 pandemic influenza A H1N1 in pilgrims.

INTRODUCTION: The World Health Organization's persistent reporting of global outbreaks of influenza A viruses, including the 2009 pandemic swine A H1N1 strain (H1N1pdm09), justified the targeted surveillance of pilgrims during their annual congregation that pools more than two million people from around 165 nations in a confined area of Makkah city in the Kingdom of Saudi Arabia (KSA). METHODOLOGY: A total of 1,600 pilgrims were included in the targeted surveillance of influenza A and the 2009 pandemic swine H1N1 strain in the Hajj (pilgrimage) season of 2010. Each pilgrim responded to a demographic and health questionnaire. Collected oropharyngeal swabs were analyzed by real-time PCR for influenza A viruses, and positive samples were further analyzed for the presence of H1N1pdm09. Fisher's exact test was applied in the analysis of the significance of the distribution of influenza-positive pilgrims according to demographic characters. RESULTS: A total of 120 pilgrims (7.5%) tested positive for influenza A viruses by real-time PCR. Nine out of the 120 influenza-A-positive pilgrims (7.5%) were positive for H1N1pdm09. Demographics played a significant role in those pilgrims who tested positive for influenza A. CONCLUSIONS: The detection of H1N1pdm09 in pilgrims at their port of entry to the KSA was alarming, due to the high potential of trans-boundary transmission. This situation necessitates the implementation of specific prevention and control programs to limit infection by influenza A viruses.

Anti hepatitis E virus seropositivity in a group of male blood donors in Makkah, Saudi Arabia.

OBJECTIVES: To determine the seropositivity of Immunoglobulin-G and Immunoglobulin-M to hepatitis E virus in male blood donors in Makkah, Saudi Arabia. METHODS: The study was carried out from March to August 2009, in which 900 blood samples were collected from 4 different hospital blood banks in Makkah City: AL-Noor Hospital, Central Blood Bank, Maternity and Children Hospital, and Herra Hospital. All the samples were tested for Immunoglobulin-G and Immunoglobulin-M antibodies specific to hepatitis E virus using the enzyme-linked immunosorbent assay test. RESULTS: Hepatitis E virus-specific Immunoglobulin-G antibodies were detected in 168/900 (18.7%), and IgM in 39/900 (4.3%) samples. Prevalence of the former was found to be higher in non-Saudi donors. In addition, its prevalence increased with age. Moreover, its prevalence was found to be higher in uneducated donors and in donors who drank well-water. CONCLUSION: Exposure to hepatitis E virus among blood donors in Makkah City was high in comparison to the neighbouring areas in the region. Further studies are warranted to determine the true seroprevalence of the virus in the society at large.

Frequency of viral, bacterial and parasitic enteropathogens among young children with acute diarrhoea in Saudi Arabia.

OBJECTIVE: The frequency of viral, bacterial and parasitic enteropathogens among 270 paediatric patients (< 5 years of age) in various hospitals of Makkah and Jeddah cities of Saudi Arabia were investigated. METHODS: A total of 270 stool samples were collected from paediatric patients with signs and symptoms of gastroenteritis from different hospitals of Makkah and Jeddah cities of Saudi Arabia. Samples were investigated for bacterial, viral and parasitic enteropathogens using microscopic examination, immunological tests and bacterial culture techniques. RESULTS: Out of 270 stool samples tested in this study for various causative agents of gastroenteritis, total number of positive samples were 106 (39%). Of these, 90 (33%) had viral etiology, of which Rotavirus type A (serotype G) was found in the majority of cases 60 (22%), Adenovirus in 20 (7%) patients, and Astrovirus in the remaining 10 (4%) patients. Thirteen (5%) were of bacterial origins of which 9 (3%) were Salmonella species, 4 (2%) were Shigella species and only 3 (1%) of the samples were positive for Giardia lamblia. CONCLUSION: This study indicated that most of the diarrhoeal diseases in young children in Saudi Arabia are due to viral etiology, where Rotavirus was predominant followed by Adenovirus and Astrovirus. While Salmonella and Shigella represent the bacterial etiology of paediatric acute diarrhoea and only Giardia lamblia was found as a parasitic cause of diarrhoea in young children in our study.

Seroprevalence of erythrovirus B19 IgG antibody among paediatric patients in Makkah and Jeddah, Kingdom of Saudi Arabia.

OBJECTIVE: To estimate the prevalence of IgG antibodies against B19 virus (B19V) in Makkah and Jeddah, Saudi Arabia. METHODS: B19V-specific IgG antibodies were detected by a commercial indirect enzyme-linked immunosorbent assay in sera of 400 paediatric patients (185 males and 215 females) aged 1-17 years. RESULTS: Of the 400 patients, 80 (20%) had sera positive for B19V-specific IgG. The difference in the prevalence of the antibodies between genders was not statistically significant (p = 0.9). The prevalence of anti-B19V antibodies increased significantly in the age group of 12-17 years as compared to younger patients (37.5 vs. 18% in those aged 1-11 years; p = 0.006). CONCLUSION: This study indicated a high prevalence of IgG antibodies against B19V in paediatric patients with an increase in age.

SEROPREVALENCE OF ERYTHROVIRUS B19 IgG AMONG SAUDI BLOOD DONORS IN MAKKAH, SAUDI ARABIA.

OBJECTIVES: To determine the seroprevalence of immunoglobulin G (IgG) to erythrovirus B19 in Saudi blood donors in Makkah. Saudi Arabia. SUBJECTS AND METHODS: A total of 578 blood (serum) samples were tested for erythrovirus B19-specific-IgG antibody among Saudi blood donors in Makkah. Saudi Arabia. RESULTS: Erythrovirus B19-specific-IgG antibodies were detected in 441/578 (76.3%) of Saudi blood donors of different age groups. CONCLUSION: This study indicated that 76.3% of Saudi blood donors in Makkah city, Saudi Arabia, had been exposed to erythrovirus B19. This result is in accordance with previous studies performed in other countries.

Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes.

The use of genotyping assays for the detection and evaluation of drug resistance mutations within the polymerase gene of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly relevant in the clinical management of HIV-1 infection. However, genotypic resistance assays available currently have been optimised for genetic subtype B strains of the virus and many clinical centres are presented with strains from subtypes A, C, and D. In the present report, we compare the performance of two sequence-based commercially available kits, the ViroSeq Genotyping System (Applied Biosystems, Foster City, CA) and the TruGene HIV-1 Genotyping Kit (Visible Genetics, Toronto, Ontario) against a panel of 35 virus isolates from HIV-1 Group M (subtypes A-J). Full-length consensus sequences were generated by the ViroSeq genotyping system for 26 of 31 (83.8%) of the isolates tested, in contrast to the TruGene genotyping system, which generated 16 of 30 (53%) usable sequences overall. Overall, subtype B isolates were sequenced with a greater degree of success than non-subtype B isolates. Discrepancies were found between the consensus sequences reported by each system for each sample (mean difference 1.0%; range 0.0-3.2%), but these appeared to be random and did not affect interpretation of the major resistance codons. In addition, both systems were able to amplify template RNA from low copy viral load plasma samples (10(2)-10(3) RNA copies/ml) taken from a random selection of patient samples encompassing subtypes A-C. While the availability of these genotyping systems should facilitate studies of HIV-1 drug resistance in countries in which these subtypes are prevalent, the performance against subtypes other than B needs to be improved.