The Prevalence and Risk Factors of Trichosporonosis at King Abdulaziz University Hospital.

Background: Fungal infections, especially those caused have emerged as a significant medical concern over the past three decades, particularly among immunocompromised patients. However, recent studies have highlighted the increasing prevalence of fungal infections resembling yeast other than Candida, such as trichosporonosis, especially among immunosuppressed individuals worldwide. Trichosporon has been identified as a significant contributor to superficial and invasive infections. Invasive trichosporonosis, primarily affecting immunocompromised patients, poses a significant threat with high mortality rates. Purpose: The current study aimed to explore the clinical epidemiology of Trichosporon spp at King Abdulaziz University Hospital (KAUH) in Saudi Arabia. Methods: This retrospective study aimed to assess the clinical epidemiology of Trichosporon spp. infections in microbiology cultures obtained from KAUH in Saudi Arabia. The study analyzed data from patients over a five-year period, focusing on demographic, clinical, and microbiological characteristics. Results: This study encompassed 21 participants, categorized into four distinct age groups. Moreover, this study indicated T. asahii as the predominant species isolated, accounting for 90.5% of infections, followed by T. mucoides (9.5%). ICU hospitalization, diabetes mellitus, taking immunosuppressive drugs, and antifungal drugs, and the use of invasive medical equipment were identified as prominent risk factors for trichosporonosis. Urinary tract infections were the most common clinical presentation, particularly among male and elderly patients. Mortality rates were high, especially among older individuals. Conclusion: This study contributes valuable epidemiological insights into trichosporonosis, highlighting the need for enhanced surveillance and preventive strategies in healthcare settings. Further research is warranted to optimize treatment approaches and infection control measures, ultimately reducing the burden of Trichosporon infections on patient outcomes.

The microbiological profile of isolates recovered from ICU patients with traumatic brain injuries at a tertiary care center, Southern Region, Saudi Arabia.

INTRODUCTION: Traumatic head injury THI is a Neurosurgical condition in which brain function is interrupted as a result of blunt (motor vehicle accidents MVA, falls, and assaults) or penetrating trauma. Nearly half of all injuries are caused by head trauma. Head traumas are a leading cause of death and organ loss in young people, where this population accounts for the vast majority of TBI patients. METHODOLOGY: This retrospective cohort study was conducted at Asir Central Hospital, KSA with data from 2015 to 2019. Records of bacterial cultures and outcomes such as length of stay in the hospital were analyzed. In addition, treatment outcomes were also analyzed. RESULTS: A total of 300 ICU patient samples (69 patients) were included. Patients' ages ranged from 13 to 87 years with a mean age of 32.4 ± 17.5 years old. The most frequently reported diagnosis was RTA (71 %), followed by SDH (11.6 %), The most isolated organisms from the recovered samples were Klebsiella pneumoniae (27 %), followed by Pseudomonas aeruginosa (14.7 %). Regarding susceptibility, Tigecycline was the most sensitive (44 %), followed by Gentamicin (43.3 %). A total of 36 (52.2 %) patients stayed for less than one month, 24 (34.8 %) stayed for 1-3 months, and 7 (10.1 %) stayed for 3-6 months. The mortality rate in our study population was (40.6 %) as 28 patients died. CONCLUSION: The prevalence of pathogens in TBI needs to be determined in different institutions for the establishment of effective empiric antibiotic treatment following infections in traumatic brain injuries. This will ultimately help to improve treatment outcomes. In neurosurgical patients undergoing cranial procedures after trauma, a hospital-standardized antibiotic policy is effective in achieving low rates of bacterial infections especially MDR infections.

Evaluation of the Antibacterial Activity of Quinoxaline Derivative Compound Against Methicillin-Resistant Staphylococcus aureus.

Background: While the frequency of methicillin-resistant Staphylococcus aureus (MRSA) continues to rise globally, there is a fear regarding an increase in vancomycin resistance among S. aureus strains. As far back as the 1960s, MRSA was one of the world's most prevalent antibiotic-resistant bacteria. Among hospitalized patients and community members, MRSA is the cause of a significant number of infections. As a result of its resistance to classical beta-lactam and, in some cases, vancomycin antibiotics, efforts must be made as soon as feasible to find a new approach to fighting MRSA. Purpose: This study is designed to evaluate the antibacterial activity of quinoxaline derivative compound against MRSA in comparison with vancomycin as a reference drug. Methods: Sixty MRSA isolates were subjected to susceptibility testing by broth microdilution method for quinoxaline derivative compound and vancomycin. Each drug's minimal inhibitory concentration (MIC) was determined and compared. Results: Among the sixty MRSA isolates, most of the quinoxaline derivative compound MIC findings (56.7%) were 4 µg/mL compared to vancomycin MIC values (63.3%) of 4 µg/mL. In comparison, 20% of quinoxaline derivative compound MIC readings were 2 µg/mL, while the vancomycin MIC results were 6.7%. However, the overall proportion of MIC readings at ≤2 µg/mL for both antibacterial agents was equal (23.3%). None of the isolates were resistant to vancomycin. Conclusion: This experiment revealed that most MRSA isolates were associated with low MICs (1-4 µg/mL) for quinoxaline derivative compound. Overall, the susceptibility of the quinoxaline derivative compound signifies a promising efficacy against MRSA and may set a novel treatment approach.

Detection of Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC® CARBA NP and Xpert™Carba-R Assay.

Introduction: Carbapenem-resistant Enterobacteriaceae (CRE) infections resist nearly most available antimicrobials, resulting in poor clinical outcomes. Saudi Arabia has a relatively high CRE prevalence. This study aims to evaluate the sensitivity of Rapidec Carba NP test and GeneXpert Carba-R assay compared with conventional manners for detection of carbapenemase-producing Enterobacteriaceae. Methods: This is a cross-sectional study including a total of 90 CRE isolates examined at two tertiary hospitals in KSA from October 2020 to December 2021. Gram-negative Enterobacteriaceae were identified by using Vitek 2 system and were furtherly tested for imipenem and meropenem susceptibility by E- test strips, followed by Rapidec Carba NP test and the Xpert™Carba-R assay. Results: Carbapenem-resistant K. pneumoniae (78.9%) and carbapenem-resistant E. coli (14.4%) were the two most common isolates species. Colistin (98.9%) and tigecycline (88.9%) were the most effective antibiotics against CRE isolates, followed by amikacin (52.2%), gentamicin (33.3%), cotrimoxazole (15.6%), and ciprofloxacin (8.9%). blaOXA-48 was the predominant carbapenemase gene (44.4%), followed by blaNDM (32.2%). blaKPC gene was not detected. The Rapidec Carba NP and the Xpert™Carba-R demonstrated an overall sensitivity of 69.3% and 88%, respectively, in comparison to gold standard detection of meropenem and imipenem resistance by Vitek 2 system and E- test strips. Discussion: RAPIDEC® CARBA NP may be a beneficial screening test for detecting CRE, but for confirmation of the results, Xpert Carba-R assay is more sensitive, significantly lowering the turnaround time compared to reference traditional methods. The information on carbapenemase genes may be used for epidemiologic purposes and outbreak management.

Prevalence of Carbapenem-Resistant Enterobacteriaceae in Western Saudi Arabia and Increasing Trends in the Antimicrobial Resistance of Enterobacteriaceae.

PURPOSE:  The aim of the study is to estimate the prevalence rate of carbapenem-resistant Enterobacteriaceae (CRE) and to determine the types of carbapenemase genes present in patients admitted to King Abdulaziz Medical City (KAMC-J) and King Abdulaziz University Hospital (KAUH), both in Jeddah, Saudi Arabia. METHODS:  A total of 180 isolates were analyzed which were included on the basis of retrospective chart review of patients from KAMC-J and KAUH between 1st April 2017 to 30th March 2019. The prevalence of carbapenemase genes ( blaIMP, blaVIM, blaKPC, blaNDM-1, and blaOXA-48) was evaluated by Xpert® Carba-R (Cepheid, Sunnyvale, CA, USA). We assessed the CRE prevalence and described their susceptibility to antimicrobial agents based on antibiogram reports.  Results: Klebsiella pneumoniae showed a higher frequency of bla OXA-48 (79%) than bla NDM (11.7%) genes (p=0.007). The CRE prevalence in KAUH was 8% in 2017 and increased to 13% in 2018. In KAMC-J, the prevalence was 57% in 2018 and 61% in 2019. K. pneumoniae was found to be the most frequently isolated causative organism followed by Escherichia coli . The  bla OXA-48 (76.1%) gene was predominant among overall isolates followed by bla NDM (13.9%); both genes coexisted in 6.1% of the isolates. CONCLUSION:  During the study period, the prevalence of CRE considerably rose in the two tertiary care institutions from western Saudi Arabia. In the CRE isolates, bla OXA-48 was discovered to be the most common gene. We recommend an antimicrobial resistance surveillance system to detect the emergence of resistant genes through use of new rapid diagnostic tests and monitor antimicrobial use in order to improve clinical outcomes of CRE infections given the severity of infection associated with the CRE isolates as well as the limited treatment options available.

Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia.

The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, blaADC-25, blaOXA-23, and blaOXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia.

Arabiibacter massiliensis gen. nov. sp. nov., New Anaerobic Bacterium Isolated from the Human Gut.

Using microbial culturomics, we were able to isolate strain Marseille-P3078 from a stool sample of a healthy 50-year-old Saudi Arabian woman. To this end, we used taxonogenomics that combines phenotypic, biochemical and genomic analyses, to describe this bacterium. Cells from strain Marseille-P3078 are anaerobic and Gram-negative rods that are motile and unable to sporulate. Its genome size is 3,377,914-bp-long with a 66.33 mol% G + C content. Based on its phenotypic and genomic features, including a 94.6% 16S rRNA similarity with Paraeggerthella hongkongensis strain JCM 14552, its closest phylogenetic neighbor withstanding in nomenclature, we propose that strain Marseille-P3078T (= CSUR P3078 = DSM 104007) is the representative strain of a new genus for which we propose the name Arabiibacter massiliensis gen. nov., sp. nov.

Small intestinal bacterial overgrowth among patients with celiac disease unresponsive to a gluten free diet.

BACKGROUND/AIMS: Little is known about the relationship between small intestinal bacterial overgrowth (SIBO) and celiac disease (CeD) in patients who are unresponsive to a gluten-free diet (GFD). This study aimed to determine the SIBO prevalence in patients with CeD who are unresponsive to a GFD. MATERIALS AND METHODS: We conducted a case-control study from July 2012 to September 2014. We included 32 patients with CeD who were unresponsive to a GFD and 52 healthy age- and sex-matched controls. Demographic, clinical, and laboratory data were obtained from patients' medical records. Antitissue transglutaminase antibody determined by enzyme-linked immunosorbent assay was recorded, and lactulose hydrogen breath test (LHBT) was used to detect SIBO in all participants. Microbiological analysis, including jejunal aspirates obtained using upper endoscopy, was performed for only 20 patients with CeD. RESULTS: A total of 10 (31%) of 32 patients with CeD and 4 (7.7%) of 52 controls tested positive for LHBT, with a statistically significant difference (p=0.007). Of 20 cultures, 3 (15%) were positive with no statistically significant correlation between the cultures and LHBT (p=0.05). In a subgroup analysis of children who were 18 years old or younger, 7/24 (29.2%) patients with CeD had a positive LHBT compared with 3/32 (9.4%) controls, but this difference was not statistically significant (p=0.08). CONCLUSION: The prevalence of SIBO was 31% in unresponsive patients with CeD according to LHBT and 15% in the quantitative culture of the jejunal aspirate, which is comparable with the published Western literature.

Genomic and antimicrobial resistance genes diversity in multidrug-resistant CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah.

BACKGROUND: Whole genome sequencing has revolutionized epidemiological investigations of multidrug-resistant pathogenic bacteria worldwide. Aim of this study was to perform comprehensive characterization of ESBL-positive isolates of Escherichia coli obtained from clinical samples at the King Abdulaziz University Hospital utilizing whole genome sequencing. METHODS: Isolates were identified by MALDI-TOF mass spectrometry. Genome sequencing was performed using a paired-end strategy on the MiSeq platform. RESULTS: Nineteen isolates were clustered into different clades in a phylogenetic tree based on single nucleotide polymorphisms in core genomes. Seventeen sequence types were identified in the extended-spectrum ß-lactamase (ESBL)-positive isolates, and 11 subtypes were identified based on distinct types of fimH alleles. Forty-one acquired resistance genes were found in the 19 genomes. The blaCTX-M-15 gene, which encodes ESBL, was found in 15 isolates and was the most predominant resistance gene. Other antimicrobial resistance genes (ARGs) found in the isolates were associated with resistance to tetracycline (tetA), aminoglycoside [aph(3″)-Ib, and aph(6)-Id], and sulfonamide (sul1, and sul2). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA were commonly found in several genomes. CONCLUSION: Several other ARGs were found in CTX-M-positive E. coli isolates confer resistance to clinically important antibiotics used to treat infections caused by Gram-negative bacteria.

Publisher Correction: Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Draft genome sequence of a clinical Acinetobacter baumannii isolate of new sequence type ST1688 from Saudi Arabia.

OBJECTIVES: Acinetobacter baumannii has emerged as a prevalent multidrug-resistant nosocomial pathogen worldwide. Here we report the draft genome sequence of A. baumannii strain Ab174 isolated from a neonatal patient diagnosed with acute peritonitis. METHODS: The draft genome sequence of A. baumannii Ab174 was determined using a MiSeq platform (Illumina Inc., San Diego, CA) using v.3, 2×30-bp chemistry. Genomic assembly was performed using SPAdes 3.9 algorithm. RESULTS: The draft genome of A. baumannii Ab174 is 3 747 065bp in length and was classified as a new sequence type (ST1688). The genome of A. baumannii Ab174 has a G+C content of 39% and harbours two plasmids. The antimicrobial resistance gene blaADC-25 and the virulence factor gene for penicillin-binding protein G (pbpG) as well as 17 genomic islands and 14 insertion sequences were identified in the genome of A. baumannii Ab174. CONCLUSION: The genome sequence of A. baumannii strain Ab174 can be used as a reference sequence for the new ST1688. These data will facilitate further understanding of genomic variation in isolates from different geographical regions.

In vitro evaluation of methicillin-resistant and methicillin-sensitive Staphylococcus aureus susceptibility to Saudi honeys.

BACKGROUND: Honey has been increasingly recognized as a potential therapeutic agent for treatment of wound infections. There is an urgent need for assessment and evaluation of the antibacterial properties against wound pathogens of honeys that have not yet been tested. METHODS: Ten Saudi honeys collected from different geographical locations were screened initially for their antibacterial potential against methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) by the agar well diffusion method. Manuka honey (UMF-12) was used for comparison. Of the tested honeys, the honey that exhibited the greatest antibacterial activity in the agar well diffusion assay was further evaluated for its minimum inhibitory concentration (MIC) against ten MRSA clinical isolates and three American Type Culture Collection (ATCC) reference strains by the microbroth dilution method. RESULTS: Locally produced honeys exhibited variable antibacterial activity against the tested isolates in the agar well diffusion assay. They were unable to exhibit antibacterial activity against MSSA and MRSA at 25% dilutions (w/v) in catalase solution. However, Sumra and Talha honeys showed a zone of inhibition at 50% dilutions (w/v) in catalase solution. This finding means that both honeys possess weak non-peroxide-based antibacterial activity. Moreover, Sumra honey showed a larger inhibition zone at 50 and 25% dilutions (w/v) in distilled water than Manuka honey against both MSSA and MRSA. This result demonstrates that Sumra honey has more hydrogen peroxide-related antibacterial activity or total antibacterial activity than Manuka honey. In addition, MIC results obtained through a microbroth dilution assay showed that Sumra honey inhibited the growth of all MRSA clinical isolates (n = 10) and reference strains [MRSA (ATCC 43300) and MSSA (ATCC 29213)] at lower concentrations (12.0% v/v) than those required for Manuka honey-mediated inhibition (14.0% v/v). This result means that Sumra honey has more peroxide or synergistic antibacterial activity than Manuka honey. An equivalent MIC (15.0% v/v) was observed for E. coli (ATCC 25922) between Manuka honey and Sumra honey. CONCLUSIONS: Sumra honey may be used as an alternative therapeutic agent for infected wounds and burns, where additional hydrogen peroxide-related antibacterial activity is needed. In the future, the physiochemical characteristics of Sumra honey may be evaluated and standardized.

Antimicrobial Susceptibility and Molecular Characterization of Clinical Strains of Acinetobacter baumannii in Western Saudi Arabia.

Acinetobacter baumannii has emerged as a problematic multidrug-resistant (MDR) pathogen worldwide. The aim of this study was to characterize clinical isolates of A. baumannii from Jeddah, a coastal city in the western region of Saudi Arabia that has an ∼50% expatriate population. In this study, 135 nonrepetitive clinical isolates of A. baumannii were identified through MALDI-TOF and susceptibility was determined with VITEK-2 systems and broth microdilution method. Genotypic characterization of the isolates was performed by using M13 primer typing and polymerase chain reaction screening was performed for carbapenemase genes, insertion sequences, metallo-ß-lactamases, and cephalosporinase genes. The isolates were recovered from heterogeneous clinical specimens, and the majority of the cases of A. baumannii infection were acquired in the hospital and predominantly involved patients who were older than 50 years. Total, 58.5% of the isolates were MDR, and 55.6% isolates were resistant to carbapenem antibiotics. Approximately half of the isolates were resistant to ceftazidime, and cefepime among the ß-lactam antibiotics and ciprofloxacin from the quinolone group. The blaOXA-23-like gene and ISAba1 upstream of blaOXA-23-like were detected in 92% of the carbapenem-resistant isolates, while all carbapenem-resistant isolates were found to carry blaOXA-51-like, and blaADC-type cephalosporinase gene. The blaIMP gene was detected in 84% isolates, and two isolates carried the blaNDM-1 gene. Data demonstrate the coexistence of multiple carbapenem resistance determinants in A. baumannii from the western region of Saudi Arabia.

Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia.

Background: Enterococcus faecalis is a ubiquitous member of the gut microbiota and has emerged as a life- threatening multidrug-resistant (MDR) nosocomial pathogen. The aim of this study was to survey the prevalence of multidrug-resistant and epidemiologically important strains of E. faecalis in the western region of Saudi Arabia using phenotypic and whole genome sequencing approaches. Methods: In total, 155 patients positive for E. faecalis infection were included in this study. The isolates were identified by MALDI-TOF, and screen for antimicrobial resistance using VITEK-2 system. Genome sequencing was performed with paired-end strategy using MiSeq platform. Results: Seventeen sequence types (STs) were identified through multilocus sequence typing (MLST) analysis of the E. faecalis genomes, including two novels STs (ST862 and ST863). The most common STs in the Saudi patients were ST179 and ST16 from clonal complex 16 (CC16). Around 96% (n = 149) isolates were MDR. The antibiotics quinupristin/dalfopristin, clindamycin, and erythromycin demonstrated almost no coverage, and high-level streptomycin, gentamycin, and ciprofloxacin demonstrated suboptimal coverage. Low resistance was observed against vancomycin, linezolid, and ampicillin. Moreover, 34 antimicrobial resistance genes and variants, and three families of insertion sequences were found in the E. faecalis genomes, which likely contributed to the observed antimicrobial resistance. Twenty-two virulence factors, which were mainly associated with biofilm formation, endocarditis, cell adherence, and colonization, were detected in the isolates. Conclusions: Diverse STs of E. faecalis, including strains associated with common nosocomial infections are circulating in the healthcare facility of Saudi Arabia and carried multi-drug resistance, which has important implications for infection control.

Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East.

Tuberculosis (TB) represents a significant challenge to public health authorities, especially with the emergence of drug-resistant (DR) and multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis. We sought to examine the genomic variations among recently isolated strains of M. tuberculosis in two closely related countries with different population demography in the Middle East. Clinical isolates of M. tuberculosis from both Egypt and Saudi Arabia were subjected to phenotypic and genotypic analysis on gene and genome-wide levels. Isolates with MDR phenotypes were highly prevalent in Egypt (up to 35%) despite its relatively stable population structure (sympatric pattern). MDR-TB isolates were not identified in the isolates from Saudi Arabia despite its active guest worker program (allopatric pattern). However, tuberculosis isolates from Saudi Arabia, where lineage 4 was more prevalent (>65%), showed more diversity than isolates from Egypt, where lineage 3 was the most prevalent (>75%). Phylogenetic and molecular dating analyses indicated that lineages from Egypt were recently diverged (~78 years), whereas those from Saudi Arabia were diverged by over 200 years. Interestingly, DR isolates did not appear to cluster together or spread more widely than drug-sensitive isolates, suggesting poor treatment as the main cause for emergence of drug resistance rather than more virulence or more capacity to persist.

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut.

As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.

Impact of mass migrations on the clonal variation of clinical Staphylococcus aureus strains isolated from the Western region of Saudi Arabia.

OBJECTIVES: A rapid molecular typing system was used to determine the impact of mass migration on the clonal variation of Staphylococcus aureus isolates recovered from King Abdulaziz University Hospital (KAUH) Jeddah, in the western region of Saudi Arabia. This region experiences an annual influx of millions of pilgrims. METHODS: SmaI-multiplex PCR typing (SMT) was used for the initial analysis of strains and the resulting data subsequently supported by Multi-Locus Sequence Typing (MLST). RESULTS: A total of 89 S. aureus isolates were SMT typed and revealed a high degree of genetic variation, with 40 SMT profiles detected among the isolates. Representatives of all forty SMT types were subsequently analysed by MLST, identifying 26 sequence types. A novel sequence type (ST), named ST3303, was identified in two methicillin-sensitive S. aureus (MSSA) isolates. MSSA strains exhibited more diversity than methicillin-resistant S. aureus (MRSA) strains, with community acquired MSSA and MRSA strains reaching alarmingly high levels. CONCLUSION: The relatively high degree of genetic diversity found among S. aureus isolates of single hospital was attributed to the fact that Jeddah is the principal gateway to Mecca, visited each year by millions of pilgrims from many countries. The observed diversity clearly reflects the impact of such mass migrations in the rapid dissemination of strains world-wide. Our findings suggest the importance of surveillance programmes in locations affected by mass migrations, both to monitor their impact on endemic strains and for the detection of pandemic strains. SMT provides a cost-effective and sensitive typing method for achieving this objective.

Molecular characterization, antimicrobial resistance and clinico-bioinformatics approaches to address the problem of extended-spectrum ß-lactamase-producing Escherichia coli in western Saudi Arabia.

The goal of this study was to genotypically characterize extended-spectrum ß-lactamase-producing Escherichia coli isolates from the western region of Saudi Arabia and to identify active antibiotics against these isolates using phenotypic and molecular modeling. In total, 211 ESBL-producing E. coli isolates recovered from heterogeneous clinical specimens were identified by MALDI-TOF. Thirty-two sequence types (STs) were identified from a multilocus sequence typing (MLST) analysis of ESBL-producing E. coli, including a novel ST (ST8162). The most common ST in the Saudi and expatriate population was ST131, followed by ST38. All the isolates were multidrug resistant (MDR), and >95% of the isolates were resistant to third-generation (ceftriaxone and ceftazidime) and fourth-generation (cefepime) cephalosporins. The ESBL-positive E. coli isolates primarily harbored the blaCTX-M and blaTEM genes. No resistance was observed against the carbapenem antibiotic group. All the ESBL-producing E. coli isolates were observed to be susceptible to a ceftazidime/avibactam combination. Molecular interaction analyses of the docked complexes revealed the amino acid residues crucial for the binding of antibiotics and inhibitors to the modeled CTX-M-15 enzyme. Importantly, avibactam displayed the most robust interaction with CTX-M-15 among the tested inhibitors in the docked state (∆G = -6.6 kcal/mol). The binding free energy values for clavulanate, tazobactam and sulbactam were determined to be -5.7, -5.9 and -5.2 kcal/mol, respectively. Overall, the study concludes that 'ceftazidime along with avibactam' should be carefully used as a treatment option against only carbapenem-resistant MDR ESBL-producing E. coli in this region.

Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH).

BACKGROUND: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. METHODS: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. RESULTS: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages. CONCLUSIONS: We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.