Decline in ESBL Production and Carbapenem Resistance in Urinary Tract Infections among Key Bacterial Species during the COVID-19 Pandemic.

The COVID-19 pandemic has led to significant changes in healthcare practices, including increased antibiotic usage. This study aimed to investigate the impact of the pandemic on the prevalence of extended-spectrum ß-lactamase (ESBL) production and carbapenem resistance among key bacterial species causing urinary tract infections (UTIs). Conducted at King Fahad Medical City in Riyadh from January 2018 to December 2022, the study analyzed urine samples from 9697 UTI patients. Patients were categorized into 'pre-COVID-19' and 'during COVID-19' groups. Bacterial isolates were identified, and antimicrobial susceptibility testing was performed following guidelines. ESBL production was detected using the Double-Disc Synergy Test. Escherichia coli and Klebsiella pneumoniae were the main pathogens. During the pandemic, ESBL production decreased in E. coli by 1.9% and in K. pneumoniae by 6.0%. Carbapenem resistance also declined, with E. coli displaying a 1.2% reduction and K. pneumoniae and Pseudomonas aeruginosa displaying 10.7% and 7.9% reductions, respectively. Notably, logistic regression analysis revealed that the odds of ESBL presence were 10% lower during the COVID-19 pandemic (OR 0.91; 95% CI 0.83-0.99; p = 0.040), and there was a significant reduction in the odds of carbapenem resistance (OR 0.43; 95% CI 0.37-0.51; p < 0.001). This study reveals a significant decrease in ESBL production and carbapenem resistance among UTI pathogens during the COVID-19 pandemic, hinting at the impact of modified antibiotic and healthcare approaches. It emphasizes the need for persistent antimicrobial resistance surveillance and policy adaptation to address resistance challenges, offering key directions for future public health actions.

Multidrug-Resistant Proteus mirabilis Infections and Clinical Outcome at Tertiary Hospital in Riyadh, Saudi Arabia.

Background: Proteus mirabilis (P. mirabilis) is known to cause various infections, most commonly urinary tract infections, and is a threat to hospitalized patients, especially in long-stay departments that utilize invasive devices. This study aims to fill the knowledge gap regarding P. mirabilis epidemiology and antimicrobial resistance in Saudi Arabia. It investigates epidemiological patterns, resistance characteristics, and clinical outcomes among P. mirabilis patients at King Fahad Medical City in Riyadh from 2019 to 2021. Methods: A total of 598 P. mirabilis isolated from diverse clinical specimens, including the clinical information of 78 intensive care unit (ICU) patients, were included in the current study. The Phoenix BD instrument was used for complete identification and sensitivity testing of Proteus spp. Demographic, clinical, and outcome data were reported and compared using statistical analysis. Results: Pan-drug-resistant isolates were identified in 2019 (n = 6), although multi- and extensively drug-resistant isolate frequencies were greatest among all patients in 2019. The highest susceptibility levels were observed for piperacillin-tazobactam, carbapenems, and cephalosporins antibiotics. In contrast, Cephalothin, trimethoprim-sulfamethoxazole, and ampicillin had the lowest susceptibilities. Urine infections with a positive culture of P. mirabilis were significantly higher in females and non-ICU patients (p <0.001), but respiratory infections were significantly higher in ICU patients (p <0.001). Moreover, ICU patients infected with P. mirabilis and undergoing renal dialysis have a 7.2-fold (P 0.034) higher risk of death than those not receiving dialysis. Conclusion: Hospitalized patients are at risk of fatal consequences due to P. mirabilis infection. It is crucial to conduct further investigation to fully understand the severity of this issue and take necessary measures to prevent it.

The transmutation of Escherichia coli ATCC 25922 to small colony variants (SCVs) E. coli strain as a result of exposure to gentamicin.

BACKGROUND: Small colony variants (SCVs) are biotypes of bacteria that have a size of approximately one-tenth or less of the wild types and has distinct characteristics comparing to the wild type strains. Clinical SCVs are usually associated with persistent infection and require a long-term treatment program with antibiotics. In Saudi Arabia, there are few studies about SCVs Escherichia coli for this reason, this study is aimed to investigate the ability of gentamicin to mutate E. coli ATCC 25922 to produce small SCVs and investigate the genotypes and phenotypes changes and stress tolerance comparing to clinical SCVs E. coli and normal clinical E. coli Isolated from blood samples. METHODS: In this investigation, four clinical blood samples were collected ted from patients and the cultivation and isolation were carried out in KFMC between December 2019 and February 2021. The identification of positive blood culture samples was done using phoenix MD. Non-SCV E. coli ATCC25922 were mutated to SCV using exposure to increasing gradual concentrations of gentamicin at 100-generation intervals. Biochemical features and susceptibility to standard antibiotics using automated Phoenix MD 50 and. The survival assays were done using several stresses including heat shock, low pH, high osmotic pressure, and oxidative pressure. Virulence genes screening included the detection of genes that encoded to α-haemolysin, CS12 fimbriae, F17-like fimbrial adhesion, P-related fimbriae, yersiniabactin siderophore system, P-fimbriae, aerobactin, iron-regulated genes using PCR and gel electrophoresis. RESULTS: The data from the mutating E. coli ATCC 25922 small colony test with gentamicin revealed that the first emergence of the multidrug resistance (MDR) SCV E. coli strain occurred at generation number 250, corresponding to a gentamicin concentration of 57 g/ml. Pathogenicity islands detection revealed that all tested E. coli strains have PAI IV 536 genes on their chromosomes furthermore, mutated SCV E. coli ATCC 25922 acquired PAII CFT073 and PAI IV 536. Survival tests showed no significant differences changes in tolerance of mutated SCVs comparing to parental strain. CONCLUSION: The present work concluded that gentamicin sub-MIC concentration gradual exposure can induce mutation responsible for SCV formation and evolving of MDR E. coli strains. The mutated SCVs evolved high-level aminoglycoside resistance for gentamicin and resistance to amikacin, it also developed resistance to 2 cephalosporin antibiotics cefuroxime, and cephalothin and a resistance to aztreonam.

Bacterial Pathogens and Antimicrobial Susceptibility Patterns of Urinary Tract Infections in Children during COVID-19 2019-2020: A Large Tertiary Care Center in Saudi Arabia.

BACKGROUND: One of the most prevalent bacterial infections in children is urinary tract infection (UTI), which has become a major concern with increasing resistance of the pathogens to the routinely used antimicrobial agents. The aim of the study is to determine the antimicrobial susceptibility patterns of pediatric UTI-causing pathogens, including ESBL-producing bacteria, in Saudi Arabia. METHODS: This cross-sectional retrospective study was conducted to ascertain the frequency of isolation and the antimicrobial resistance pattern of uropathogens among children aged 0-15 years. The data from the urine cultures was collected during 2019-2020 at the King Fahad Medical City, a major tertiary hospital in Riyadh, Saudi Arabia. A total of 1022 urine samples from patients diagnosed with urinary tract infections (UTIs) were collected for this study. Microbial species present in the samples were cultured and identified using standard biochemical techniques. To assess the resistance of these strains to antimicrobial drugs, an in vitro method was employed, and the criteria set by the Clinical Laboratory Standard Institute (CLSI) were followed. In addition, a double-disc synergy test was conducted to identify strains of E. coli that produce extended-spectrum beta-lactamase (ESBL). RESULTS: The predominant pathogens were E. coli (58.6%), followed by Klebsiella sp. (23.9%). E. coli isolates were more sensitive to meropenem and ertapenem in 99.2% of cases, followed by amikacin (99%). Klebsiella sp. were sensitive to amikacin in 97.1% of cases, followed by meropenem and ertapenem (92.2% in both). The highest sensitivities of antimicrobials toward ESBL were for meropenem and ertapenem (100% in both), followed by amikacin (99%). CONCLUSIONS: Our study recommends using local antibiotic sensitivity data for empirical UTI treatment. Amikacin, ertapenem, and meropenem are effective intravenous options. Cephalosporin, cefuroxime, amoxicillin/clavulanic acid, and nitrofurantoin are suitable oral choices. No significant changes in antimicrobial susceptibility were observed during the COVID-19 pandemic. Further research is needed to assess potential pandemic-related alterations.

Genomic Characterization of Colistin-Resistant Isolates from the King Fahad Medical City, Kingdom of Saudi Arabia.

BACKGROUND: Whole-genome sequencing is one of the best ways to investigate resistance mechanisms of clinical isolates as well as to detect and identify circulating multi-drug-resistant (MDR) clones or sub-clones in a given hospital setting. METHODS: Here, we sequenced 37 isolates of Acinetobacter baumannii, 10 Klebsiella pneumoniae, and 5 Pseudomonas aeruginosa collected from the biobank of the hospital setting of the King Fahad Medical City. Complete phenotypic analyses were performed, including MALDI-TOF identification and antibiotic susceptibility testing. After the genome assembly of raw data, exhaustive genomic analysis was conducted including full resistome determination, genomic SNP (gSNP) analysis, and comparative genomics. RESULTS: Almost all isolates were highly resistant to all tested antibiotics, including carbapenems and colistin. Resistome analysis revealed many antibiotic resistance genes, including those with resistance to ß-lactams, aminoglycosides, macrolides, tetracyclines, sulfamids, quinolones, and phenicols. In A. baumannii isolates, the endemic carbapenemase blaOXA-23 gene was detected in 36 of the 37 isolates. Non-synonymous mutations in pmrB were detected in almost all of the isolates and likely mediated colistin resistance. Interestingly, while classical analyses, such as MLST, revealed the predominance of an ST2 clone in A. baumannii isolates, the genomic analysis revealed the presence of five circulating sub-clones and identified several isolate transmissions between patients. In the 10 K. pneumoniae isolates, several resistance genes were identified, and the observed carbapenem resistance was likely mediated by overexpression of the detected extended-spectrum-ß-lactamase (ESBL) genes associated with low membrane permeability as few carbapenemase genes were detected with just blaOXA-48 in three isolates. Colistin resistance was mediated either by non-synonymous mutations in the MgrB regulator, PmrA, PmrB, and PhoQ proteins or the presence of the MCR-1 protein. Here, gSNP analysis also revealed the existence of bacterial clones and cases of isolate transmissions between patients. The five analyzed P. aeruginosa isolates were highly resistant to all tested antibiotics, including carbapenems mediated by loss or truncated OprD porin, and colistin resistance was associated with mutations in the genes encoding the PmrA, PmrB, or PhoQ proteins. CONCLUSION: We demonstrate here the usefulness of whole-genome sequencing to exhaustively investigate the dissemination of MDR isolates at the sub-clone level. Thus, we suggest implementing such an approach to monitor the emergence and spread of new clones or sub-clones, which classical molecular analyses cannot detect. Moreover, we recommend increasing the surveillance of the endemic and problematic colistin resistance mcr-1 gene to avoid extensive dissemination.

A synergic action of colistin, imipenem, and silver nanoparticles against pandrug-resistant Acinetobacter baumannii isolated from patients.

BACKGROUND: The upgrowth and rapid prevalence of pandrug-resistant Acinetobacter baumannii strains that have a pathogenic activity to cause several infections are of considerable influence on the health of communities worldwide. No infections by these bacterial strains were recorded before 1998, and currently, the numbers are on the rise. METHODS: The A. baumannii strains were isolated from male and female patients in Medical Microbiology Department, King Fahd Medical City (KFMC) in Riyadh, Saudi Arabia between 1/1/2020 to 29/12/2020. The statistical analysis was performed base on sex, age, source of samples, and response to commercially available antibiotics. The A. baumannii strains that resisted all the antibiotics including colistin and imipenem were selected for the synergic test. RESULTS: The data showed that 62.28%, 77.07% of 342 A. baumannii strains were isolated from males and patients over 35 years of age. A. baumannii strains (pandrug-A. baumannii) that can resist all tested antibiotics were 8.19%. The major source of the A. baumannii isolates was the respiratory system (>50%). Among all isolates (N = 342), azidothymidine-resistant A. baumannii strains were more than 85%. There is a statistically significant difference (P < 0.05) in the number of colistin-resistant A. baumannii strains isolated from males comparing with the female. The combinations of colistin and silver nanoparticles or imipenem and silver nanoparticles resulted in synergistic action led to reduction of MICs of colistin, imipenem, and silver nanoparticles (more than four-fold reduction). Also, the combinations of colistin and imipenem had high synergistic action. CONCLUSION: The pandrug-resistant A. baumannii strains may represent a current and future threat that must be fought, and the synergy action of antibiotics and nanoparticles may be one of the available, rapid, and easy strategies to confront this global problem.