Sahar Althawadi’s research while affiliated with King Faisal Specialist Hospital and Research Centre and other places

Background Twenty percent of lung donors in our transplant program carry respiratory carbapenem‐resistant (CR) gram‐negative bacteria (GNB), most commonly CR Acinetobacter baumannii . Universal multiplex panel testing of lung transplant donors was introduced in June 2022 as a strategy to expedite CR‐GNB detection and optimize perioperative antibiotic prophylaxis. We herein describe our experiences with this approach. Methods Retrospective single‐center cohort study including 53 adult patients who underwent lung‐only transplantation between June 2022 and December 2023. Results The most common bacteria identified by the multiplex panel were Staphylococcus aureus ( n = 20), A. baumannii ( n = 13), Klebsiella pneumoniae ( n = 13), and Pseudomonas aeruginosa ( n = 10). The panel detected 6/9 A. baumannii , 2/2 CR K. pneumoniae , 1/1 CR P. aeruginosa , and 7/8 methicillin‐resistant S. aureus that were grown on conventional cultures, corresponding to negative predictive values of 94%, 100%, 100%, and 98%. Based on panel or culture results, IV tigecycline was administered as prophylaxis in 19% of patients, colistin in 17%, and novel beta‐lactams in 15%. Conclusion The multiplex panel rapidly detected donor CR‐GNB with a high negative predictive value and resulted in clinical effects of reducing broad‐spectrum antibiotic prescriptions and maintaining adequate posttransplant outcomes. Prospective studies with predefined outcomes are needed to compare panel‐directed therapy against current standards of care. image

Objective In this study, we aim to estimate the risk of developing clinical multidrug-resistant organism (MDRO) infection with carbapenem-resistant Enterobacterales (CRE), methicillin-resistant Staphylococcus aureus (MRSA), or vancomycin-resistant enterococci (VRE) in colonized patients compared with non-colonized admitted to high-risk areas with a main focus on CRE colonization/infection. Design and setting Retrospective cohort study conducted at a tertiary care facility. Methods This study included patients enrolled in active surveillance testing (AST) for CRE, MRSA, or VRE during the year 2021. Development of relevant invasive infection within 365 days of the AST result was collected as the primary outcome. The association between MDRO colonization and infection was calculated using the risk ratio. The prevalence of CRE organisms and carbapenemase genes is presented. Results A total of 19,134 ASTs were included in the analysis (4,919 CRE AST, 8,303 MRSA AST, and 5,912 VRE AST). Patient demographics were similar between colonized and non-colonized groups. Colonization was associated with an increased risk of infection in the 3 cohorts (CRE, MRSA, and VRE), with risk ratios reported as 4.6, 8.2, and 22, respectively. Most patients (88%) develop CRE infection with the same colonizing carbapenemase gene. Oxa-48/NDM Klebsiella pneumoniae was the most common organism detected in CRE infection. Conclusions The study demonstrated that colonization with CRE, MRSA, or VRE is a risk factor for developing infections caused by the respective bacteria. The high percentage of match between carbapenemase genes detected in colonization and infection indicates that screening results might be used to inform infection management and treatment.

Stenotrophomonas maltophilia is a nonfermenting gram-negative bacterium associated with multiple nosocomial outbreaks. Antibiotic resistance increases healthcare costs, disease severity, and mortality. Multidrug-resistant infections (such as S. maltophilia infection) are difficult to treat with conventional antimicrobials. This study aimed to investigate the isolation rates, and resistance trends of S. maltophilia infections over the past 19 years, and provide future projections until 2030. In total, 4466 patients with S. maltophilia infection were identified. The adult and main surgical intensive care unit (ICU) had the highest numbers of patients (32.2%), followed by the cardiology department (29.8%), and the paediatric ICU (10%). The prevalence of S. maltophilia isolation increased from 7% [95% confidence interval (CI) 6.3–7.7%] in 2004–2007 to 15% [95% CI 10.7–19.9%] in 2020–2022. Most S. maltophilia isolates were resistant to ceftazidime (72.5%), levofloxacin (56%), and trimethoprim-sulfamethoxazole (14.05%), according to our study. A consistent and significant difference was found between S. maltophilia-positive ICU patients and non-ICU patients (P = 0.0017) during the three-year pandemic of COVID-19 (2019–2021). The prevalence of S. maltophilia isolates is expected to reach 15.08% [95% CI 12.58–17.59%] by 2030. Swift global action is needed to address this growing issue; healthcare authorities must set priorities and monitor infection escalations and treatment shortages.

Purpose This study aims to describe the prevalence and the fluctuations of respiratory viral infections among the pediatric population in a tertiary care center during 2019–2023, parallel with the COVID-19 pandemic, and the specific preventative measures applied in the region during this time. Methods In this observational study, we extracted all respiratory virus PCR tests collected from pediatric patients (< 15 years old) between January 2019 and March 2023. Data on the positivity rate and prevalence of 18 respiratory viruses were presented over the study period. Results The lowest rate for the studied respiratory viruses was observed in 2020/2021 (during the COVID-19 pandemic), followed by a gradual increase in positive cases in the 2021/2022 season. Timing (seasonality) was altered during 2022/2023 with an early circulation of respiratory viruses in May-June followed by an early start of the usual respiratory viruses’ season in September, leading to prolonged respiratory virus activity. Most respiratory viruses were circulating at unprecedented levels during the 2022/2023 season, with rhinovirus/enterovirus being the most commonly detected virus in all seasons. Other viruses that had atypical activity after the COVID-19 pandemic were influenza A(H3) virus, adenovirus, and parainfluenza 3 virus. Conclusion Our study demonstrates the extended influence of the COVID-19 pandemic and its associated community restriction measures on the timing and distribution of other respiratory viruses. Continuous monitoring of changes in the circulation of respiratory viruses is crucial for the success of related public health measures such as vaccination distributions and epidemic preparedness.

Human parechovirus, a member of the Picornaviridae family (PeVs), can lead to severe infections, including severe meningitis, meningoencephalitis, and sepsis-like syndrome. We report a case of human parechovirus-related encephalitis in a 52-year-old woman diagnosed with glioblastoma multiforme. She underwent surgical resection in June 2022. Unfortunately, her disease recurred, and she underwent a second resection in August 2022, followed by radiation therapy and Temozolomide therapy. She presented to the hospital with acute confusion followed by seizures, necessitating intubation for airway support. A cerebrospinal fluid (CSF) sample was obtained and processed using the Biofire FilmArray, which reported the detection of HSV-1. Despite being on Acyclovir, the patient did not show signs of improvement. Consequently, a second CSF sample was obtained and sent for next-generation sequencing (NGS), which returned a positive result for Parechovirus. In this presented case, the patient exhibited symptoms of an unknown infectious cause. The utilization of NGS and metagenomic analysis helped identify Parechovirus as the primary pathogen present, in addition to previously identified HSV. This comprehensive approach facilitated a thorough assessment of the underlying infection and guided targeted treatment. In conclusion, the application of NGS techniques and metagenomic analysis proved instrumental in identifying the root cause of the infection.

According to the World Health Organization (WHO), the JN.1 variant currently has the highest global prevalence among SARS-CoV-2 variants. However, based on available evidence, the overall public health risk associated with JN.1 is still considered low. In our hospital surveillance system, we have been closely monitoring SARS-CoV-2 mutations. In this study, we report on the characteristics and clinical manifestations of patients during the surge of the JN.1 variant, with a special focus on organ transplant patients as a high-risk group. We conducted whole genome sequencing on 151 nasopharyngeal samples from PCR-confirmed SARS-CoV-2-infected patients collected between September 2023 and January 2024. Our findings revealed that during the surge of the JN.1 variant, the average age of patients was 40 years, with an equal infection rate among males and females (50% each). Our investigation showed that the JN.1 variant predominantly infected patients with comorbidities or organ transplant recipients (57.6%). Additionally, patients with comorbidities or organ transplants exhibited a higher number of mutations. Among our organ transplant cohort, we observed that an increased total number of spike mutations was associated with a lower risk of developing severe disease (OR = 0.96, 95% CI: 0.93–0.98). In conclusion, although the JN.1 variant may not prove to be deadly, it is crucial to acknowledge the ongoing emergence of concerning variants, which provide new pathways for the virus to evolve. Therefore, active surveillance of the evolving SARS-CoV-2 virus is essential to effectively respond to variants of concern.

The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies.

During the analysis of a collection of Pseudomonas strains linked to an outbreak in an intensive care unit at King Faisal Specialist Hospital and Research Center in 2019, one isolate (CFS3442 T ) was identified phenotypically as Pseudomonas aeruginosa . However, whole-genome sequencing revealed its true identity as a member of the genus Stenotrophomonas , distinct from both P. aeruginosa and Stenotrophomonas maltophilia . The isolate demonstrated: (i) a significant phylogenetic distance from P. aeruginosa ; (ii) considerable genomic differences from several S. maltophilia reference strains and other Stenotrophomonas species; and (iii) unique phenotypic characteristics. Based on the combined geno- and phenotypic data, we propose that this isolate represents a novel species within the genus Stenotrophomonas , for which the name Stenotrophomonas riyadhensis sp. nov. is proposed. The type strain is CFS3442 T (=NCTC 14921 T =LMG 33162 T ).