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Fulltext Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait

Altawalah H, Alfouzan W, Al-Fadalah T, Zalzala MA, Ezzikouri S

Heliyon, 2024 Apr 30;10(8):e29855.
PMID: 38681623 DOI: 10.1016/j.heliyon.2024.e29855

BACKGROUND: The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic.
METHODS: We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen.
RESULTS: Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years).
CONCLUSION: Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.
Fulltext Antimicrobial resistance pattern in clinical Escherichia coli and Pseudomonas aeruginosa isolates obtained from a secondary-care hospital prior to and during the COVID-19 pandemic in Kuwait

Alali WQ, Abdo NM, AlFouzan W, Dhar R

Germs, 2022 Sep;12(3):372-383.
PMID: 37680673 DOI: 10.18683/germs.2022.1341

INTRODUCTION: The study objective was to compare the prevalence of antimicrobial resistance (AMR) in clinical Escherichia coli and Pseudomonas aeruginosa isolates obtained from a secondary-care hospital prior to and during the COVID-19 pandemic in Kuwait.
METHODS: A retrospective descriptive study was conducted based on AMR profiles of clinical Escherichia coli and Pseudomonas aeruginosa isolates. The AMR data represented isolates from five specimen types (body fluids; blood; respiratory; wound, bone, or other tissues; and urine) of patients admitted to four wards (surgical, medical, pediatric, and maternal-postnatal). Tested isolates between January 2019 and February 2020 represented the pre-COVID-19 pandemic period in Kuwait, whereas those from February 2020 until April 2021 represented the 'during COVID-19' period.
RESULTS: A total of 1,303 isolates (57.2% E. coli and 42.8% P. aeruginosa) were analyzed. For ceftazidime, ertapenem and meropenem, the prevalence of AMR in E. coli was significantly (p<0.05) lower in pre-COVID-19 wards compared to that during COVID-19, whereas for other antibiotics (i.e., cefepime, gentamicin, and trimethoprim/sulfamethoxazole), the prevalence of AMR in pre-COVID-19 was significantly higher than that during COVID-19. The prevalence of AMR to gentamicin in P. aeruginosa isolates from non-COVID-19 wards (52.8%) was significantly higher (p<0.001) than that from COVID-19 wards (35.0%) and from the pre-COVID-19 period (32.9%). The multidrug-resistance (MDR) prevalence was 37.4% for E. coli and 32.1% for P. aeruginosa isolates. The odds of MDR in E. coli isolates from the COVID-19 medical wards were significantly lower (OR=0.27, [95%CI: 0.09-0.80], p=0.018) compared to the pre-COVID-19 wards. The odds of MDR E. coli and P. aeruginosa isolates by COVID-19 status stratified by specimen type were not different (p>0.05).
CONCLUSIONS: No major differences in AMR in E. coli and P. aeruginosa prevalence by specimen type and wards prior to and during the COVID-19 pandemic was observed at this hospital. The high reported MDR prevalence calls for better infection control and prevention.
Genomic characterization and identification of multiple drug resistance genes in clinical isolates of Acinetobacter baumannii through whole genome sequencing

Habibi N, Mustafa AS, Nasser K, Al-Obaid I, Alfouzan W, Uddin S, et al.

Mol Biol Rep, 2025 Feb 15;52(1):233.
PMID: 39954144 DOI: 10.1007/s11033-025-10353-1

BACKGROUND: Acinetobacter baumannii is a notorious nosocomial pathogen universally in healthcare settings. Its natural competent characteristics for genetic recombination are responsible for acquired antibiotic resistance and render it untreatable through commonly used antibiotics. Hence, characterizing the A. baumannii genomes for multidrug resistance carriage is of paramount importance. The study aimed to characterize the whole genome of clinical isolates of A. baumannii to identify specifically the types of antibiotic resistance genes, drug classes and mobile genetic elements. We also aimed to determine the significant multi-locus sequence tags (MLSTs). The phylogeny of the isolates was established with other clinical strains distributed globally.
METHODS AND RESULTS: Fifteen clinical isolates (isolated from tracheal secretion, urine and bronchoalveolar lavage) were subjected to whole genome sequencing. Raw sequences were assembled using SPAdes and species were identified using KmerFinder 3.2. The assembled genomes were annotated using the Prokka v1.14.6. Resfinder 4.6.0 was used to determine antibiotic resistance genes. The sequences were aligned against seven housekeeping genes aka sequence tags (STs) available within the MLST database (v 2.0.9). MobileGeneticElement finder (v1.0.3) were used for profiling mobile genetic elements associated with the antibiotic resistance genes. The genomes of nosocomial A. baumannii were assembled with an average N50 of 23,480 and GC content of 38%. There were approximately 3700 CDs, 53 tRNA and 3 rRNA. About 80% of the isolates were ST2 type. The genomes possessed antibiotic resistance genes (n = 24) belonging to 17 drug classes. The predicted phenotype was multidrug resistant. Among the mobile genetic elements, 12 insertion sequences and 2 composite transposons were also found. The mode of antibiotic resistance was mostly through antibiotic inactivation in all the isolates.
CONCLUSIONS: The results imply the occurrence of multidrug resistant genes in clinical isolates of A. baumannii strains in the healthcare settings of Kuwait. A more comprehensive survey should be undertaken for antimicrobial resistance monitoring on a regular basis for surveillance, contact tracing, and potential mitigation in clinical settings.
Fulltext Non-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics

Albert MJ, Bulach D, Alfouzan W, Izumiya H, Carter G, Alobaid K, et al.

PLoS Negl Trop Dis, 2019 04;13(4):e0007293.
PMID: 30986214 DOI: 10.1371/journal.pntd.0007293

Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals-Al Farwaniya and Al Amiri-in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world. The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates.
Whole genome sequencing analysis demonstrates therapy-induced echinocandin resistance in Candida auris isolates

Spruijtenburg B, Ahmad S, Asadzadeh M, Alfouzan W, Al-Obaid I, Mokaddas E, et al.

Mycoses, 2023 Dec;66(12):1079-1086.
PMID: 37712885 DOI: 10.1111/myc.13655

Candida auris is an emerging, multidrug-resistant yeast, causing outbreaks in healthcare facilities. Echinocandins are the antifungal drugs of choice to treat candidiasis, as they cause few side effects and resistance is rarely found. Previously, immunocompromised patients from Kuwait with C. auris colonisation or infection were treated with echinocandins, and within days to months, resistance was reported in urine isolates. To determine whether the development of echinocandin resistance was due to independent introductions of resistant strains or resulted from intra-patient resistance development, whole genome sequencing (WGS) single-nucleotide polymorphism (SNP) analysis was performed on susceptible (n = 26) and echinocandin-resistant (n = 6) isolates from seven patients. WGS SNP analysis identified three distinct clusters differing 17-127 SNPs from two patients, and the remaining isolates from five patients, respectively. Sequential isolates within patients had a maximum of 11 SNP differences over a time period of 1-10 months. The majority of isolates with reduced susceptibility displayed unique FKS1 substitutions including a novel FKS1M690V substitution, and nearly all were genetically related, ranging from only three to six SNP differences compared to susceptible isolates from the same patient. Resistant isolates from three patients shared the common FKS1S639F substitution; however, WGS analysis did not suggest a common source. These findings strongly indicate that echinocandin resistance is induced during antifungal treatment. Future studies should determine whether such echinocandin-resistant strains are capable of long-term colonisation, cause subsequent breakthrough candidiasis, have a propensity to cross-infect other patients, or remain viable for longer time periods in the hospital environment.