To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR detect SARS-CoV-2 in nasopharyngeal swabs without extraction. Nasopharyngeal specimens positive and other coronaviruses collected universal viral transport (UVT) medium were pre-processed by several commercial laboratory-developed methods tested assays using different master mixes. The results compared that standard approach involves Incubation at 65°C 10 minutes along with...

During the COVID-19 pandemic in Qatar, many patients who were severely ill colonized and infected by Candida auris, an invasive multidrug-resistant yeast pathogen that spreads through nosocomial transmission within healthcare facilities. Here, we investigated molecular epidemiology of these C. auris isolates mechanisms associated with antifungal drug resistance.Whole genomes 76 clinical isolates, including 65 from collected March 2020 to June 2021, nine major hospitals sequenced on Illumina...

Candida glabrata is a commensal yeast of the gastrointestinal tract and skin humans. However, it causes opportunistic infections in immunocompromised patients, second most common pathogen causing bloodstream infections. Although there are many studies on epidemiology C. infections, fine- large-scale geographical nature remain incompletely understood. Here we investigated both population structure through genome sequencing 80 clinical isolates obtained from six tertiary hospitals Qatar by...

To the Editors: Probiotics are used in medical practice as an adjuvant therapy for various conditions. Although probiotics deemed safe, their use may pose a risk certain vulnerable populations. A 7-month-old male infant born at 32 weeks of gestation had short bowel syndrome due to necrotizing enterocolitis. He was on intestinal lengthening and rectal dilation regimen. Twenty-four hours after last procedure, patient developed fever, tachycardia, high output from gastrostomy tube stoma...

Background: Infections in sterile body sites are serious despite their low incidence. Accurate diagnosis is crucial for effective antimicrobial management. This study assesses the diagnostic yield of multiplex polymerase chain reaction (PCR) identifying bacterial pathogens site specimens other than blood and CSF. Methods: Bacterial pathogen PCR panels were independently developed validated by laboratories at Hamilton Regional Laboratory Medicine Program (HRLMP) Canada Sidra Qatar....

Introduction: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on molecular characteristic of their antimicrobial resistance determinants children is limited. Aim: To determine characteristics ESBL-producing Escherichia coli and Klebsiella pneumoniae pediatric population Qatar. Methods: Whole-genome sequencing (WGS) was performed E. K. isolates recovered from screening clinical specimens patients at Sidra...

Antibiotic resistance is a growing public health problem globally, incurring and cost burdens. The occurrence of antibiotic-resistant bacterial infections has increased significantly over the years. Gram-negative bacteria display broadest range, with species expressing extended-spectrum β-lactamases (ESBLs), AmpC, carbapenemases. All carbapenem-resistant Enterobacteriaceae (CRE) isolates from pediatric urinary tract (UTIs) between October 2015 November 2019 (n = 30). underwent antimicrobial...

The incidence of bloodstream infections (BSI) with extended spectrum beta-lactamase (ESBL) producing and carbapenemase Enterobacterales (CPE) is increasing at an alarming rate, for which only limited therapeutic options remain available. Rapid identification these bacteria along their antibiotic resistance mechanisms in positive blood cultures Gram-negative will allow early initiation effective therapy limit the overuse broad-spectrum antibiotics BSI (1).

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by high prevalence asymptomatic colonization, particularly infants. Many laboratory diagnostic methods are available, but there continues to be controversy over optimal testing approach diagnose CDI children. We evaluated commonly used C. commercial tests our hospital at Sidra Medicine Doha, Qatar. Between June and December 2023, 374 consecutive stool samples from patients aged 0–18 years old...

Abstract Introduction Escherichia coli ST1193 is an emerging high-risk clone associated with the production of plasmid-mediated CTX-type extended-spectrum β-lactamases. However, this has seldom been found to contain plasmids carrying carbapenemase genes. We report two epidemiologically unlinked multidrug-resistant (MDR) clinical isolates E. harbouring NDM-type genes from Gulf region. Methods The were identified by MALDI-TOF MS and antibiotic susceptibility testing was performed using VITEK...

Klebsiella oxytoca is an opportunistic human pathogen causing nosocomial infection. We report the draft genome of extended-spectrum β-lactamase-producing K. isolate harboring mcr-9 gene, a recently discovered colistin resistance analog, from Qatar. The statistics, along with sequence type and mechanisms, are predicted for assembled genome.

The novelty of the coronavirus disease 2019 (COVID-19) has led some researchers to use influenza models and changes in activity infer impact social distancing measures mitigate transmission severe acute respiratory syndrome 2 (SARS-CoV-2).1, However, it been argued that effectiveness school closure reduce is not transferrable COVID-19 pandemic given alleged lower attack rate children compared with adults greater basic reproductive number SARS-CoV-2 as opposed influenza.3 Sidra Medicine main...

Whole-genome sequencing was used to characterize carbapenemase-producing Enterobacterales (CPE) strains recovered from rectal screening swab samples obtained children at a tertiary-care pediatric hospital in Qatar during 3-year period. A total of 72 CPE isolates 61 fecal carriers were characterized. Escherichia coli (47 [65.3%]) and Klebsiella pneumoniae (22 [30.6%]) the most common species identified. High levels genetic diversity observed for both species. These produced 78 carbapenemases,...

Abstract Peritoneal dialysis (PD)–associated peritonitis constitutes a major complication associated with the procedure. PD-associated caused by nontuberculous mycobacteria, usually as result of an infection related to PD catheter, has been reported in adults and is significant complications poor outcome. The management Mycobacterium abscessus particularly challenging because this species resistant many antimicrobials commonly used treat mycobacterial species. We present here second case M....

### What you need to know A previously healthy and fully vaccinated (including 13-valent pneumococcal conjugate vaccine) 22 month old boy is brought the emergency department because of a 12 hour history high fever (up 40°C). He had low grade fever, runny nose, cough, decreased oral intake for past two days. On examination, he did not look severely ill but was febrile (38.3°C). His respiratory rate 45 breaths/minute (normal range 25-40 breaths/min at 18-24 months old), heart 140 beats/minute...

Key Clinical Message Streptococcus gordonii ‐associated endocarditis is a rare occurrence, raising diagnostic challenges, and often associated with considerable morbidity. However, vigilance can prevent devastating consequences. Abstract rarely reported but We describe three cases of infective caused by S. during four‐week period in 2023, the use whole‐genome sequencing to determine whether these isolates were genetically related. The available literature was reviewed.

Better diagnostic tools are needed to improve the diagnosis of Clostridioides difficile infections (CDI) and reduce overtreatment colonized children. In this study, we evaluated two polymerase chain reaction (PCR) assays (Cepheid GeneXpert C. Gastroenteritis PCR Panel by QIAstat-Dx) as a standalone method in combination with cycle threshold (Ct) value positive samples predict presence free toxins. We also clinical impact reporting toxin production results provided comments alongside our...

Bloodstream infections (BSIs) are life-threatening for which a timely initiation of appropriate antimicrobial therapy is critical. Antibiotic susceptibility testing (AST) directly performed on positive blood culture broths can help initiate targeted antibiotic sooner than the standard AST colonies isolated solid media after overnight incubation. Faster results improve clinical outcomes, and reduce broad-spectrum consumption healthcare-associated costs in sepsis. In this study, we evaluated...

Invasive fungal infections (IFI) are a major cause of mortality and morbidity in patients with chronic granulomatous disease (CGD). We report comment on case IFI caused by Rasamsonia argillacea 16-year-old female CGD. Additionally, we briefly review discuss the most challenging aspects identification treatment this species.