Clinical and epidemiological characteristics of multi-drug resistant Enterobacterales isolated from King Fahad Hospital of the University, AlKhobar, Saudi Arabia.

Multi-drug resistant (MDR) Enterobacterales remain a major clinical problem. Infections caused by carbapenem-resistant strains are particularly difficult to treat. This study aimed to assess the clinical and epidemiological characteristics of MDR Enterobacterales isolates. A total of 154 non-repetitive clinical isolates, including Escherichia coli (n = 66), Klebsiella pneumoniae (n = 70), and other Enterobacterales (n = 18), were collected from the Diagnostic Microbiology Laboratory at King Fahad Hospital of the University. Most E. coli isolates were collected from urine specimens (n = 50, 75.8%) and resistance against the third and fourth-generation cephalosporins (ceftriaxone, ceftazidime, cefixime, and cefepime) and fluoroquinolones (ciprofloxacin and levofloxacin) was assessed. Clonal relatedness analysis using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) revealed two clones (E. coli A and B), each comprising two strains. Most K. pneumoniae samples were collected from respiratory specimens (27.1%, 20 samples), and the strains showed overall resistance to most of the antimicrobials tested (54%‒100%). Moreover, clonal-relatedness analysis using ERIC-PCR revealed seven major clones of K. pneumoniae. These findings suggest nosocomial transmission among some identical strains and emphasize the importance of strict compliance with infection prevention and control policies and regulations. Environmental reservoirs could facilitate this indirect transmission, which needs to be investigated.

Microbiological trends and mortality risk factors of central line-associated bloodstream infections in an academic medical center 2015-2020.

BACKGROUND: Despite tremendous efforts to prevent central line-associated bloodstream infections, they still remain life-threatening complications among hospitalized patients with significant morbidity and mortality worldwide. The emerging antibiotic-resistant bacteria and other risk factors, including patient comorbidities, complicate patient management. METHODS: A single-center retrospective observational study was conducted at King Fahad Hospital of the University, Eastern Province, Saudi Arabia. Hospitalized patients with confirmed central line-associated bloodstream infections between January 2015 and December 2020 were included. The primary objectives were to investigate the trends in antibiotic susceptibility patterns of the causative agents, coexisting comorbid conditions, and other risk factors associated with mortality. RESULTS: A total of 214 patients with confirmed central line-associated bloodstream infections were included (CLABSI). The overall 30-day mortality rate was 33.6%. The infection rates per 1000 central line days for medical, surgical, and pediatric intensive care units were 4.97, 2.99, and 4.56 per 1000 CL days, respectively. The overall microbiological trends showed a predominance of Gram-negative agents, a steady increase of fungal CLABSI up to 24.0% in 2020, and a high prevalence of multidrug resistance up to 47% of bacterial CLABSI. In addition, the study indicates a significant negative surviving correlation with diabetes mellitus, cardiovascular disease, lung disease, chronic kidney disease, and the presence of ≥ 3 comorbidities (P < 0.05). CONCLUSION: The microbiological trends of the study population demonstrated a steady increase of CLABSI caused by Candida spp. with a predominance of Gram-negative pathogens. Stratifying the patients according to relevant mortality risk factors, including patient comorbidities, will help reduce CLABSI rates and improve patient outcomes.

Clinical and Microbiological Characteristics of Candidemia Cases in Saudi Arabia.

Purpose: Candidemia and antifungal resistance are major healthcare challenges. The aim of this study is to describe the frequency of candidemia cases, distribution of Candida spp., and the associated risk factors for mortality in an academic institution in Saudi Arabia over an 18-month period. We also evaluated the susceptibility patterns of Candida blood isolates. Methods: Candidemia cases were collected from King Fahad Hospital of the University over the period between July 1st, 2020 through December 31st, 2021. They were prospectively reviewed for the preceding risk factors and antifungal (AF) susceptibility, testing results to fluconazole (FL), voriconazole (VO), itraconazole (IT), posaconazole (PO), caspofungin (CASP), anidulafungin (AND), micafungin (MYC), flucytosine (FLC) and amphotericin B (AMPB) using a broth microdilution kit (Sensititre™ YeastOne). Results: A total of 48 candidemia isolates were included that were isolated from 43 patients. The median age of cases was 62 ± 23.3 years (60.4% males and 83% ICU patients). Independent risk factors for mortality at 30 days in candidemia patients were age, COVID-19 co-infection, and use of tocilizumab. The most commonly isolated species were C. glabrata and C. parapsilosis (22.9% each) followed by C. albicans (18.75%). AF resistance for ≥1 antifungal was detected in 39.3% of 33 cases tested, with no cross-resistance identified. Resistance rates for each AF were as follows: FL (18%), VO (6%), IT (6%), PO (9%) and AMPB (3%). No resistance was seen for echinocandins apart from one C. krusei strain showing an intermediate result for CASP. Conclusion: The study showed an overall high rate of non-albicans Candida, with the predominance of C. parapsilosis and C. glabrata, representing a therapeutic challenge. AF resistance rate was high which emphasizes the importance of continuing surveillance and providing accurate and reliable tools in the laboratories for rapid speciation and susceptibility testing.

Antimicrobial Resistance in Ventilator-Associated Pneumonia: Predictive Microbiology and Evidence-Based Therapy.

Ventilator-associated pneumonia (VAP) is a serious intensive care unit (ICU)-related infection in mechanically ventilated patients that is frequent, as more than half of antibiotics prescriptions in ICU are due to VAP. Various risk factors and diagnostic criteria for VAP have been referred to in different settings. The estimated attributable mortality of VAP can go up to 50%, which is higher in cases of antimicrobial-resistant VAP. When the diagnosis of pneumonia in a mechanically ventilated patient is made, initiation of effective antimicrobial therapy must be prompt. Microbiological diagnosis of VAP is required to optimize timely therapy since effective early treatment is fundamental for better outcomes, with controversy continuing regarding optimal sampling and testing. Understanding the role of antimicrobial resistance in the context of VAP is crucial in the era of continuously evolving antimicrobial-resistant clones that represent an urgent threat to global health. This review is focused on the risk factors for antimicrobial resistance in adult VAP and its novel microbiological tools. It aims to summarize the current evidence-based knowledge about the mechanisms of resistance in VAP caused by multidrug-resistant bacteria in clinical settings with focus on Gram-negative pathogens. It highlights the evidence-based antimicrobial management and prevention of drug-resistant VAP. It also addresses emerging concepts related to predictive microbiology in VAP and sheds lights on VAP in the context of coronavirus disease 2019 (COVID-19).

Bloodstream Infections Caused by Drug Resistant Ralstonia species: A Case Series During the COVID-19 Pandemic.

Ralstonia spp. is an emerging, non-fermentative Gram-negative rod that demonstrates multidrug resistance. Herein, four cases of bloodstream infections (BSI) caused by R. mannitolilytica or R. pickettii are presented. All the cases had comorbidities that predisposed them to this opportunistic infection. The microbiological assessment showed carbapenemase genes carried out in two strains with minimal inhibitory concentrations > 32 µg/mL to imipenem and meropenem. Fluoroquinolones and trimethoprim-sulphamethoxazole were the most potent agents showing activity against 3/4 strains (75%), although treatment should be susceptibility-dependent for each strain. This case series highlights the possibility of co-infection by a rare organism during the COVID-19 pandemic and the importance of the readiness of diagnostic laboratories to support the diagnosis of uncommon pathogens.

Diagnosis of group A streptococcal pharyngitis in the paediatric emergency department using a fluorescence-based RADT: predicted impact on antibiotic prescription.

Introduction. Using rapid antigen diagnostic tests (RADTs) in clinical practice has shown excellent specificity but often has diminished sensitivity.Gap Statement. Local data for evaluating the diagnostic performance of a new fluorescence-based RADT and its influence on the antibiotic prescription rate are not available.Aim. To evaluate the accuracy of fluorescent immunoassay (FIA)-RADTs for diagnosing group A streptococcal (GAS) pharyngitis among children and its estimated effect as a point of care test (POCT) on the antibiotic prescription rate at the paediatric emergency department.Methodology. A prospective study was conducted, comprising children 3 to 14 years old presenting with pharyngitis. Throat swab culture and FIA-RADTs were performed on all samples. Conventional PCR was performed on the discordant samples.Results. A total of 246 children were included in this study. The sensitivity, specificity, and positive and negative predictive values of the FIA-RADT, based on culture results and PCR detection combined, were 95.6, 96.8, 94.6 and 97.4 %, respectively. Antibiotics have been prescribed to 162 (65.9 %) children; however, if FIA-RADTs had been added in the clinical practice as a POCT, only 92 (37.4 %) children would have received antibiotics in total. Additionally, implementation of FIA-RADTs would significantly reduce the antibiotic prescription rate from 48.8 and 60.6 % to 9.5 and 31.9 % among patients with clinical scores of 2 and 3, respectively.Conclusion. The new FIA-RADT is simple, prompt and reliable. It is helpful in clinical settings and may be used to reduce antibiotic overprescription, especially for children who have a low risk for GAS pharyngitis, according to the clinical score.

Nano-treatment of HEPA filters in COVID-19 isolation rooms in an academic medical center in Saudi Arabia.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread globally. The major reservoir for SARS-CoV-2 transmission remains controversial, with the airborne route remaining a possible transmission vehicle for carrying the virus within indoor environments. This study aimed to detect contamination of SARS-CoV-2 in high-efficiency particulate air (HEPA) filters within hospital isolation rooms of confirmed COVID-19 patients, exploring the role of nano-treatment of these filters with silver and titanium dioxide nanoparticles (Ag/TiO2 NPs). MATERIALS AND METHODS: We investigated the effectiveness of Ag-NPs/TiO2-treated HEPA filters in the air of rooms occupied by patients with confirmed COVID-19 in a university teaching hospital in the Eastern province of Saudi Arabia during the first wave of the pandemic. Ag/TiO2 NPs were designed and coated on HEPA filters to examine the filtration efficiency and antiviral ability in the presence of aerosolized virus particles. A total of 20 viral swab samples were collected from five patients' rooms before and after treatment with nanoparticle-prepared solutions into the sterile virus-transporting media. Samples were evaluated for SARS-CoV-2 with a reverse transcription-polymerase chain reaction. RESULTS: Two samples taken from the HEPA filter air exhaust outlets prior to nano-treatment tested positive for SARS-CoV-2 RNA in the intensive care unit, which has stringent aerosolization control procedures, suggesting that small virus-laden droplets may be displaced by airflow. All air samples collected from the HEPA filters from the rooms of patients with confirmed COVID-19 following nano-treatment were negative. CONCLUSION: We recommend further experimental exploration using a larger number of HEPA filters in areas with aerosol-generating procedures, along with viability studies on the HEPA filters to facilitate decision-making in high-risk facilities regarding the replacement, storage, and disposal of HEPA filters in wards occupied by cases diagnosed with a highly transmissible disease.

Pneumococcal empyema: Resistance patterns, fitness cost and serotype distribution.

BACKGROUND: Streptococcus pneumoniae is a recognized etiology of invasive infections including parapneumonic empyema, and its resistance to antibiotics is evolving worldwide, raising concerns of encountering untreatable strains. This study measured the serotype distribution, antimicrobial susceptibility and biological cost incurred by resistance of pneumococci from pleural samples. METHODS: The serotype profiles, susceptibility results and growth rates were phenotypically determined for a panel of clinical strains of S. pneumoniae from cases of empyema between 2011 and 2019. RESULTS: Of 24 empyema cases, the isolated strains belonged to seven serotypes in the following descending order; 19A, 11A/D, 19F, 3, 7F, 1/6B while two strains remained non-typable. Penicillin susceptibility was shown in <80% of the isolates, while parenteral cephalosporins (cefuroxime and ceftriaxone) demonstrated activity in 83.3 and 95.8% respectively. High resistance frequency was noted for macrolides and sulfonamides, but the strains were uniformly sensitive to respiratory fluroquinolones, vancomycin and linezolid. The macrolide-resistant strain exhibited a high growth rate, suggesting a possible beneficial effect. Phenotypes with mono-resistance to sulfonamides and clindamycin were equally fit as the susceptible counterpart strains. Resistance to multiple antimicrobial agents resulted in a high degree of fitness deficit, while other resistant phenotypes were less fit. CONCLUSIONS: The pneumococcal conjugate vaccine PCV13 serotypes still circulate in the community. The data indicate that resistance to certain antimicrobials incurs an apparent fitness cost in pneumococci which may limit the dissemination of such strains while low fitness cost, seen in case of resistance to macrolides, may contribute to the spread of resistant clones.

Eleven-Year surveillance of methicillin-resistant Staphylococcus aureus infections at an Academic Health Centre.

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen associated with nosocomial and community infections. There is a continual focus on the epidemiology of this public health threat owing to the increase in its spread and rapid development of resistance. Aim: We aimed to demonstrate the time trend of antibiotic resistance by describing the epidemiology of MRSA infections at an academic health centre. Methodology: We retrospectively reviewed cases during an 11-year period (from January 2009 to December 2019) with positive cultures for MRSA from various clinical sites in King Fahad Hospital of the University, to understand their clinical and microbiological profiles. Screening and colonisation samples were excluded. Results: A total of 1338 MRSA isolates were identified, with an increasing trend from 5.2% to 14.5% during 2009-2019. Skin and soft tissue samples were the most common source (52.4%) of MRSA infections. Vancomycin activity remained stable against MRSA, and only one isolate showed resistance to linezolid (< 1%). A significant reduction in susceptibility to clindamycin (p = 0.003), trimethoprim-sulfamethoxazole (p = 0.001), and rifampin (p < 0.0001) was detected over the study period. Conclusions: MRSA infections still represent a significant burden on healthcare systems. Our data support the need for constant local and regional surveillance to devise relevant protocols to manage MRSA infections. Empirical therapy needs to consider the changing antimicrobial susceptibility trends among MRSA isolates.

Low levels of soluble DPP4 among Saudis may have constituted a risk factor for MERS endemicity.

Most of the cases of Middle East respiratory syndrome coronavirus (MERS-CoV) were reported in Saudi Arabia. Dipeptidyl peptidase-4 (DPP4) was identified as the receptor for the virus. The level of soluble DPP4 (sDPP4) was found to be reduced in MERS-CoV infected patients while high levels of sDPP4 were suggested to be protective against MERS-CoV in animal models. We investigated whether the Saudi population has lower levels of sDPP4 which makes them more susceptible to MERS-CoV infection and, therefore, could explain the larger number of cases from the country. Blood samples were collected from 219 Saudi blood donors and 200 blood donors from other ethnic groups. The plasma level of sDPP4 was measured by ELISA and the following SNPs in the DPP4 gene; rs35128070, rs1861978, rs79700168, and rs17574, were genotyped by TaqMan SNP genotyping assay. The average level of plasma sDDP4 was significantly lower in Saudis than other Arabs and non-Arabs (P value 0.0003 and 0.012, respectively). The genotypes AG of rs35128070 and GT of rs1861978 were significantly associated with lower sDPP4 among Saudis (P value 0.002 for each). While both genotypes AA and AG of rs79700168 and rs17574 were associated with significantly lower average sDPP4 level in Saudis compared to other ethnic groups (P value 0.031 and 0.032, and 0.027 and 0.014, respectively). Herein, we report that the Saudi population has lower levels of plasma sDPP4 than other ethnic groups, which is associated with genetic variants in the DPP4 gene. This may have contributed to increase the susceptibility of the Saudi population to MERS-CoV infection and could be a factor in the long-lasting persistence of the virus in the country.

Bacterial and Fungal Coinfection in Critically Ill COVID-19 Cases and Predictive Role of Procalcitonin During the First Wave at an Academic Health Center.

BACKGROUND: Coinfection at various sites can complicate the clinical course of coronavirus disease of 2019 (COVID-19) patients leading to worse prognosis and increased mortality. We aimed to investigate the occurrence of coinfection in critically ill COVID-19 cases, and the predictive role of routinely tested biomarkers on admission for mortality. METHODS: This is a retrospective study of all SARS-CoV-2-infected cases, who were admitted to King Fahad Hospital of the University between March 2020 and December 2020. We reviewed the data in the electronic charts in the healthcare information management system including initial presentation, clinical course, radiological and laboratory findings and reported all significant microbiological cultures that indicated antimicrobial therapy. The mortality data were reviewed for severely ill patients who were admitted to critical care units. RESULTS: Of 1091 admitted patients, there were 70 fatalities (6.4%). 182 COVID-19 persons were admitted to the critical care service, of whom 114 patients (62.6%) survived. The in-hospital mortality was 13.4%. Coinfection was noted in 67/68 non-survivors, and Gram-negative pathogens (Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumanni) represented more than 50% of the etiological agents. We noted that the serum procalcitonin on admission was higher for non-survivors (Median = 1.6 ng/mL ± 4.7) than in survivors (Median = 0.2 ng/mL ± 4.2) (p ≤ 0.05). CONCLUSION: Coinfection is a serious complication for COVID-19 especially in the presence of co-morbidities. High levels of procalcitonin on admission may predict non-survival in critically ill cases in whom bacterial or fungal co-infection is likely.

The Environmental Deposition of Severe Acute Respiratory Syndrome Coronavirus 2 in Nosocomial Settings: Role of the Aerosolized Hydrogen Peroxide.

BACKGROUND: Data on the role of aerosolized hydrogen peroxide (AHP) systems in the control of the COVID-19 pandemic are still emerging. This study provides evidence of the environmental shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the hospital environment, and the efficacy of AHP to eliminate it. METHODS: A total of 324 environmental sites (224 surfaces and 100 air samples) belonging to 54 patient rooms were contextually collected and tested for genes of SARS-CoV-2 using RT-PCR assays and Xpert® Xpress SARS-CoV-2. RESULTS: The SARS-CoV-2 viral genome was detected in seven sites (2.5%) of three patients' rooms, including six highly touched surfaces and one air sample. Viral shedding was directly related to the distance from the patient, with 1, 1.9, and 3.5% of samples testing positive at 3, 2, and 1 meter, respectively (P-value=0.02). None of the sites showed the viral genome following application of 6% AHP. Of note, the viral genome was detected at 2 meters of a mildly symptomatic case on a face mask in the absence of aerosol generating procedures. CONCLUSION: Our data support the possible role of the hospital environment as a source of infection, and the efficacy of AHP to eliminate the virus. Further studies are needed to address the viability of the pathogen in these nosocomial sites and the cost-effectiveness of routine hospital disinfection procedures using AHP for SARS-CoV-2.

Predictive Role of Targeted, Active Surveillance Cultures for Detection of Methicillin-Resistant Staphylococcus aureus.

INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) colonisation is an important source of healthcare-acquired infections. Reliable screening strategies for MRSA colonisation are essential for the timely implementation of infection control measures. AIM: This study determined reliable MRSA screening sites to predict colonisation in resource-limited settings and estimated the impact of missed MRSA cases when shifting from multi- to single-site screening. METHODOLOGY: A cross-sectional study was conducted in patients with positive MRSA surveillance cultures from the routinely screened sites (nasal, axillary, groin, and throat) from January 2009 to December 2019. RESULTS: A total of 1906 screening tests were positive for MRSA cultures (n = 1345 patients). As a single site, the nasal cavity showed the highest MRSA detection, with a sensitivity of 66.8% (95% CI = 64-69) with 277.9 missed isolation days. Screening three or more anatomical sites detected 97-100% of MRSA cases, with 0-24.5 missed isolation days. Screening the axilla and groin separately or in combination showed a good clinical utility index (CUI) of >0.6 to <0.8, while an excellent CUI was obtained upon screening other site samples (>0.8). The combined nasal and throat cultures demonstrated a sensitivity of 93.2 (95% CI = 91-94) with 57.2 missed isolation days. CONCLUSION: Multi-site screening is the optimal strategy for minimising MRSA exposure within a healthcare facility. For active MRSA surveillance, a combination of nasal and throat cultures can provide a practical approach in low-resource settings compared to nasal sampling alone.

Predictors of Illness Severity in COVID-19 Cases in Saudi Arabia.

PURPOSE: Multiple studies worldwide have reported the clinical and epidemiological features of coronavirus disease 2019 (COVID-19), with limited reports from the Middle East. This study describes the clinical and epidemiological features of COVID-19 cases in the Eastern Province of Saudi Arabia and identified factors associated with the severity of illness. PATIENTS AND METHODS: This was an observational study of 341 COVID-19 cases. These cases were reported in the first three months after the first case in the country was identified. Clinical and demographic data were analyzed and described to identify the effects of age, sex, and ethnicity on illness severity. In addition, the duration of viral shedding and cycle threshold (Ct) values of real-time PCR were evaluated as predictors of severity. RESULTS: The median age was 45 years. Males were twice as likely to be infected than females (p <0.0001). The duration of viral shedding ranged from 9 to 36 days. The most common clinical presentations include fever, shortness of breath, cough, myalgia, sore throat, vomiting, and headache. Critical cases were significantly higher in men (23% vs 8.7%), senior adults (>65 years), individuals of Bengali ethnicity, and in patients with comorbidities including diabetes, hypertension, and dyslipidemia (p =0.001). The case fatality rate was found to be 10%. The fatality was significantly higher in males than females (13.8% vs 2.6%), and in Asians (17.9%) than Arabs (6%) and Africans (0) (p =0.002). No association was found between viral load, represented by the RT-PCR cycle threshold (Ct) values, and severity of illness. CONCLUSION: Age, sex, and ethnicity are important predictors of COVID-19 severity. The cycle threshold (Ct) of the SARS-CoV-2 RT-PCR test cannot be used as a predictor of the criticality of illness.

The diagnostic impact of implementing a molecular-based algorithm to standard mycobacterial screening at a reference laboratory with an intermediate prevalence for non-respiratory samples.

Rapid, reliable results can be given by molecular, direct detection and identification of the Mycobacterium tuberculosis (MTB/Mtb) complex from clinical samples. The Xpert MTB/RIF assay is an assay that has been availablefor more than a decade for identification of Mycobacterium tuberculosis and resistance to rifampicin. However, there is minimal evidence on its clinical usefulness in paucibacillary, non-respiratory samples. The Xpert MTB/RIF assay clinical utility index, its diagnostic characteristics and the number required to diagnose 2935 non-respiratory specimens submitted for routine mycobacterial work-up in a reference laboratory in an intermediate prevalence setting per specimen form were evaluated. The Xpert MTB/RIF assay showed a variable clinical utility index and number required to diagnose (NND) depending on the type of specimen, which was moderate in tissue biopsies (NND = 1.8) and excellent in pus and urine samples, compared to acid-fast microscopy and culture as a gold standard technique (NND = 1.1 and 1.2). Microscopy, on the other hand, consistently showed a weak to fair index of clinical usefulness in all specimen forms, with in NND of 2.3-12.5. The NND for detecting tuberculous infection in the cerebrospinal fluid by the Xpert MTB/RIF assay was noted to be 1.2, with a moderate clinical utility index of 0.8. The evidence presented indicates that the overall appropriate diagnostic utility of the Xpert MTB/RIF assay is clinically successful in most non-respiratory samples. To check the cost-effectiveness and prognostic effect of integrating this completely automated molecular-based assay into the routine testing algorithm for non-respiratory mycobacterial specimens, further data must be collected.

Inverse correlation between biofilm production efficiency and antimicrobial resistance in clinical isolates of Pseudomonas aeruginosa.

This study assessed the correlation between biofilm formation in Pseudomonas aeruginosa strains with both the level of antibiotic resistance, and the number of virulence- and biofilm-related genes encoded. A total of sixty-six, non-replicate and prospectively collected P. aeruginosa strains were identified and tested. Potential ampD mutations that may impose resistance to extended-spectrum ß-lactam (ESBL) agents were further explored. Of the sixty-six tested isolates, 40 demonstrated the multidrug resistance (MDR) phenotype, while twenty-six were non-MDR strains. An inverse correlation was observed between antibiotic resistance and the potential capacity to form biofilms. In addition, no correlation was observed between novel ampD mutations and the tendency for MDR isolates to acquire a ß-lactam-resistant phenotype. The present study emphasizes the need for enhanced infection preventive measures in various hospital units, since both MDR and non-MDR P. aeruginosa isolates exhibited a high level of biofilm-forming capacity and the presence of virulence-associated genes.

A seven-year surveillance of Candida bloodstream infection at a university hospital in KSA.

OBJECTIVES: Candidemia incidence has increased in the past few years, with high mortality. Previous studies have reported a variable distribution of Candida spp. among different regions. This study aimed to identify the species found in Candida bloodstream infections, routine antifungal susceptibility testing, and mortality outcomes in an academic medical centre. METHODS: Between January 2012 and December 2018, the positive blood cultures for candidemia infection were retrieved and statistically analysed for species prevalence, susceptibility pattern, and crude mortality at 14, 30, 60 and 90 days. RESULTS: Of 156 candidemia cases, a majority (69.2%) was caused by non-albicans Candida spp. After Candida albicans (30.8%), Candida tropicalis and Candida parapsilosis were the second and third most frequeunt isolates spp, each counting for 23.7%. Acquired resistance was detected in 14.8% of candidemia strains. No other antifungal resistance was detected. The overall crude mortality rates of all species were 29.3%, 47.9%, 56.4%, and 58.0% at 14, 30, 60, and 90 days, respectively. A higher mortality rate was noted in cases of Candida krusei infection (crude mortality 71.4-100%, p = 0.002). CONCLUSION: In this study, a considerable shift to non-albicans Candida causing most bloodstream infections was observed. As such infections pose a serious threat to hospitalised patients, microbiology laboratories are urged to adopt rapid diagnostic and minimal inhibitory concentration-based testing for the detection of susceptible dose-dependent phenotypes. Prospective studies are essential to consider the prognosis of bloodstream infections by various Candida species in a multivariate model.

Pooled Specimen Testing Using Automated Cartridge-Based System for COVID-19: The Cost on Sensitivity.

BACKGROUND: Pooled specimen screening for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can improve laboratory testing capacity. This study assessed the impact of pooling and retesting individual swabs on the overall detection rate and reduction in the frequency of retesting. METHODS: One hundred respiratory swabs specimens were tested individually and in pools of three or five samples using the Cepheid's Xpert® Xpress SARS-CoV-2 test kit. The optimum number of samples per pool was calculated using the application 'A Shiny App for Pooled Testing'. RESULTS: Twenty-five pools were generated from 101 samples. Out of 13 pools that contained five samples each, three pools gave true positive results. While out of the 12 pools that contained three samples each, five pools gave true positive results. Four samples gave a false negative pool result. The overall sensitivity and specificity of the assay in the pools were 66.6% and 100%, respectively. The cycle threshold was reduced in most of the pools compared to individual sample tests. CONCLUSION: The overall pooled test had a remarkable impact on laboratory resources. Yet, caution is warranted when selecting the cases for pooled testing, since the reduction in sensitivity can significantly impact and increase the risk of exposure to infection.

Prevalence of the SARS-CoV-2 Infection Among Post-Quarantine Healthcare Workers.

BACKGROUND: Coronavirus disease 2019 is an emerging highly communicable disease. Nosocomial transmission needs to be prevented through the implementation of stringent screening and infection control measures. OBJECTIVE: The objective of the study is to estimate the prevalence of severe acute respiratory syndrome- coronavirus 2 (SARS-CoV-2) infection among health care workers (HCWs) post quarantine period. METHODS: This is a prospective, observational study conducted at a teaching University hospital in Alkhobar, Saudi Arabia, during the period between May 1 and June 15, 2020. All (HCWs) joining work back from the quarantine areas had a real-time polymerase chain reaction (qRT-PCR) test for SARS-CoV-2. The demographic and clinical data from the staff were collected. RESULTS: Of the 301 HCWs screened, 18 (6%) had positive PCR. The age means of the positive cases was 32.9 Y ± 8.7 compared to 33.8 Y ± 7.0 in the negatively tested group (p value = 0.90). Of the 18 PCR-positive HCWs, 7 (38.9%) were male. Majority of those who tested positive were trainees (8.2%) followed by nurses (5.1%). In PCR-positive group, a clear epidemiological exposure was found in 4/18 cases (22.2%). Male gender and residency in specific districts were observed more in the positive cases (p value = 0.01 and 0.0001, respectively). In regards to symptoms, most of the positive PCR tested HCWs (n=12, 66.7%) remained asymptomatic. Most prevalent initial symptoms were gastrointestinal symptoms (diarrhea, abdominal pain) in six HCWs representing 33.3%. No significant difference was noted in co-morbidities reported by both groups. CONCLUSION: Health care workers tested post-quarantine period were found to be at risk of SARS-CoV-2 infection despite very minimal or no known risks of exposure, where most of them were asymptomatic. This potentially carries risk of nosocomial transmission inside healthcare facilities. Implanting policies for routine post-quarantine screening for HCWs is recommended.

Whole Genome Sequencing of Ceftolozane-Tazobactam and Ceftazidime-Avibactam Resistant Pseudomonas aeruginosa Isolated from a Blood Stream Infection Reveals VEB and Chromosomal Metallo-Beta Lactamases as Genetic Determinants: A Case Report.

Pseudomonas aeruginosa is a common gram-negative bacillus in nosocomial settings. Consideration of this organism is important due to its potential to acquire multi-drug resistance through various mechanisms causing severe infections, particularly in immunocompromised hosts. Here, we present a challenging case of a blood stream infection caused by a drug-resistant strain of P. aeruginosa in a debilitated young patient. A 31-year-old male patient with a complex history of multiple trauma following a vehicle accident that required several surgical interventions, is plagued by persistent bacteremia. An extensively drug-resistant strain of P. aeruginosa was repeatedly isolated that continued to grow in the patient's blood cultures despite treatment with meropenem and colistin for an extended period. In addition to phenotypic characterization, the complete genome of the strain was sequenced and a genomic view was provided regarding its antimicrobial resistance (AMR) patterns, efflux pump genes, virulence determinants, phageomic signals, and genomic islands. The strain belongs to sequence type ST357 with dominant Class A (VEB), Class B, Class C (PDC-11) and D (OXA-10, OXA-50) ß-lactamases, and injectosomes (type III secretion system) known to mediate high virulence. The pool of extended spectrum ß-lactamases genes and the upregulated chromosomal efflux system are likely to account for the extended resistance pattern in this strain. In light of the global spread of ST357 isolates, it is essential to continue monitoring their resistance patterns and evaluate effective epidemiological tools to define the genetic determinants of emerging resistance. Intensified infection control measures are continuously required to stop dissemination of such strains in an institution where susceptible hosts are at risk of acquiring them.