Antimicrobial Resistance and Infection Control, Nov 18, 2023
Background Despite tremendous efforts to prevent central line-associated bloodstream infections, ... more 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.
Dormancy models for Mycobacterium tuberculosis play important roles in understanding various aspe... more Dormancy models for Mycobacterium tuberculosis play important roles in understanding various aspects of tuberculosis pathogenesis and in the testing of novel therapeutic regimens. By simulating the latent tuberculosis infection, in which the bacteria exist in a non-replicative state, the models demonstrate reduced susceptibility to antimycobacterial agents. This minireview outlines the models available for simulating latent tuberculosis both in vitro and in several animal species. Additionally, this minireview discusses the advantages and disadvantages of these models for investigating the bacterial subpopulations and susceptibilities to sterilization by various antituberculosis drugs.
Candidemia and antifungal resistance are major healthcare challenges. The aim of this study is to... more 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 crossresistance 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.
Background: Data on the role of aerosolized hydrogen peroxide (AHP) systems in the control of the... more 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.
Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen a... more 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.
Journal of Taibah University Medical Sciences, Jun 1, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Pseudomonas aeruginosa is a common gram-negative bacillus in nosocomial settings. Consideration o... more 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 drugresistant 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) β-lactamases, and injectosomes (type III secretion system) known to mediate high virulence. The pool of extended spectrum βlactamases 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.
Background: Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seek... more Background: Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seeking shelter in other European countries. Aim: We aimed to investigate the prevalence and the molecular epidemiology of multidrug-resistant Gram-negative (MDRGN) bacteria and meticillin-resistant Staphylococcus aureus (MRSA) in Ukrainian patients at admittance to the University Hospital Frankfurt, Germany. Methods: We performed screening and observational analysis of all patients from March until June 2022. Genomes of MDRGN isolates were analysed for antimicrobial resistance, virulence genes and phylogenetic relatedness. Results: We included 103 patients (median age: 39 ± 23.7 years), 57 of whom were female (55.3%; 95% confidence interval (CI): 45.2-5.1). Patients were most frequently admitted to the Department of Paediatrics (29/103; 28.2%; 95% CI: 19.7-37.9). We found 34 MDRGN isolates in 17 of 103 patients (16.5%; 95% CI: 9.9-25.1). Ten patients carried 21 carbapenem-resistant (CR) bacteria, five of them more than one CR isolate. Four of six patients with war-related injuries carried eight CR isolates. In six of 10 patients, CR isolates caused infections. Genomic characterisation revealed that the CR isolates harboured at least one carbapenemase gene, bla NDM-1 being the most frequent (n = 10). Core genome and plasmid analysis revealed no epidemiological connection between most of these isolates. Hypervirulence marker genes were found in five of six Klebsiella pneumoniae CR isolates. No MRSA was found. Conclusion: Hospitals should consider infection control strategies to cover the elevated prevalence of MDRGN bacteria in Ukrainian patients with war-related injuries and/or hospital pretreatment and to prevent the spread of hypervirulent CR isolates.
النوعية محددة تكن لم العزالت من 94 أصل من 24% أن لألهتمام مستخلصات 53 بني... more النوعية محددة تكن لم العزالت من 94 أصل من 24% أن لألهتمام مستخلصات 53 بني من .cpsA املدبر للجني سلبية كانت 18% و املقاومة احادية)17%(9 كانت النوعية محددة الرئوية املكورات 5 و املاكرواليد ضد املقاومة احادية)5.6%(3 و البنسلني ضد املقاومة للجينات العالية النسبة تختلف لم مقاومة. غير)9.4%(املكورات فإن وباملثل)p=0.76(املصلي للنمط وفقا ً كبيرا ً اختالفا عالية مقاومة معدالت لها cpsA+ و cpsA-النوعية محددة غير الرئوية .)47%(واملاكروليدات)62.5%(للبنسلني الكبسولي النوع ظهور على الضوء البيانات هذه تسلط اخلامتة: وعالوة)p=0.001 29 املريض عمر (متوسط 11A ً سابقا املعروف تبني النوعية محددة غير املستخلصات من عالية نسبة فإن ذلك، على اللقاحات تغطيها ال محتملة منطية غير رئوية املصلية األمناط ظهور املتاحة. Objectives: To study serotype distribution and antimicrobial resistance to beta-lactams and macrolides in pneumococci causing respiratory diseases after the introduction of the 13-valent pneumococcal conjugate vaccine in Saudi Arabia. Methods: This is a hospital-based and a cross-sectional prospective surveillance study conducted at King Fahad Hospital of the University, AlKhobar, Kingdom of Saudi Arabia, in which respiratory pneumococcal isolates collected between 2012 and 2014 were serotyped by multiplex sequential polymerase chain reaction)PCR(and Pneumotest-Latex. Resistance genes to beta-lactams and macrolides were detected by multiplex PCR. Results: The most common serotypes encountered were 11A, 19A, 17F, 23F, 3, and 19F, representing 64% of the typeable strains. Interestingly, 24% of the 94 isolates were not typeable and 18% were negative for the housekeeping gene cpsA. Among the 53 typeable pneumococci isolates, 36)67.9%(carried genes encoding resistance to both penicillin and macrolides, 9)17%(were penicillin-monoresistant, 3)5.6%(were macrolide-monoresistant, and 5)9.4%(were designated non-resistant. The high rate of resistance genes did not significantly differ according to serotype)p=0.76(. Similarly, non-typeable pneumococci)cpsA+ and cpsA-(had high rates of resistance to both penicillin)62.5%(and macrolides)47%(. Conclusion: These data highlight the emergence of a previously rare capsular type, 11A)mean patient age, 29 years; p=0.001(. Moreover, the high percentage of non-typeable isolates shows the emergence of possible atypical pneumococcal serotypes not covered by available vaccines.
This study assessed the correlation between biofilm formation in Pseudomonas aeruginosa strains w... more 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 β-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 β-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.
Ralstonia spp. is an emerging, non-fermentative Gram-negative rod that demonstrates multidrug res... more 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 trimethoprimsulphamethoxazole 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.
This study analyzed the genotype, antibiotic resistance, and biofilm formation of Acinetobacter b... more This study analyzed the genotype, antibiotic resistance, and biofilm formation of Acinetobacter baumannii strains and assessed the correlation between biofilm formation, antibiotic resistance, and biofilm-related risk factors. A total of 207 non-replicate multi-drug-resistant A. baumannii strains were prospectively isolated. Phenotypic identification and antimicrobial susceptibility testing were carried out. Isolate biofilm formation ability was evaluated using the tissue culture plate (TCP), Congo red agar, and tube methods. Clonal relatedness between the strains was assessed by enterobacterial repetitive intergenic consensus-PCR genotyping. Of the 207 isolates, 52.5% originated from an intensive care unit setting, and pan resistance was observed against ceftazidime and cefepime, with elevated resistance (99-94%) to piperacillin/tazobactam, imipenem, levofloxacin, and ciprofloxacin. alongside high susceptibility to tigecycline (97.8%). The Tissue culture plate, Tube method, and Congo red agar methods revealed that 53.6%, 20.8%, and 2.7% of the strains were strong biofilm producers, respectively, while a significant correlation was observed between biofilm formation and device-originating respiratory isolates (p = 0.0009) and between biofilm formation in colonized vs. true infection isolates (p = 0.0001). No correlation was detected between antibiotic resistance and biofilm formation capacity, and the majority of isolates were clonally unrelated. These findings highlight the urgent need for implementing strict infection control measures in clinical settings.
Electronic journal of general medicine, Jul 1, 2023
A lack of evidence of accuracy for various testing modalities for carbapenem-resistant Enterobact... more A lack of evidence of accuracy for various testing modalities for carbapenem-resistant Enterobacterales (CRE) reduces the efficiency of screening and delays the isolation of carriers. This study examined the performance of phenotypic detection of CRE in comparison to molecular testing. A cross-sectional study was conducted in an academic medical institution in Saudi Arabia on CRE-screened patients during a 36-month period (April 1, 2019, through March 31, 2022). Cases were followed up for their susceptibility status by the phenotypic gradient method and genotypes. Of 3,116 samples tested, 359 carbapenemase genes were detected in 297 strains (9.5%) belonging to 292 patients. Oxacilliniase-48 (OXA-48) was the most frequently detected genotype (n=190, 64%), followed by a combined New Delhi metallo-B-lactamase (NDM)/OXA-48 genotype (n=77, 25.9%). Variable missed isolation days were encountered for various genotypes (0-18.5 days), with an excellent clinical utility index obtained for screening the OXA-48 genotype phenotypically. The data provided some insights into the predictive role and shortcomings of the e-test alone in CRE screening. While it provided a reasonable approach in a CRE population dominated by OXA-48 genotypes, it was more likely to miss the NDM-incurred carbapenemase. Thus, local epidemiology in an institution must be considered when designing a local screening protocol in addition to consideration of cost and turnaround time.
Rapid, reliable results can be given by molecular, direct detection and identification of the Myc... more 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.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Feb 9, 2009
underlying cause coded as J65 (pneumoconiosis associated with tuberculosis) or J92.0 (pleural pla... more underlying cause coded as J65 (pneumoconiosis associated with tuberculosis) or J92.0 (pleural plaque with presence of asbestos) also were included in the underlying cause-of-death tabulation for asbestosis if code J61 also was listed on the death certificate. ‡Alaska,
Streptococcus pseudopneumoniae is a distinct pathogen and the available evidence suggests its sig... more Streptococcus pseudopneumoniae is a distinct pathogen and the available evidence suggests its significance in lower respiratory tract infections. The purpose of this study is to investigate the occurrence of this new species in patients presenting with community-acquired pneumonia in a university hospital setting using routine laboratory tests. Sputum samples (n = 213) submitted to the microbiology laboratory for culture from cases clinically diagnosed as community-acquired pneumonia are studied. Optochin variability in ambient air and 5% CO2 was the criterion used to identify S. pseudopneumoniae. Disc-diffusion and E-test on Muller Hinton blood-based agar were used for antibiotic susceptibility testing following Clinical Laboratory Standard Institute breakpoints. Out of the screened isolates, only six (3%) were identified as S. pseudopneumoniae. None of the commercial tests differentiated the pathogens from viridans streptococci so diagnostic laboratories need to provide an alternative identification algorithm. The six isolates showed susceptibility to penicillin, and five isolates were susceptible to vancomycin, but one exhibited low-level resistance (minimum inhibitory concentration [MIC]: 1 μg/mL). All isolates showed high-level resistance to macrolides (MIC: 24- &gt; 256 μg/mL). Although S. pseudopneumoniae strains were not sufficiently frequent to justify routine additional incubation of sputum samples in ambient air, the high resistance pattern is alarming. Further surveillance is needed in diagnostic laboratories to understand the epidemiology and clinical significance of the newly described pathogen.
Bacteremia due to Campylobacter spp. is rarely reported, and Campylobacter fetus is the species m... more Bacteremia due to Campylobacter spp. is rarely reported, and Campylobacter fetus is the species most commonly exhibiting vascular tropism, as occurred in this case report describing the diagnosis of C. fetus bacteremia in an infant presenting with respiratory tract infection. A 5-month-old baby, with undiagnosed failure to thrive, presented to the acute care service with a high fever and respiratory symptoms of 2 days duration. The initial clinical and laboratory diagnosis suggested bacteremia, but there was difficulty with recovery and identification of the organism from blood. Subsequent laboratory testing confirmed C. fetus as the etiological agent. Campylobacter isolated from blood culture bottles may give atypical laboratory features, rendering its identification challenging. Thus, such an infrequent species might be underestimated in frequency, and it should be considered in diagnostic laboratories, when a gram-negative organism with atypical findings is encountered in respiratory samples or blood culture bottles.
The Malaysian Journal of Medical Science, Dec 22, 2021
Background: Pooled specimen screening for the severe acute respiratory syndrome coronavirus 2 (SA... more 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.
Antimicrobial Resistance and Infection Control, Nov 18, 2023
Background Despite tremendous efforts to prevent central line-associated bloodstream infections, ... more 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.
Dormancy models for Mycobacterium tuberculosis play important roles in understanding various aspe... more Dormancy models for Mycobacterium tuberculosis play important roles in understanding various aspects of tuberculosis pathogenesis and in the testing of novel therapeutic regimens. By simulating the latent tuberculosis infection, in which the bacteria exist in a non-replicative state, the models demonstrate reduced susceptibility to antimycobacterial agents. This minireview outlines the models available for simulating latent tuberculosis both in vitro and in several animal species. Additionally, this minireview discusses the advantages and disadvantages of these models for investigating the bacterial subpopulations and susceptibilities to sterilization by various antituberculosis drugs.
Candidemia and antifungal resistance are major healthcare challenges. The aim of this study is to... more 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 crossresistance 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.
Background: Data on the role of aerosolized hydrogen peroxide (AHP) systems in the control of the... more 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.
Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen a... more 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.
Journal of Taibah University Medical Sciences, Jun 1, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Pseudomonas aeruginosa is a common gram-negative bacillus in nosocomial settings. Consideration o... more 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 drugresistant 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) β-lactamases, and injectosomes (type III secretion system) known to mediate high virulence. The pool of extended spectrum βlactamases 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.
Background: Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seek... more Background: Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seeking shelter in other European countries. Aim: We aimed to investigate the prevalence and the molecular epidemiology of multidrug-resistant Gram-negative (MDRGN) bacteria and meticillin-resistant Staphylococcus aureus (MRSA) in Ukrainian patients at admittance to the University Hospital Frankfurt, Germany. Methods: We performed screening and observational analysis of all patients from March until June 2022. Genomes of MDRGN isolates were analysed for antimicrobial resistance, virulence genes and phylogenetic relatedness. Results: We included 103 patients (median age: 39 ± 23.7 years), 57 of whom were female (55.3%; 95% confidence interval (CI): 45.2-5.1). Patients were most frequently admitted to the Department of Paediatrics (29/103; 28.2%; 95% CI: 19.7-37.9). We found 34 MDRGN isolates in 17 of 103 patients (16.5%; 95% CI: 9.9-25.1). Ten patients carried 21 carbapenem-resistant (CR) bacteria, five of them more than one CR isolate. Four of six patients with war-related injuries carried eight CR isolates. In six of 10 patients, CR isolates caused infections. Genomic characterisation revealed that the CR isolates harboured at least one carbapenemase gene, bla NDM-1 being the most frequent (n = 10). Core genome and plasmid analysis revealed no epidemiological connection between most of these isolates. Hypervirulence marker genes were found in five of six Klebsiella pneumoniae CR isolates. No MRSA was found. Conclusion: Hospitals should consider infection control strategies to cover the elevated prevalence of MDRGN bacteria in Ukrainian patients with war-related injuries and/or hospital pretreatment and to prevent the spread of hypervirulent CR isolates.
النوعية محددة تكن لم العزالت من 94 أصل من 24% أن لألهتمام مستخلصات 53 بني... more النوعية محددة تكن لم العزالت من 94 أصل من 24% أن لألهتمام مستخلصات 53 بني من .cpsA املدبر للجني سلبية كانت 18% و املقاومة احادية)17%(9 كانت النوعية محددة الرئوية املكورات 5 و املاكرواليد ضد املقاومة احادية)5.6%(3 و البنسلني ضد املقاومة للجينات العالية النسبة تختلف لم مقاومة. غير)9.4%(املكورات فإن وباملثل)p=0.76(املصلي للنمط وفقا ً كبيرا ً اختالفا عالية مقاومة معدالت لها cpsA+ و cpsA-النوعية محددة غير الرئوية .)47%(واملاكروليدات)62.5%(للبنسلني الكبسولي النوع ظهور على الضوء البيانات هذه تسلط اخلامتة: وعالوة)p=0.001 29 املريض عمر (متوسط 11A ً سابقا املعروف تبني النوعية محددة غير املستخلصات من عالية نسبة فإن ذلك، على اللقاحات تغطيها ال محتملة منطية غير رئوية املصلية األمناط ظهور املتاحة. Objectives: To study serotype distribution and antimicrobial resistance to beta-lactams and macrolides in pneumococci causing respiratory diseases after the introduction of the 13-valent pneumococcal conjugate vaccine in Saudi Arabia. Methods: This is a hospital-based and a cross-sectional prospective surveillance study conducted at King Fahad Hospital of the University, AlKhobar, Kingdom of Saudi Arabia, in which respiratory pneumococcal isolates collected between 2012 and 2014 were serotyped by multiplex sequential polymerase chain reaction)PCR(and Pneumotest-Latex. Resistance genes to beta-lactams and macrolides were detected by multiplex PCR. Results: The most common serotypes encountered were 11A, 19A, 17F, 23F, 3, and 19F, representing 64% of the typeable strains. Interestingly, 24% of the 94 isolates were not typeable and 18% were negative for the housekeeping gene cpsA. Among the 53 typeable pneumococci isolates, 36)67.9%(carried genes encoding resistance to both penicillin and macrolides, 9)17%(were penicillin-monoresistant, 3)5.6%(were macrolide-monoresistant, and 5)9.4%(were designated non-resistant. The high rate of resistance genes did not significantly differ according to serotype)p=0.76(. Similarly, non-typeable pneumococci)cpsA+ and cpsA-(had high rates of resistance to both penicillin)62.5%(and macrolides)47%(. Conclusion: These data highlight the emergence of a previously rare capsular type, 11A)mean patient age, 29 years; p=0.001(. Moreover, the high percentage of non-typeable isolates shows the emergence of possible atypical pneumococcal serotypes not covered by available vaccines.
This study assessed the correlation between biofilm formation in Pseudomonas aeruginosa strains w... more 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 β-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 β-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.
Ralstonia spp. is an emerging, non-fermentative Gram-negative rod that demonstrates multidrug res... more 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 trimethoprimsulphamethoxazole 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.
This study analyzed the genotype, antibiotic resistance, and biofilm formation of Acinetobacter b... more This study analyzed the genotype, antibiotic resistance, and biofilm formation of Acinetobacter baumannii strains and assessed the correlation between biofilm formation, antibiotic resistance, and biofilm-related risk factors. A total of 207 non-replicate multi-drug-resistant A. baumannii strains were prospectively isolated. Phenotypic identification and antimicrobial susceptibility testing were carried out. Isolate biofilm formation ability was evaluated using the tissue culture plate (TCP), Congo red agar, and tube methods. Clonal relatedness between the strains was assessed by enterobacterial repetitive intergenic consensus-PCR genotyping. Of the 207 isolates, 52.5% originated from an intensive care unit setting, and pan resistance was observed against ceftazidime and cefepime, with elevated resistance (99-94%) to piperacillin/tazobactam, imipenem, levofloxacin, and ciprofloxacin. alongside high susceptibility to tigecycline (97.8%). The Tissue culture plate, Tube method, and Congo red agar methods revealed that 53.6%, 20.8%, and 2.7% of the strains were strong biofilm producers, respectively, while a significant correlation was observed between biofilm formation and device-originating respiratory isolates (p = 0.0009) and between biofilm formation in colonized vs. true infection isolates (p = 0.0001). No correlation was detected between antibiotic resistance and biofilm formation capacity, and the majority of isolates were clonally unrelated. These findings highlight the urgent need for implementing strict infection control measures in clinical settings.
Electronic journal of general medicine, Jul 1, 2023
A lack of evidence of accuracy for various testing modalities for carbapenem-resistant Enterobact... more A lack of evidence of accuracy for various testing modalities for carbapenem-resistant Enterobacterales (CRE) reduces the efficiency of screening and delays the isolation of carriers. This study examined the performance of phenotypic detection of CRE in comparison to molecular testing. A cross-sectional study was conducted in an academic medical institution in Saudi Arabia on CRE-screened patients during a 36-month period (April 1, 2019, through March 31, 2022). Cases were followed up for their susceptibility status by the phenotypic gradient method and genotypes. Of 3,116 samples tested, 359 carbapenemase genes were detected in 297 strains (9.5%) belonging to 292 patients. Oxacilliniase-48 (OXA-48) was the most frequently detected genotype (n=190, 64%), followed by a combined New Delhi metallo-B-lactamase (NDM)/OXA-48 genotype (n=77, 25.9%). Variable missed isolation days were encountered for various genotypes (0-18.5 days), with an excellent clinical utility index obtained for screening the OXA-48 genotype phenotypically. The data provided some insights into the predictive role and shortcomings of the e-test alone in CRE screening. While it provided a reasonable approach in a CRE population dominated by OXA-48 genotypes, it was more likely to miss the NDM-incurred carbapenemase. Thus, local epidemiology in an institution must be considered when designing a local screening protocol in addition to consideration of cost and turnaround time.
Rapid, reliable results can be given by molecular, direct detection and identification of the Myc... more 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.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Feb 9, 2009
underlying cause coded as J65 (pneumoconiosis associated with tuberculosis) or J92.0 (pleural pla... more underlying cause coded as J65 (pneumoconiosis associated with tuberculosis) or J92.0 (pleural plaque with presence of asbestos) also were included in the underlying cause-of-death tabulation for asbestosis if code J61 also was listed on the death certificate. ‡Alaska,
Streptococcus pseudopneumoniae is a distinct pathogen and the available evidence suggests its sig... more Streptococcus pseudopneumoniae is a distinct pathogen and the available evidence suggests its significance in lower respiratory tract infections. The purpose of this study is to investigate the occurrence of this new species in patients presenting with community-acquired pneumonia in a university hospital setting using routine laboratory tests. Sputum samples (n = 213) submitted to the microbiology laboratory for culture from cases clinically diagnosed as community-acquired pneumonia are studied. Optochin variability in ambient air and 5% CO2 was the criterion used to identify S. pseudopneumoniae. Disc-diffusion and E-test on Muller Hinton blood-based agar were used for antibiotic susceptibility testing following Clinical Laboratory Standard Institute breakpoints. Out of the screened isolates, only six (3%) were identified as S. pseudopneumoniae. None of the commercial tests differentiated the pathogens from viridans streptococci so diagnostic laboratories need to provide an alternative identification algorithm. The six isolates showed susceptibility to penicillin, and five isolates were susceptible to vancomycin, but one exhibited low-level resistance (minimum inhibitory concentration [MIC]: 1 μg/mL). All isolates showed high-level resistance to macrolides (MIC: 24- &gt; 256 μg/mL). Although S. pseudopneumoniae strains were not sufficiently frequent to justify routine additional incubation of sputum samples in ambient air, the high resistance pattern is alarming. Further surveillance is needed in diagnostic laboratories to understand the epidemiology and clinical significance of the newly described pathogen.
Bacteremia due to Campylobacter spp. is rarely reported, and Campylobacter fetus is the species m... more Bacteremia due to Campylobacter spp. is rarely reported, and Campylobacter fetus is the species most commonly exhibiting vascular tropism, as occurred in this case report describing the diagnosis of C. fetus bacteremia in an infant presenting with respiratory tract infection. A 5-month-old baby, with undiagnosed failure to thrive, presented to the acute care service with a high fever and respiratory symptoms of 2 days duration. The initial clinical and laboratory diagnosis suggested bacteremia, but there was difficulty with recovery and identification of the organism from blood. Subsequent laboratory testing confirmed C. fetus as the etiological agent. Campylobacter isolated from blood culture bottles may give atypical laboratory features, rendering its identification challenging. Thus, such an infrequent species might be underestimated in frequency, and it should be considered in diagnostic laboratories, when a gram-negative organism with atypical findings is encountered in respiratory samples or blood culture bottles.
The Malaysian Journal of Medical Science, Dec 22, 2021
Background: Pooled specimen screening for the severe acute respiratory syndrome coronavirus 2 (SA... more 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.
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