COVID-19 related multisystem inflammatory syndrome in children (MIS-C): a case series from a tertiary care pediatric hospital in Qatar.

BACKGROUND: Multisystem Inflammatory Syndrome in Children (MIS-C) is a severe complication of coronavirus disease 2019 (COVID-19) in children, which is increasingly being reported worldwide. Here we report the first case series of 7 children diagnosed with MIS-C in Qatar. METHODS: Clinical features and outcomes of COVID-19 positive patients admitted to Sidra Medicine, Qatar from June to October 2020, who met the WHO case definition for MIS-C were reviewed. RESULTS: The mean age in our case series was 5.6 years, of which 71.4% were males. All patients were previously healthy but had a history of COVID-19 infection. Fever, rash, vomiting and abdominal pain were the most common symptoms (70-100%). The average hospitalization was 12.9 days with no case fatalities. Laboratory findings included lymphopenia and thrombocytopenia in most patients, as well as evidence of coagulopathy and elevated inflammatory markers such as C-reactive protein, ferritin and procalcitonin. Many patients (71.4%) required inotropic support in intensive care, while only one required respiratory support. Although all patients had elevated cardiac biomarkers, cardiovascular involvement was observed in 42.9% of patients with one patient developing a giant coronary aneurysm. All patients received intravenous immunoglobulin (IVIG) and 86% of patients received corticosteroids, with two patients requiring treatment with IL-1 inhibitors. CONCLUSIONS: Our report is one of the first reports on MIS-C from Asia. Although clinical features and outcomes are not significantly different from those reported elsewhere, lack of case fatalities in our cohort may indicate that early recognition and prompt medical attention is necessary for a favorable outcome in MIS-C.

Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report.

BACKGROUND: Infections with multidrug-resistant organisms (MDRO) pose a serious threat to patients with dysregulated immunity such as in hemophagocytic lymphohistiocytosis (HLH), but such infections have rarely been comprehensively characterized. Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. CASE PRESENTATION: A previously healthy, six-year-old boy presented with a 45-day history of fever prior to a diagnosis of hemophagocytic lymphohistiocytosis and hemorrhagic colitis, both associated with CMV. On hospital admission, the patient was found to be colonized with multiple, multidrug-resistant (MDR) bacteria including vancomycin-resistant enterococci (VRE) and carbapenamase-producing organisms (CPO). He eventually developed respiratory, urine and bloodstream infections with highly drug-resistant, including pandrug-resistant bacteria, which could not be controlled by antibiotic treatment. Antiviral therapy also failed to contain his CMV infection and the patient succumbed to overwhelming bacterial and viral infection. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. CONCLUSIONS: The case highlights both the risk of acquiring MDR superbugs and the severity of these infections in HLH patients.

Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16.

Objectives: Globally there is an increased prevalence of carbapenem-resistant Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs) in the hospital setting. This increase prompted the Canadian Nosocomial Infection Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and infections identified from patients in CNISP-participating hospitals between 2010 and 2016. Methods: Participating acute care facilities across Canada submitted CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from medical records using a standardized questionnaire. WGS was conducted on all CRAs and data underwent single nucleotide variant analysis, resistance gene detection and MLST. Results: The 7 year incidence rate of CRA was 0.02 per 10 000 patient days and 0.015 per 1000 admissions, with no significant increase observed over the surveillance period (P > 0.73). Ninety-four CRA isolates were collected from 58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%) was the most common due to two separate clusters, followed by the OXA-23 group (41.9%). Patients with a travel history were associated with 38.8% of CRA cases. The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA cases. Colistin was the most active antimicrobial agent (95.8% susceptibility). Conclusions: CRA remains uncommon in Canadian hospitals and the incidence did not increase from 2010 to 2016. Almost half of the cases were from two clusters harbouring OXA-235-group enzymes. Previous medical treatment during travel outside of Canada was common.

Enterobacter cloacae Complex Isolates Harboring blaNMC-A or blaIMI-Type Class A Carbapenemase Genes on Novel Chromosomal Integrative Elements and Plasmids.

Carbapenem-resistant Enterobacter cloacae complex isolates submitted to a reference laboratory from 2010 to 2015 were screened by PCR for seven common carbapenemase gene groups, namely, KPC, NDM, OXA-48, VIM, IMP, GES, and NMC-A/IMI. Nineteen of the submitted isolates (1.7%) were found to harbor Ambler class A blaNMC-A or blaIMI-type carbapenemases. All 19 isolates were resistant to at least one carbapenem but susceptible to aminoglycosides, trimethoprim-sulfamethoxazole, tigecycline, and ciprofloxacin. Most isolates (17/19) gave positive results with the Carba-NP test for phenotypic carbapenemase detection. Isolates were genetically diverse by pulsed-field gel electrophoresis macrorestriction analysis, multilocus sequence typing, and hsp60 gene analysis. The genes were found in various Enterobacter cloacae complex species; however, blaNMC-A was highly associated with Enterobacter ludwigii Whole-genome sequencing and bioinformatics analysis revealed that all NMC-A (n = 10), IMI-1 (n = 5), and IMI-9 (n = 2) producers harbored the carbapenemase gene on EludIMEX-1-like integrative mobile elements (EcloIMEXs) located in the identical chromosomal locus. Two novel genes, blaIMI-5 and blaIMI-6, were harbored on different IncFII-type plasmids. Enterobacter cloacae complex isolates harboring blaNMC-A/IMI-type carbapenemases are relatively rare in Canada. Though mostly found integrated into the chromosome, some variants are located on plasmids that may enhance their mobility potential.

Results from the Canadian Nosocomial Infection Surveillance Program on Carbapenemase-Producing Enterobacteriaceae, 2010 to 2014.

Carbapenemase-producing Enterobacteriaceae (CPE) are increasing globally; here we report on the investigation of CPE in Canada over a 5-year period. Participating acute care facilities across Canada submitted carbapenem-nonsusceptible Enterobacteriaceae from 1 January 2010 to 31 December 2014 to the National Microbiology Laboratory. All CPE were characterized by antimicrobial susceptibilities, pulsed-field gel electrophoresis, multilocus sequence typing, and plasmid restriction fragment length polymorphism analysis and had patient data collected using a standard questionnaire. The 5-year incidence rate of CPE was 0.09 per 10,000 patient days and 0.07 per 1,000 admissions. There were a total of 261 CPE isolated from 238 patients in 58 hospitals during the study period. blaKPC-3 (64.8%) and blaNDM-1 (17.6%) represented the highest proportion of carbapenemase genes detected in Canadian isolates. Patients who had a history of medical attention during international travel accounted for 21% of CPE cases. The hospital 30-day all-cause mortality rate for the 5-year surveillance period was 17.1 per 100 CPE cases. No significant increase in the occurrence of CPE was observed from 2010 to 2014. Nosocomial transmission of CPE, as well as international health care, is driving its persistence within Canada.

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection: A Randomized Clinical Trial.

IMPORTANCE: Clostridium difficile infection (CDI) is a major burden in health care and community settings. CDI recurrence is of particular concern because of limited treatment options and associated clinical and infection control issues. Fecal microbiota transplantation (FMT) is a promising, but not readily available, intervention. OBJECTIVE: To determine whether frozen-and-thawed (frozen, experimental) FMT is noninferior to fresh (standard) FMT in terms of clinical efficacy among patients with recurrent or refractory CDI and to assess the safety of both types of FMT. DESIGN, SETTING, AND PARTICIPANTS: Randomized, double-blind, noninferiority trial enrolling 232 adults with recurrent or refractory CDI, conducted between July 2012 and September 2014 at 6 academic medical centers in Canada. INTERVENTIONS: Patients were randomly allocated to receive frozen (n = 114) or fresh (n = 118) FMT via enema. MAIN OUTCOMES AND MEASURES: The primary outcome measures were clinical resolution of diarrhea without relapse at 13 weeks and adverse events. Noninferiority margin was set at 15%. RESULTS: A total of 219 patients (n = 108 in the frozen FMT group and n = 111 in the fresh FMT group) were included in the modified intention-to-treat (mITT) population and 178 (frozen FMT: n = 91, fresh FMT: n = 87) in the per-protocol population. In the per-protocol population, the proportion of patients with clinical resolution was 83.5% for the frozen FMT group and 85.1% for the fresh FMT group (difference, -1.6% [95% CI, -10.5% to ∞]; P = .01 for noninferiority). In the mITT population the clinical resolution was 75.0% for the frozen FMT group and 70.3% for the fresh FMT group (difference, 4.7% [95% CI, -5.2% to ∞]; P < .001 for noninferiority). There were no differences in the proportion of adverse or serious adverse events between the treatment groups. CONCLUSIONS AND RELEVANCE: Among adults with recurrent or refractory CDI, the use of frozen compared with fresh FMT did not result in worse proportion of clinical resolution of diarrhea. Given the potential advantages of providing frozen FMT, its use is a reasonable option in this setting. TRIAL REGISTRATION: clinicaltrials.gov Identifier:NCT01398969.

Longitudinal clinical findings and outcome among patients with Cryptococcus gattii infection in British Columbia.

BACKGROUND: Cryptococcus gattii (Cg) infection emerged in British Columbia in 1999. A longitudinal, clinical description of patients has not been reported. METHODS: Medical records were reviewed for Cg patients identified through surveillance (1999-2007). Risk factors for Cg mortality were explored using multivariate Cox regression; longitudinal patterns in serum cryptococcal antigen (SCrAg) titers and the probability of chest cryptococcomas over time were estimated using cubic B-splines in mixed-effects regression models. RESULTS: Among 152 patients, 111 (73.0%) were culture confirmed. Isolated lung infection was present in 105 (69.1%) patients; 47 (30.9%) had central nervous system infection, with or without lung involvement. Malignancy was the provisional diagnosis in 64 (42.1%) patients. Underlying diseases were present in 91 (59.9%) patients; 23 (15.1%) were immunocompromised, and 23 (15.1%) had asymptomatic disease. There were only 2 (1.8%) culture positive relapses, both within 12 months of follow-up. The estimated median time to resolution of lung cryptococcomas and decline in SCrAg titer to <1:8 was 2.8 and 2.9 years, respectively. Cg-related and all-cause mortality among culture-confirmed cases at 12 months' follow-up was 23.3% and 27.2%, respectively. Cg-related mortality was associated with age >50 years (hazard ratio [HR], 15.6; 95% confidence interval [CI], 1.9-130.5) and immunocompromise (HR, 5.8; CI, 1.5-21.6). All Cg-related mortality occurred among culture-positive cases within 1 year of diagnosis. CONCLUSIONS: Cryptococcomas and serum antigenemia were slow to resolve. However, late onset of failed therapy or relapse was uncommon, suggesting that delayed resolution of these findings does not require prolongation of treatment beyond that recommended by guidelines.

Antimicrobial co-resistance patterns of gram-negative bacilli isolated from bloodstream infections: a longitudinal epidemiological study from 2002-2011.

BACKGROUND: Increasing multidrug resistance in gram-negative bacilli (GNB) infections poses a serious threat to public health. Few studies have analyzed co-resistance rates, defined as an antimicrobial susceptibility profile in a subset already resistant to one specific antibiotic. The epidemiologic and clinical utility of determining co-resistance rates are analyzed and discussed. METHODS: A 10-year retrospective study from 2002-2011 of bloodstream infections with GNB were analyzed from three hospitals in Greater Vancouver, BC, Canada. Descriptive statistics were calculated for antimicrobial resistance and co-resistance. Statistical analysis further described temporal trends of antimicrobial resistance, correlations of resistance between combinations of antimicrobials, and temporal trends in co-resistance patterns. RESULTS: The total number of unique blood stream isolates of GNB was 3280. Increasing resistance to individual antimicrobials was observed for E. coli, K. pneumoniae, K. oxytoca, E. cloacae, and P. aeruginosa. Ciprofloxacin resistance in E. coli peaked in 2006 at 40% and subsequently stabilized at 29% in 2011, corresponding to decreasing ciprofloxacin usage after 2007, as assessed by defined daily dose utilization data. High co-resistance rates were observed for ceftriaxone-resistant E. coli with ciprofloxacin (73%), ceftriaxone-resistant K. pneumoniae with trimethoprim-sulfamethoxazole (83%), ciprofloxacin-resistant E. cloacae with ticarcillin-clavulanate (91%), and piperacillin-tazobactam-resistant P. aeruginosa with ceftazidime (83%). CONCLUSIONS: Increasing antimicrobial resistance was demonstrated over the study period, which may partially be associated with antimicrobial consumption. The study of co-resistance rates in multidrug resistant GNB provides insight into the epidemiology of resistance acquisition, and may be used as a clinical tool to aid prescribing empiric antimicrobial therapy.

Changing epidemiology of methicillin-resistant Staphylococcus aureus in Canada.

OBJECTIVES: To compare the demographics, antimicrobial susceptibilities and molecular epidemiology of community-associated (CA) and healthcare-associated (HA) methicillin-resistant Staphylococcus aureus (MRSA) in Canada. METHODS: Between 2007 and 2011, 1266 MRSA were collected from inpatients and outpatients attending tertiary-care medical centres across Canada. Susceptibility testing was performed using broth microdilution and isolates were characterized by spa typing and PCR to detect the Panton-Valentine leucocidin (PVL) gene. Detection of heterogeneous vancomycin-intermediate S. aureus (hVISA) was performed using the Etest macromethod and confirmed by population analysis profiling. RESULTS: The annual proportion of S. aureus that were methicillin resistant decreased from 26.1% in 2007 to 19.3% in 2011 (P= 0.0002). Of 1266 MRSA isolated, 366 (28.9%) were CA-MRSA genotypes and 868 (68.6%) were HA-MRSA genotypes. The proportion of MRSA represented by CA-MRSA genotypes increased from 19.7% to 36.4% between 2007 and 2011 (P < 0.0001). CMRSA10 (USA300) was the predominant CA-MRSA genotype (22.1%); the most common HA-MRSA genotype was CMRSA2 (USA100/800) (58.1%). PVL was detected in 328/366 (89.6%) of CA-MRSA genotypes and 6/868 (0.7%) of HA-MRSA genotypes. The hVISA phenotype was detected in 7/27 (25.9%) of MRSA with a vancomycin MIC of 2 mg/L. CONCLUSIONS: The most frequent CA-MRSA genotype was CMRSA10 (USA300), while CMRSA2 (USA100/800) was the predominant HA-MRSA genotype. Despite a decrease in the numbers of MRSA, the proportion of CMRSA10 (USA300) CA-MRSA has risen significantly between 2007 and 2011 in Canada.

A prospective randomized trial of povidone-iodine prophylactic cleansing of the rectum before transrectal ultrasound guided prostate biopsy.

PURPOSE: Transrectal ultrasound guided prostate biopsy can lead to urinary tract infections in 3% to 11% and sepsis in 0.1% to 5% of patients. We investigated the efficacy of rectal cleansing with povidone-iodine before transrectal ultrasound guided prostate biopsy to reduce infectious complications. MATERIALS AND METHODS: Between 2009 and 2011, 865 men were prospectively randomized to rectal cleansing (421) or no cleansing (444) before transrectal ultrasound guided prostate biopsy. Patients received ciprofloxacin prophylaxis and rectal swab cultures were obtained before transrectal ultrasound guided prostate biopsy. Patients completed a telephone interview 7 days after undergoing the biopsy. The primary end point was the rate of infectious complications, a composite end point of 1 or more of 1) fever greater than 38.0C, 2) urinary tract infection or 3) sepsis (standardized definition). Chi-square significance testing was performed for differences between groups and a multivariate analysis was performed to assess risk factors for infectious complications. RESULTS: Infectious complications were observed in 31 (3.5%) patients, including 11 (2.6%) treated and 20 (4.5%) control patients (p = 0.15). Sepsis was observed in 4 (1.0%) treated and 7 (1.6%) control patients (p = 0.55). On multivariate analysis resistance to ciprofloxacin in the rectal swab culture (p = 0.002) and a history of taking ciprofloxacin in the 3 months preceding transrectal ultrasound guided prostate biopsy (p = 0.009) predicted infectious complications. CONCLUSIONS: Rectal cleansing with povidone-iodine before transrectal ultrasound guided prostate biopsy was safe, but the 42% relative risk reduction of infectious complications was not statistically significant. Patients who have received ciprofloxacin within 3 months of transrectal ultrasound guided prostate biopsy should be considered for alternate prophylaxis or possibly a delay of biopsy beyond 3 months.

Ciprofloxacin resistance in the faecal carriage of patients undergoing transrectal ultrasound guided prostate biopsy.

UNLABELLED: WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Transrectal ultrasound guided prostate biopsies (TRUSBx) are associated with a spectrum of complications, including most significantly infection, which affects up to 5% of patients. In the most severe cases, infection leads to sepsis, a life-threatening complication. Escherichia coli is the primary responsible pathogen. Although antibiotic prophylaxis with fluoroquinolones is routinely used, there is evidence that the infection rate after TRUSBx is increasing, and this appears to be due to an increasing prevalence of ciprofloxacin-resistant rectal flora. This is the largest prospective clinical trial to date analysing the rectal flora of men undergoing prostate biopsies. We determined the microbial and antibiotic sensitivity profiles from 849 patients. Ciprofloxacin-resistant Gram-negative organisms were identified in the rectal flora of 19.0% of men. Furthermore, fluoroquinolone use within 6 months preceding a TRUSBx and the presence of a prosthetic heart valve were significant predictors of ciprofloxacin resistance on rectal swab. Determining the prevalence of rectal fluoroquinolone resistance has important implications in evaluation of the suitability of prophylactic regimens. Antimicrobial profiles derived from rectal swabs pre-biopsy may prove useful in guiding targeted antibiotic prophylaxis. OBJECTIVES: To establish the prevalence of ciprofloxacin-resistant bacteria in patients undergoing transrectal ultrasound guided prostate biopsies (TRUSBx) and to determine whether this predicts subsequent infectious complications. To identify risk factors for harbouring ciprofloxacin-resistant flora. PATIENTS AND METHODS: Any patient undergoing a TRUSBx from 2009 to 2011 was eligible for enrolment in this prospective study. Pre-biopsy rectal and urine cultures and post-biopsy urine cultures were obtained and antimicrobial susceptibility was determined. Univariate and multivariate analyses were performed to identify independent patient risk factors associated with ciprofloxacin-resistant rectal flora. RESULTS: A total of 865 patients underwent TRUSBx, of whom 19.0% were found to have ciprofloxacin-resistant Gram-negative coliforms. Escherichia coli was the most prevalent Gram-negative rectal isolate (80.9%) and accounted for 90.6% of ciprofloxacin resistance. Patient characteristics that conferred an increased risk of harbouring ciprofloxacin-resistant organisms included a history of a heart valve replacement (P < 0.05) and ciprofloxacin use in the past 3 months (P < 0.05). Infectious complications were observed in 3.6% (n = 31) of the patient population and 48% of these patients grew ciprofloxacin-resistant organisms on the pre-biopsy rectal swab (P < 0.001). CONCLUSIONS: Antimicrobial resistance to ciprofloxacin in the rectal flora was common, particularly in patients with recent ciprofloxacin use and a heart valve replacement. Despite a significant correlation between those patients who developed infections and the detection of ciprofloxacin-resistant organisms, only 9.0% (n = 15) of the total group with ciprofloxacin resistance developed an infectious complication. Future studies will need to evaluate the cost effectiveness and clinical utility of a pre-biopsy rectal culture in targeting antibiotic prophylaxis.

Ten-year review of candidemia in a Canadian tertiary care centre: Predominance of non-albicans Candida species.

OBJECTIVE: To review the epidemiology and associated risk factors for candidemia at a tertiary care centre, in view of recent reports on the changing epidemiology of bloodstream infection due to Candida species. METHODS: Between January 2000 and December 2009, patients with blood culture samples positive for Candida species were identified using the microbiology laboratory information system. Patient data were collected by retrospective chart review of clinical characteristics including demographic data, underlying medical diagnoses and risk factors. RESULTS: A total of 266 candidemia episodes were included in the final analysis. Fifty-nine per cent of these episodes occurred in males and 51% were in patients >60 years of age. The most common risk factor for candidemia was previous antibiotic use (85%). The most frequent species was Candida albicans (49%), followed by Candida glabrata (30%). C albicans was the predominant species in all study years with the exception of 2002, in which C glabrata was more frequent. The likelihood of recovering a non-albicans Candida species was found to be significantly associated with previous antifungal therapy (P=0.0004), immunosuppressive therapy (P=0.002), abdominal surgery (P=0.003) and malignancy (P=0.05). Mixed candidemia was found in 10 episodes (4%); 80% grew C albicans and C glabrata. Risk factors for mixed candidemia were not significantly different from those with monomicrobial candidemia. CONCLUSION: C albicans remains the most commonly isolated species in this setting, consistent with findings from other Canadian centres. However, non-albicans Candida species were overall predominant. Mixed-species candidemia does not appear to be more prevalent in patients with identified risk factors.

OBJECTIF: Analyser l'épidémiologie et les facteurs de risque connexes de septicémie à Candida dans un centre de soins tertiaires, compte tenu des récents rapports sur l'évolution de l'épidémiologie des bactériémies causées par des espèces de Candida. MÉTHODOLOGIE: Entre janvier 2000 et décembre 2009, les chercheurs ont déterminé les patients dont l'hémoculture était positive aux espèces de Candida au moyen du système d'information du laboratoire de microbiologie. Ils ont colligé les données à leur sujet au moyen de l'analyse rétrospective des caractéristiques cliniques contenues dans leur dossier, y compris les données démographiques, les diagnostics médicaux sous-jacents et les facteurs de risque. RÉSULTATS: Au total, 266 épisodes de septicémie à Candida ont été inclus dans l'analyse finale. Cinquante-neuf pour cent d'entre eux s'étaient produits chez des hommes, et 51 % chez des patients de plus de 60 ans. La prise antérieure d'antibiotiques était le principal facteur de risque de septicémie à Candida (85 %), et les espèces les plus fréquentes, le Candida albicans (49 %), suivies du Candida glabrata (30 %). Le C albicans était l'espèce prédominante dans toutes les années d'étude, sauf en 2002, où il était détrôné par le C glabrata. La possibilité de dépister une autre espèce que le C albicans s'associait nettement à une thérapie anti-fongique antérieure (P=0,0004), à une thérapie immunosuppressive (P=0,002), à une chirurgie abdominale (P=0,003) et à une tumeur maligne (P=0,05). Dans dix épisodes (4 %), les chercheurs ont observé une septicémie à Candida mixte, dont 80 % d'association de C albicans et de C glabrata. Les facteurs de risque de septicémie à Candida mixte ne différaient pas de manière significative de ceux des septicémies à Candida monomicrobiennes. CONCLUSION: Le C albicans demeure l'espèce la plus isolée dans ce contexte, ce qui correspond aux observations d'autres centres canadiens. Cependant, dans l'ensemble, les autres espèces que le C albicans étaient prédominantes. Les septicémies à Candida mixtes ne semblent pas plus prévalentes chez les patients ayant des facteurs de risque déterminés.

New Delhi metallo-ß-lactamase in Klebsiella pneumoniae and Escherichia coli, Canada.

Multidrug-resistant Klebsiella pneumoniae and Escherichia coli isolates harboring New Delhi metallo-ß-lactamase (NDM-1) were isolated from a patient who had returned to Canada from India. The NDM-1 gene was found on closely related incompatibility group A/C type plasmids. The occurrence of NDM-1 in North America is a major public health concern.

Performance and Impact on Initial Antibiotic Choice of Direct Identification of Pathogens from Pediatric Blood Culture Bottles Using an In-House MALDI-TOF MS Protocol.

The performance and early therapeutic impact of direct identification by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF; DIMT) on pediatric blood culture bottles using in-house-developed methods to obtain microbial pellets for spectrometric analysis have seldom been studied. During a 2-year period (June 2018 to May 2020), DIMT was performed on broths from positive pediatric blood culture bottles using an in-house-developed method. Organism identifications with a score of ≥1.6 were notified to treating clinicians. Therapeutic modifications that occurred after the communication of DIMT were reviewed through the electronic medical records. DIMT was performed on 530 pediatric positive blood culture bottles. Among 505 monomicrobial bottles, identifications from 298 (97.7%) deemed as bloodstream infections (BSI) and 189 (94.5%) as contaminations had DIMT notified to clinicians. All identifications were correct except for one Streptococcus mitis incorrectly reported as Streptococcus pneumoniae. Therapy modifications resulting from DIMT occurred in 27 (8.3%) patients with BSI. Deescalation from effective or ineffective broad-spectrum regimens occurred mainly in Enterococcus faecalis bacteremia, whereas appropriate escalation from an ineffective regimen with narrower spectrum occurred mainly in bacteremia caused by AmpC-ß-lactamase-producing Enterobacterales. Escalation therapy was instituted significantly faster than deescalation therapy (median time, 0.75 versus 10.5 h [P = 0.01]). DIMT also enabled clinicians to confirm contamination in nearly one-half of patients with contaminated blood cultures. Our DIMT method applied to positive pediatric blood culture bottles demonstrated reliable performance for the rapid identification of pathogens. Our DIMT approach allowed therapeutic optimization in BSI, especially involving microorganisms with intrinsic antibiotic resistance, and was helpful in the early identification of likely contaminants. IMPORTANCE We demonstrate the performance and early impact on the antimicrobial management of bloodstream infections of an inexpensive, in-house preparation method for direct identification of bloodstream pathogens in pediatric blood culture bottles by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.

Evaluation of Rapid Immunochromatographic Tests for the Direct Detection of Extended Spectrum Beta-Lactamases and Carbapenemases in Enterobacterales Isolated from Positive Blood Cultures.

NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech) are two rapid in vitro immunochromatographic assays that are widely used for the detection of the most common extended spectrum beta-lactamases (ESBL) and carbapenemases in Enterobacterales. ESBL and carbapenemases are leading causes of morbidity and mortality worldwide and their rapid detection from positive blood cultures is crucial for early initiation of effective antimicrobial therapy in bloodstream infections (BSI) involving antibiotic-resistant organisms. In this study, we developed a rapid workflow for positive blood cultures for direct identification of Enterobacterales by MALDI-TOF mass-spectrometry, followed by detection of ESBL and carbapenemases using NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech). The workflow was evaluated using Enterobacterales isolates (n = 114), primarily Klebsiella species (n = 50) and Escherichia coli (n = 40). Compared to the standard testing approach in our institution using BD Phoenix, our new testing approach demonstrates 100% sensitivity and specificity for organism identification and detection of ESBL and carbapenemases. Implementation of a rapid workflow in diagnostic microbiology laboratories will enable more effective antimicrobial management of patients with BSI due to ESBL- and carbapenemase-producing Enterobacterales. IMPORTANCE The incidence of bloodstream infections (BSI) with extended spectrum beta-lactamase (ESBL) producing and carbapenemase producing Enterobacterales (CPE) is increasing at an alarming rate, for which only limited therapeutic options remain available. Rapid identification of these bacteria along with their antibiotic resistance mechanisms in positive blood cultures with Gram-negative bacteria will allow for early initiation of effective therapy and limit the overuse of broad-spectrum antibiotics in BSI (1). In this study we evaluated a combined approach of testing positive blood cultures directly, using MALDI-TOF MS followed by rapid immunochromatographic tests, for the detection of ESBLs and CPEs. Our approach demonstrates 100% sensitivity and specificity for the identification of Enterobacterales and detection of ESBLs and CPEs in positive blood culture with a turnaround time (TAT) of ≤60 min compared to a TAT of 48 h required by conventional culture and susceptibility testing methods.

Fecal Carriage and Molecular Characterization of Carbapenemase-Producing Enterobacterales in the Pediatric Population in Qatar.

Whole-genome sequencing was used to characterize carbapenemase-producing Enterobacterales (CPE) strains recovered from rectal screening swab samples obtained from children at a tertiary-care pediatric hospital in Qatar during a 3-year period. A total of 72 CPE isolates recovered from 61 fecal carriers were characterized. Escherichia coli (47 isolates [65.3%]) and Klebsiella pneumoniae (22 isolates [30.6%]) were the most common species identified. High levels of genetic diversity were observed for both species. These 72 isolates produced 78 carbapenemases, characterized as either NDM-type (41 enzymes [52.6%]) or OXA-48-type (37 enzymes [47.4%]). NDM-5 (24 enzymes [30.8%]), NDM-1 (15 enzymes [19.2%]), and OXA-181 (15 enzymes [19.2%]) were the most common variants detected within each type. Twenty-three NDM producers exhibited difficult-to-treat resistance, compared with only 2 of the OXA-48 producers. Multiple comorbidities were identified in 88.5% of the patients, whereas recent travel history to countries in which CPE are endemic was documented for 57.4% of the patients. All 9 blaOXA-48-type-gene-containing E. coli sequence type 38 (ST38) strains were isolated from patients without international travel history. The mean quarterly incidence of fecal carriage decreased more than 6-fold after the implementation of coronavirus disease 2019 (COVID-19)-related international travel restrictions in Qatar in mid-March 2020. Our data suggest that NDM-type and OXA-48-type carbapenemases expressed by a large diversity of E. coli and K. pneumoniae genotypes are largely dominant in the pediatric population of Qatar. Although our data indicate successful local expansion of E. coli ST38 strains harboring blaOXA-244 genes, at least within health care settings, blaOXA-48-type and blaNDM-type genes appear to have been mainly introduced sporadically by asymptomatic carriers who visited or received health care in some nearby countries in which the genes are endemic. IMPORTANCE To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.

Potential influence of rapid diagnostics on timeliness of management decisions for patients with positive blood cultures.

Background: The Accelerate Pheno system (AXDX) provides rapid identification (ID; 90 minutes) and antimicrobial susceptibility testing (AST; approximately 7 hours) from positive blood culture (BC) bottles. We assessed the potential of AXDX results to influence more timely antibiotic interventions with a convenience sample of 158 positive BCs. Methods: BCs with a mono-microbial Gram stain likely to be on the AXDX panel were run in parallel with the standard of care (SOC). Using results from the SOC, the medical microbiologist on call (MMOC) noted interventions made at the time of BC Gram stain and when ID and AST results were available. The timing of MMOC intervention was noted and compared with fastest potential SOC time and AXDX time. Results: Of 158 specimens selected for analysis, 144 were evaluable. ID was available 11.9 hours and AST 27.7 hours faster than SOC. Correct ID was provided for 85.2% of specimens and AST for 59.0% of specimens, with 97.5% essential agreement compared with the SOC. One hundred and thirteen clinical interventions were made on 100 specimens: 54.9% were narrowing; 33.6%, escalation; 6.2%, consultation with ID; and 3.5%, further investigation. If AXDX data had been used immediately once available, interventions would have been possible 24 hours earlier for ID interventions and 39 hours earlier for AST results. Conclusions: Results from rapid diagnostic panels such as AXDX have the potential to support timely antimicrobial de-escalation and other decisions to benefit patients, especially if paired with stewardship interventions.

Historique: Le système Accelerate Pheno (AXDX) permet de procéder à une identification rapide (ID; 90 minutes) et à des tests de susceptibilité antimicrobienne (AST; environ sept heures) à partir de bouteilles d'hémoculture (BH) positives. À l'aide d'un échantillon de commodité de 158 BH positives, les auteurs ont évalué le potentiel de résultats du système AXDX pour favoriser des interventions antibiotiques plus opportunes. Méthodologie: Les auteurs ont comparé les BH présentant une coloration de Gram monomicrobienne susceptible de se trouver sur le panel AXDX avec la norme de soins (NdS). À l'aide des résultats de la NdS, le microbiologiste médical sur appel (MMSA) a consigné les interventions effectuées au moment de la coloration de Gram de la BH et lorsque les résultats de l'ID et de l'AST étaient disponibles. Le moment de l'intervention du MMSA était consigné et comparé avec la durée de la NdS au potentiel le plus rapide et la durée de l'AXDX. Résultats: Des 158 échantillons sélectionnés en vue d'être analysés, 144 étaient évaluables. L'ID était disponible 11,9 heures et l'AST, 27,7 heures plus rapidement que la NdS. L'ID exacte était fournie pour 85,2 % des échantillons et l'AST exacte, pour 59,0 % des échantillons, selon une entente essentielle de 97,5 % par rapport à la NdS. Cent treize interventions ont été effectuées sur 100 échantillons : 54,9 % visaient à réduire le spectre, 33,6 %, à accroître la médication, 6,2 %, à demander une consultation avec l'ID et 3,5 %, à obtenir des explorations plus approfondies. Si les données de l'AXDX avaient été utilisées dès l'obtention des résultats, il aurait été possible d'agir 24 heures plus rapidement pour les interventions d'ID et 39 heures plus rapidement pour les résultats de l'AST. Conclusions: Les résultats des panels diagnostiques rapides comme l'AXDX ont le potentiel de favoriser une désescalade antimicrobienne et d'autres décisions au profit des patients, surtout s'ils s'associent à des interventions de gestion.

Gaseous nitric oxide bactericidal activity retained during intermittent high-dose short duration exposure.

Previously, we have shown that gaseous Nitric oxide (gNO) has great potential as an effective topical anti-infective agent for non-healing wounds due to its non-specific antimicrobial properties. These same antimicrobial attributes may be useful for pulmonary infections. However, gNO would have limited usefulness as an inhaled antimicrobial agent as continuous exposure to the concentration required for a bactericidal effect (160-200 ppm) leads to methemoglobinemia. To overcome this problem, we investigated whether a thirty minute exposure of 160 ppm every four hours would retain the same antimicrobial effect as continuous delivery. In vitro, exposure of clinical multi-drug resistant Staphylococcus aureus and Escherichia coli strains isolated from the lungs of nosocomial pneumonia patients and a lethal antibiotic-resistant strain of Pseudomonas aeruginosa, isolated from a deceased cystic fibrosis patient resulted in over a 5 log(10) reduction in bacterial load after multiple thirty minute treatments (4 cycles) every four hours to 160 ppm gNO. The intermittent regimen required 320 (SD=0)ppm h for 100% lethality whereas the continuous exposure required 800 (SD=160)ppm h. We have also shown that selection for a gNO resistant phenotype did not lead to decrease sensitivity to gNO therapy (p>0.05). In addition, no host cellular toxicity was observed in human THP-1 monocytes and macrophages following intermittent delivery of a high concentration of gNO, and the proliferation and migration of pulmonary epithelial cells was not adversely affected by the administration of intermittent high-dose gNO. These results justify further studies that should focus on whether intermittent delivery of 160 ppm of gNO every four hours can technically be administered while keeping inhaled NO(2) levels less than 2 ppm and methemoglobin saturation less than 2.5 percent.

FilmArray respiratory panel assay: An effective method for detecting viral and atypical bacterial pathogens in bronchoscopy specimens.

The BioFire FilmArray Respiratory Panel (FA RP) is a rapid multiplexed molecular assay approved for detection of viral and atypical bacterial pathogens in nasopharyngeal specimens. This study aimed to evaluate the performance of the BioFire FilmArray Respiratory Panel v1.7 on bronchoscopy specimens. We tested 133 bronchial specimens (87 archived and 46 prospectively collected) with the FA RP and compared the results to the Luminex NxTAG Respiratory Pathogen Panel (NxTAG RPP). After discordant analysis, 123 specimens gave concordant results using the FA RP and the NxTAG RPP for an overall agreement of 93.9% (kappa = 0.88 [95% CI 0.80-0.96]), a positive percent agreement of 93.7% (95% CI 83.7-97.7) and a negative percent agreement of 94.1% (95% CI 84.9-98.1). In conclusion, the BioFire FilmArray RP performed reliably to detect a broad range of respiratory pathogens in bronchoscopy specimens.