The COVID-19 pandemic has strongly impacted healthcare settings. We assess changes in blood culture practices and results during the COVID-19 era. All blood culture vials processed between January 1, ...2017, and December 31, 2020, by 3 clinical laboratories were included. A baseline period from January 1, 2017 to December 31, 2019, was compared to the year 2020. COVID-19 “waves” were defined as follows: “wave 1” from March 16 to May 10, 2020, and “wave 2” from October 29 to December 14, 2020. A mean of 143.5 and 158.6 vials per day were processed in 2019 and 2020 respectively. Up to 300 and 220 vials per day were processed during waves 1 and 2. Among positive vials, a higher rate of contaminant was noticed during wave 1 (55.9% vs 45.0%; P < 0.0001) and interwave (46.0% vs 38.6%; P < 0.0001) in comparison to previous years. The prevalence of contaminants returned to the baseline level during wave 2. Streptococcus pneumonia prevalence fell in 2020 in comparison to the baseline (0.4% vs 1.4%; P < 0.0001). The COVID-19 pandemic was associated with an increase in the number of blood culture vials processed, the rate of contaminants, and a fall in the number of pneumococcal bloodstream infections.
Abstract
Background
Linezolid-resistant enterococci (LRE) causing infections that are challenging to treat are rising, highlighting the need for reliable screening of LRE clinical isolates.
...Objectives
To evaluate the ability of the broth microdilution (BMD) method for LRE detection and to assess the performance of seven commercially available techniques for linezolid susceptibility testing.
Methods
A collection of 100 clinical isolates (80 Enterococcus faecium and 20 Enterococcus faecalis), including 20 optrA-positive isolates, 17 poxtA-positive isolates and 1 optrA/poxtA-positive E. faecium isolate, were studied. MICs were determined after 18 h Day 1 (D1) and 42 h Day 2 (D2) of incubation and interpreted following EUCAST and CLSI guidelines, which currently provide different interpretative breakpoints. Performance of commercial techniques was compared with BMD results.
Results
MIC50/D1 and MIC50/D2 were both 8 mg/L, while MIC90/D1 and MIC90/D2 were 16 and 32 mg/L, respectively. MICD1 values for poxtA-positive isolates were lower than those for optrA-positive isolates. Proportions of susceptible isolates at D1 and D2 were 48% and 41%, respectively, according to EUCAST breakpoints and 35% and 13%, respectively, according to CLSI criteria (the proportions of isolates categorized as intermediate following CLSI recommendations were 13% and 28% at D1 and D2, respectively). Percentage susceptibility assessed by the commercially available techniques was always higher. The four commercial methods allowing MIC determination provided an overall essential agreement of ≥90% at D1. Categorical agreement and error rates were generally improved at D2.
Conclusions
Non-automated methods (Sensititre and UMIC) and, to a lesser extent, gradient strip Etest appear to show an acceptable correlation with the BMD reference method for the detection of isolates with low MICs of linezolid after prolonged incubation.
The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood ...cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the
gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18
genes detected by the BCID2 were not confirmed. No carbapenemase,
, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections.
Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.
Ventilator-associated pneumonia is a frequent cause of ICU-acquired infections. These infections are associated with high morbidity and mortality. The increase in antibiotic resistance, particularly ...among Gram-negative bacilli, makes the choice of empiric antibiotic therapy complex for physicians. Multidrug-resistant organisms (MDROs) related infections are associated with a high risk of initial therapeutic inadequacy. It is, therefore, necessary to quickly identify the bacterial species involved and their susceptibility to antibiotics. New diagnostic tools have recently been commercialized to assist in the management of these infections. Moreover, the recent enrichment of the therapeutic arsenal effective on Gram-negative bacilli raises the question of their place in the therapeutic management of these infections. Most national and international guidelines recommend limiting their use to microbiologically documented infections. However, many clinical situations and, in particular, the knowledge of digestive or respiratory carriage by MDROs should lead to the discussion of the use of these new molecules, especially the new combinations with beta-lactamase inhibitors in empirical therapy. In this review, we present the current epidemiological data, particularly in terms of MDRO, as well as the clinical and microbiological elements that may be taken into account in the discussion of empirical antibiotic therapy for patients managed for ventilator-associated pneumonia.
Ceftolozane/tazobactam (CTZ/TZ) exhibits time-dependent antimicrobial activity, and prolonged infusion can better achieve the pharmacodynamic target than an intermittent bolus. We aimed to compare ...the use of prolonged or continuous infusion with intermittent administration of CTZ/TZ for the treatment of infections caused by multidrug-resistant
Pseudomonas aeruginosa
. We performed a multicentric prospective cohort study to evaluate continuous, prolonged, or intermittent infusion of CTZ/TZ. We assessed the plasma concentration as a function of the duration of infusion and then performed a simulation of the percentage of patients who would reach the PK/PD targets, set at 100% ƒT
> MIC
or 100% ƒT
>4 MIC
. Seventy-two patients were enrolled with a median IQR age of 48.5 32.4–63.2 years. Fifty-seven (79%) were hospitalized in an intensive care unit. Thirty-seven (51.4%) were immunosuppressed, and the in-hospital mortality rate was 15.2%. The major site of infection was the respiratory tract (66.7%). The PK/PD objectives (100% ƒT
>4 MIC
) were achieved for all patients infected with strains with CTZ/TZ MICs < 4 mg/L, regardless of the mode of administration. In contrast, intermittent bolus administration and prolonged infusion did not achieve the PK/PD objectives when the CTZ/TZ MICs were ≥ 4 mg/L. However, the PK/PD objectives (100% ƒT
>4 MIC
) were achieved for strains with MICs up to 8 mg/L in patients receiving continuous infusion of CTZ/TZ. A dosing regimen of 2 g/1 g CTZ/TZ administered every 8 h as a 1-h intravenous infusion, as currently recommended, did not provided adequate coverage to achieve a sufficient probability of target attainment for
P. aeruginosa
strains with MICs ≥ 4 mg/L.
The major virulence factors of
(
) are enterotoxins A (TcdA) and B (TcdB). The study of toxins is a crucial step in exploring the virulence of this pathogen. Currently, the toxin purification process ...is either laborious and time-consuming in
or performed in heterologous hosts. Therefore, we propose a streamlined method to obtain functional toxins in
. Two
strains were generated, each harboring a sequence encoding a His-tag at the 3' end of
630∆
or
genes. Each toxin gene is expressed using the P
promoter, which is inducible by anhydro-tetracycline. The obtained purification yields were 0.28 mg and 0.1 mg per liter for rTcdA and rTcdB, respectively. In this study, we successfully developed a simple routine method that allows the production and purification of biologically active rTcdA and rTcdB toxins with similar activities compared to native toxins.
Blood culturing (BC) remains the gold standard for bloodstream diagnosis but its workflow is slow. We aimed reducing this time by implementing a new automated incubator with a 24/7 BC workflow. With ...this new strategy, time to incubation was shorter (1.52 h vs 6.82 h), positivity rates were higher (10.6% vs 8.9%,
p<
0.05), and the number of BSI diagnostics increased (16.1% vs 13.8% patients and 2.3 vs 1.9 density episode per 1000 hospital days). Our results show that implementing automatic loading of BC bottles with a 24/7 strategy not only shortened time to diagnosis but significantly increased the BSI diagnosis rate.
•The ID NOW COVID-19 assay is a rapid molecular biology test based on nicking endonuclease amplification reaction (NEAR) evaluated prospectively in the emergency department.•Nasopharyngeal swabs ...directly tested with the ID NOW COVID-19 assay yielded good performance.•When the ID NOW COVID-19 test was performed in the laboratory using the VTM samples, the sensitivity decreased significantly.•ID NOW COVID-19 assay, performed as a point of care test in the ED using dry swabs, provides a rapid and reliable alternative to laboratory-based RT-PCR methods.
Rapid testing for COVID-19 has been clearly identified as an essential component of the strategy to control the SARS-CoV-2 epidemic, worldwide. The ID NOW COVID-19 assay is a simple, user-friendly, rapid molecular biology test based on nicking and extension amplification reaction (NEAR).
The aim of this study was to evaluate the ID NOW COVID-19 assay when used as a point-of-care test (POCT) in our Emergency Department (ED).
This prospective study enrolled 395 consecutive patients; paired nasopharyngeal swabs were collected from each study participant. The first swab was tested with the ID NOW COVID-19 assay at the point-of-care by ED nurses. The second swab was diluted in viral transport medium (VTM) and sent to the clinical microbiology department for analysis by both the RT-PCR Simplexa test COVID-19 Direct assay as the study reference method, and the ID NOW COVID-19 assay performed in the laboratory.
Nasopharyngeal swabs directly tested with the ID NOW COVID-19 assay yielded a sensitivity, specificity, PPV and NPV of 98.0%, 97.5%, 96.2% and 98.7%, respectively, in comparison with the RT-PCR study reference assay. When the ID NOW COVID-19 assay was performed in the laboratory using the VTM samples, the sensitivity decreased to 62.5% and the NPV to 79.7%. Three false negative test results were reported with the ID NOW COVID-19 assay when performed using undiluted swabs directly in the ED; these results were obtained from patients with elevated CT values (> 30).
We demonstrated that the ID NOW COVID-19 assay, performed as a point of care test in the ED using dry swabs, provides a rapid and reliable alternative to laboratory-based RT-PCR methods
Patients with viral respiratory infections often present symptoms compatible with bloodstream infections. Consequently, the winter period commonly associated with epidemic respiratory illnesses shows ...an increase in the number of blood cultures (BC) and to occasional saturation of automated BC systems. Here, we explored the seasonal variations in BC samples and the potential impact of shortening the incubation time of BC when automated BC systems are close to saturation. A retrospective study was conducted during a 3-year period in 4 hospitals located in the Paris region, France. All aerobic and anaerobic bottles were included, except pediatric bottles and those sampled for suspicion of endocarditis. The number of BC bottles collected during the winter period was compared to the annual baseline. All bottles positive after a 4-day incubation were analyzed regarding clinical and microbiological findings. The number of BC bottles was significantly higher during the winter periods, compared to the annual baseline (up to 14%). A total of 292,349 BC bottles were analyzed with 23,363 (8.0%) positive, including 236 (1%) after a 4-day incubation. Of these 236 bottles, 76 (64.8%) were positive with a contaminant, 78 (33.1%) with a clinically significant microorganism identified for the same patient in the previous 4 days, and only 5 (2.1%) with a clinically significant microorganism not previously identified. Winter periods were associated with a significant increase in BC samples. Shortening the incubation time of BC bottles from 5 to 4 days seems a relevant option when automated BC systems are close to saturation.
Zoonotic species of
Capnocytophaga
genus belong to the oral microbiota of dogs and cats. They may be responsible for serious human infections, mainly after animal bites, with a high mortality rate. ...In France, only few cases have been reported and no multicenter study has been conducted. Our aim was to describe the French epidemiology of
Capnocytophaga
zoonosis. We conducted a multicenter (21 centers) retrospective non-interventional, observational study in France describing the epidemiology of
Capnocytophaga
zoonosis (
C. canimorsus
,
C. cynodegmi
,
C. canis
) over 10 years with regard to clinical and bacteriological data. From 2009 to 2018, 44 cases of
Capnocytophaga
zoonotic infections were described (
C. canimorsus
,
n
= 41;
C. cynodegmi
,
n
= 3). We observed an increase (2.5 times) in the number of cases over the study period (from the first to the last 5 years of the study). The most frequent clinical presentations were sepsis (
n
= 37), skin and soft tissue infections (
n
= 12), meningitis (
n
= 8), osteoarticular infections (
n
= 6), and endocarditis (
n
= 2). About one-third of patients with sepsis went into septic shock. Mortality rate was 11%. Mortality and meningitis rates were significantly higher for alcoholic patients (
p
= 0.044 and
p
= 0.006, respectively). Other comorbidities included smoking, splenectomy, diabetes mellitus, and immunosuppressive therapy are associated to zoonotic
Capnocytophaga
infection. Eighty-two percent of cases involved contact with dogs, mostly included bites (63%). Despite all isolates were susceptible to the amoxicillin-clavulanic acid combination, three of them were resistant to amoxicillin.
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