Real life turnaround time of blood cultures in the clinical microbiology laboratory: results of the first Italian survey, May 2015

Diagnostic and antibiotic use practices among COVID-19 and non-COVID-19 patients in the Indonesian National Referral Hospital

BACKGROUND

Little is known about diagnostic and antibiotic use practices in low and middle-income countries (LMICs) before and during COVID-19 pandemic. This information is crucial for monitoring and evaluation of diagnostic and antimicrobial stewardships in healthcare facilities.

METHODS

We linked and analyzed routine databases of hospital admission, microbiology laboratory and drug dispensing of Indonesian National Referral Hospital from 2019 to 2020. Patients were classified as COVID-19 cases if their SARS-CoV-2 RT-PCR result were positive. Blood culture (BC) practices and time to discontinuation of parenteral antibiotics among inpatients who received a parenteral antibiotic for at least four consecutive days were used to assess diagnostic and antibiotic use practices, respectively. Fine and Grey subdistribution hazard model was used.

RESULTS

Of 1,311 COVID-19 and 58,917 non-COVID-19 inpatients, 333 (25.4%) and 18,837 (32.0%) received a parenteral antibiotic for at least four consecutive days. Proportion of patients having BC taken within ±1 calendar day of parenteral antibiotics being started was higher in COVID-19 than in non-COVID-19 patients (21.0% [70/333] vs. 18.7% [3,529/18,837]; p<0.001). Cumulative incidence of having a BC taken within 28 days was higher in COVID-19 than in non-COVID-19 patients (44.7% [149/333] vs. 33.2% [6,254/18,837]; adjusted subdistribution-hazard ratio [aSHR] 1.71, 95% confidence interval [CI] 1.47-1.99, p<0.001). The median time to discontinuation of parenteral antibiotics was longer in COVID-19 than in non-COVID-19 patients (13 days vs. 8 days; aSHR 0.73, 95%Cl 0.65-0.83, p<0.001).

CONCLUSIONS

Routine electronic data could be used to inform diagnostic and antibiotic use practices in LMICs. In Indonesia, the proportion of timely blood culture is low in both COVID-19 and non-COVID-19 patients, and duration of parenteral antibiotics is longer in COVID-19 patients. Improving diagnostic and antimicrobial stewardship is critically needed.

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.

Collection, transport and storage procedures for blood culture specimens in adult patients: recommendations from a board of Italian experts

Bloodstream infections (BSIs) remain a potentially life-threatening condition. The gold standard for the diagnosis of BSI is still blood cultures (BCs), and the diagnostic yield depends on clinical and technical factors that have an impact on collection and transportation. Hence, monitoring of the entire pre-analytical process from blood collection to transportation to the microbiology laboratory is critical. To optimize the clinical impact of the diagnostic and therapeutic procedures, a multidisciplinary approach and univocal protocols are mandatory. A board of specialists discussed the available evidence on the pre-analytical process and produced the present document to guide physicians and nurses on the ideal execution of BC: (1) timing and preparation for blood collection; (2) skin antisepsis; (3) blood volume; (4) sampling method and safety; (5) medium to be used; (6) time to BC transportation; and (7) quality assurance and quality management.

Compliance of clinical microbiology laboratories with recommendations for the diagnosis of bloodstream infections: Data from a nationwide survey in Italy

In 2014, the Italian Working Group for Infections in Critically Ill Patient of the Italian Association of Clinical Microbiologists updated the recommendations for the diagnostic workflow for bloodstream infections (BSI). Two years after publication, a nationwide survey was conducted to assess the compliance with the updated recommendations by clinical microbiology laboratories. A total of 168 microbiologists from 168 laboratories, serving 204 acute care hospitals and postacute care facilities, were interviewed during the period January–October 2016 using a questionnaire consisting of nineteen questions which assessed the level of adherence to various recommendations. The most critical issues were as follows: (a) The number of sets of blood cultures (BC) per 1,000 hospitalization days was acceptable in only 11% of laboratories; (b) the minority of laboratories (42%) was able to monitor whether BCs were over or under‐inoculated; (c) among the laboratories monitoring BC contamination (80%), the rate of contaminated samples was acceptable in only 12% of cases;(d) the Gram‐staining results were reported within 1 hr since BC positivity in less than 50% of laboratories. By contrast, most laboratories received vials within 2–4 hr from withdrawal (65%) and incubated vials as soon as they were received in the laboratory (95%). The study revealed that compliance with the recommendations is still partial. Further surveys will be needed to monitor the situation in the future.

Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey

OBJECTIVES

High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories.

METHODS

We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.

RESULTS

Responses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC.

CONCLUSIONS

Laboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.

Blood Culture Turnaround Time in U.S. Acute Care Hospitals and Implications for Laboratory Process Optimization

The rapid identification of blood culture isolates and antimicrobial susceptibility test (AST) results play critical roles for the optimal treatment of patients with bloodstream infections. Whereas others have looked at the time to detection in automated culture systems, we examined the overall time from specimen collection to actionable test results. We examined four points of time, namely, blood specimen collection, Gram stain, organism identification (ID), and AST reports, from electronic data from 13 U.S. hospitals for the 11 most common, clinically significant organisms in septic patients. We compared the differences in turnaround times and the times from when specimens were collected and the results were reported in the 24-h spectrum. From January 2015 to June 2016, 165,593 blood specimens were collected, of which, 9.5% gave positive cultures. No matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was used during the study period. Across the 10 common bacterial isolates (n = 6,412), the overall median (interquartile range) turnaround times were 0.80 (0.64 to 1.08), 1.81 (1.34 to 2.46), and 2.71 (2.46 to 2.99) days for Gram stain, organism ID, and AST, respectively. For all positive cultures, approximately 25% of the specimens were collected between 6:00 a.m. and 11:59 a.m. In contrast, more of the laboratory reporting times were concentrated between 6:00 a.m. and 11:59 a.m. for Gram stain (43%), organism ID (78%), and AST (82%), respectively (P < 0.001). The overall average turnaround times from specimen collection for Gram stain, organism ID, and AST were approximately 1, 2, and 3 days, respectively. The laboratory results were reported predominantly in the morning hours. Laboratory automation and work flow optimization may play important roles in reducing the microbiology result turnaround time.