A Multicenter Evaluation of Blood Culture Practices, Contamination Rates, and the Distribution of Causative Bacteria

Underutilization and Quality Gaps in Blood Culture Processing in Public Hospitals of Peru

Correct processing of blood cultures may impact individual patient management, antibiotic stewardship, and scaling up of antimicrobial resistance surveillance. To assess the quality of blood culture processing, we conducted four assessments at 16 public hospitals across different regions of Peru. We assessed the following standardized quality indicators: 1) positivity and contamination rates, 2) compliance with recommended number of bottles/sets and volume of blood sampled, 3) blood culture utilization, and 4) possible barriers for compliance with recommendations. Suboptimal performance was found, with a median contamination rate of 4.2% (range 0-15.1%), with only one third of the participating hospitals meeting the target value of < 3%; and a median positivity rate of 4.9% (range 1-8.1%), with only 6 out of the 15 surveilled hospitals meeting the target of 6-12%. None of the assessed hospitals met both targets. The median frequency of solitary blood cultures was 71.9% and only 8.9% (N = 59) of the surveyed adult bottles met the target blood volume of 8 - 12 mL, whereas 90.5% (N = 602) were underfilled. A high frequency of missed opportunities for ordering blood cultures was found (69.9%, 221/316) among patients with clinical indications for blood culture sampling. This multicenter study demonstrates important shortcomings in the quality of blood culture processing in public hospitals of Peru. It provides a national benchmark of blood culture utilization and quality indicators that can be used to monitor future quality improvement studies and diagnostic stewardship policies.

Pre-hospital antibiotic therapy preceded by blood cultures in a physician-manned mobile emergency care unit

BACKGROUND

Rapid recognition and antibiotic treatment, preferably preceded by blood cultures (BCs), is a mainstay in sepsis therapy. The objective of this investigation was to determine if pre-hospital BCs were feasible and drawn with an acceptably low level of contamination and to investigate whether pre-hospital antibiotics were administered on correct indications.

METHODS

We performed a register-based study in a pre-hospital physician-manned mobile emergency care unit (MECU) operating in a mixed urban/rural area in Denmark. All patients who received pre-hospital antibiotics by the MECU from November 2013 to October 2018 were reviewed. Outcome measures were characterisation of microbial findings and subsequent in-hospital confirmation of the pre-hospital indication for antibiotics.

RESULTS

One-hundred-and-nineteen patients received antibiotics pre-hospitally. Six were excluded. One-hundred-and-thirteen patients were included in the study. BCs were drawn in 107 of the 113 patients (94.7% [88.8%-98.0%]). We found a true pathogen of sepsis in 29 (27.1% [19.0%-36.6%]) of these 107 patients. Nine (8.4% [3.9%-15.4%]) patients had contaminated pre-hospital BCs. Forty-nine of all patients (36.3% [27.4%-45.9%]) had causative pathogens in either their BCs or other samples confirming the pre-hospital tentative diagnosis. Eighty-two (72.6% [63.4%-80.5%]) patients received antibiotic therapy in-hospitally, while 27 (23.9% [16.4%-32.8%]) were assigned an in-hospital diagnosis not associated with infection. Four (3.5% [1.0%-8.8%]) patients died in hospital before a diagnosis was established.

CONCLUSIONS

Pre-hospital administration of antibiotics preceded by BCs is feasible, although with somewhat high blood culture contamination rates. Antibiotics are administered on reasonable indications.

Non-linear relationships between children age and pneumococcal vaccine coverage: Important implications for vaccine prevention strategies

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) is an important pathogen causing both invasive and non-invasive infections in children, with significant morbidity and mortality worldwide. This study aimed to determine the potential relationships between age and vaccine coverage and between multiple phenotype-genotype characteristics of S. pneumoniae isolated from children.

METHODS

All S. pneumoniae isolates were tested for antimicrobial susceptibility, virulence genes, serotypes, and sequence types. The restricted cubic spline models were used to reveal potential relationships between children age and pneumococcal vaccine coverage.

RESULTS

For capsular-based vaccines, we observed a high coverage rate of 13-valent pneumococcal conjugate vaccine (PCV13, 85.8%) and a significantly non-linear relationship between children age and vaccine coverage (including PCV7, PCV10, and PCV13), with marked fluctuations in children aged < 2 years. For protein-based and pilus-based vaccine candidates, we demonstrated dynamic non-linear relationships between age and vaccine coverage, maintaining a stable and high coverage rate of ply and lytA for all age groups. Moreover, there were significantly high-dimensional corresponding relationships among multiple phenotype-genotype characteristics of S. pneumoniae isolates (such as ST271 associated with serotype 19F, PI-2, and extensively drug-resistance).

CONCLUSIONS

Our findings suggest that the age for high PCV coverage being children aged ≥ 2 years and also provide important evidence for supporting ply and lytA as priority candidate targets for the development of new-generation protein vaccines.

Revealing antibiotic cross-resistance patterns in hospitalized patients through Bayesian network modelling

OBJECTIVES

Microbial resistance exhibits dependency patterns between different antibiotics, termed cross-resistance and collateral sensitivity. These patterns differ between experimental and clinical settings. It is unclear whether the differences result from biological reasons or from confounding, biasing results found in clinical settings. We set out to elucidate the underlying dependency patterns between resistance to different antibiotics from clinical data, while accounting for patient characteristics and previous antibiotic usage.

METHODS

Additive Bayesian network modelling was employed to simultaneously estimate relationships between variables in a dataset of bacterial cultures derived from hospitalized patients and tested for resistance to multiple antibiotics. Data contained resistance results, patient demographics and previous antibiotic usage, for five bacterial species: Escherichia coli (n = 1054), Klebsiella pneumoniae (n = 664), Pseudomonas aeruginosa (n = 571), CoNS (n = 495) and Proteus mirabilis (n = 415).

RESULTS

All links between resistance to the various antibiotics were positive. Multiple direct links between resistance of antibiotics from different classes were observed across bacterial species. For example, resistance to gentamicin in E. coli was directly linked with resistance to ciprofloxacin (OR = 8.39, 95% credible interval 5.58-13.30) and sulfamethoxazole/trimethoprim (OR = 2.95, 95% credible interval 1.97-4.51). In addition, resistance to various antibiotics was directly linked with previous antibiotic usage.

CONCLUSIONS

Robust relationships among resistance to antibiotics belonging to different classes, as well as resistance being linked to having taken antibiotics of a different class, exist even when taking into account multiple covariate dependencies. These relationships could help inform choices of antibiotic treatment in clinical settings.

The Clinical Impact of Rapid Molecular Microbiological Diagnostics for Pathogen and Resistance Gene Identification in Patients With Sepsis: A Systematic Review

Fast microbiological diagnostics (MDx) are needed to ensure early targeted antimicrobial treatment in sepsis. This systematic review focuses on the impact on antimicrobial management and patient outcomes of MDx for pathogen and resistance gene identification compared with blood cultures. PubMed was searched for clinical studies using either whole blood directly or after short-term incubation. Twenty-five articles were retrieved describing the outcomes of 8 different MDx. Three interventional studies showed a significant increase in appropriateness of antimicrobial therapy and a nonsignificant change in time to appropriate therapy. Impact on mortality was conflicting. Length of stay was significantly lower in 2 studies. A significant decrease in antimicrobial cost was demonstrated in 6 studies. The limitations of this systematic review include the low number and observed heterogeneity of clinical studies. In conclusion, potential benefits of MDx regarding antimicrobial management and some patient outcomes were reported. More rigorous intervention studies are needed focusing on the direct benefits for patients.

Reduction in the processing of possible blood culture contaminants by the application of a selection criterion

Possible blood culture (BC) contaminants are generally considered to be skin flora species including coagulase-negative Staphylococci (CNS), Corynebacterium species, Micrococcus species, Bacillus species and Propionibacterium acnes. Prior to October 1, 2016 all possible BC contaminants were fully processed (identification, susceptibility testing) in our laboratory. In order to reduce the laboratory workload from October 1, 2016 a possible contaminant was only processed if it was present in more than one BC pair drawn from the same patient within the same day. The two-year study period was divided in two periods namely period A from January 1, 2016 to September 30, 2016 (first 9 months) and period B from October 1, 2016 to December 31, 2017 (last 15 months). A series of indices (INs) were calculated including among others the Working Rate IN (WR) defined as the total isolates divided to the total number of BCs submitted per month and the CNS Rate (CNSR) defined as the total number of CNS processed divided to the total number of BCs submitted per month. A 23.08% reduction in the CNSR was noted (from 3.51% in period A to 2.70% in period B) whereas the overall WR was reduced from 7.19% in period A to 6.84% in period B. Furthermore, the total number of contaminants processed per month divided to the total number of isolates processed per month was reduced from 54.50% in period A to 42.41% in period B. The reduction in the INs recorded is of great value since it was achieved by the implementation of a simple criterion easily applicable and without any cost.

Best Practices of Blood Cultures in Low- and Middle-Income Countries

Bloodstream infections (BSI) have a substantial impact on morbidity and mortality worldwide. Despite scarcity of data from many low- and middle-income countries (LMICs), there is increasing awareness of the importance of BSI in these countries. For example, it is estimated that the global mortality of non-typhoidal Salmonella bloodstream infection in children under 5 already exceeds that of malaria. Reliable and accurate diagnosis of these infections is therefore of utmost importance. Blood cultures are the reference method for diagnosis of BSI. LMICs face many challenges when implementing blood cultures, due to financial, logistical, and infrastructure-related constraints. This review aims to provide an overview of the state-of-the-art of sampling and processing of blood cultures, with emphasis on its use in LMICs. Laboratory processing of blood cultures is relatively straightforward and can be done without the need for expensive and complicated equipment. Automates for incubation and growth monitoring have become the standard in high-income countries (HICs), but they are still too expensive and not sufficiently robust for imminent implementation in most LMICs. Therefore, this review focuses on "manual" methods of blood culture, not involving automated equipment. In manual blood cultures, a bottle consisting of a broth medium supporting bacterial growth is incubated in a normal incubator and inspected daily for signs of growth. The collection of blood for blood culture is a crucial step in the process, as the sensitivity of blood cultures depends on the volume sampled; furthermore, contamination of the blood culture (accidental inoculation of environmental and skin bacteria) can be avoided by appropriate antisepsis. In this review, we give recommendations regarding appropriate blood culture sampling and processing in LMICs. We present feasible methods to detect and speed up growth and discuss some challenges in implementing blood cultures in LMICs, such as the biosafety aspects, supply chain and waste management.

Use of hair nets and face masks to decrease blood culture contamination rates

Owing to a persistently high blood culture contamination rate of 3.2% exceeding the target rate of <3%, a midwestern United States hospital began a series of 3 additive interventions. After collecting phlebotomist data for approximately 3 months, reporting of individual contamination rates commenced. A specialized trainer reeducated staff with high rates, which resulted in a modest decrease in contamination rates (3.2% to 2.8%, P = 0.23). A second, additional intervention requiring phlebotomists to wear hair nets and face masks resulted in marked improvement from a mean of 2.8% to 1.1% (P < .0001). In a final, third addition, whenever possible, the replacement of nursing staff by phlebotomy staff for blood specimen collection did not result in a significant change in mean contamination (P = 0.81). Overall, the mean contamination rate progressively declined in a stepwise manner from 3.2% to 1.2% (P = .0013), with the greatest decline after adding hair nets and face masks.

Estimation of missed bloodstream infections without the third blood culture set: a retrospective observational single-centre study

OBJECTIVES

The question of whether to obtain two or three sets of blood cultures to assess the aetiology of bloodstream infections (BSIs) remains open to debate. Few studies have assessed the proportion of BSIs missed without the third blood culture set (BCS). The aim of our study was to determine the proportion of BSIs that would be missed without the third BCS in a hospital where obtaining three BCSs is the standard of care.

METHODS

We performed a descriptive retrospective study in Hospital Gregorio Marañón (Madrid) from 2010 to 2013. We included all episodes of BSI in which three BCSs were systematically obtained.

RESULTS

We included 4000 episodes of BSI between 2010 and 2013. Without the third BCS, we would have missed 298 (7.5%) episodes of BSI: 141 (47.3%) by gram-positive microorganisms, 147 (49.3%) by gram-negative microorganisms, and 10 (3.4%) by yeasts. In 132/298 (44.3%) of the episodes another clinical sample was obtained within a week of the BCS extraction; in 101/298 (33.9%), the same microorganism was present in a significant clinical sample other than blood.

CONCLUSIONS

Our data suggest that performing a third BCS is useful, as not doing this could result in an unacceptable number of BSIs going undetected.

Phenotypic and molecular characterization of Streptococcus pneumoniae in pre-conjugate vaccine era: A Chinese hospital-based retrospective study

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) is an important pathogen in causing global morbidity and mortality among children. This study aimed to determine phenotypic and molecular characteristics of S. pneumoniae causing infections in children under five years in China.

METHODS

A hospital-based retrospective study was conducted. All 537 S. pneumoniae isolates were tested for antimicrobial susceptibility by E-test method, molecular characteristics including resistance genes, virulence genes and serotypes by multiplex polymerase chain reaction (PCR) method, and sequence types (STs) by sequencing seven housekeeping genes. Minimum spanning tree and correspondence analysis were used to reveal the potential relationship between serotypes and STs.

RESULTS

Most of S. pneumoniae isolates were resistant to erythromycin (93.9%) and tetracycline (86.4%), with the predominant resistance genes being erm(B) (92.6%) and tet(M) (95.5%). The prevalent serotypes were 19F, 6B, 19A, 23F and 14, the coverage rate of PCV13 was high in 85.8%, and the predominant STs were ST271, ST320, ST3173, ST81 and ST876. A significant correlation existed between STs and serotypes, with ST271/19F and ST320/19A as the most prevalent clones. Notably, ST271/19F and ST320/19A isolates were associated with resistance to specific antibiotics and carrying of mef(A/E), rlrA and sipA genes.

CONCLUSIONS

Our findings suggest the introduction of PCV13 vaccine to Chinese children, and underscore the value of monitoring multiple characteristics to detect new epidemiologic trends and provide implications for the formulation of multivalent pneumococcal vaccines.