Understanding Bacterial Isolates in Blood Culture and Approaches Used to Define Bacteria as Contaminants: A Literature Review

Clinical predictors of bacteraemia in neonates with suspected early-onset sepsis in Malawi: a prospective cohort study

OBJECTIVES

We studied neonates with suspected early-onset sepsis (EOS, sepsis developing in the first 72 hours after delivery) in Malawi to (1) describe clinical characteristics and microbiological findings, (2) identify which patient characteristics may be associated with pathogen positivity on blood culture, and (3) describe mortality and its potential determinants.

DESIGN

Prospective observational study (May 2018-June 2019).

SETTING

Neonatal ward in Queen Elizabeth Central Hospital, the largest government hospital in Malawi.

PATIENTS

All neonates with suspected EOS in whom a blood culture was obtained.

RESULTS

Out of 4308 neonatal admissions, 1244 (28.9%) had suspected EOS. We included 1149 neonates, of which 109 blood cultures had significant growth (9.5%). The most commonly isolated pathogens were Staphylococcus aureus, Klebsiella pneumoniae, Enterobacter cloacae, Escherichia coli and Acinetobacter baumanii. Many of the Gram negatives were extended-spectrum beta lactamase-producing Enterobacteriaceae, and these were 40-100% resistant to first-line and second-line antimicrobials. Gestational age (GA) of <32 weeks was associated with pathogen-positive blood cultures (<28 weeks: adjusted OR (AOR) 2.72, 95% CI 1.04 to 7.13; 28-32 weeks: AOR 2.26, 95% CI 1.21 to 4.21; p=0.005). Mortality was 17.6% (202/1149) and associated with low birth weight (<1000 g: AOR 47.57, 95% CI 12.59 to 179.81; 1000-1500 g: AOR 11.31, 95% CI 6.97 to 18.36; 1500-2500 g: AOR 2.20, 95% CI 1.42 to 3.39; p<0.001), low Apgar scores at 5 min (0-3: AOR 18.60, 95% CI 8.81 to 39.27; 4-6: AOR 4.41, 95% CI 2.81 to 6.93; p<0.001), positive maternal venereal disease research laboratory status (AOR 2.53, 95% CI 1.25 to 5.12; p=0.001) and congenital anomalies (AOR 7.37, 95% CI 3.61 to 15.05; p<0.001). Prolonged rupture of membranes was inversely associated with mortality (AOR 0.43, 95% CI 0.19 to 0.98; p 0.007).

CONCLUSION

In Malawi, EOS was suspected in nearly a third of neonatal admissions and had a high mortality. Ten per cent were culture-confirmed and predicted by low GA. To reduce the impact of suspected neonatal sepsis in least developed countries, improved maternal and antenatal care and development of rapid point of care methods to more accurately guide antimicrobial use could simultaneously improve outcome and reduce antimicrobial resistance.

How to interpret a paediatric blood culture

Blood culture is one of the most important diagnostic tests in medicine, considering the significant morbidity and mortality associated with bloodstream infection (BSI). However, it is an often misused and misinterpreted test in everyday paediatric practice. In this article, we explore the evidence related to paediatric blood cultures, with the aim of providing clear and clinically-relevant recommendations for its judicious use.

Improved diagnostic prediction of the pathogenicity of bloodstream isolates of Staphylococcus epidermidis

With an estimated 440,000 active cases occurring each year, medical device associated infections pose a significant burden on the US healthcare system, costing about $9.8 billion in 2013. Staphylococcus epidermidis is the most common cause of these device-associated infections, which typically involve isolates that are multi-drug resistant and possess multiple virulence factors. S. epidermidis is also frequently a benign contaminant of otherwise sterile blood cultures. Therefore, tests that distinguish pathogenic from non-pathogenic isolates would improve the accuracy of diagnosis and prevent overuse/misuse of antibiotics. Attempts to use multi-locus sequence typing (MLST) with machine learning for this purpose had poor accuracy (~73%). In this study we sought to improve the diagnostic accuracy of predicting pathogenicity by focusing on phenotypic markers (i.e., antibiotic resistance, growth fitness in human plasma, and biofilm forming capacity) and the presence of specific virulence genes (i.e., mecA, ses1, and sdrF). Commensal isolates from healthy individuals (n = 23), blood culture contaminants (n = 21), and pathogenic isolates considered true bacteremia (n = 54) were used. Multiple machine learning approaches were applied to characterize strains as pathogenic vs non-pathogenic. The combination of phenotypic markers and virulence genes improved the diagnostic accuracy to 82.4% (sensitivity: 84.9% and specificity: 80.9%). Oxacillin resistance was the most important variable followed by growth rate in plasma. This work shows promise for the addition of phenotypic testing in clinical diagnostic applications.

Prevalence and antimicrobial resistance patterns of bacteria isolated from cerebrospinal fluid among children with bacterial meningitis in China from 2016 to 2018: a multicenter retrospective study

Background

Pediatric bacterial meningitis (PBM) remains a devastating disease that causes substantial neurological morbidity and mortality worldwide. However, there are few large-scale studies on the pathogens causing PBM and their antimicrobial resistance (AMR) patterns in China. The present multicenter survey summarized the features of the etiological agents of PBM and characterized their AMR patterns.

Methods

Patients diagnosed with PBM were enrolled retrospectively at 13 children’s hospitals in China from 2016 to 2018 and were screened based on a review of cerebrospinal fluid (CSF) microbiology results. Demographic characteristics, the causative organisms and their AMR patterns were systematically analyzed.

Results

Overall, 1193 CSF bacterial isolates from 1142 patients with PBM were obtained. The three leading pathogens causing PBM were Staphylococcus epidermidis (16.5%), Escherichia coli (12.4%) and Streptococcus pneumoniae (10.6%). In infants under 3 months of age, the top 3 pathogens were E. coli (116/523; 22.2%), Enterococcus faecium (75/523; 14.3%), and S. epidermidis (57/523; 10.9%). However, in children more than 3 months of age, the top 3 pathogens were S. epidermidis (140/670; 20.9%), S. pneumoniae (117/670; 17.5%), and Staphylococcus hominis (57/670; 8.5%). More than 93.0% of E. coli isolates were sensitive to cefoxitin, piperacillin/tazobactam, cefoperazone/sulbactam, amikacin and carbapenems, and the resistance rates to ceftriaxone, cefotaxime and ceftazidime were 49.4%, 49.2% and 26.4%, respectively. From 2016 to 2018, the proportion of methicillin-resistant coagulase-negative Staphylococcus isolates (MRCoNS) declined from 80.5 to 72.3%, and the frequency of penicillin-resistant S. pneumoniae isolates increased from 75.0 to 87.5%. The proportion of extended-spectrum β-lactamase (ESBL)-producing E. coli fluctuated between 44.4 and 49.2%, and the detection rate of ESBL production in Klebsiella pneumoniae ranged from 55.6 to 88.9%. The resistance of E. coli strains to carbapenems was 5.0%, but the overall prevalence of carbapenem-resistant K. pneumoniae (CRKP) was high (54.5%).

Conclusions

S. epidermidis, E. coli and S. pneumoniae were the predominant pathogens causing PBM in Chinese patients. The distribution of PBM causative organisms varied by age. The resistance of CoNS to methicillin and the high incidence of ESBL production among E. coli and K. pneumoniae isolates were concerning. CRKP poses a critical challenge for the treatment of PBM.

Preventing Bloodstream Infections and Death in Zambian Neonates: Impact of a Low-cost Infection Control Bundle

BACKGROUND

Sepsis is a leading cause of neonatal mortality in low-resource settings. As facility-based births become more common, the proportion of neonatal deaths due to hospital-onset sepsis has increased.

METHODS

We conducted a prospective cohort study in a neonatal intensive care unit in Zambia where we implemented a multifaceted infection prevention and control (IPC) bundle consisting of IPC training, text message reminders, alcohol hand rub, enhanced environmental cleaning, and weekly bathing of babies ≥1.5 kg with 2% chlorhexidine gluconate. Hospital-associated sepsis, bloodstream infection (BSI), and mortality (>3 days after admission) outcome data were collected for 6 months prior to and 11 months after bundle implementation.

RESULTS

Most enrolled neonates had a birth weight ≥1.5 kg (2131/2669 [79.8%]). Hospital-associated mortality was lower during the intervention than baseline period (18.0% vs 23.6%, respectively). Total mortality was lower in the intervention than prior periods. Half of enrolled neonates (50.4%) had suspected sepsis; 40.8% of cultures were positive. Most positive blood cultures yielded a pathogen (409/549 [74.5%]), predominantly Klebsiella pneumoniae (289/409 [70.1%]). The monthly rate and incidence density rate of suspected sepsis were lower in the intervention period for all birth weight categories, except babies weighing <1.0 kg. The rate of BSI with pathogen was also lower in the intervention than baseline period.

CONCLUSIONS

A simple IPC bundle can reduce sepsis and death in neonates hospitalized in high-risk, low-resource settings. Further research is needed to validate these findings in similar settings and to identify optimal implementation strategies for improvement and sustainability.

CLINICAL TRIALS REGISTRATION

NCT02386592.

Rectal screening displays high negative predictive value for bloodstream infection with (ESBL-producing) Gram-negative bacteria in neonates with suspected sepsis in a low-resource setting neonatal care unit

OBJECTIVES

We analysed the concordance of rectal swab isolates and blood culture for Gram-negative bacteria (GNB) isolates in neonates with a suspicion of neonatal sepsis admitted to a neonatal care unit in Haiti.

METHODS

We matched pairs of blood and rectal samples taken on the date of suspected sepsis onset in the same neonate. We calculated the proportion of rectal isolates in concordance with the blood isolates by species and genus. We calculated the negative predictive value (NPV) for GNB and extended-spectrum β-lactamase (ESBL)-producing GNB for all rectal and blood isolate pairs in neonates with suspected sepsis.

RESULTS

We identified 238 blood and rectal samples pairs, with 238 blood isolate results and 309 rectal isolate results. The overall concordance in genus and species between blood and rectal isolates was 22.3% [95% confidence interval (CI) 17.4-28.0%] and 20.6% (95% CI 16.0-26.2%), respectively. The highest concordance between blood and rectal isolates was observed for samples with no bacterial growth (65%), followed byKlebsiella pneumoniae (18%) and Klebsiella oxytoca (12%). The NPV of detecting GNB bacterial isolates in rectal samples compared with those in blood samples was 81.6% and the NPV for ESBL-positive GNB was 92.6%.

CONCLUSIONS

The NPV of rectal swab GNB isolates was high in all patient groups and was even higher for ESBL-positive GNB. Clinicians can use the results from rectal swabs when taken simultaneously with blood samples during outbreaks to inform the (de-)escalation of antibiotic therapy in those neonates that have an ongoing sepsis profile.

Improving adherence to facility protocol and reducing blood culture contamination in an intensive care unit: A quality improvement project

BACKGROUND

Blood culture contamination (BCC) is a safety and quality indicator for intensive care units (ICUs). BCC rates in our ICU ranged from 2.90% to 6.70% in 2017.

OBJECTIVE

This quality improvement project aimed to reduce the contamination rate from a mean of 4.52% to <3.0% in 1 year by improving the adherence of nurses to the facility protocol during blood collection.

METHODS

This project used a before-after design. It was conducted by a leadership team in a 32-bed ICU where approximately 4000 cultures are drawn annually. We observed the performance of ICU nurses during blood collection, interviewed them regarding the difficulties they encountered with protocol adherence, and conducted a cause-and-effect analysis to identify the main problems. Based on a literature review, we developed and implemented a countermeasure protocol, including a standardised medical order, an online learning program, a weekly departmental report and individual feedback routine, and phlebotomy training to address these problems in 2 months.

RESULTS

The interview results indicated that blood contamination resulted from the environment, difficult phlebotomy, and the inadequate knowledge and skill of the nurses. The countermeasure protocol reduced the average BCC rate from 4.52% to 2.59% during the intervention period and to 0.59% during the 10-month postintervention period. Nursing adherence to the standard protocol for blood culture collection also improved.

CONCLUSIONS

BCC in ICUs is multifactorial. By optimising the work environment, offering skill training, and reinforcing education and individualised feedback, we successfully reduced BCC in our unit to a sustainable low rate.

Reporting and Categorization of Blood Culture Contaminants in Infants and Young Children: A Scoping Review

BACKGROUND

Blood cultures are obtained routinely for infants and young children for the evaluation for serious bacterial infection. Isolation of organisms that represent possible contaminants poses a management challenge. The prevalence of bacteremia reported in this population is potentially biased by inconsistent contaminant categorization reported in the literature. Our aim was to systematically review the definition and reporting of contaminants within the literature regarding infant bacteremia.

METHODS

A search of studies published between 1986 and mid-September 2016 was conducted using Medline/PubMed. Included studies examined children aged 0 to 36 months for whom blood culture was performed as part of a serious bacterial infection evaluation. Studies that involved children in an intensive care unit, prematurely born children, and immunocompromised children or those with an indwelling catheter/device were excluded. Data extracted included contaminant designation methodology, organisms classified as contaminants and pathogens, and contamination and bacteremia rates.

DISCUSSION

Our search yielded 1335 articles, and 69 of them met our inclusion criteria. The methodology used to define contaminants was described in 37 (54%) study reports, and 16 (23%) reported contamination rates, which ranged from 0.5% to 22.8%. Studies defined contaminants according to organism species (n = 22), according to the patient's clinical management (n = 4), and using multifactorial approaches (n = 11). Many common organisms, particularly Gram-positive cocci, were inconsistently categorized as pathogens or contaminants.

CONCLUSIONS

Reporting and categorization of blood culture contamination are inconsistent within the pediatric bacteremia literature, which limits our ability to estimate the prevalence of bacteremia. Although contaminants are characterized most frequently according to organism, we found inconsistency regarding the classification of certain common organisms. A standardized approach to contaminant reporting is needed.

Impact of chlorhexidine baths on suspected sepsis and bloodstream infections in hospitalized neonates in Zambia

INTRODUCTION

Sepsis is the leading cause of infectious morbidity and mortality among hospitalized neonates. In high-resource pediatric and adult intensive care units, use of aqueous chlorhexidine (CHG) solution has been associated with reduced risk of bloodstream infections (BSI).

OBJECTIVES

To assess the impact of bathing of neonates with 2% CHG on BSI, suspected sepsis, and mortality in a low-income country neonatal care unit.

METHODS

We conducted a secondary analysis of data from the Sepsis Prevention in Neonates in Zambia (SPINZ) study, a prospective observational cohort study performed at a large public referral hospital in Lusaka, Zambia. The SPINZ study assessed the impact of an infection control bundle (consisting of alcohol hand rub, SMS hygiene reminders, enhanced environmental cleaning, and CHG baths for babies ≥1.5 kg) on sepsis, BSI, and all-cause mortality. Episodic shortages in study staffing resulted in some enrolled babies not receiving a CHG bath. Using Longitudinal Targeted Maximum Likelihood Estimation and Cox proportional hazards regression to adjust for observed confounding, we estimated the causal effect of receiving a CHG bath within the first 3 days of life on suspected sepsis, BSI, and death among inborn babies enrolled during the study implementation and intervention phases.

RESULTS

The majority of inborn, enrolled babies ≥1.5 kg received a CHG bath within 3 days of NICU admission (864 of 1233, 70%). We found that CHG bathing reduced the hazard rate of BSI among inborn babies ≥1.5 kg by a factor of 0.58 (p = 0.10, 95% CI: 0.31, 1.11), corresponding to an absolute risk reduction of 9.6 percentage points within a week of admission (p = 0.002, 95% CI: 3.4-15.7 percentage points). We did not find a statistically significant effect of CHG bathing on culture-negative sepsis (p = 0.54) or death (p = 0.85).

CONCLUSION

In our single center study, CHG bathing at admission was associated with a reduced risk of BSI due to a pathogenic organism after adjusting for potential confounding. Our results suggest that CHG may be an effective intervention for preventing neonatal sepsis in high-risk, low-income country settings.

Two Blood Cultures With Age-Appropriate Volume Enhance Suspected Sepsis Decision-Making

Background

Multiple blood cultures have been shown to improve pathogen yield and antimicrobial stewardship for adult patients with suspected serious bacterial infection (SBI). For children, the use of multiple blood cultures is less common and volume recommendations are more complicated, often resulting in single cultures with low volume.

Methods

In 2010, Children’s Hospital Colorado instituted electronic medical record (EMR) decision support to recommend collection of 2 blood cultures before administration of antibiotics for suspected SBI. Recommended blood culture volumes were calculated by age rather than weight. We evaluated all children admitted to inpatient units between 2008 and 2009 (pre-intervention) and 2011 and 2013 (postintervention) who received antibiotics in the hospital after having blood cultures drawn in the emergency department, excluding those with a length of stay >8 days. We compared blood culture yield, isolate classification (pathogen vs contaminant), and antimicrobial modifications before and after the interventions.

Results

A total of 3948 children were included in the study. EMR guidelines were associated with a significantly higher number of children with multiple blood cultures drawn before antibiotic administration (88.0% vs 12.3%; P < .001) and an increased percentage of blood cultures with the recommended volume (74.3% vs 15.2%; P < .001), resulting in a significantly higher pathogen isolation rate and improved antimicrobial decisions. Multiple cultures helped define the role of common contaminants in the clinical decision process.

Conclusions

Multiple blood cultures with age-based volumes taken before starting antibiotics increase pathogen isolation rates and appropriate modification of antimicrobial treatment in children.

Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data

BACKGROUND

There is a pressing need to understand better the extent and distribution of antimicrobial resistance on a global scale, to inform development of effective interventions. Collation of datasets for meta-analysis, mathematical modelling and temporo-spatial analysis is hampered by the considerable variability in clinical sampling, variable quality in laboratory practice and inconsistencies in antimicrobial susceptibility testing and reporting.

METHODS

The Microbiology Investigation Criteria for Reporting Objectively (MICRO) checklist was developed by an international working group of clinical and laboratory microbiologists, infectious disease physicians, epidemiologists and mathematical modellers.

RESULTS

In keeping with the STROBE checklist, but applicable to all study designs, MICRO defines items to be included in reports of studies involving human clinical microbiology data. It provides a concise and comprehensive reference for clinicians, researchers, reviewers and journals working on, critically appraising, and publishing clinical microbiology datasets.

CONCLUSIONS

Implementation of the MICRO checklist will enhance the quality and scientific reporting of clinical microbiology data, increasing data utility and comparability to improve surveillance, grade data quality, facilitate meta-analyses and inform policy and interventions from local to global levels.

Caracterización de pacientes pediatricos con hemocultivos positivos del servicio de cuidado intensivo pediátrico del Hospital San José Bogotá, abril 2012 a 2017

Introducción: El cultivo de la sangre es el método más utilizado en la búsqueda de infecciones del paciente pediátrico porque orienta la terapia antimicrobiana.Objetivo: Determinar la incidencia de hemocultivos positivos y su caracterización microbiológica en pacientes de cuidado intensivo pediátrico del Hospital de San José, Bogotá-Colombia.Materiales y métodos: Descripción de hemocultivos positivos en pacientes pediátricos de la unidad desde abril de 2012 a 2017. Se determinó la incidencia de hemocultivos positivos y se describió la población estudiada y los gérmenes aislados incluido su perfil de antibiograma.Resultados: Ingresaron 1773 pacientes a la UCIP, 241 pacientes (13,6%) fueron hemocultivados, de los cuales 80 (33,2%) fueron positivos, pero 50% de estos fueron catalogados como contaminaciones. La mediana de edad fue de 21 meses, con 64% de sexo masculino. El 57% fue ventilado y 45% tuvieron un catéter central. La mortalidad fue de 15,4%. La patología más frecuentemente fue respiratoria (75%). De los gérmenes no contaminantes el más frecuente aislado fue Staphylococcus aureus (30%), seguido de Klebsiella pneumoniae (17,5%) y Streptococcus pneumoniae (17,5%). El germen contaminante más frecuente fue Staphylococcus epidermidis (47,5%).Conclusión: La frecuencia de hemocultivos positivos es baja y es frecuente que se aíslen gérmenes contaminantes. El patrón fue similar a lo reportado por la red GREBO.

Epidemiology of Cerebrospinal Fluid Cultures and Time to Detection in Term Infants

BACKGROUND

Although meningitis is rare in previously healthy term infants, lumbar puncture is often performed to evaluate for source of illness. This study was performed to determine the time to detection for positive cerebrospinal fluid (CSF) cultures and to provide an update on the current epidemiology of bacterial meningitis in term infants.

METHODS

This study was a multicenter, retrospective review of positive CSF cultures in infants ≤90 days of age. Specimens were drawn in the emergency department or inpatient setting between January 2000 and December 2013. Cultures were deemed true pathogens or contaminant species based on the attending physician's treatment plan. Cultures from premature infants, an operative source, or those with significant medical history were excluded.

RESULTS

A total of 410 positive CSF culture results were included, with 53 (12.9%) true pathogens and 357 (87.1%) contaminant species. The mean ± SD time to detection for true pathogens was 28.6 ± 16.8 hours (95% confidence interval, 24-33.2); for contaminant species, it was 68.1 ± 36.2 hours (95% confidence interval, 64.3-71.9). Forty-three true-positive cases (81.1%) were positive in ≤36 hours. The most common pathogen was group B Streptococcus (51%), followed by Escherichia coli (13%) and Streptococcus pneumoniae (9%).

CONCLUSIONS

The majority of pathogenic bacteria in CSF exhibit growth within 36 hours. Most growth from CSF cultures in febrile infants is treated as contamination. The epidemiology of meningitis has remained constant, with group B Streptococcus as the predominant pathogen, despite changes noted in the epidemiology of bacteremia in this population.

Classification of Blood Culture Isolates Into Contaminants and Pathogens on the Basis of Clinical and Laboratory Data

The multisite community-based study, Aetiology of Neonatal Infection in South Asia (ANISA), uses blood culture as the gold standard for identifying the etiology of neonatal infection. Considering the importance of this age-old diagnostic tool and the risk of contamination, ANISA has employed rigorous measures to prevent contamination at all stages of blood collection, processing and culture. Because contamination may still occur, an independent expert group evaluates the routinely collected clinical and laboratory data to determine whether a blood culture isolate is a contaminant or a true pathogen. This article describes the methodology used by ANISA to determine whether a blood culture isolate is likely to be a true pathogen or a contaminant in neonatal sepsis.