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

Hossain, Belal MSc; Islam, Mohammad Shahidul MSc; Rahman, Atiqur MSc; Marzan, Mahfuza MSc; Rafiqullah, Iftekhar MSc; Connor, Nicholas E. MSc; Hasanuzzaman, Mohammad MSc; Islam, Maksuda BA; Hamer, Davidson H. MD; Hibberd, Patricia L. MD, PhD; Saha, Samir K. PhD

The Pediatric Infectious Disease Journal: May 2016 - Volume 35 - Issue 5 - p S45–S51
doi: 10.1097/INF.0000000000001106
ANISA Supplement

Background: Interpretation of blood culture isolates is challenging due to a lack of standard methodologies for identifying contaminants. This problem becomes more complex when the specimens are from sick young infants, as a wide range of bacteria can cause illness among this group.

Methods: We used 43 key words to find articles published between 1970 and 2011 on blood culture isolates and possible contaminants in the PubMed database. Experts were also consulted to obtain other relevant articles. Selection of articles followed systematic methods considering opinions from more than 1 reviewer.

Results: After reviewing the titles of 3869 articles extracted from the database, we found 307 relevant to our objective. Based on the abstracts, 42 articles were selected for the literature review. In addition, we included 7 more articles based on cross-references and expert advice. The most common methods for differentiating blood culture isolates were multiple blood cultures from the same subject, antibiograms and molecular testing. Streptococcus pneumoniae, Hemophilus influenzae, Neisseria meningitidis and group A and B streptococcus were always considered as pathogens, whereas Bacillus sp., Diphtheroids, Propionibacterium and Micrococcus were commonly regarded as contaminants. Coagulase-negative staphylococci were the most frequent isolates and usually reported as contaminants unless the patient had a specific condition, such as long-term hospitalization or use of invasive devices (catheters).

Conclusions: Inaccurate interpretation of blood culture may falsely guide treatment and also has long-term policy implications. The combination of clinical and microbiological knowledge, patient’s clinical history and laboratory findings are essential for appropriate interpretation of blood culture.

From the *Child Health Research Foundation, Dhaka, Bangladesh; Centre for Child and Adolescent Health, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; Department of Global Health and Center for Global Health and Development, Boston University School of Public Health, Boston, Massachusetts; and §Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts.

Accepted for publication January 10, 2016.

The ANISA study is funded by the Bill & Melinda Gates Foundation (Grant No. OPPGH5307). The authors have no other funding or conflicts of interest to disclose.

Address for correspondence: Belal Hossain, MSc, Child Health Research Foundation, Department of Microbiology, Dhaka Shishu (Children) Hospital, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh. E-mail:

This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially.

The Aetiology of Neonatal Infection in South Asia (ANISA) study is one of the largest initiatives for obtaining data on the etiology of community-acquired neonatal infections in the region.1 A wide range of bacteria can cause bloodstream infection in young infants, but many of these organisms are also part of normal skin flora.2 Contamination of blood culture during specimen collection and processing is common and accounts for up to half of all positive blood culture results.3 This situation can lead to incorrect treatment and has policy implications for designing appropriate strategies for the prevention and management of young infant infections.4,5 Considering this, ANISA has undertaken an elaborate initiative to prevent contamination during blood collection. Despite these efforts, bacterial contamination in blood culture may still occur. With this situation in mind, we conducted a review of relevant literature to understand different approaches to differentiating true bacterial pathogens from contaminants in blood culture. In this article, we narrate the summary of that review.

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Based on the preliminary observations of 3 peer-reviewed articles,5–7 we selected 43 key words to be used independently or in combinations to carry out the search process. We looked for articles that had both the phrases “blood culture” and “contamination” either in the title or in the abstract or that contained the phrase blood culture and any of the key words in the title (Table 1). We limited our search to the National Institutes of Health PubMed database and articles published between 1970 and 2011. Screening of articles for final use was done in 3 steps. First, each selected title was reviewed by 2 individuals, and all articles deemed irrelevant by them were excluded from subsequent screening. A third reviewer made a final decision where the first 2 reviewers disagreed. Second, each abstract was reviewed by 2 individuals. We discarded case reports and articles that did not use blood culture for etiology detection. After these 2 steps, 3 individuals carried out a full review of the selected articles and rated each one from A to C based on its relevance. Articles were selected for analysis if at least 2 reviewers scored an article as “A.” In addition to this screening, we included some articles from cross-references and others suggested by experts in neonatology.



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Search Outcomes

Through the search strategies, we extracted 3869 articles and checked the titles for their relevance to our objectives. Of these articles, 307 were marked for the next step, review of the abstracts. After reviewing the abstract, 168 articles went through a full-text screening. From this screening, 42 articles were selected for a full-text review of blood culture outcome interpretations and their relevance to infection.8–49 In addition, we included 2 relevant articles from cross-references50,51 and 5 articles based on expert advice,52–56 which were not captured in our search methodologies (Fig. 1). The selected articles were from various parts of the world: Africa (n = 4), Asia (n = 8), Australia (n = 1), Europe (n = 11), North America (n = 21) and South America (n = 1). One article reported bacterial etiology from multicenter studies in Asia and Africa, and 3 were review articles. Of these articles, 5.5% (n = 3) were published in the 1980s, 21.8% (n = 12) in the 1990s, 54.5% (n = 30) from 2000 to 2010 and 16.4% (n = 9) in 2011. Twenty-three articles contained information about strategies to define blood culture isolates and 4 contained information about strategies or methods to reduce blood culture contamination; 13 articles were etiological studies, 3 were reviews and 6 were on other related topics. A brief summary of the primary features of the selected articles is shown in Table 2.





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Identity of Blood Culture Isolates

Research confirmed that both Gram-positive and Gram-negative bacteria cause bloodstream infections. Gram-negative bacteria predominated during the neonatal period, whereas Gram-positive bacteria were more common in older patients.56 Hemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis and group A and B streptococcus were reported as potential causes of bloodstream infection in children; these organisms were described as a true cause in all the studies reviewed.8,10,11,46,52,55,56 Bacillus sp., Diphtheroids, Propionibacterium and Micrococcus were common contaminants in blood culture.9,16,18,41,44,50,55 Coagulase-negative Staphylococci (CoNS) were the most frequent isolates.30,51 These bacteria are commonly found in skin flora,2 and 85% of the time they occur during blood collection.3 Therefore, many studies considered these as contaminants, and they were labeled as pathogens only under certain conditions, such as when a patient used invasive devices (catheters)20,22,26,31,34,47 or stayed in an intensive care unit for a long time.14,15,17,32,43 Other common bloodstream pathogens were Staphylococcus aureus, Salmonella sp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter sp., Enterobacter sp., Proteus sp. and Candida sp.8,10–12,52,55,56 S. aureus, K. pneumoniae and E. coli are sometimes found in skin flora2 and thus may often appear in the culture as a contaminant. Hence, these pathogens need special review when they are found in blood cultures.

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Strategies for Interpreting Blood Culture Isolates

Researchers linked multiple clinical and microbiological parameters to define blood culture isolates where the isolates were not obvious blood-borne pathogens. The parameters, as described in detail below, include (i) type of bacteria; (ii) antibiogram of the isolate; (iii) antibiotic therapy response of the patient; (iv) time-to-positivity (TTP) of the blood culture and (v) isolation of the same bacterium from a second blood culture done at the same time or on follow-up.5

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Type of Bacteria

In all clinical research, identity of a bacterium was a major criterion to consider it as a true pathogen.5 Bacteria such as S. pneumoniae, H. influenzae and N. meningitidis were always considered as pathogens regardless of the patient’s clinical condition.5,8,10–12,52,55,56 Many researchers considered CoNS, Bacillus sp., Diphtheroids, Propionibacterium and Micrococcus as contaminants.55 E. coli and other potential bacteria were reviewed case-by-case to determine their association with illness.

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Antibiogram of the Isolate

In many studies, drug susceptibility patterns were correlated with treatment outcomes to decide whether to label isolated bacteria as pathogens. An isolate was considered as a pathogen when the patient showed clinical improvement in response to treatment and the isolated organism was susceptible to the drug used for treatment, or the patient showed no clinical improvement and the isolated organism was resistant to the treatment drug. An isolate was considered as a contaminant if the patient did not respond to an antibiotic to which the respective isolate was susceptible or responded to an antibiotic to which the isolate was not susceptible.5,31,32,39,50

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TTP is measured based on the time the blood culture bottle remains in the incubator and is inversely proportional to the magnitude of bacteria in the blood. Infected blood has a higher inoculum compared with contaminated blood and should have a shorter incubation time to yield growth.5 Thus, any blood culture that yields growth within a short duration has a higher probability of being a true pathogen.34

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Multiple Blood Culture Vials or Repeat Blood Cultures

Blood culture in duplicate was ideal to exclude contamination, that is, to confirm the isolate as a true pathogen. In many studies, multiple blood cultures (more than 2 within a 12-hour period) were performed, and if more than 1 culture was positive for the same bacterium, then the isolate was considered as a true pathogen.5,29,30,32

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Genotyping and Plasmid Profiles

The genetic fingerprints of isolated bacteria from the same patient are good tools for differentiating contaminants from opportunistic pathogens. In some studies, the plasmid or DNA profiles of 2 strains isolated from the same patient were compared, and if they matched, then they were considered as true pathogens.17,23,27,48 These molecular techniques were mainly used to differentiate contaminant CoNS from pathogenic ones.

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Blood culture contamination is a long-standing challenge in clinical microbiology as normal skin flora also consists of potential pathogens. The aim of this literature review was to extract existing information on defining blood culture isolates. The findings of this review assisted the ANISA study team and an external expert panel to develop a guideline for properly interpreting blood culture outcomes. This landscape analysis shows that a wide range of bacteria can cause infection in humans, especially at an early age. Some bacteria were universally considered either as pathogens or as contaminants, whereas some needed to be reviewed case-by-case. The process for assigning causality is never straightforward in an etiology study, and it requires integration of clinical knowledge, practical experience and expert opinion.

This review has some potential limitations. The literature search was designed to capture articles reporting blood culture contamination, so it could have missed studies that reported blood culture isolates but did not discuss contamination. In addition, our search was limited to PubMed and articles published in English. Therefore, we may have not seen useful articles published in other languages. We tried to compensate for such limitations by the inclusion of relevant cross-references and articles suggested by experts.

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The current review provides an insight into our existing knowledge about classifying blood culture isolates as true pathogens or contaminants based on an integrated algorithm and case-specific clinical and microbiological information. ANISA aims to use these findings to prevent the misclassification of blood culture results at 2 stages: (i) reduction of contamination by employing preventive strategies and (ii) teasing out contaminants from the isolates.

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1. Saha SK, Arifeen SE, Schrag SJ. Aetiology of Neonatal Infection in South Asia (ANISA): an initiative to identify appropriate program priorities to save newborns. Pediatr Infect Dis J. 2016;35(Suppl 1):S6–S8
2. Mullany LC, Saha SK, Shah R, et al. Impact of 4.0% chlorhexidine cord cleansing on the bacteriologic profile of the newborn umbilical stump in rural Sylhet District, Bangladesh: a community-based, cluster-randomized trial. Pediatr Infect Dis J. 2012;31:444–450
3. Weinstein MP, Towns ML, Quartey SM, et al. The clinical significance of positive blood cultures in the 1990s: a prospective comprehensive evaluation of the microbiology, epidemiology, and outcome of bacteremia and fungemia in adults. Clin Infect Dis. 1997;24:584–602
4. Alahmadi YM, Aldeyab MA, McElnay JC, et al. Clinical and economic impact of contaminated blood cultures within the hospital setting. J Hosp Infect. 2011;77:233–236
5. Hall KK, Lyman JA. Updated review of blood culture contamination. Clin Microbiol Rev. 2006;19:788–802
6. Bryan CS. Clinical implications of positive blood cultures. Clin Microbiol Rev. 1989;2:329–353
7. Weinstein MP. Current blood culture methods and systems: clinical concepts, technology, and interpretation of results. Clin Infect Dis. 1996;23:40–46
8. Adhikari M, Coovadia YM, Singh D. A 4-year study of neonatal meningitis: clinical and microbiological findings. J Trop Pediatr. 1995;41:81–85
9. Berkley JA, Lowe BS, Mwangi I, et al. Bacteremia among children admitted to a rural hospital in Kenya. N Engl J Med. 2005;352:39–47
10. Kohli-Kochhar R, Omuse G, Revathi G. A ten-year review of neonatal bloodstream infections in a tertiary private hospital in Kenya. J Infect Dev Ctries. 2011;5:799–803
11. Sigaúque B, Roca A, Mandomando I, et al. Community-acquired bacteremia among children admitted to a rural hospital in Mozambique. Pediatr Infect Dis J. 2009;28:108–113
12. Ashkenazi-Hoffnung L, Kaufman Z, Bromberg M, et al. Seasonality of Bacillus species isolated from blood cultures and its potential implications. Am J Infect Control. 2009;37:495–499
13. Huang SY, Tang RB, Chen SJ, et al. Coagulase-negative staphylococcal bacteremia in critically ill children: risk factors and antimicrobial susceptibility. J Microbiol Immunol Infect. 2003;36:51–55
14. Huang YC, Wang YH, Su LH, et al. Determining the significance of coagulase-negative staphylococci identified in cultures of paired blood specimens from neonates by species identification and strain clonality. Infect Control Hosp Epidemiol. 2006;27:70–73
15. Matrai-Kovalskis Y, Greenberg D, Shinwell ES, et al. Positive blood cultures for coagulase-negative staphylococci in neonates: does highly selective vancomycin usage affect outcome? Infection. 1998;26:85–92
16. Quiambao BP, Simoes EA, Ladesma EA, et al. Serious community-acquired neonatal infections in rural Southeast Asia (Bohol Island, Philippines). J Perinatol. 2007;27:112–119
17. Bradford R, Abdul Manan R, Daley AJ, et al. Coagulase-negative staphylococci in very-low-birth-weight infants: inability of genetic markers to distinguish invasive strains from blood culture contaminants. Eur J Clin Microbiol Infect Dis. 2006;25:283–290
18. Arnason S, Thors VS, Gudnason T, et al. [Bacteraemia in children in Iceland 1994-2005]. Laeknabladid. 2008;94:523–529
19. Burnie JP, Naderi-Nasab M, Loudon KW, et al. An epidemiological study of blood culture isolates of coagulase-negative staphylococci demonstrating hospital-acquired infection. J Clin Microbiol. 1997;35:1746–1750
20. Guerti K, Devos H, Ieven MM, et al. Time to positivity of neonatal blood cultures: fast and furious? J Med Microbiol. 2011;60(pt 4):446–453
21. Klingenberg C, Sundsfjord A, Rønnestad A, et al. Phenotypic and genotypic aminoglycoside resistance in blood culture isolates of coagulase-negative staphylococci from a single neonatal intensive care unit, 1989-2000. J Antimicrob Chemother. 2004;54:889–896
22. Koksal F, Yasar H, Samasti M. Antibiotic resistance patterns of coagulase-negative staphylococcus strains isolated from blood cultures of septicemic patients in Turkey. Microbiol Res. 2009;164:404–410
23. Krause R, Haberl R, Wölfler A, et al. Molecular typing of coagulase-negative staphylococcal blood and skin culture isolates to differentiate between bacteremia and contamination. Eur J Clin Microbiol Infect Dis. 2003;22:760–763
24. Leyssene D, Gardes S, Vilquin P, et al. Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture. Eur J Clin Microbiol Infect Dis. 2011;30:1537–1541
25. Mulder JG, Degener JE. Slime-producing properties of coagulase-negative staphylococci isolated from blood cultures. Clin Microbiol Infect. 1998;4:689–694
26. Schuetz P, Mueller B, Trampuz A. Serum procalcitonin for discrimination of blood contamination from bloodstream infection due to coagulase-negative staphylococci. Infection. 2007;35:352–355
27. Senger SS, Saccozza ME, Yuce A. Compatibility of pulsed-field gel electrophoresis findings and clinical criteria commonly used to distinguish between true coagulase-negative staphylococcal bacteremia and contamination. Infect Control Hosp Epidemiol. 2007;28:992–996
28. Viagappan M, Kelsey MC. The origin of coagulase-negative staphylococci isolated from blood cultures. J Hosp Infect. 1995;30:217–223
29. Al Wohoush I, Rivera J, Cairo J, et al. Comparing clinical and microbiological methods for the diagnosis of true bacteraemia among patients with multiple blood cultures positive for coagulase-negative staphylococci. Clin Microbiol Infect. 2011;17:569–571
30. Beekmann SE, Diekema DJ, Doern GV. Determining the clinical significance of coagulase-negative staphylococci isolated from blood cultures. Infect Control Hosp Epidemiol. 2005;26:559–566
31. Benjamin DK Jr., Stoll BJ, Gantz MG, et al.Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. Neonatal candidiasis: epidemiology, risk factors, and clinical judgment. Pediatrics. 2010;126:e865–e873
32. Calnen G, Campognone P, Peter G. Coagulase-negative staphylococcal bacteremia in newborns. Clin Pediatr (Phila). 1984;23:542–544
33. Chandran AU, Rennie R. Routine antimicrobial susceptibility testing of coagulase-negative staphylococci isolated from blood cultures: is it necessary? Clin Microbiol Infect. 2005;11:1037–1040
34. Haimi-Cohen Y, Shafinoori S, Tucci V, et al. Use of incubation time to detection in BACTEC 9240 to distinguish coagulase-negative staphylococcal contamination from infection in pediatric blood cultures. Pediatr Infect Dis J. 2003;22:968–974
35. Herwaldt LA, Geiss M, Kao C, et al. The positive predictive value of isolating coagulase-negative staphylococci from blood cultures. Clin Infect Dis. 1996;22:14–20
36. Kim SD, McDonald LC, Jarvis WR, et al. Determining the significance of coagulase-negative staphylococci isolated from blood cultures at a community hospital: a role for species and strain identification. Infect Control Hosp Epidemiol. 2000;21:213–217
37. Kirchhoff LV, Sheagren JN. Epidemiology and clinical significance of blood cultures positive for coagulase-negative staphylococcus. Infect Control. 1985;6:479–486
38. Kassis C, Rangaraj G, Jiang Y, et al. Differentiating culture samples representing coagulase-negative staphylococcal bacteremia from those representing contamination by use of time-to-positivity and quantitative blood culture methods. J Clin Microbiol. 2009;47:3255–3260
39. Khatib R, Riederer KM, Clark JA, et al. Coagulase-negative staphylococci in multiple blood cultures: strain relatedness and determinants of same-strain bacteremia. J Clin Microbiol. 1995;33:816–820
40. Nataro JP, Corcoran L, Zirin S, et al. Prospective analysis of coagulase-negative staphylococcal infection in hospitalized infants. J Pediatr. 1994;125(5 pt 1):798–804
41. Segal GS, Chamberlain JM. Resource utilization and contaminated blood cultures in children at risk for occult bacteremia. Arch Pediatr Adolesc Med. 2000;154:469–473
42. Seybold U, Reichardt C, Halvosa JS, et al. Clonal diversity in episodes with multiple coagulase-negative Staphylococcus bloodstream isolates suggesting frequent contamination. Infection. 2009;37:256–260
43. Sidebottom DG, Freeman J, Platt R, et al. Fifteen-year experience with bloodstream isolates of coagulase-negative staphylococci in neonatal intensive care. J Clin Microbiol. 1988;26:713–718
44. Souvenir D, Anderson DE Jr., Palpant S, et al. Blood cultures positive for coagulase-negative staphylococci: antisepsis, pseudobacteremia, and therapy of patients. J Clin Microbiol. 1998;36:1923–1926
45. Struthers S, Underhill H, Albersheim S, et al. A comparison of two versus one blood culture in the diagnosis and treatment of coagulase-negative staphylococcus in the neonatal intensive care unit. J Perinatol. 2002;22:547–549
46. Weston EJ, Pondo T, Lewis MM, et al. The burden of invasive early-onset neonatal sepsis in the United States, 2005-2008. Pediatr Infect Dis J. 2011;30:937–941
47. Zaidi AK, Harrell LJ, Rost JR, et al. Assessment of similarity among coagulase-negative staphylococci from sequential blood cultures of neonates and children by pulsed-field gel electrophoresis. J Infect Dis. 1996;174:1010–1014
48. García P, Benítez R, Lam M, et al. Coagulase-negative staphylococci: clinical, microbiological and molecular features to predict true bacteraemia. J Med Microbiol. 2004;53(pt 1):67–72
49. Peltola H. Burden of meningitis and other severe bacterial infections of children in Africa: implications for prevention. Clin Infect Dis. 2001;32:64–75
50. Kim NH, Kim M, Lee S, et al. Effect of routine sterile gloving on contamination rates in blood culture: a cluster randomized trial. Ann Intern Med. 2011;154:145–151
51. Thylefors JD, Harbarth S, Pittet D. Increasing bacteremia due to coagulase-negative staphylococci: fiction or reality? Infect Control Hosp Epidemiol. 1998;19:581–589
52. Arifeen SE, Saha SK, Rahman S, et al. Invasive pneumococcal disease among children in rural Bangladesh: results from a population-based surveillance. Clin Infect Dis. 2009;48(suppl 2):S103–S113
53. Stoll BJ, Hansen N, Fanaroff AA, et al. Changes in pathogens causing early-onset sepsis in very-low-birth-weight infants. N Engl J Med. 2002;347:240–247
54. Stoll BJ, Hansen NI, Sánchez PJ, et al.Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. Early onset neonatal sepsis: the burden of group B Streptococcal and E. coli disease continues. Pediatrics. 2011;127:817–826
55. The WHO Young Infants Study Group. . Bacterial etiology of serious infections in young infants in developing countries: results of a multicenter study. Pediatr Infect Dis J. 1999;18(suppl 10):S17–S22
56. Zaidi AK, Thaver D, Ali SA, et al. Pathogens associated with sepsis in newborns and young infants in developing countries. Pediatr Infect Dis J. 2009;28(1 suppl):S10–S18

neonatal; infection; blood culture; contamination; review; ANISA

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