Serum PCR in diagnosis of neonatal sepsis caused by bacteria and enteroviruses.
Main Article Content
Abstract
Although blood culture is considered the gold standard for detection of neonatal infections of bloodstream, its result can take from 48-72 h and has low sensitivity. In this study, we determined the usefulness of the panbacterial polymerase chain reaction (PCR) and the panviral RT-PCR in serum, as tests for the early diagnosis of neonatal sepsis. We studied 195 patients with the clinical diagnosis of neonatal sepsis, up to the age of 28 days, hospitalized in the Neonatal Intensive Care Unit (NICU) of the Hospital Infantil de México “Federico Gómez”, and 195 umbilical cord samples obtained from healthy newborns. Blood cultures, and DNA / RNA extraction were done with a system of primers of the rRNA 16s region, which is highly conserved in a large number of bacteria and a highly conserved non-coding enteroviral 5´ (5’-NCR) region, respectively. The results showed that among the 90 newborns with sepsis and negative PCR, 19 were randomly selected to perform RT-PCR; 26% of them had a positive result. Statistical analysis included the PCR test’s sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) using the clinical diagnosis as the gold standard. PCR sensitivity was 77%, specificity was 83%, PPV was 92% and the NPV was 59%. In summary, panbacterial PCR is useful, quick and effective in the diagnosis of sepsis and should be used as a complement to the microbiological and clinical diagnoses. Although the frequency of enteroviral sepsis was low, in newborns with a negative panbacterial PCR, a panviral RT-PCR is recommended. Our results indicate that molecular diagnosis provides the balance of cost-benefit.
Keywords:
Early diagnosis, Neonatal sepsis, Polymerase chain reaction, Reverse transcriptase polymerase chain reaction
Article Details
How to Cite
REY-PINEDA, Guillermo del et al.
Serum PCR in diagnosis of neonatal sepsis caused by bacteria and enteroviruses..
Medical Research Archives, [S.l.], v. 9, n. 3, mar. 2021.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/2353>. Date accessed: 28 dec. 2024.
doi: https://doi.org/10.18103/mra.v9i3.2353.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
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Early neonatal sepsis, incidence and associated risk factors in a public hospital in western Mexico. Rev Chilena Infectol 2015; 32: 387-392. doi: 10.4067/S0716-10182015000500003
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17. Gérard HC, Wang Z, Wang GF, El-Gabalawy H, Goldbach-Mansky R, Li Y et al. Chromosomal DNA from a variety of bacterial species is present in synovial tissue from patients with various forms of arthritis. Arthritis Rheum 2001; 44: 1689-97. doi: 10.1002/1529-0131(200107)44:7<1689::AID-ART293>3.0.CO;2-K
18. Iizuka N, Kuge S, Nomoto A. Complete nucleotide sequence of the genome of coxsackie B1. Virology 1987; 156: 64-73. doi: 10.1016/0042-6822(87)90436-3
19. Zoll GJ, Melchers WJF, Kopecka H, Jambroes G, Van der Piel HJA, Galama JMD. General primer-mediated polymerase chain reaction for detection of enterovirus: application for diagnostic routine and persistent infections. J Clin Microbiol 1992; 30: 160-165. doi: 10.1128/JCM.30.1.160-165.1992
20. García-Elorriaga G, Esparza-García A, Méndez-Rojas C, del Rey-Pineda G, González-Bonilla C. CSF RT-PCR standardization in pediatric patients with enteroviral central nervous system infection. Rev Invest Clin 2012; 64: 59-66.
21. Tsai MH, Chu SM, Lee CW, Hsu JF, Huang HR, Chiang MC et al. Recurrent late-onset sepsis in the neonatal intensive care unit: incidence, clinical characteristics and risk factors. Clin Microbiol Infect 2014; 20: O928–O935. doi: 10.1111/1469-0691.12661
22. Chiabi A, Takou V, Mah E, Nguefack S, Siyou H, Takou V et al. Risk Factors for Neonatal Mortality at the Yaounde Gynaeco-Obstetric and Pediatric Hospital, Cameroon. Iran J Pediatr 2014; 24: 393-400.
23. Tsai MH, Chu SM, Hsu JF, Lien R, Huang HR, Chiang MC et al. Polymicrobial bloodstream infection in neonates: Microbiology, clinical characteristics, and risk factors. PLoS ONE 2014; 9: e83082. doi: 10.1371/journal.pone.0083082
24. Tsai MH, Chu SM, Hsu JF, Lien R, Huang HR, Chiang MC et al. Risk factors and outcomes for multidrug-resistant Gram-Negative bacteremia in the NICU. Pediatrics 2014; 133: e322-e329. doi: 10.1542/peds.2013-1248
25. Bhandari V, Wang C, Rinder C, Rinder H. Hematologic profile of sepsis in neonates: neutrophil CD64 as a diagnostic marker. Pediatrics 2008; 65:19-25. doi: 10.1542/peds.2007-1308
26. Lahra MM, Beeby PJ, Jeffery HE. Intrauterine inflammation, neonatal sepsis, and chronic lung disease: a 13-year hospital cohort study. Pediatrics 2009; 123:1314–19. doi: 10.1542/peds.2008-0656
27. van den Hoogen A, Gerards LJ, Verboon-Maciolek MA, Fleer A, Krediet TG. Long-term trends in the epidemiology of neonatal sepsis and antibiotic susceptibility of causative agents. Neonatology 2010; 97:22–8. doi: 10.1159/000226604
28. Borges Peixoto P, Henrique Massinhani F, Netto Dos Santos KR, Cardoso Chamon R, Beatriz Silva R, Lopes Correa FE et al. Methicillin-resistant Staphylococcus epidermidis isolates with reduced vancomycin susceptibility from bloodstream infections in a neonatal intensive care unit. J Med Microbiol.2020; 9:41-45.doi: 10.1099/jmm.0.001117
29. Huggard D, Powell J, Kirkham C, Power L, O'Connell NH, Philip RK. Time to positivity (TTP) of neonatal blood cultures: a trend analysis over a decade from Ireland. J Matern Fetal Neonatal Med. 2021; 34:780-786.doi: 10.1080/14767058.2019.1617687
30. Chaves F, García- Alvarez M, Sanz F, Alba C, Otero JR. Nosocomial spread of a Staphylococcus hominis subsp. novobiosepticus strain causing sepsis in a neonatal intensive care unit. J Clin Microbiol 2005; 43:4877–4879. doi: 10.1128/JCM.43.9.4877-4879.2005
31. Furtado I, Niz Xavier PC, Martinelli Tavares LV, Alves F, Fonseca Martins S, de Sousa Martins A et al. Enterococcus faecium and Enterococcus faecalis in Blood of newborns with suspected nosocomial infection. Rev Inst Med Trop. Sao Paulo 2014; 56:77-80. doi: 10.1590/S0036-46652014000100012
32. Reier-Nilsen T, Farstad T, Nakstad B, Lauvrak V, Steinbakk M. Comparison of broad range 16S rDNA PCR and conventional blood culture for diagnosis of sepsis in the newborn: a case control study. BMC Pediatrics 2009; 9:5. doi: 10.1186/1471-2431-9-5
33. El Gawhary S, El-Anany M, Hassan R, Ali D, El Gameel el Q. The Role of 16S rRNA Gene Sequencing in Confirmation of Suspected Neonatal Sepsis. J Trop Pediatr 2016; 62:75-80. doi: 10.1093/tropej/fmv066
34. El-Amir MI, El-Feky MA, Abo Elwafa DA, Abd-Elmawgood EA. Rapid diagnosis of neonatal sepsis by PCR for detection of 16S rRNA gene, while blood culture and PCR results were similar in E.coli-predominant EOS cases. Infect Drug Resist. 2019; 12:2703-2710. doi: 10.2147/IDR.S213958
35. Morriss FH Jr, Lindower JB, Bartlett HL, Atkins DL, Kim JO, Klein JM et al. Neonatal Enterovirus Infection: Case Series of Clinical Sepsis and Positive Cerebrospinal Fluid Polymerase Chain Reaction Test with Myocarditis and Cerebral White Matter Injury Complications. Am J Perinatol Rep 2016; 6:e344-e351. doi: 10.1055/s-0036-1593406
36. Schröder D, Siauw C, Wirbelauer J. Rare Differential Diagnosis of a Neonatal Bacterial Sepsis: The Neonatal Viral Myocarditis. Z Geburtshilfe Neonatol. 2018; 222:82-85. doi: 10.1055/s-0043-121222
37. Chuang YY, Huang YC. Enteroviral infection in neonates. J Microbiol Immunol Infect. 2019; 52:851-857. doi: 10.1016/j.jmii.2019.08.018
38. Pammi M, Flores A, Versalovic J, Leeflang MM. Molecular assays for the diagnosis of sepsis in neonates. Cochrane Database Syst Rev. 2017; 2:CD011926.
doi: 10.1002/14651858.CD011926
2. Chu SM, Hsu JF, Lee CW, Lien R, Huang HR, Chiang MC, Fu RH, Tsai MH. Neurological complications after neonatal bacteremia: the clinical characteristics, risk factors, and outcomes. PLoS ONE 2014; 9: e105294. doi: 10.1371/journal.pone.0105294
3. Rohit A, Maiti B, Shenoy S, Karunasagar I. Polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) for rapid diagnosis of neonatal sepsis. Indian J Med Res 2016; 143: 72-78. doi: 10.4103/0971-5916.178613
4. Pérez RO, Lona JC, Quiles M, Verdugo MA, Ascencio EP, Benítez EA.
Early neonatal sepsis, incidence and associated risk factors in a public hospital in western Mexico. Rev Chilena Infectol 2015; 32: 387-392. doi: 10.4067/S0716-10182015000500003
5. Leal YA, Álvarez-Nemegyei J, Velázquez JR, Rosado-Quiab U, Diego-Rodríguez N, Paz-Baeza E et al. Risk factors and prognosis for neonatal sepsis in southeastern Mexico: analysis of a four-year historic cohort follow-up. BMC Pregnancy Childbirth 2012; 12:48. doi: 10.1186/1471-2393-12-48
6. Korber F, Iris Zeller I, Grünstäudl M, Willinger B, Apfalter P, Hirschl AM et al. SeptiFast versus blood culture in clinical routine – A report on 3 years experience. Wien Klin Wochenschr 2017; 129:427-434. doi: 10.1007/s00508-017-1181-3
7. StraubJ, Paula H, Mayr M, Kasper D, Assadian O, Berger A et al. Diagnostic accuracy of the ROCHE Septifast PCR system for the rapid detection of blood pathogens in neonatal sepsis – A prospective clinical trial. PLoS ONE 2017; 12: e0187688. https://doi.org/10.1371/journal.pone.0187688.
8. Dong Y, Speer CP. The role of Staphylococcus epidermidis in neonatal sepsis: guarding angel or pathogenic devil? Int J Med Microbiol 2014; 304:513-20. doi: 10.1016/j.ijmm.2014.04.013
9. Dutta S, Narang A, Chakraborty A, Pallab Ray P. Diagnosis of Neonatal Sepsis Using Universal Primer Polymerase Chain Reaction Before and After Starting Antibiotic Drug Therapy. Arch Pediatr Adolesc Med 2009; 163:6-11. doi: 10.1001/archpediatrics.2008.513
10. Liu CL, Ai HW, Wang WP, Chen L, Hu HB, Ye T et al. Comparison of 16S rRNA gene PCR and blood culture for diagnosis of neonatal sepsis. Arch Pediatr 2014; 21:162-9. doi: 10.1016/j.arcped.2013.11.015
11. Lindamood KE, Fleck P, Narla A, Vergilio JA, Degar BA, Baldwin M et al. Neonatal enteroviral sepsis/meningoencephalitis and hemophagocytic lymphohistiocytosis: Diagnostic challenges. Am J Perinatol 2010; 28:337-46. doi: 10.1055/s-0030-1268710
12. Schlapbach LJ, Ersch J, Balmer C, Prêtre R, Tomaske M, Caduff R et al. Enteroviral myocarditis in neonatos. J Pediatr Child Health 2013; 49: E451–E454. doi: 10.1111/jpc.12248
13. Bhat AA, Shamim A, Gul S, Akther R, Bhat I. Neonatal sepsis- Early detection comparing Procalcitonin and CRP as markers and newer tools. IJMDS 2016; 5:1048-1055. doi:10.19056/ijmdsjssmes/2016/v5i1/83574
14. Chandna A, Rao MN, Srinivas M, Shyamala S. Rapid diagnostic tests in neonatal septicemia. Indian J Pediatr 1988; 55:947-53. doi: 10.1007/BF02727835
15. Chomczynski P. A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques 1993; 15: 532-7.
16. García-Elorriaga G, Cortés-Torres N, Ballesteros-del Olmo JC, del Rey-Pineda G, González-Bonilla C. The usefulness of the buffy coat smear and panbacterial polymerase chain reaction in early diagnosis of neonatal sepsis. Rev Invest Clin 2012; 64: 275-283.
17. Gérard HC, Wang Z, Wang GF, El-Gabalawy H, Goldbach-Mansky R, Li Y et al. Chromosomal DNA from a variety of bacterial species is present in synovial tissue from patients with various forms of arthritis. Arthritis Rheum 2001; 44: 1689-97. doi: 10.1002/1529-0131(200107)44:7<1689::AID-ART293>3.0.CO;2-K
18. Iizuka N, Kuge S, Nomoto A. Complete nucleotide sequence of the genome of coxsackie B1. Virology 1987; 156: 64-73. doi: 10.1016/0042-6822(87)90436-3
19. Zoll GJ, Melchers WJF, Kopecka H, Jambroes G, Van der Piel HJA, Galama JMD. General primer-mediated polymerase chain reaction for detection of enterovirus: application for diagnostic routine and persistent infections. J Clin Microbiol 1992; 30: 160-165. doi: 10.1128/JCM.30.1.160-165.1992
20. García-Elorriaga G, Esparza-García A, Méndez-Rojas C, del Rey-Pineda G, González-Bonilla C. CSF RT-PCR standardization in pediatric patients with enteroviral central nervous system infection. Rev Invest Clin 2012; 64: 59-66.
21. Tsai MH, Chu SM, Lee CW, Hsu JF, Huang HR, Chiang MC et al. Recurrent late-onset sepsis in the neonatal intensive care unit: incidence, clinical characteristics and risk factors. Clin Microbiol Infect 2014; 20: O928–O935. doi: 10.1111/1469-0691.12661
22. Chiabi A, Takou V, Mah E, Nguefack S, Siyou H, Takou V et al. Risk Factors for Neonatal Mortality at the Yaounde Gynaeco-Obstetric and Pediatric Hospital, Cameroon. Iran J Pediatr 2014; 24: 393-400.
23. Tsai MH, Chu SM, Hsu JF, Lien R, Huang HR, Chiang MC et al. Polymicrobial bloodstream infection in neonates: Microbiology, clinical characteristics, and risk factors. PLoS ONE 2014; 9: e83082. doi: 10.1371/journal.pone.0083082
24. Tsai MH, Chu SM, Hsu JF, Lien R, Huang HR, Chiang MC et al. Risk factors and outcomes for multidrug-resistant Gram-Negative bacteremia in the NICU. Pediatrics 2014; 133: e322-e329. doi: 10.1542/peds.2013-1248
25. Bhandari V, Wang C, Rinder C, Rinder H. Hematologic profile of sepsis in neonates: neutrophil CD64 as a diagnostic marker. Pediatrics 2008; 65:19-25. doi: 10.1542/peds.2007-1308
26. Lahra MM, Beeby PJ, Jeffery HE. Intrauterine inflammation, neonatal sepsis, and chronic lung disease: a 13-year hospital cohort study. Pediatrics 2009; 123:1314–19. doi: 10.1542/peds.2008-0656
27. van den Hoogen A, Gerards LJ, Verboon-Maciolek MA, Fleer A, Krediet TG. Long-term trends in the epidemiology of neonatal sepsis and antibiotic susceptibility of causative agents. Neonatology 2010; 97:22–8. doi: 10.1159/000226604
28. Borges Peixoto P, Henrique Massinhani F, Netto Dos Santos KR, Cardoso Chamon R, Beatriz Silva R, Lopes Correa FE et al. Methicillin-resistant Staphylococcus epidermidis isolates with reduced vancomycin susceptibility from bloodstream infections in a neonatal intensive care unit. J Med Microbiol.2020; 9:41-45.doi: 10.1099/jmm.0.001117
29. Huggard D, Powell J, Kirkham C, Power L, O'Connell NH, Philip RK. Time to positivity (TTP) of neonatal blood cultures: a trend analysis over a decade from Ireland. J Matern Fetal Neonatal Med. 2021; 34:780-786.doi: 10.1080/14767058.2019.1617687
30. Chaves F, García- Alvarez M, Sanz F, Alba C, Otero JR. Nosocomial spread of a Staphylococcus hominis subsp. novobiosepticus strain causing sepsis in a neonatal intensive care unit. J Clin Microbiol 2005; 43:4877–4879. doi: 10.1128/JCM.43.9.4877-4879.2005
31. Furtado I, Niz Xavier PC, Martinelli Tavares LV, Alves F, Fonseca Martins S, de Sousa Martins A et al. Enterococcus faecium and Enterococcus faecalis in Blood of newborns with suspected nosocomial infection. Rev Inst Med Trop. Sao Paulo 2014; 56:77-80. doi: 10.1590/S0036-46652014000100012
32. Reier-Nilsen T, Farstad T, Nakstad B, Lauvrak V, Steinbakk M. Comparison of broad range 16S rDNA PCR and conventional blood culture for diagnosis of sepsis in the newborn: a case control study. BMC Pediatrics 2009; 9:5. doi: 10.1186/1471-2431-9-5
33. El Gawhary S, El-Anany M, Hassan R, Ali D, El Gameel el Q. The Role of 16S rRNA Gene Sequencing in Confirmation of Suspected Neonatal Sepsis. J Trop Pediatr 2016; 62:75-80. doi: 10.1093/tropej/fmv066
34. El-Amir MI, El-Feky MA, Abo Elwafa DA, Abd-Elmawgood EA. Rapid diagnosis of neonatal sepsis by PCR for detection of 16S rRNA gene, while blood culture and PCR results were similar in E.coli-predominant EOS cases. Infect Drug Resist. 2019; 12:2703-2710. doi: 10.2147/IDR.S213958
35. Morriss FH Jr, Lindower JB, Bartlett HL, Atkins DL, Kim JO, Klein JM et al. Neonatal Enterovirus Infection: Case Series of Clinical Sepsis and Positive Cerebrospinal Fluid Polymerase Chain Reaction Test with Myocarditis and Cerebral White Matter Injury Complications. Am J Perinatol Rep 2016; 6:e344-e351. doi: 10.1055/s-0036-1593406
36. Schröder D, Siauw C, Wirbelauer J. Rare Differential Diagnosis of a Neonatal Bacterial Sepsis: The Neonatal Viral Myocarditis. Z Geburtshilfe Neonatol. 2018; 222:82-85. doi: 10.1055/s-0043-121222
37. Chuang YY, Huang YC. Enteroviral infection in neonates. J Microbiol Immunol Infect. 2019; 52:851-857. doi: 10.1016/j.jmii.2019.08.018
38. Pammi M, Flores A, Versalovic J, Leeflang MM. Molecular assays for the diagnosis of sepsis in neonates. Cochrane Database Syst Rev. 2017; 2:CD011926.
doi: 10.1002/14651858.CD011926