Emerging Antimicrobial Resistance in Neonatal Sepsis

By Muhammad Almas Hashmi, Munir Akmal Lodhi, Kiran Mushtaq Toor, Awais Tahir, Huma Saleem Khan, Rabia Aziz

Affiliations

1. Department of Paediatrics, Fauji Foundation Hospital, Rawalpindi, Foundation University, Islamabad, Pakistan

doi: 10.29271/jcpsp.2020.12.1312

ABSTRACT
Objective: To determine the frequency and antimicrobial sensitivity pattern of microbial agents causing neonatal sepsis.
Study Design: Descriptive study.
Place and Duration of Study: Neonatal ICU, Fauji Foundation Hospital, Rawalpindi; Foundation University, Islabambad, from May 2017 to April 2019.
Methodology: Data of all neonates admitted with sepsis during study period was retrieved from computer database. Age at admission, gender, duration of hospital stay and culture reports were recorded. Culture positive patients were further analysed regarding their antibiotic sensitivity.
Results: A total of 1,070 neonates, male:female = 1.36:1, mostly newborn, were included in the study. Total mortality was 182 (17%). Blood culture was positive in 79 (7.4%). Gram positive organisms were identified in 37 (46.8%) Staphylococci in 29 (36.7%), Enterococci 7 (8.9%), Corynebacterium species in 1 (1.3%). Gram negative were isolated in 42 (53.2%) Acinetobacter Baumanni in 14 (17.7%), Klebsiella in 12 (15.2%), Enterobacter spp. In 7 (8.8%), E.coli in 5 (6.3%), Pseudomonas in 2 (2.5%) and Proteus in 1 (1.3%) and Serratia in 1 (1.3%) each. Sensitivity pattern of Gram positive organisms was: vancomycin 30/37 (81.1%), ciprofloxacin 13/37 (35.1%) and Gentimicin 12/37 (32.4%). Gram negative organisms sensitivity pattern was: meropenem 12/42 (28.6%), chloramphenical 10/42 (23.8%), gentimicin 6/42 (14.3%), ciprofloxacin 5/42 (11.9%). Highly resistant strains of Klebsiella (13/14) and Acinitobacter (5/12) were sensitive to colomycin only.
Conclusion: Common organisms responsible for neonatal sepsis were Styphylococci, Acinitobacter, Klebsiella and E.Coli. Gram positive organisms showed sensitivity to vancomycin and gentamicin. Gram negative organisms were highly sensitive to colomycin.

Key Words: Neonatolgy, Neonatal sepsis, Antimicrobial sensitivity, Neonatal mortality.

INTRODUCTION

Neonatal sepsis is defined as a syndrome of hemodynamic and clinical manifestations caused by a pathogenic infective organism.^1,2

Neonatal sepsis is one of the major contributors to mortality in neonatal intensive care setup. Mortality rates as high as 14.6% to 36%, higher in neonatal sepsis associated with prematurity and low birth weight.³ In a study from Ghana, neonatal sepsis was responsible for 8.3% of total deaths in a neonatal intensive care setup.⁴

Causitive organisms vary depending upon the onset of sepsis. In early onset, presenting within 72 hours of life, gram positive organisms were found to occur more frequently.
 

In data from American Neonatology Network, main etiology for early onset neonatal sepsis was Streptococcus agalactae accounting for 43% of cases while E.coli accounts for 29% of cases.⁵ On the other hand, in late-onset neonatal sepsis patients, i.e. those presenting beyond 72 hours of life, conagulase negative Staphylococci and Staphylococcus aureus were predominantly encountered while E. Coli accounted for only 7% of cases.⁶

Additional problems are presented by the fact that microbial yield of most of the culture methods is limited. In one study, only 8.98% for all blood culture specimen taken from neonates with suspected neonatal sepsis were positive for a pathological organism.⁷ This makes the rational and empiric choice of antibiotics an extremely important determinant of outcome. The problem is compounded by rapidly emerging antimicrobial resistance. In a recent study from Nepal, the organisms causing neonatal sepsis were found to be highly resistant to common antibiotics like cefotaxime, gentimicin, ciprofloxacin and chloramphenical. Good sensitivity was observed with carbapenems and calomycin for gram negative organisms and vancomycin for Gram positive organisms.⁸

Klebsiella is among the commonest Gram negative organisms causing neonatal sepsis in some of the recent studies. The source of these organisms may include delivery rooms, operating rooms or neonatal areas.^9,10 Microbial pattern and antimicrobial sensitivity keeps on evolving and at times, varies between different locations and healthcare setups. This makes it necessary to review the treatment guidelines in accordance with the recent data. This study was conducted to determine the frequency of different microbial agents causing neonatal sepsis and determine their antimicrobial sensitivity pattern.

METHODOLOGY

Thisdescriptive study was conducted in NICU of Fauji Foundation Hospital, Foundation University, Islamabad from May 2017 to April 2019. After obtaining ethical approval from the Institution Review Board, data of all neonates admitted in NICU during the study period was retrieved from computer database by consecutive non-probability sampling. Age at admission, gender, duration of hospital stay and culture reports were recorded. Culture positive patients were further analysed regarding their antibiotic sensitivity patterns. Antibiotic sensitivity was tested in a stepwise manner; sensitivity to common antibiotics was tested first and only highly resistant organisms were tested for sensitivity to antibiotics like colomycin.

All data was recorded and analysed suing SPSS version 20. Descriptive variables including culture positivity, gram staining, gender, onset of neonatal sepsis, outcome and organism identified were described as frequencies and percentages, while continuous variables including age and hospital stay were subjected to normality testing. As both variables were non-parametric, they were described as median and interquartile range. Data was divided into groups based upon the onset of sepsis (early onset within 3 days of life and late onset beyond 3 days of life), and culture positivity. Comparison between the groups was done using Mann Whittney-U test and Chi-square test for quantitative and qualitative variables respectively. P-value of less than 0.05 was considered significant.

RESULTS

A total of 1,070 neonates, males 617 (57.7%) and females 453(42.3%), were entered into study after removing duplicates. Median age at time of admission was 0 days (newborn) with an interquartile range of 0 - 1.9 days. Blood culture was positive in 79 (7.4%) patients. Median duration of admission was 5.5 days with an interquartile range of 2.9 - 9.7 days. Total number of expired neonates was 182 giving an expiry rate of 17%.

Among all, 886 (82.8%) neonates presented with early onset neonatal sepsis (within 3 days of life) while 184 (17.2%) presented with late onset of neonatal sepsis (beyond 3 days of life).

Table I: Demographic Features of Study Population.

		Early presentation (<72 hours) (n=886)	Latepresentation (>72 hours) (N=184)	p-value
Gender	Male	506 (57.11%)	111 (60.33%)	0.422*
	Female	380 (42.89%)	73 (39.67%)
Organism identified	Gram +ive	25 (2.82%)	12 (6.52%)	<0.001*
	Gram –ive	16 (1.80%)	26 (14.13%)
Expiryrate		141 (15.91%)	41 (22.28%)	0.036*
Duration of admission (days)	Median	4.7	10.4	<0.001#
	IQR (Q1 - Q3)	2.6 - 8.3	5.8 - 17.6
Chi-square test;   #Mann-WhittneyU-Test.

Table II: Gram positive organisms; Antibiotic Sensitivity (n=37).

Organism	No	Doxycycline	Chloramphenical	Vancomycin	Linezolid	Ciprofloxacin
MRSA	19	13 (68.42%)	14 (73.68%)	19 (100%)	16 (84.21%)	5 (26.31%)
MRSE	1	1 (100%)	1 (100%)	1 (100%)	1 (100%)	0 (0%)
MSSA	8	6 (75%)	5 (62.5%)	6 (75%)	8 (100%)	5 (62.50%)
Coagulase negative staphylococcus	1	1 (100%)	0 (0%)	1 (100%)	1 (100%)	1 (100%)
Enterococcus spp	7	2 (28.57%)	2 (28.57%)	3 (42.86%)	3 (42.86%)	1 (14.29%)
Corynebacteriumspp	1	1 (100%)	0 (0%)	1 (100%)	1 (100%)	1 (100%)
Total	37	24 (64.86%)	22 (59.46%)	31 (83.78%)	30 (81.08%)	13 (35.13%)
MRSA: Methycillin Resistant Staphylococcus Aureus;   MRSE:Methycillin Resistant Staphylococcus Epidermidis;   MSSA:Methycillin Sensitive Staphylococcus Aureus.

Table III: Gram negative Organisms; Antibiotic Sensitivity (n=42).

Organism	No.	Ciprofloxacin	Gentimicin	Meropenem	Colomycin	Chloramphenical
Klebsiella	12	2 (16.67%)	2 (16.67%)	3 (25%)	11 (91.67%)	2 (16.67%)
Acinetobacter Baumanni	14	0 (0%)	0 (0%)	0 (0%)	14 (100%)	1 (7.14%)
E.coli	5	4 (80%)	3 (60%)	4 (80%)	Not Tested	2 (40%)
Enterobacter spp.	7	0 (0%)	0 (0%)	1 (14.29%)	3/3 (100%)	5 (71.43%)
Proteus	1	0 (0%)	0 (0%)	1 (100%)	Not Tested	0 (0%)
Pseudomonas	2	1 (50%)	0 (0%)	2 (100%)	Not Tested	0 (0%)
Serratia	1	1 (100%)	0 (0%)	1 (100%)	Not Tested	0 (0%)
Total	42	8 (19.0%)	5 (11.9%)	12 (28.6%)	28/29 (96.55%)	8 (19.0%)

Age at onset was the most significant determinant of microbiological spectrum and outcome. Culture proven sepsis was much more frequent in neonates with late onset sepsis and they had significantly higher frequency of gram negative organisms and higher expiry rate. However, there was no difference of gender among late onset and early onset sepsis (Table I).

Blood culture was positive in 79 (7.4%). Gram positive organisms were identified in 37 (46.8%) out of 79 patients; Staphylococci in 29 (36.7%), Enterococci 7 (8.9%), Corynebacterium species in 1 (1.3%). Gram negative organisms were isolated in 42 (53.2%) patients; Acinetobacter baumanni in 14 (17.7%), Klebsiella in 12 (15.2%), Enterobacter spp. In 7 (8.9%), E.coli in 5 (6.3%), Pseudomonas in 2(2.5%), Proteus in 1 (1.3%) and Serratia in 1 (1.3%).

Penicillin, ampicillin, cephradine, cefotaxime, ceftazidime, cefoperazone/salbactum and aztreonam showed very high resistance pattern with 5% or less organism isolated having sensitivity to these antibiotics. Sensitivity pattern of Gram positive organisms was:vancomycin 30/37 (81.1%), chloramphenical 26/37 (70.3%), ciprofloxacin 13/37 (35.1%) and gentimicin 12/37 (32.4%) (Table II). Gram negative organisms showed meropenem 12/42 (28.6%), chloramphenical 10/42 (23.8%), gentimicin 6/42 (14.3%) ciprofloxacin 5/42 (11.9%). Highly resistant strains of Klebsiella and Acinitobacter showed a high sensitivity (100%) to colomycin, but were resistant to all other antibiotics tested. Out of total 14 strains of Acinetobacter isolated; 13(92.9%) were sensitive only to colomycin while among 12 strains of Klebsiella isolated 5 (41.7%) were sensitive to colomycin only (Table III). No organism showed complete resistant.

Overall mortality 182 (17%). There was no significant difference of expiry rate between culture-positive and culture-negative cases (p = 0.89). Among culture-positive sepsis patient, there was no significant difference of mortality between early onset and late onset sepsis (p = 0.090). Median hospital stay in culture-negative neonates was 5.3 days with interquartile range of 2.9 -9.1 days while culture-positive patients had a median hospital stay of 9.6 days with interquartile range of 4.0 - 17.6. The hospital stay was significantly longer in culture-positive patients (p =<0.001).

DISCUSSION

Neonatal sepsis is a very important cause of neonatal mortality that importantly is potentially treatable. Most of the patients in the study presented within 72 hours of life and had early onset sepsis with slight male predominance.

Culture positivity rate in the current study was 7.4%. The rate is low because all neonates were included in the study as blood cultures we sent for every neonate irrespective of clinical features suggestive of sepsis. Culture positivity rates reported in different studies are variable ranging from 19.56% to 48%.^11,12

Gram-positive and Gram-negative organisms were encountered in 37 (46.8%) and 42 (53.2%) of cases. Most common organisms were Staphyllococcus  aureus, Acinetobacter and Klebsiella in descending order. Group B Streptococcus was not isolated in any case and E. coli was encountered in only 6.3% of culture positive cases. Similar bacteriological pattern was documented in the study done. in Nepal where Klebsiella, Enterobacter and Acinetobacter were the predominant Gram negative organisms and Staphyllococci were the predominant gram positive organisms. Other studies have also reported similar results. In a meta-analysis of neonatal sepsis data from Pakistan, Klebsiella and E. coli were the predominant causative organisms.^8,13,14

Gram positive organisms showed a high sensitivity towards vancomycin and linezolid while gram negative organisms showed a high sensitivity towards colomycin. High resistance was observed towards most of the common antibiotics. These ominous findings are endorsed by the results of numerous contemporary studies.^15,16Duration of hospital stay was significantly higher in culture-positive patients which is self-explanatory.

Overall mortality was 17% and rate was significantly higher in neonates with late-onset sepsis. However, among culture positive sepsis patients, there was no significant difference of expiry rate in early-onset and late-onset sepsis.This outcome is comparable with studies from India, Nepal and Egypt.^16,17

Multiple local studies demonstrate the evolving etiological and antimicrobial sensitivity pattern of neonatal sepsis. A study published in 2012 shows a predominance of Staphylococci and E.coli with intermediate sensitivity to penicillins and third generation cephalosporins while aminoglycosides, flouroquinolones, carbapenems and vancomycin showed high level of sensitivity and low resistance.¹⁸A study from Peshawar published in 2016, showed a predominance of E.coli and staphalococcusaureus with high sensitivity towards carbapenems and flouroquinolones.¹⁹ Both these studies showed a low frequency of Klebsiella and Acinetobacter was not reported in either study. A more recent study from Karachi has reported a high frequency of highly resistant gram negative bacteria responsive only to colomycin.²⁰

Bacteriological and antimicrobial sensitivity pattern is variable and rapidly changing. Colomycin resistance is also starting to emerge gradually as one organism reported in current study. There is a need for careful and continuous antimicrobial sensitivity surveillance and update of treatment guidelines accordingly. Development of newer antimicrobial agents is also need of the day.

CONCLUSION

Common organisms indentified in our study were Styphylococci, Acinitobacter, Klebsiella and E.coli. Gram positive organisms showed sensitivity to vancomycin, chlormphenical and gentamicin. Gram negative organisms were highly sensitive to colomycin, but only sparsely sensitive to meropenem, chloramphnical and gentimicin. Klebsiella pnueumonie and Acinetobacter isolated were highly resistant to most of the antibiotics tested.

ETHICAL APPROVAL:
Ethical approval was obtained from the Institutional Review Board of Fauji Foundation Hospital Rawalpindi, before starting data collection.

PATIENTS' CONSENT:
As data was collected from the computer database, consent was not taken from the parents / guardians.

CONFLICT OF INTEREST:
The authors declared no conflict of interest.

AUTHORS' CONTRIBUTION: 
MAH: Data acquisition, data analysis, writeup. 
MAL: Critical review.
KMT: Writeup. 
AT, HSK, RA: Drafting, critical revision. 

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