Skip to main content

Prevalence of gram-negative bacteria and their antibiotic resistance in neonatal sepsis in Iran: a systematic review and meta-analysis



Neonatal sepsis, particularly gram-negative (GN) bacteria-induced, is a significant cause of morbidity and mortality in newborns. Healthcare professionals find this issue challenging because of antibiotic resistance. This study aims to combine findings to identify the prevalence of GN bacteria and their antibiotic resistance in Iranian neonates with sepsis.


This systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). The literature search was performed through international databases, including (PubMed/MEDLINE, EMBASE, Scopus, and Web of Science), Iranian local databases (Magiran, Iranmedex, Irandoc, Scimed, and SID), and the first 100 records of Google Scholar. Analytical cross-sectional study checklist from the Joanna Briggs Institute (JBI) was used for the quality assessment of included studies. Comprehensive Meta-Analysis Software Version 2 was used to conduct the meta-analysis. The between-study heterogeneity was investigated by I2 statistics.


The prevalence of GN bacteria was estimated to be 53.6% [95% CI: 45.9– 61.1: P = 0.362] in Iranian neonates with sepsis, based on 31 studies with a sample size of 104,566. klebsiella pneumoniae (K.pneumonia) (23.2% [95% CI: 17.5–30.0, P < 0.001]) followed by Escherichia coli (E.coli) (13.5% [95% CI: 9.4–18.9, P < 0.001]) were more prevalent among GN bacteria. The highest resistance in K.pneumoniae was observed in Cefixime (80.6%, [95% CI: 56.3–93.1, P = 0.018]). E.coli showed greater resistance to Ampicillin (61.8%, [95% CI: 44.2–76.5, P = 0.188]. The prevalence of GN bacteria in Iranian neonates with sepsis has a decreasing trend based on the year, as shown by a meta-regression model (P < 0.0004).


GN pathogens, particularly K.pneumoniae, and E.coli, are the leading cause of neonatal sepsis in Iran. GN bacteria showed the highest resistance to Third-generation cephalosporin and Aminoglycosides.

Peer Review reports


The neonatal mortality rate is a crucial health indicator. Infections cause almost one-fourth (23%) of neonatal deaths worldwide, with 15% of these deaths resulting from neonatal sepsis [1]. Sepsis is a systemic inflammatory reaction caused by microorganisms invading the bloodstream, leading to extreme symptoms such as fever and shock [2]. Neonatal sepsis is classified into early-onset sepsis (EOS) and late-onset sepsis (LOS). EOS is defined as sepsis within 72 h of birth, and LOS defines as sepsis occurring at or after 72 h of life [3]. Early detection of neonatal sepsis is challenging, so antibiotics are given empirically when sepsis is suspected to prevent severe consequences.

The unnecessary use of broad-spectrum antibiotics in empirical therapy leads to an increase in multidrug-resistant microorganisms in neonatal intensive care units (NICU) and puts a high burden on developing countries. The world health organization (WHO) defines antibiotic resistance as a major public health issue that requires immediate attention [4].

Gram-negative (GN) bacteria-induced neonatal sepsis is a crucial cause of morbidity and mortality in neonates [5]. Neonatal GN sepsis is becoming more prevalent globally, with a concerning rise in multidrug-resistant infections [3, 6]. It has been estimated that 214,000 deaths from neonatal sepsis are attributed to resistant pathogens annually [7]. Sepsis is the fourth leading cause of neonatal mortality in Iran, with an estimated 16% prevalence in hospitalized neonates [8,9,10]. The high use of empirical and prophylactic antibiotics goes against the recommended therapies [11]. Healthcare professionals face a challenge due to antibiotic resistance. We conducted a systematic review and meta-analysis of published data on gram-negative neonatal sepsis from various regions of Iran due to the increasing evidence of multidrug resistance in neonatal sepsis caused by GN bacteria. The aim was to determine the prevalence of gram-negative bacteria and their antibiotic resistance pattern in neonatal sepsis.

Materials and methods

The systematic review followed the Preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines for systematic reviews and meta-analyses [12]. The review methods were not established prior to the conduct of the review.

Eligibility criteria

Cross-sectional studies reporting bacterial blood culture and antibiotic resistance/sensitivity testing for neonates with sepsis were included if published in English or Persian language, performed in Iranian hospitals, and used a recognized standard for interpreting antibiotic susceptibility testing (European Committee on Antimicrobial Susceptibility Testing (EUCAST), Clinical and Laboratory Standards Institute (CLSI), British Society for Antimicrobial Chemotherapy). According to the WHO definition, a neonate or newborn infant is a child who is under 28 days old. Any samples over 28 days in age were excluded from the studies. Studies that only reported antibiotic sensitivity were excluded from the analysis. Studies that only reported gram-positive bacteria were excluded. Review studies, letters, case reports, and conference papers were excluded.

Information sources and search strategy

Four international electronic databases (PubMed/MEDLINE, EMBASE, Scopus, and Web of Science) and five Iranian databases (Magiran, Iranmedex, Irandoc, Scimed, and SID) underwent a broad electronic search. Additionally, we manually searched the first 100 records on Google Scholar. The databases were searched from the beginning up until July 28, 2023. Additionally, the references of included studies were searched for other potentially essential studies. Experts in neonatology and library science were consulted to select the search keywords. The used keywords in this study were as follows: ‘sepsis’, ‘septicemia’, ‘bacteremia’, ‘blood infection’, ‘infant’, ‘newborn’, ‘neonate’, ‘antibiotic resistance’, ‘antimicrobial resistance’, ‘Prevalence’, and their Persian equivalent. Our search was restricted to English and Persian publications. Detailed search strategies for PubMed database available in Supplementary file 1.

Study selection

All records have been imported to EndNote X8 and duplicates were eliminated. The records were screened by two reviewers, who independently considered inclusion and exclusion criteria based on title and abstract (MST, KM). The full-text of the selected articles was reviewed independently by two different reviewers (PRH, NM). Any disagreement was resolved through discussion among at least three reviewers (KM, MST, NM) until they reached a consensus.

Data extraction and data items

We used a researcher made data extraction checklist. The data extraction sheet underwent a pilot test on 10 randomly selected articles, followed by revisions and approval by consensus among researchers. The data items collected for every study consisted of author names, publication year, province, duration, hospital type, sample size (categorized by gender), positive culture (categorized by gender), early or late-onset sepsis, pathogen type, and antibiotic resistance. Data extraction was done by two reviewers independently. In case of disagreement, a third author was involved.

Quality assessment

The quality of the included studies was assessed using the analytical cross-sectional study checklist from the Joanna Briggs Institute (JBI) [13]. The checklist has eight questions that are signed with the answer “Yes”, “No”, and “Unclear”. Articles that scored above 7 were considered high-quality, while those between 4 and 6 were medium-quality, and those below 4 were low-quality. Two reviewers (MN and TSS) conducted the quality assessment and resolved discrepancies through consensus.

Synthesis of results

The Mantel–Haenszel method was used in performing a meta-analysis with comprehensive meta-analysis (CMA) (Version 2) software. Statistical heterogeneity was evaluated through the calculation of I2 statistics. We utilized a fixed or random-effect model with a 95% confidence interval (CI) depending on the level of heterogeneity. In the following of Cochrane criteria if the heterogeneity was ≥ 50 we used the random-effect model. To investigate sources of heterogeneity, sensitivity, and subgroup analyses were conducted, as well as meta-regression models. For each variable, the event rate was determined alongside a 95% CI. Egger's test and funnel plots were used to evaluate the presence of publication bias.


Study selection

Figure 1 displays the flow diagram according to PRISMA guidelines, illustrating the search process and study selection. A total of 717 titles were retrieved from the databases. After removing duplicates, 191 papers were screened by title and abstract for possible inclusion in the study. After applying the eligibility criteria, 48 full-text articles remained for assessment. Based on the exclusion criteria, 17 articles were excluded after the assessment (Age of patients in seven studies was above 28 days, five studies reported just gram-positive bacteria, in two studies only antibiotic sensitivity was reported, two review studies and one study was conference paper). The review included 31 articles [14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44] that met the eligibility criteria.

Fig. 1
figure 1

The follow diagram of the literature selection process

Characteristics of the selected studies

The studies that were included were published between 1998 and 2021, with the majority conducted in Iran's Center (n = 10) [35,36,37,38,39,40,41,42,43,44] based on geographical location, followed by the Northwest (n = 5) [30,31,32,33,34], West (n = 5) [25,26,27,28,29], North (n = 4) [14,15,16,17], East (n = 4) [21,22,23,24], and South (n = 3) [18,19,20]. The duration of the studies varied from six months to 10 years. Of all the studies, 22 were conducted in NICUs of maternity hospitals and nine in NICUs of children's hospitals. Studies assessed 104,566 neonates, among whom 6348 patients had positive blood cultures (6.07% of all cultures). Of all isolates, 69.8% were GN bacteria. Out of 24 studies that report blood cultures based on gender, 2474 males and 1919 females were found to have positive blood cultures. According to Table 1, sepsis was divided into EOS (n = 1030) and LOS (n = 486) into 12 studies.

Table 1 Characteristics of included studies

Assessment quality of articles

Table 2 displays the results of the methodological evaluation of the included studies. The methodological quality of the studies included had a final score range of 5 to 8.

Table 2 Methodological evaluation of included studies

There were six high-quality studies and 25 medium-quality studies. All studies were included eventually. All studies highlighted Q8 as the most important quality aspect, which confirmed the use of the right statistical analysis. Also, question number 6 which implied “Were strategies to deal with confounding factors stated?” was addressed in seven studies [14, 22, 28, 31, 37, 38, 41].

Total prevalence of gram-negative bacteria and sensitivity analysis

There was a high rate of heterogeneity in the prevalence of GN bacteria (I2 = 96.026, P < 0.001). According to 31 studies with a sample size of 104,566, GN bacteria in neonates with sepsis was estimated to be 53.6% [95% CI: 45.9– 61.1: P = 0.362] (Fig. 2). The studies conducted by Bahmani [29] and Rajabi [38] reported the lowest and highest prevalence of GN bacteria as 9.5% and 95.8%, respectively (Fig. 2).

Fig. 2
figure 2

Prevalence of Gram Negative bacteria in neonates with sepsis in Iran

Sensitivity analysis for the prevalence of GN bacteria in Fig. 3 shows that after removing one study at a time, the result is still robust.

Fig. 3
figure 3

Sensitivity analysis for the prevalence of Gram Negative bacteria in neonates with sepsis in Iran

Subgroup analysis of the prevalence of gram-negative bacteria cause neonatal sepsis based on geographical region

Among GN bacteria that caused neonatal sepsis, Klebsiella pneumoniae (K.pneumonia) (23.2% [95% CI: 17.5–30.0, P < 0.001]) followed by Escherichia coli (E.coli) (13.5% [95% CI: 9.4–18.9, P < 0.001]) were more prevalent. However, this pattern varied between different regions. As shown in Table 3, in the Center, Northwest, and West of Iran, K.pneumonia had the highest prevalence rate among GN bacteria causing neonatal sepsis (24.6% [95%CI: 16.1–35.6, P < 0.001], 17.4% [95%CI: 10.2–28.0, P < 0.001], and 19.6% [95%CI: 7.5–42.2, P = 0.012], respectively). Also, in the East, North, and South of Iran, E.coli (32.0% [95%CI: 18.0–50.1, P < 0.001], 34.4% [95%CI: 21.1–90.5, P = 0.009], and 28.8% [95% CI: 4.6–77.2, P = 0.403], respectively) had the highest prevalence rate.

Table 3 Subgroup analysis for the prevalence of Gram-negative bacteria in neonates with sepsis in Iran

Subgroup analysis of the prevalence of Gram-negative bacteria cause neonatal sepsis based on hospital

Hospitals exhibited varying patterns of GN bacteria prevalence. The data in Table 3 shows that E.coli (23.3%, [95% CI: 20.6 -28.8, P < 0.001]) and K.pneumonia (20.3%, [95% CI: 15.4–33.7, P < 0.001]) were the most common bacteria found in maternity hospitals. While in the children’s hospitals, K.pneumonia (20.5%, [95% CI: 11.8–33.2, P < 0.001]) followed by Enterobacter (11.6%, [95% CI: 5.9–21.7, P < 0.001]) were more prevalent.

Prevalence of antibiotic resistance in gram-negative bacteria

There was a high level of heterogeneity in antibiotic resistance prevalence among GN bacteria (I2 = 96.18, P < 0.001). Cefixime had the highest resistance rate among third-generation cephalosporins (62.0%, [95% CI: 45.8–75.9, P = 0.146]) as shown in Fig. 4. Ampicillin and Amikacin had the highest resistance rates among penicillin and aminoglycosides, respectively (58.6%, [95% CI: 47.3- 69.0, P = 0.137] and 51.4%, [95% CI: 42.7–60.0, P = 0.616]).

Fig. 4
figure 4

Prevalence of antibiotic resistant in Gram-negative bacteria among neonates with sepsis in Iran

Subgroup analysis of the prevalence of antimicrobial resistance based on geographic region

Figure 5 displays the pattern of antibiotic resistance rate in different regions of Iran. Ampicillin was found to have the highest rate of antibiotic resistance among neonates with sepsis in the Center of Iran (72.8%, [95% CI: 58.1–83.7, P = 0.003]). High resistance to Gentamicin (86.7%, [95% CI: 59.8- 96.6, P = 0.013]) was observed in the Eastern region of Iran. Ceftriaxone showed the highest resistance rate in the North, Northwest, and West regions (75.8%, [95% CI: 44.8–92.4, P = 0.098], 57.9% [95% CI: 29.9–81.6, P = 0.593] and 57.7%, [95% CI: 27.8–82.9, P = 0.629], respectively). The South of Iran had the highest resistance to Amikacin at 63.0% [95% CI: 40.4–81.0, P = 0.117]. Imipenem showed the lowest resistance in the Center of Iran (11.9%, [95% CI: 3.9–31.0, P = 0.001]). Both East and West regions exhibited low resistance to Cephalothin (9.7%, [95% CI: 1.6- 41.2, P = 0.017] and 34.7%, [95% CI: 11.9–67.7, P = 0.366]). Gentamicin showed the lowest resistance rate in the North of Iran (27.6%, [95% CI: 10.9–54.4, P = 0.097]). Cotrimoxazole had the lowest resistance in the South (45.1% [95% CI: 20.7–72.1, P = 0.751]). Northwest had the lowest resistance rate for Ciprofloxacin (28.9%, [95% CI: 15.2–48.1, P = 0.032]).

Fig. 5
figure 5

Prevalence of antimicrobial resistance on gram negative bacteria based on geographic region

Subgroup analysis of the prevalence of antimicrobial resistance based on the type of bacteria

Cefixime was less effective against K.pneumonia, the most resistant GN bacteria causing neonatal sepsis (80.7%, [95% CI: 56.2–93.2, P = 0.018]). E.coli was more resistant to Ampicillin (61.7%, [95% CI: 44.3–76.5, P = 0.188]), Enterobacter was resistant to Cephalothin (74.2%, [95% CI: 36.6–91.4, P = 0.052]) and Acinetobacter was resistant to Cefotaxime (90.0%, [95% CI: [95% CI: 64.7- 97.8, P = 0.007]). Pseudomonas aeruginosa (P.aeruginosa) was more resistant to Ceftizoxime (94.7%, [95% CI: 79.5–98.8, P < 0.001]). Table 4 displays the antibiotic resistance pattern of two common GN bacteria. Supplementary file 2, Table S1 demonstrates the resistance pattern of other bacteria.

Table 4 Subgroup analysis for the antibiotic resistance pattern among two more prevalent gram-negative bacteria


In Iran, there has been a statistically significant decreasing trend in the prevalence of GN bacteria in neonates with sepsis in recent years, as shown by a meta-regression model that considers the published year of studies (P < 0.001) (Fig. 6). The meta-regression model revealed that Ampicillin resistance has been on the rise in recent years in the Center of Iran (P < 0.001), while Gentamicin resistance has significantly decreased in the Northwest. The other antibiotics did not exhibit a significant trend (P < 0.001).

Fig. 6
figure 6

Meta-regression model for the prevalence of gram negative bacteria in neonates with sepsis according to the published year of studies

Publication bias

Based on the funnel plot in Fig. 7 and the results of Egger's test, Publication bias was not observed among the included studies (p = 0.295).

Fig. 7
figure 7

Funnel plot for investigating of publication bias in the included studies


Our study analyzed the occurrence of GN bacteria and their antibiotic resistance in septic neonates from Iran. Based on the meta-analysis, the occurrence of GN bacteria was found to be 53.6%. Based on the year of studies, the meta-regression model for GN bacteria exhibited a significant decreasing trend. Different studies have reported neonatal sepsis caused by GN agents ranging from 18 to 78% [45,46,47]. In two systematic reviews conducted in Iran in 2020, Akbarian-Rad et al.[8] reported that Enterobacter (23.04%) and K.pneumonia (17.54%) were common neonatal sepsis GN pathogens after combining 22 articles with a sample size of 14,683. In a review of 17 studies (sample size: 89,472), Akya et al. [9] found that K.pneumonia (24.2%) and P.aeruginosa (16.6%) were the main causative pathogens of neonatal sepsis. The results of our meta-analysis of 31 studies with a total of 104,566 Iranian neonates with sepsis showed that K.pneumonia (23.2%) was the most prevalent GN bacteria, followed by E.coli (13.5%). The advantages of this study over previously published meta-analyses include a larger sample size, the use of cross-sectional studies, and the exclusion of studies with samples over 28 days old. These factors, which were not accounted for in previous meta-analyses, can impact the final evaluation and accuracy of prevalence. Our findings are supported by a 2014 systematic review in resource-limited countries, which demonstrated that in Africa, South-East Asia, and the Middle East, K.pneumonia is often the cause of neonatal sepsis more than other pathogens [48]. Moreover, a systematic review carried out in 2021 in developing countries [49] discovered that K.pneumonia (26.36%) and E.coli (15.30%) were the dominant pathogens responsible for neonatal sepsis. Geographical variation in GN bacteria prevalence was observed among Iranian neonates with sepsis through region-based subgroup analysis. The highest prevalence rate of E.coli was found in the East and North of Iran, at 32.0% and 34.4%, respectively. A systematic review and meta-analysis carried out in Iran in 2019 found that the prevalence rates of urinary tract infection (UTI) and asymptomatic bacteriuria (ASB) in pregnant women were 9.8% and 8.7%, respectively [50]. A higher prevalence of UTI and ASB was observed in the North and East of Iran than in other regions. In addition, E.coli was reported as the predominant microorganism involved in UTI (61.6% [95%CI: 51.6–70.7]) and ASB (63.22% [95%CI: 51.2–73.8]). One reason for the alignment of the results of the current study with that study may be the fact that newborns can get gram-negative bacteria from the vaginal fecal flora of the mother and the environment. Differences in socioeconomic factors, quality healthcare, and racial diversity may explain the variation in neonatal GN bacteria prevalence across geographic regions. The prevalence of GN agents in neonatal with sepsis in Iran, based on the type of hospital, shows that E.coli (23.3%) has the highest prevalence in maternity hospitals and K.pneumonia (20.5%) is more prevalent in children’s hospitals. The rate of prevalence of K.pneumonia in children’s hospitals from 26 to 48% has been reported by various authors [51, 52]. Another study reported K.pneumonia as the most frequently isolated pathogen (32.5%) among extramural admissions [53]. K.pneumonia handles a significant proportion of hospital-acquired infections, such as septicemias [51, 53].

WHO recommends Ampicillin-Gentamicin as the first-line treatment for neonatal sepsis in low- and middle-income countries [54]. Ampicillin and aminoglycoside (Amikacin/Gentamicin) are the primary empirical antibiotics for neonatal sepsis in Iranian NICUs [21]. According to our meta-analysis, nearly 54.0% of GN pathogens that were isolated showed resistance to the WHO-recommended first-line antibiotics. Excessive and irrational use of antibiotics in hospitals may be the cause of high resistance in Iran [11]. The findings of this study align with those of other studies when it comes to levels of resistance to first-line antibiotics [55, 56]. In Africa, Asia, and South America, other reports indicate that 50–80% of neonates have a high resistance rate to commonly used antibiotics, like aminoglycosides, cephalosporins, and ampicillin [57,58,59,60,61]. Depending on the region, the resistance pattern in Iran varied. The increased resistance of GN bacteria to Ampicillin in Iran's Center and its upward trend over the past decade highlights the urgency to re-evaluate the current treatment protocols and implement antibiotic stewardship. The resistance to Gentamicin has lowered in Northwest Iran, perhaps because Amikacin is now the preferred first-line treatment. Local prevention policies and clinical management decisions can be influenced by geographical variations. Ampicillin resistance was observed in both E.coli and K.pneumonia in the current study. Germany, China, and Africa also reported similar findings [48, 62, 63]. A United States report found that 67% of E.coli isolates were resistant to Ampicillin and 17% were resistant to aminoglycosides. Additionally, nearly 10% of the isolates were resistant to both Ampicillin and Gentamicin [64]. Another similar report in 2015–2017 in the United States shows 7.8% of neonatal sepsis caused by E.coli in NICU was resistant to both Ampicillin and Gentamicin [65]. According to previous studies, resistance in E.coli and K.pneumoniae is commonly acquired through plasmidmediated extended-spectrum beta-lactamase (ESBL) production, which has been recognized as a significant threat to public health for the past two decades [66, 67]. ESBL-producing multidrug-resistant bacteria cause infections that are resistant to a variety of beta-lactams, such as third-generation cephalosporins [68]. The effectiveness of third-generation cephalosporins as a second-line treatment is still being debated [63]. Our study found a high level of resistance (57.3%) to third-generation cephalosporins. The reviewed articles in this study were laboratory-based, exploring the resistance of GN bacteria to various types of antibiotic discs. According to the results, Cefixime was found to have the highest resistance in K.pneumoniae. In Iran, Cefixime isn't used as a treatment for neonatal sepsis and Cefotaxime is the second-line treatment for sepsis among third-generation cephalosporins. Acinetobacter showed the highest level of resistance to Cefotaxime. Other studies have reported the high resistance of Acinetobacter to Cefotaxime [69, 70]. Antimicrobial resistance patterns in GN bacteria in Iran make it difficult to choose the right antibiotic for initial empirical therapy. In the NICU, selecting the right empirical antibiotics and treatment duration for suspected sepsis has a lot of variation. Recent studies indicate that implementing NICU-specific antimicrobial stewardship programs (ASP) can significantly reduce the use of inappropriate antibiotics [71, 72]. The use of ASP along with suitable antimicrobial treatments can reduce the negative impact caused by antibiotic resistance in newborns.

Excessive use of broad-spectrum antibiotics in NICUs has led to a serious problem of infections caused by multidrug-resistant GN bacteria in some developing countries. Developed countries face this problem with less severity. The occurrence of multidrug-resistant GN bacteria in the present study is akin to that of China and India [63, 73]. Multidrug resistance was found in more than 50% of GN bloodstream isolates in the present study. This level of resistance highlights the significance of GN multidrug resistance in Iranian neonates. Improving infection control strategies should be prioritized. The essential method for preventing GN multidrug resistance colonization and infection is to restrict horizontal transmission. Infection control measures, such as proper hand hygiene, suitable gloving, disinfection, decontamination, and sterilization practices, should be taken seriously. It is important to prevent unit overcrowding and understaffing. NICU-specific ASPs play a crucial role in reducing resistance. Neonatal ESBL bacterial sepsis incidence can be reduced by limiting cephalosporin. Nevertheless, an important challenge is to minimize the use of third-generation cephalosporins and carbapenems. Additional clinical research is urgently required to address these challenges.

In this meta-analysis, most studies did not differentiate between EOS or LOS cases in sepsis. Unfortunately, grouping by sepsis type for analysis was not feasible. The neonates were not classified based on gender, so a detailed analysis could not be conducted. Another limitation of this study was the uneven distribution of samples across the study regions.

The study's findings are crucial for WHO's antibiotic recommendations for neonatal sepsis. Many neonates may not receive sufficient coverage from common first-line and second-line antibiotics. Therefore, these findings can aid in the creation of NICU-specific antibiotic use guidelines.


The study emphasizes that K.pneumoniae and E.coli are the most frequent gram-negative pathogens that cause neonatal sepsis in Iran. The distribution of sepsis-causative pathogens differs among hospitals and regions, as shown in this systematic review. GN bacteria showed the greatest resistance to third-generation cephalosporin and aminoglycosides. Neonatologists in Iranian hospitals should carefully discuss this alarming result and consider changing the treatment regimen if needed.

Availability of data and materials

The datasets generated during and/or analyzed during the current study are available from the corresponding author (Email: and first author (Email: on reasonable request.



Asymptomatic bacteriuria


Antimicrobial stewardship programs


Confidence interval


Clinical and Laboratory Standards Institute


Comprehensive meta-analysis


Early-onset sepsis


Escherichia coli


Extended-spectrum beta-lactamase


European Committee on Antimicrobial Susceptibility Testing




Joanna briggs institute


Klebsiella pneumoniae


Late-onset sepsis


Neonatal intensive care units


Preferred reporting items for systematic reviews and meta-analysis


Pseudomonas aeruginosa


Urinary tract infection


World health organization


  1. Amuka JI, Asogwa FO, Ugwuanyi RO, Onyechi T. Neonatal deaths and challenges of public health: where do we need urgent intervention in developing countries? Health Care Women Int. 2020;41(2):227–37.

    PubMed  Google Scholar 

  2. Randolph AG, McCulloh RJ. Pediatric sepsis: important considerations for diagnosing and managing severe infections in infants, children, and adolescents. Virulence. 2014;5(1):179–89.

    PubMed  Google Scholar 

  3. Tsai MH, Wu IH, Lee CW, Chu SM, Lien R, Huang HR, Chiang MC, Fu RH, Hsu JF, Huang YC. Neonatal gram-negative bacillary late-onset sepsis: a case-control-control study on a prospectively collected database of 5,233 admissions. Am J Infect Control. 2016;44(2):146–53.

    PubMed  Google Scholar 

  4. World Health O. Global action plan on antimicrobial resistance. Geneva: World Health Organization; 2015.

    Google Scholar 

  5. Wen SCH, Ezure Y, Rolley L, Spurling G, Lau CL, Riaz S, Paterson DL, Irwin AD. Gram-negative neonatal sepsis in low- and lower-middle-income countries and WHO empirical antibiotic recommendations: a systematic review and meta-analysis. PLoS Med. 2021;18(9): e1003787.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Schlapbach LJ, Straney L, Alexander J, MacLaren G, Festa M, Schibler A, Slater A. Mortality related to invasive infections, sepsis, and septic shock in critically ill children in Australia and New Zealand, 2002–13: a multicentre retrospective cohort study. Lancet Infect Dis. 2015;15(1):46–54.

    PubMed  Google Scholar 

  7. Laxminarayan R, Matsoso P, Pant S, Brower C, Røttingen JA, Klugman K, Davies S. Access to effective antimicrobials: a worldwide challenge. Lancet (London, England). 2016;387(10014):168–75.

    PubMed  Google Scholar 

  8. Akbarian-Rad Z, Riahi SM, Abdollahi A, Sabbagh P, Ebrahimpour S, Javanian M, Vasigala V, Rostami A. Neonatal sepsis in Iran: a systematic review and meta-analysis on national prevalence and causative pathogens. PLoS One. 2020;15(1): e0227570.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Akya A, Rostamian M, Rezaeian S, Ahmadi M, Janatolmakan M, Sharif SA, Ahmadi A, Weisi S, Chegene Lorestani R. Bacterial causative agents of neonatal sepsis and their antibiotic susceptibility in Neonatal Intensive Care Units (NICUs) and Neonatal Wards in Iran: a Systematic Review. Arch Pediatr Infect Dis. 2020;8(2): e92212.

    Google Scholar 

  10. Moftian N, Samad Soltani T, Mirnia K, Esfandiari A, Tabib MS, Rezaei Hachesu P. Clinical risk factors for early-onset sepsis in neonates: an international delphi study. Iran J Med Sci. 2023;48(1):57–69.

    PubMed  PubMed Central  Google Scholar 

  11. Fahimzad A, Eydian Z, Karimi A, Shiva F, Armin S, Mansour Ghanaei R, Fallah F, Rafiei Tabatabaei S, Shirvani F, Rahbar M, et al. Antibiotic prescribing pattern in neonates of seventeen Iranian Hospitals. Arch Pediatr Infect Dis. 2017;5(4): e61630.

    Google Scholar 

  12. Moher D, Liberati A, Tetzlaff J, Altman DG. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. 2009;6(7): e1000097.

    PubMed  PubMed Central  Google Scholar 

  13. Porritt K, Gomersall J, Lockwood C. JBI’s systematic reviews: study selection and critical appraisal. Am J Nurs. 2014;114(6):47–52.

    PubMed  Google Scholar 

  14. Karambin M, Zarkesh M. Entrobacter, the most common pathogen of neonatal septicemia in rasht, iran. Iran J Pediatr. 2011;21(1):83–7.

    PubMed  PubMed Central  Google Scholar 

  15. Fatehi T, Anvari M, Ranji N. Investigating antibiotic resistance and the frequency of SHVand TEM Extended Expecterum Beta Lactamase Genes in klebsiella penumoniea Isolated from Blood Samples of Neonates Admitted to Some Health Centers in Rasht. Iran J Med Microbiol. 2017;11(4):57–63.

    Google Scholar 

  16. Rafati MR, Farhadi R, Nemati-Hevelai E, Chabra A. Determination of frequency and antibiotic resistance of common bacteria in late onset sepsis at the neonatal ward in Booali-Sina Hospital of Sari. Iran J Babol Univ Med Sci. 2014;16(6):64–71.

    Google Scholar 

  17. Mozafari A, Asghari F, Hosseini S. Bacterial etiology and antibiotic resistance of neonotal sepsis. Med J Tabriz Uni Med Sciences Health Services. 2006;27(4):107–10.

    Google Scholar 

  18. Shahian M, Pishva N, Kalani M. Bacterial etiology and antibiotic sensitivity patterns of early-late onset neonatal sepsis among Newborns in Shiraz, Iran 2004–2007. Iran J Med Sci. 2010;35(4):293–8.

    Google Scholar 

  19. Sedigh Ebrahim-Saraie H, Motamedifar M, Mansury D, Halaji M, Hashemizadeh Z, Ali-Mohammadi Y. Bacterial etiology and antibacterial susceptibility patterns of pediatric bloodstream infections: a two year study from Nemazee Hospital, Shiraz. Iran J Compr Ped. 2016;7(1): e29929.

    Google Scholar 

  20. Rezaei A, Javanmardi F, Pirbonyeh N, Parsa HR, Eskandari kootahi z, Emami A: prevalence and antibiotic susceptibility of escherichia coli isolated from early-onset sepsis in Shiraz, Iran. Infec Epidemiol Microbiol. 2021; 7(4):305-310

  21. Behmadi H, Borji A, Taghavi-Rad A, Soghandi L, Behmadi R. Prevalence and antibiotic resistance of neonatal sepsis pathogens in neyshabour. Iran Arch Pediatr Infect Dis. 2016;4(2): e33818.

    Google Scholar 

  22. Mohammadi N, Gharebaghi M, Maamuri GA. Determination of bacterial causes of sepsis in premature newborns. Med J Tabriz Uni Med Sciences Health Services. 2007;29(4):67–71.

    Google Scholar 

  23. Boskabadi H, Heidari E, Bagheri F, Zakerihamidi M. Antibiotic susceptibility patterns in the NICU of Ghaem Hospital of Mashhad. Int J Med Lab. 2021;8(1):17–26.

    Google Scholar 

  24. Falahi J, Khaledi A, Esmaeili D, Ghazvini K, Rostami H. Prevalence and types of bacteria associated with neonatal sepsis in neonatal ward from Ghaem hospital of Mashhad. Iran Der Pharmacia Lettre. 2016;8(3):240–5.

    Google Scholar 

  25. Aletayeb SMH, Khosravi AD, Dehdashtian M, Kompani F, Mortazavi SM, Aramesh MR. Identification of bacterial agents and antimicrobial susceptibility of neonatal sepsis: A 54-month study in a tertiary hospital. African J Microbiol Res. 2011;5(5):528–31.

    Google Scholar 

  26. Monsef A, Eghbalian F. Antibiotic sensitivity pattern of common bacterial pathogens in NICU and neonatal ward in Hamedan province of Iran. Health. 2010;2(06):625.

    Google Scholar 

  27. Dezfoulimanesh Z, Tohidnia MR, Darabi F, Almasi A. Prevalence of bacterial and antibiotic sensitivity in septicemia of neonates admitted to Kermanshah Imam Reza Hospital (2007–2008). J Kermanshah Univ Med Sci. 2011;15(2): e79381.

    Google Scholar 

  28. Nikkhoo B, Lahurpur F, Delpisheh A, Rasouli MA, Afkhamzadeh A. Neonatal blood stream infections in tertiary referral hospitals in Kurdistan Iran. Italian J Pediatr. 2015;41:43.

    Google Scholar 

  29. Bahmani N. Bacterial etiology and antibiotic resistance patterns in neonatal sepsis in the West of Iran. Int J Pediatr. 2021;9(11):14737–46.

    CAS  Google Scholar 

  30. Ghotaslou R, Ghorashi Z, Nahaei MR. Klebsiella pneumoniae in neonatal sepsis: a 3-year-study in the pediatric hospital of Tabriz Iran. Jap J Infect Dis. 2007;60(2–3):126–8.

    Google Scholar 

  31. Mahallei M, Rezaee MA, Mehramuz B, Beheshtirooy S, Abdinia B. Clinical symptoms, laboratory, and microbial patterns of suspected neonatal sepsis cases in a children’s referral hospital in northwestern Iran. Medicine. 2018;97(25): e10630.

    PubMed  PubMed Central  Google Scholar 

  32. Hosseini MB, Abdoli Oskouei S, Heidari F, Sadat Sharif A, Salimi Z, Sharif SAA. Determination of the frequency of microbial agents and drug susceptibility pattern of the neonatal sepsis in the neonatal intensive care unit at Alzahra Hospital, Tabriz Iran. Iran J Neonatol. 2019;10(4):33–40.

    CAS  Google Scholar 

  33. Gheybi S, Fakour Z, Karamyar M, Khashabi J, Ilkhanizadeh B, Asghari Sana F, Mahmoudzadeh H, Majlesi AH. Coagulase negative staphylococcus, the most common cause of neonatal septicemia in Urmia. Iran Iran J Pediatrics. 2008;18(3):237–43.

    Google Scholar 

  34. Bakhsi khaniki G, Asgharisana F, Gaibi S. Study of the role of common bacterial etiology in neonatal sepsis in Urumiah Shahid arefian hospital. New Cellular Molecular Biotechnol J. 2011; 1(3):17–21.

  35. Sharif MR, Hosseinian M, Moosavi GA, Sharif AR. Etiology of bacterial sepsis and bacterial drug resistance in hospitalized neonates of Shahid Beheshti Hospital of Kashan in 1375 and 1376. Feyz J Kashan Univ Med Sci. 2000;3(4):71–7.

    Google Scholar 

  36. Malakan Rad E, Momtazmanesh N. Neonatal sepsis due to klebsiella: frequency, outcome and antibiotic sensitivity. Iran J Public Health. 2004;33(2):43–8.

    Google Scholar 

  37. Movahedian A, Moniri R, Mosayebi Z. Bacterial culture of neonatal sepsis. Iran J Public Health. 2006;35(4):84–9.

    Google Scholar 

  38. Rajabi Z, Akbari N, Mardaneh J, Soltan DM. Antimicrobial susceptibility of isolated from neonatal blood and urine infections in neonatal intensive care unit (nicu), imam hossein hospital of tehran. J Microb Biotechnol. 2012;4(12):53–9.

    Google Scholar 

  39. Behjati S. Reporting of antimicrobial susceptibility and microorganisms in neonatal sepsis in Children Medical Center Hospital. Tehran Univ Med J. 1998;56(2):22–4.

    Google Scholar 

  40. Rabirad N, Mohammadpoor M, Lari AR, Shojaie A, Bayat R, Alebouyeh M. Antimicrobial susceptibility patterns of the gram-negative bacteria isolated from septicemia in Children’s Medical Center, Tehran Iran. J Prev Med Hygiene. 2014;55(1):23–6.

    CAS  Google Scholar 

  41. Marzban A, Samaee H, Mosavinasab N. Changing trend of empirical antibiotic regimen: experience of two studies at different periods in a neonatal intensive care unit in Tehran. Iran Acta Medica Iranica. 2010;48(5):312–5.

    PubMed  Google Scholar 

  42. Haj Ebrahim Tehrani F, Moradi M, Ghorbani N. Bacterial etiology and antibiotic resistance patterns in neonatal sepsis in Tehran during 2006–2014. Iran J Pathol. 2017; 12(4):356–361.

  43. Rajabi Z, Soltan Dallal MM. Study on bacterial strains causing blood and urinary tract infections in the neonatal intensive care unit and determination of their antibiotic resistance pattern. Jundishapur J Microbiol. 2015;8(8): e19654.

    PubMed  PubMed Central  Google Scholar 

  44. Mahmoudi S, Mahzari M, Banar M, Pourakbari B, Haghi Ashtiani MT, Mohammadi M, Keshavarz Valian S, Mamishi S. Antimicrobial resistance patterns of Gram-negative bacteria isolated from bloodstream infections in an Iranian referral paediatric hospital: a 5.5-year study. J Glob Antimicrob Resist. 2017; 11:17–22.

  45. Almohammady MN, Eltahlawy EM, Reda NM. Pattern of bacterial profile and antibiotic susceptibility among neonatal sepsis cases at Cairo University Children Hospital. J Taibah Univ Med Sci. 2020;15(1):39–47.

    PubMed  PubMed Central  Google Scholar 

  46. Peterside O, Pondei K, Akinbami FO. Bacteriological profile and antibiotic susceptibility pattern of neonatal sepsis at a Teaching Hospital in Bayelsa State. Nigeria Trop Med Health. 2015;43(3):183–90.

    PubMed  Google Scholar 

  47. Shehab El-Din EMR, El-Sokkary MMA, Bassiouny MR, Hassan R. Epidemiology of neonatal sepsis and implicated pathogens: a study from Egypt. Biomed Res Int. 2015;2015: 509484.

    PubMed  PubMed Central  Google Scholar 

  48. Le Doare K, Bielicki J, Heath PT, Sharland M. Systematic review of antibiotic resistance rates among Gram-negative bacteria in children with sepsis in resource-limited countries. J Pediatr Infect Dis Soc. 2015;4(1):11–20.

    Google Scholar 

  49. Zelellw DA, Dessie G, Worku Mengesha E, Balew Shiferaw M, Mela Merhaba M, Emishaw S. A systemic review and meta-analysis of the leading pathogens causing neonatal sepsis in developing countries. Biomed Res Int. 2021;2021:6626983.

    PubMed  PubMed Central  Google Scholar 

  50. Azami M, Jaafari Z, Masoumi M, Shohani M, Badfar G, Mahmudi L, Abbasalizadeh S. The etiology and prevalence of urinary tract infection and asymptomatic bacteriuria in pregnant women in Iran: a systematic review and Meta-analysis. BMC Urol. 2019;19(1):43.

    PubMed  PubMed Central  Google Scholar 

  51. Gajul SV, Mohite ST, Mangalgi SS, Wavare SM, Kakade SV. Klebsiella Pneumoniae in septicemic neonates with special reference to extended spectrum β-lactamase, AmpC, Metallo β-lactamase production and multiple drug resistance in tertiary care hospital. J Lab Phys. 2015;7(1):32–7.

    CAS  Google Scholar 

  52. Mukherjee S, Mitra S, Dutta S, Basu S. Neonatal sepsis: the impact of carbapenem-resistant and hypervirulent Klebsiella pneumoniae. Front Med. 2021;8: 634349.

    Google Scholar 

  53. You T, Zhang H, Guo L, Ling KR, Hu XY, Li LQ. Differences in clinical characteristics of early- and late-onset neonatal sepsis caused by Klebsiella pneumoniae. Int J Immunopathol Pharmacol. 2020;34:2058738420950586.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. World Health O: Pocket book of hospital care for children: guidelines for the management of common childhood illnesses, 2nd ed. edn. Geneva: World Health Organization; 2013.

  55. Versporten A, Bielicki J, Drapier N, Sharland M, Goossens H. The Worldwide Antibiotic Resistance and Prescribing in European Children (ARPEC) point prevalence survey: developing hospital-quality indicators of antibiotic prescribing for children. J Antimicrob Chemother. 2016;71(4):1106–17.

    CAS  PubMed  Google Scholar 

  56. Majigo M, Makupa J, Mwazyunga Z, Luoga A, Kisinga J, Mwamkoa B, Kim S, Joachim A. Bacterial aetiology of neonatal sepsis and antimicrobial resistance pattern at the regional referral Hospital, Dar es Salam, Tanzania; a call to strengthening antibiotic stewardship program. Antibiotics (Basel, Switzerland). 2023;12(4):767.

  57. Akturk H, Sutcu M, Somer A, Aydın D, Cihan R, Ozdemir A, Coban A, Ince Z, Citak A, Salman N. Carbapenem-resistant Klebsiella pneumoniae colonization in pediatric and neonatal intensive care units: risk factors for progression to infection. Braz J Infect Dis. 2016;20(2):134–40.

    PubMed  PubMed Central  Google Scholar 

  58. Nour I, Eldegla HE, Nasef N, Shouman B, Abdel-Hady H, Shabaan AE. Risk factors and clinical outcomes for carbapenem-resistant Gram-negative late-onset sepsis in a neonatal intensive care unit. J Hosp Infect. 2017;97(1):52–8.

    CAS  PubMed  Google Scholar 

  59. Ding Y, Wang Y, Hsia Y, Sharland M, Heath PT. Systematic review of carbapenem-resistant Enterobacteriaceae causing neonatal sepsis in China. Ann Clin Microbiol Antimicrob. 2019;18(1):36.

    PubMed  PubMed Central  Google Scholar 

  60. Okomo U, Akpalu ENK, Le Doare K, Roca A, Cousens S, Jarde A, Sharland M, Kampmann B, Lawn JE. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in sub-Saharan Africa: a systematic review and meta-analysis in line with the STROBE-NI reporting guidelines. Lancet Infect Dis. 2019;19(11):1219–34.

    CAS  PubMed  Google Scholar 

  61. Patel SJ, Green N, Clock SA, Paul DA, Perlman JM, Zaoutis T, Ferng YH, Alba L, Jia H, Larson EL, et al. Gram-Negative bacilli in infants hospitalized in the neonatal intensive care unit. J Pediatr Infect Dis Soc. 2017;6(3):227–30.

    Google Scholar 

  62. Tessema B, Lippmann N, Knüpfer M, Sack U, König B. Antibiotic resistance patterns of bacterial isolates from neonatal sepsis patients at University Hospital of Leipzig, Germany. Antibiotics (Basel, Switzerland). 2021;10(3):323.

  63. Li JY, Chen SQ, Yan YY, Hu YY, Wei J, Wu QP, Lin ZL, Lin J. Identification and antimicrobial resistance of pathogens in neonatal septicemia in China-A meta-analysis. Int J Infect Dis. 2018;71:89–93.

    CAS  PubMed  Google Scholar 

  64. Flannery DD, Akinboyo IC, Mukhopadhyay S, Tribble AC, Song L, Chen F, Li Y, Gerber JS, Puopolo KM. Antibiotic susceptibility of escherichia coli among infants admitted to neonatal intensive care units across the US From 2009 to 2017. JAMA Pediatr. 2021;175(2):168–75.

    PubMed  Google Scholar 

  65. Stoll BJ, Puopolo KM, Hansen NI, Sánchez PJ, Bell EF, Carlo WA, Cotten CM, D’Angio CT, Kazzi SNJ, Poindexter BB, et al. Early-Onset Neonatal Sepsis 2015 to 2017, the Rise of Escherichia coli, and the Need for Novel Prevention Strategies. JAMA Pediatr. 2020;174(7): e200593.

    PubMed  PubMed Central  Google Scholar 

  66. Yadav KK, Adhikari N, Khadka R, Pant AD, Shah B. Multidrug resistant Enterobacteriaceae and extended spectrum β-lactamase producing Escherichia coli: a cross-sectional study in National Kidney Center, Nepal. Antimicrob Resist Infecti Control. 2015;4(1):42.

    Google Scholar 

  67. Hayati M, Indrawati A, Mayasari N, Istiyaningsih I, Atikah N. Molecular detection of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolates of chicken origin from East Java, Indonesia. Vet World. 2019;12(4):578–83.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Padmini N, Ajilda AAK, Sivakumar N, Selvakumar G. Extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae: critical tools for antibiotic resistance pattern. J Basic Microbiol. 2017;57(6):460–70.

    CAS  PubMed  Google Scholar 

  69. Lowings M, Ehlers MM, Dreyer AW, Kock MM. High prevalence of oxacillinases in clinical multidrug-resistant Acinetobacter baumannii isolates from the Tshwane region, South Africa - an update. BMC Infect Dis. 2015;15:521.

    PubMed  PubMed Central  Google Scholar 

  70. Pacifici G, Marchini G. Clinical pharmacology of cefotaxime in neonates and infants: effects and pharmacokinetics. Int J Pediatr. 2017;5(11):6111–38.

    CAS  Google Scholar 

  71. Cantey JB, Patel SJ. Antimicrobial stewardship in the NICU. Infect Dis Clin North Am. 2014;28(2):247–61.

    PubMed  Google Scholar 

  72. Nzegwu NI, Rychalsky MR, Nallu LA, Song X, Deng Y, Natusch AM, Baltimore RS, Paci GR, Bizzarro MJ. Implementation of an Antimicrobial Stewardship Program in a Neonatal Intensive Care Unit. Infect Control Hosp Epidemiol. 2017;38(10):1137–43.

    PubMed  Google Scholar 

  73. Chandel DS, Johnson JA, Chaudhry R, Sharma N, Shinkre N, Parida S, Misra PR, Panigrahi P. Extended-spectrum beta-lactamase-producing Gram-negative bacteria causing neonatal sepsis in India in rural and urban settings. J Med Microbiol. 2011;60(Pt 4):500–7.

    PubMed  PubMed Central  Google Scholar 

Download references


Not applicable.


Financial resources for the design of the present study were providing by the Tabriz University of Medical Sciences, Tabriz, Iran.

Author information

Authors and Affiliations



N.M conceived the study; K.M, M.S.T, N.M, and P.R.H searched for relevant literature, extracted data, and drafted the manuscript; M.A.Z and N.M analyzed and interpreted data. P.R.H, T.S.S, and A.E assisted with the search, revising, and writing of the manuscript; The final manuscript was read and approved by all authors.

Corresponding author

Correspondence to Kayvan Mirnia.

Ethics declarations

Ethics approval and consent to participate

This research was a part of a Ph.D. thesis approved by Tabriz University of Medical Sciences Research Ethics Committee (IR.TBZMED.REC.1399.031).

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1. 

Pubmed search strategy. 

Additional file 2. 

Subgroup analysis for the antibiotic resistance pattern among gram-negative bacteria in Iranian neonates with sepsis. 

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moftian, N., Rezaei-hachesu, P., Arab-Zozani, M. et al. Prevalence of gram-negative bacteria and their antibiotic resistance in neonatal sepsis in Iran: a systematic review and meta-analysis. BMC Infect Dis 23, 534 (2023).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: