As shown in Fig. 1, 7,094 articles were identified from the electronic search. After removing duplicates, 5,819 articles remained. Of these, 5,132 articles were excluded due to the absence of all specified keywords simultaneously. Following a thorough review of titles and abstracts, an additional 517 articles were excluded. Subsequent intensive full-text scrutiny led to the exclusion of 147 articles that did not meet the selection criteria. Ultimately, we included 23 articles, conducted between 1975 and 2022, including four case–control studies [19,20,21,22], and nineteen case series [23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41].

In total, 5,475 newborn patients with gastrointestinal infections were recruited in the twenty-three studies. Among these patients, 791 experienced intestinal perforation [25, 26, 31], 3,140 presented with diarrhea [20, 24, 30, 36], 174 exhibited gastroenteritis [29, 33, 39], 1127 were diagnosed with necrotizing enterocolitis (NEC) [19, 21,22,23, 27, 28, 32, 34, 35, 38, 40, 41], 18 suffered from rectal bleeding [27], and 225 were asymptomatic [37]. More characteristics of the included studies are presented in Table 1.

Table 1 Study characteristicsQuality assessment of the included studies

The quality assessment of the included studies, conducted using the JBI critical appraisal tool, is presented in Appendix Table S3. Among the 23 studies included, 7 were classified as having a low risk of bias, 15 exhibited a moderate risk of bias, and 1 showed a high risk of bias.

Diagnostic methods for neonatal gastrointestinal infections

In one study, the detection of clear pathogenic microorganisms in sepsis patients led to a 100% pathogen detection rate, which helped identify NEC patients. Excluding this study, we analyzed the diagnostic methods for neonatal intestinal infections across the remaining 22 studies. Of these, 10 employed multiple testing methods, while 12 used a single method. Blood culture was the most common diagnostic method, with a combined positive rate of 34.7% (95% CI 24.3–46.0%, I2 = 87%) among the patients tested in 9 studies. Peritoneal culture, used in 10 studies, showed a combined positivity rate of 55.8% (95% CI 33.5–77.0%, I2 = 96%) for the tested patients. Stool culture, used in 8 studies, showed a combined positivity rate of 21.3% (95% CI 10.7–34.2%, I2 = 92%) for the tested patients. Additional methods, including intestinal biopsy tissue culture, umbilical swab culture, umbilical duct culture, gastric aspirate culture, pharyngeal swab culture, enzyme immunoassay (EIA), virus isolation culture, multiplex Real-time Polymerase Chain Reaction (RT-PCR), and electron microscopy, were each used in only one study and thus were not included in the combined analysis.

Subgroup analysis and meta regression

To explore the sources of heterogeneity, a subgroup analysis and Meta-regression of neonatal intestinal infection positivity rates were conducted based on detection methods, economic development levels, regions, and sample sizes. After stratification, the Q value corresponding to the p-value was still significantly less than 0.05, indicating high heterogeneity; thus the random-effects model was applied. The results showed that the positivity rate of peritoneal culture (55.8%) was significantly higher than other detection methods. The positivity rate in high-income countries (56.5%) was the highest. In terms of regions, the positivity rate in the Americas (74.3%) was higher than in Asia (33.9%) and Europe (40.6%). The positivity rate in small sample studies (53.5%) was higher than in large sample studies (41.2%), with a statistically significant difference (P < 0.05) (Table 2). Meta-regression analysis revealed that economic development level, sample size, region, and detection methods all had significant effects on the dependent variable. However, no specific sources of heterogeneity were identified.

Table 2 Subgroup analysis of positive rate of gastrointestinal infection detection in newbornsPathogen detection rates in neonatal gastrointestinal infections

In some studies, when a pathogen is detected in a patient using multiple testing methods, and others pathogens test positive with individual methods, the case is counted as a single positive instance to avoid inflating the positive rate. After analyzing the data, we summarized the microbial spectrum of neonatal gastrointestinal infections. Escherichia showed the highest pooled positive rate (22.2%; 95% CI 8.3–40.4%, I2 = 98%), followed by Clostridium (21.8%; 95% CI 2.2–53.8%, I2 = 96%), Klebsiella (19.2%; 95% CI 8.3–33.4%, I2 = 97%), and Staphylococcus (13.6%; 95% CI 6.0–23.7%, I2 = 91%). Among fungi, Candida had the highest rate (3.8%; 95% CI 0.6–9.6%, I2 = 84%). For bacteria, Klebsiella pneumoniae had the highest rate (30.2%; 95% CI 11.3–53.5%, I2 = 95%), followed by Escherichia coli (22.7%; 95% CI 9.5–39.4%, I2 = 98%), Staphylococcus epidermidis (14.8%; 95% CI 1.3–39.2%, I2 = 88%), and Clostridium perfringens (13.6%; 95% CI 7.6–20.9%, I2 = 0%). Among viruses, Rotavirus had the highest rate (11.6%; 95% CI 1.0%–31.5%, I2 = 94%), followed by Adenovirus (4.1%; 95% CI 0.5–11.0%, I2 = 58%). Detailed data are available in Table 3.

Table 3 The positivity rate of the main pathogens causing gastrointestinal infections in newborns

In blood culture assays, Escherichia demonstrated the highest positive rate (10.0%; 95% CI 3.1–20.4%, I2 = 92%), followed by Staphylococcus (9.4%; 95% CI 4.3–16.2%, I2 = 88%). Peritoneal fluid culture assays revealed Klebsiella as having the highest positive rate (24.7%; 95% CI 6.6–49.5%, I2 = 95%), followed by Enterococcus (11.6%; 95% CI 0.6–33.5%, I2 = 96%). In stool culture assays, Escherichia exhibited the highest positive rate (11.0%; 95% CI 3.8–21.3%, I2 = 75%), followed by Campylobacter (3.9%; 95% CI 1.6%–7.2%, I2 = 15%). Detailed information can be found in Appendix Table S2.

Pathogen detection varied across patients with different symptoms, with NEC patients constituting the largest group. In NEC patients, Escherichia (24.3%; 95% CI 4.0−54.5%, I2 = 98%) and Klebsiella (22.0%; 95% CI 7.6−41.1%, I2 = 96%) were most frequently identified, with Klebsiella pneumoniae showing the highest infection rate (39.1%; 95% CI 9.3−74.4%, I2 = 97%).

Detailed NEC pathogen detection is presented in Table 4. In diarrhea cases, Vibrio and Aeromonas were the primary pathogens. For gastroenteritis, Rotavirus and Campylobacter were the most common. In gastrointestinal perforation, Staphylococcus and Escherichia predominated, while in lower gastrointestinal bleeding, Escherichia and Klebsiella were most frequently found.

Table 4 Pathogen detection in necrotizing enterocolitisSensitivity analysis

Sensitivity analysis (using the leave-one-out approach) was performed to assess the stability of the included study results. The analysis revealed that the neonatal gastrointestinal infection positivity rate ranged from 46.9 to 51.9%, indicating that the combined results were robust.

Publication bias

Funnel plots were generated to visually assess the potential for publication bias. The results indicated relatively low symmetry in the funnel plot (see Fig. 2). In conjunction with the results of Egger’s test (p = 0.0022), which showed a bias estimate of 2.8641 and standard error (SE) of 0.8196, the findings suggest the possibility of publication bias.

Fig. 2

Funnel plot of the detection positivity rates in neonates with gastrointestinal infections