Bacteria isolation

During the period from January 1st, 2020, to December 31st, 2021, a total of 271 non-replicated Salmonella strains were successfully isolated. Among these isolates, the majority (263 strains) were derived from fecal samples, while 7 strains were obtained from blood samples and 1 strain from pleural puncture fluid. Of the total isolates, 209 strains were recovered from adults, whereas 62 strains were obtained from children (below 18 years old). The monthly distribution of isolates is graphically represented in Fig. 1, highlighting a concentration of strains between May and October (summer and autumn) annually.

Fig. 1

Temporal distribution characteristics of 271 Salmonella strains originating from adults and children

Salmonella serotyping, sequence typing and phylogenetic analyse

The 271 Salmonella isolates were classified into 46 different serotypes, as depicted in Fig. 2. The most prevalent serotype was S. Enteritidis, accounting for 27.68% of the isolates (75/271), followed by S. 1,4,[5],12:i:- at 18.08% (49/271), S. Typhimurium at 9.59% (26/271), S. London at 7.38% (20/271), S. Thompson at 4.43% (12/271), S. Goldcoast at 3.69% (10/271), S. Agona at 2.58% (7/271), S. Give at 2.21% (6/271), and S. Rissen at 1.85% (5/271). Additional serotype and bacterial information can be found in Table S1. Among the 209 isolates from adults, 41 serotypes were identified, with S. Enteritidis being the most prevalent at 28.23% (59/209), followed by S. 1,4,[5],12:i:- at 13.88% (29/209), and S. Typhimurium at 10.45% (21/209). Among the 62 isolates from children, 18 serotypes were identified, with S. 1,4,[5],12:i:- being the most common at 32.26% (20/62), followed by S. Enteritidis at 25.81% (16/62), and S. Typhimurium at 8.06% (5/62). Salmonella serotypes including S. Indiana, S. Jangwani, S. 1,4,[5],12:i:-, S. Ohio, and S. Sereban were exclusively isolated from children.

Fig. 2

Phylogenetic analysis and molecular characteristics of 271 Salmonella strains. Phylogenetic tree of ST11 CRKP isolates generated by panaroo v 1.2.7 and IQ-TREE 2.1.2, including information about isolate source, serotype, ST type, ESBL/AmpC genes and antibiotic resistance profile. The ESBL includes blaCTX-M-55, blaCTX-M-65, blaCTX-M-14, blaCTX-M-27, blaCTX-M-130, and blaCTX-M-199

Phylogenetic analysis was conducted on the 271 Salmonella isolates, resulting in the identification of 54 sequence types (ST). The majority of the isolates belonged to ST11 at 27.68% (75/271), followed by ST34 at 18.08% (49/271), ST19 at 8.86% (24/271), ST155 at 7.38% (20/271), ST26 at 4.43% (12/271), ST358 at 2.95% (8/271), ST13 at 2.58% (7/271), ST516 at 2.21% (6/271), and ST469 at 1.85% (5/271). Notably, all S. Enteritidis strains belonged to ST11, S. 1,4,[5],12:i:- belonged to ST34, S. London belonged to ST155, S. Thompson belonged to ST26, S. Agona belonged to ST13, S. Give belonged to ST516, and S. Rissen belonged to ST469. S. 1,4,[5],12:i:- and S. Typhimurium exhibited a close genetic relationship, with the majority of S. Typhimurium isolates (92.31%, 24/26) belonging to ST19.

Plasmid characteristic of 271 isolates

Our findings reveal the presence of 12 distinct plasmid replicon types, including Col, IncA/C, IncFI, IncFII, IncHI, IncI, IncN, IncQ, IncR, IncX, IncY, and p0111.

S. Enteritidis predominantly harbors the IncX type plasmid, found in 64 out of 75 isolates, followed by IncFII in 60, IncFI in 58, Col in 8, and IncI in 4. Notably, 44 isolates carry three plasmid replicons, and 9 carry four different types. Specifically, S. 1,4,[5],12:i:- exhibit a diverse plasmid profile, with 8 types identified, including Col in 19 out of 49, IncFI in 3, IncFII in 3, IncHI in 13, IncI in 5, IncQ in 27, IncR in 1, and p011 in 5. Seven of these isolates carry three plasmid replicon types. In the case of S. Typhimurium, the IncFII type is the most prevalent, found in 13 out of 26 isolates, closely followed by IncFI, also in 13. Other types present include Col in 4, IncA/C in 1, IncHI in 1, IncI in 1, and IncQ in 1. S. London isolates are characterized by the IncFI type plasmid in 12 out of 20, with Col, IncI, IncQ, IncR, and IncHI types also identified in varying frequencies. A detailed account of the plasmid profiles for other serotype isolates is provided in Table S2. It is important to highlight that 74 isolates lacked plasmid replicons, spanning a range of serotypes.

Antibiotic resistance profile

AST was conducted on 19 antibiotics, and 34 of the Salmonella strains were classified as MDR. The distribution of Minimum Inhibitory Concentrations (MIC) is presented in Table 1. Overall, the resistance rates of the 271 strains to the 19 antibiotics were below 25%. The resistance rate to FOX was 4.80%. Among cephalosporin antibiotics, the resistance rates to FEP, CAZ, CRO, and CTX were 7.38%, 9.23%, 15.87%, and 16.24%, respectively. Carbapenems exhibited high sensitivity, with sensitivity rates of 100%, 100% and 99.63% for MEM, IMP, and ETP, respectively. β-lactam-β-lactamase inhibitor combinations also demonstrated good sensitivity, with rates of 96.68% for PTZ, 90.77% for F/S, 100% for CZA, and 97.05% for C/T. The resistance rates to quinolones LEV and CIP were 8.49% and 19.19%, respectively, while the resistance rate to AMI was 0.74%. The resistance rates to AZT, FOS, COL, and TGC were 12.55%, 2.95%, 22.14%, and 0.37%, respectively.

Table 1 Distribution of MIC50 and MIC90 for 19 antibiotics of 271 Salmonella strains

Differences in the antibiotic resistance profiles were observed between children and adult source isolates (Fig. 3a, b). Specifically, among the 19 antibiotics, strains isolated from children exhibited higher resistance rates, except for carbapenems, CZA, LEV, FOS, and TGC. The resistance rate of strains isolated from children to AZT was 27.42%. Notably, the resistance rates of strains isolated from children to CRO and CTX were both 30.65%.

Fig. 3

a Resistance rates of 271 Salmonella strains to 19 antibiotics; b Comparative analysis of antibiotic resistance rates in Salmonella strains derived from children and adults; c Comparative analysis of antibiotic resistance rates in Salmonella strains derived from S. Enteritidis, S. 1, 4, [5], 12:i:-, S. Typhimurium, and S. London. Statistical analysis was performed with chi-square tests. *P < 0.05; **P < 0.01; ****P < 0.0001

The comparative analysis of antibiotic resistance rates among various serotypes was conducted using a chi-square test, as depicted in Fig. 3c. For this comparison, we included serotypes with no fewer than 20 isolates: S. Enteritidis, S. 1, 4, [5], 12:i:-, S. Typhimurium, and S. London. These four predominant serotypes exhibited significantly distinct resistance profiles towards quinolones, cephalosporins, N-BIBIL, aztreonam, and colistin. Among them, strains of S. 1, 4, [5], 12:i:- showed the highest resistance rate to cephalosporins, at 28.57% (4/10), surpassing S. London with a 15% resistance rate (3/20), followed by S. Enteritidis at 8% (6/75), and S. Typhimurium at 7.69% (2/26). When it came to quinolone resistance, strains of S. London had the highest rate at 55% (11/20), followed by S. Typhimurium at 23.08% (6/26), S. 1, 4, [5], 12:i:- at 14.29% (7/49), and S. Enteritidis at 6.67% (5/ 75). Serotype S. 1, 4, [5], 12:i:- also presented the highest resistance rates towards both N-BIBIL (8.16%, 4/50) and aztreonam (24.49%, 12/50). In contrast, S. Enteritidis demonstrated the highest resistance rate towards colistin, with a striking 78.67% (59/75) of the isolates showing resistance. This detailed examination underscores the variability in antibiotic resistance among different serotypes of Salmonella, highlighting the importance of serotype-specific surveillance and antibiotic stewardship programs.

Resistance mechanism of cephalosporins and quinolones

A total of 34 isolates were found to carry ESBL genes (Fig. 4), which included blaCTX-M-55, blaCTX-M-65, blaCTX-M-14, blaCTX-M-27, blaCTX-M-130, blaCTX-M-199. Among these, thirteen isolates carried blaCTX-M-65, with the majority of them belonging to S. 1,4,[5],12:i:- (8/13). Twelve isolates carried blaCTX-M-55, distributed among S. Goldcoast (3/12), S. Agona (2/12), S. Indiana (2/12), S. Enteritidis (1/12), S. 1,4,[5],12:i:- (1/12), S. Typhimurium (1/12), and S. Muenster (1/12). Six isolates carried blaCTX-M-14, specifically found in S. Enteritidis (4/6) and S. 1,4,[5],12:i:- (2/6). One S. 1,4,[5],12:i:- isolate carried blaCTX-M-130, while one S. Kentucky isolate carried blaCTX-M-199. Notably, one S. Saintpaul isolate carried both blaCTX-M-27 and blaCTX-M-55.

Fig. 4

Distribution characteristics of ESBL genes in 34 Salmonella strains

A total of forty-three isolates exhibited resistance to cephalosporins (Fig. 5a). Among them, twenty isolates demonstrated resistance to both third and fourth generation cephalosporins, and all of these isolates carried ESBL genes. The predominant ESBL gene was blaCTX-M-55 (12), followed by blaCTX-M-14 (4), blaCTX-M-65 (2), blaCTX-M-199 (1), blaCTX-M-130 (1), and one isolate carried both blaCTX-M-27 and blaCTX-M-55. Among the remaining twenty-three isolates that were only resistant to third generation cephalosporins, thirteen carried ESBL genes, with blaCTX-M-65 (11) being the most prevalent, followed by blaCTX-M-14 (2). Eight isolates carried AmpC genes, specifically blaCMY-2 (6) and blaDHA-1(2). One isolate sa824 carried blaTEM-1 and the gene encoding penicillin-binding protein 3 (PBP3) sal, presenting resistant profile towards third generation cephalosporins, CRO and CTX.

Fig. 5

a Resistance mechanisms to cephalosporins in 43 Salmonella strains. The strains were categorized into five groups based on their resistance profiles: I, Resistant to both CRO and CTX (sa748-sa792). sa824 carried genes encoding PBP3sal. II, Resistant to both CTX and CAZ (sa784). III, Resistant to CRO, CTX, and CAZ (sa848-sa945). IV, Resistant to CRO, CTX, and FEP (sa949-sa1034). V, Resistant to CRO, CTX, FEP, and CAZ (sa759-sa1030); b Resistance mechanisms to quinolones in 53 Salmonella strains. The strains were classified into three groups based on their resistance profiles: I, Resistant to CIP (sa821-sa971), with sa971 carrying mutations in parC(p.T57S). II, Resistant to LEV (sa1036). III, Resistant to both CIP and LEV (sa758-sa908)

Fifty-three isolates exhibited resistance to quinolones (Fig. 5b). Among the thirty isolates that were solely resistant to CIP, eleven isolates carried qnrS1 as the underlying mechanism, ten isolates carried qnrB6 and aac(6′)-Ib-cr and one isolate showed parC (p.T57S) as potential mechanism. One isolate that carried qnrS1 was solely resistant to LEV. Twenty-two isolates displayed resistance to both CIP and LEV, with the majority (10/22) attributed to qnrS1 and two isolates presented mutations in gyrA and parC.