Among 1000 bacterial isolates collected from January 2022 to May 2023, 931 (93.1%) were Gram-negative bacteria, while the remaining 69 (6.9%) were Gram-positive. The predominant Gram-negative bacteria included A. baumannii (49.6%), P. aeruginosa (21%), and K. pneumoniae (18.6%), while E. coli only constituted 3.9%. Among Gram-positive bacteria, S. aureus accounted for 6.7% of all, whereas S. pneumoniae was comparatively less frequent, comprising only 0.2% of total isolates.

The occurrence of the six pathogens differed significantly in ICUs versus non-ICU wards (p < 0.05) (Fig. 1). A. baumannii, K. pneumoniae, P. aeruginosa, and S. aureus were commonly found in ICUs, while E. coli was more frequently found in non-ICU wards. Most target pathogens were identified in hospital-acquired LRTI patients with prolonged hospital stays, including A. baumannii (95.3%, 326/342), P. aeruginosa (95.1%, 137/144), K. pneumoniae (91.5%, 107/117), E. coli (80%, 16/20) and S. aureus (95.2%, 40/42).

Fig. 1

Distribution of 6 target LRTI pathogens between ICU and non-ICU sources

Antimicrobial resistance profiles of LRTI bacteria

A. baumannii exhibited high proportions of resistance to the commonly used antibiotics, including 94.8% (470/496) and 95.9% (441/460) for ceftazidime and cefepime, 88.3% (438/496) and 92.6% (426/460) for ciprofloxacin and levofloxacin, 80.4% (397/494) for gentamicin and 87.5% (434/496) for piperacillin-tazobactam (Table 2). The resistance prevalence to imipenem and meropenem was 95.5% (471/493) and 95.4% (461/483), respectively, while colistin resistance was 2.8% (14/496). The resistance proportion of A. baumannii isolates tested against ceftazidime-avibactam was 96.8% (149.0/154.0). Overall, 96.0% (476/496) of A. baumannii isolates were MDR (Table 2), and 2.8% (14/496) were PDR.

Table 2 Antimicrobial resistance patterns of Gram-negative LRTI pathogens

Among the tested P. aeruginosa isolates, resistance proportions were 48.2% (96/199) to piperacillin-tazobactam, 49.5% (103/208) to ceftazidime, 58.5% (121/207) to ciprofloxacin, 56.7% (115/203) to imipenem, 56.5% (105/186) to meropenem, and 51.2% (105/205) to gentamicin. Of total isolates, 29% (61/210) were resistant to ceftazidime-avibactam. The percentage of MDR P. aeruginosa was 56.7% (119.0/210.0).

Among the tested K. pneumoniae isolates, a high resistance prevalence was observed for ceftazidime (73.7%, 126/171), cefepime (73.2%, 90/123), ciprofloxacin (81.1%, 150/185), levofloxacin (76.1%, 108/142), gentamicin (42.7%, 79/185), piperacillin-tazobactam (73.1%, 136/186), imipenem (64.3%, 119/185) and meropenem (69.8%, 113/162). Concerningly, 34.4% of K. pneumoniae isolates displayed resistance to ceftazidime-avibactam, and 18.1% were resistant to colistin. The proportion of MDR K. pneumoniae was 78% (145/186).

Among the tested E. coli isolates, 62.9% (22/35), 50% (10/20), 79.5% (31/39), 75% (21/28), 46.2% (18/39), and 34.2% (13/38) were resistant to ceftazidime, cefepime, ciprofloxacin, levofloxacin, gentamicin and piperacillin-tazobactam, respectively. The proportions of E. coli resistant to imipenem, meropenem, and ceftazidime-avibactam were 10.3% (4/39), 7.7% (2/26), and 7.7% (3/39), respectively. None of the E. coli isolates were resistant to colistin. The MDR E. coli was 84.6% (33/39).

Among the Gram-positives, the resistance proportions of S. aureus to oxacillin, ciprofloxacin, moxifloxacin, trimethoprim-sulfamethoxazole, clindamycin, and erythromycin were 74.6% (50/67), 37.2% (16/43), 34.1% (14/41), 17.8% (8/45), 66% (31/47), and 70.2% (33/47), respectively. All S. aureus isolates were susceptible to vancomycin, teicoplanin, and ceftaroline, and 97.7% (42/43) were susceptible to linezolid. MRSA accounted for 79.1% (53/67) of S. aureus isolates (Table 3).

Table 3 Antimicrobial resistance patterns of Gram-positive LRTI pathogensIn vitro activity of ceftazidime-avibactam and other comparator agents

Overall, among the 186 K. pneumoniae and 39 E. coli, 65.6% and 89.7%, respectively, were susceptible to ceftazidime-avibactam, with MIC values ≤ 3 mg/L (MIC50, 1.5 mg/L) (Table 4, Supplementary Figs. 2, 3). For P. aeruginosa isolates, the susceptibility percentage was 69% (145/210), with MIC values ≤ 8 mg/L (MIC50, 2 mg/L) (Table 4, Supplementary Fig. 4). K. pneumoniae, E. coli, and P. aeruginosa isolates were significantly more susceptible to ceftazidime-avibactam than to ceftazidime, imipenem and meropenem. E. coli (100%, 32/32) and P. aeruginosa (99.4%, 155/156) isolates remained susceptible to colistin, however, the susceptible proportion was lower in K. pneumoniae (81.2%, 112/138) (Table 4). The MIC50 and MIC90 values of colistin were 0.19 mg/L and 8 mg/L for K. pneumoniae (n = 138), 0.75 mg/L and 1.5 mg/L for P. aeruginosa (n = 156), and 0.125 mg/L and 0.19 mg/L for E. coli isolates (n = 32), respectively.

Table 4 In vitro activity of ceftazidime-avibactam and comparators against Gram-negative bacteria

Notably, the carbapenem-resistant (CR) isolates of K. pneumoniae (n = 121), P. aeruginosa (n = 119), and E. coli (n = 2) demonstrated reduced susceptibility to ceftazidime-avibactam compared to non-CR isolates (Table S1). Among the tested isolates, only 47.1% (n = 57) of CR K. pneumoniae and 49.6% (n = 59) of CR P. aeruginosa were susceptible to ceftazidime-avibactam.

In vitro activity of ceftaroline and other comparators against S. aureus

All tested S. aureus isolates displayed susceptibility to ceftaroline with an MIC90 of 0.5 mg/L (Table 5). Ceftaroline exhibited efficacy against methicillin-susceptible S. aureus (MSSA) and MRSA with a MIC90 of ≤ 0.5 mg/L. In comparison, the three major treatment options for MRSA, vancomycin, teicoplanin, and linezolid, demonstrated efficacy against MRSA, with an MIC90 of 1 mg/L, ≤ 0.5 mg/L, and 2 mg/L, respectively (Table 5).

Table 5 In vitro activity of Ceftaroline and comparators against S. aureus isolatesAMR gene profiles and their correlation with AMR phenotypes

The presence of commonly acquired AMR genes identified by PCR assays in each bacterium is summarized in Table 6. Notably, ESBL-encoding blaCTX−M−1/blaCTX−M−9 were frequently identified in E. coli (69.2%, 27/39) and K. pneumoniae (66.1%,123/186). In contrast, these genes were only found in 5.3% (11/210) of P. aeruginosa and 2% (10/496) of A. baumannii isolates. As expected, most A. baumannii isolates carried the carbapenemase gene blaOXA−23 (86.1%, 427/496); however, this gene was also detected in 2.7% (5/186) of K. pneumoniae and 0.5% (1/210) of P. aeruginosa isolates. A high prevalence of blaOXA−48, blaNDM, and blaKPC was found in K. pneumoniae isolates with respective proportions of 39.2% (73/186), 38.2% (71/186), and 32.8% (61/186). BlaOXA−48 and blaNDM genes were also found in P. aeruginosa (1.9% and 11.9%), E. coli (10.3% and 5.1%), and A. baumannii (3.6% and 4.8%) isolates, although with lower frequencies. In S. aureus, the mecA genes were identified in 77.6% (52/67) of isolates (Table 6).

Table 6 PCR-based detection of AMR genes in LRTI pathogens

Among 64 ceftazidime-avibactam resistant K. pneumoniae isolates, various AMR gene patterns involving blaNDM were identified, each associated with an MIC50 and MIC90 value of ≥ 256 mg/L (Table 7; Fig. 2). Specifically, 11 isolates (17.2%) carried both blaNDM and ESBL gene, 51 isolates (79.7%) harboured blaNDM, ESBL gene, along with either blaOXA−48 or blaKPC. Among 61 ceftazidime-avibactam resistant P. aeruginosa isolates, 23 (37.7%) carried blaNDM, with or without blaOXA−48 and ESBL gene. No detectable AMR genes were found in 35 isolates (57.3%), and the remaining 3 isolates (4.9%) harbored only the ESBL gene. Out of 3 ceftazidime-avibactam resistant E. coli isolates, one carried blaNDM and ESBL gene; another harbored blaNDM, blaOXA−48, blaKPC and ESBL gene, while the third had no detectable AMR genes (Table 7).

Table 7 Correlation between PCR-detected AMR genes and ceftazidime-avibactam mics in E. coli, K. pneumoniae, and P. aeruginosa isolatesFig. 2

Distribution of ceftazidime-avibactam MICs by presence of AMR genes in total (below graph) and carbapenem-resistant isolates of E. coli, K. pneumoniae, and P. aeruginosa (above graph)

Notably, 9 K. pneumoniae and 2 P. aeruginosa isolates were PCR-positive for blaNDM but remained susceptible to ceftazidime-avibactam. WGS analysis of selective isolates found that these K. pneumoniae isolates harbored blaOXA−48 and a truncated blaNDM gene, missing the nucleotide region spanning positions 10–300 bp. Similarly, in the P. aeruginosa isolate, the blaNDM was truncated, lacking nucleotides from positions + 794 to 813 bp.