Clinical characteristics of ST11 Kp infected patients
To perform potential transmission route, Kp strains that isolated from inter- and intra- host were enrolled in the study. Totally, fifty-eight Kp strains isolated from thirty-six patients were incorporated into this study. Four Kp strains were isolated from one of the 36 patients. Among six patients, three isolates were detected from each patient, and two strains were obtained from each of other six patients. Additionally, the information of one strain was missing.
One strain was isolated at December in 2017, while three strains were isolated at September in 2018 and the other strains were all from 2020 year (Additional file 1: Figure S1). Most of the strains (56.9% 33/58) isolated from the respiratory tract. Fourteen strains (24.1%, 14/58) were from urine (Additional file 1: Figure S2).
The mean age of enrolled patients was 74.3±18.0 years and 18 (50.0%) were female. Thirty-four patients were admitted into six departments of the headquarters, including emergency department (17/36), ICU (9/36), Geriatric Ward (3/36), outpatient department (1/36), orthopedics department (1/36), cardiac surgery ward (1/36) and general surgery department (1/36). The other two patients hospitalized in the branch of the hospital. Most of the patients presented with cardiovascular disease. More than half of the patients were associated with cerebrovascular disease and fourteen patients (38.9%, 14/36) had diabetes. Importantly, all patients had antibiotics exposure within 90 days. The mean CCI of enrolled patients was 3.4±1.6. Notably, all patients experienced the procedure of invasive catheters, among which central intravenous catheter, urinary catheter, endotracheal tube, gastrostomy tube, drainage tube accounted for 77.8% (28/36), 91.7% (33/36), 38.9% (14/36), 86.1% (31/36) and 30.6% (11/36), respectively. Furthermore, ten patients experienced metastatic infection. Thirty-two cases (88.9%, 32/36) were identified as HAI and three (8.3%, 3/36) patients were associated with HCAI. The median SOFA of enrolled patients was 4 (Percentiles 25=1，Percentiles 75=9). Fifteen patients (41.7%%, 15/36) presented with poor prognosis. Specifically, 13 patients died within 30 days and two patients withheld the life-sustaining therapy (Table 1).
Subtyping, Antimicrobial Resistance and Virulence Profiles
All the Kp strains were identified as the ST11 (gapA3-infB3-mdh1-pgi1-phoE1-rpoB1-tonB4). Twenty-eight strains were identified as hvKp. Most of the Kp strains (98.3%, 57/58) carried yersiniabactin. IucA was positive in the 28 strains (48.3%, 28/58) and 17 isolates (29.3%, 17/58) harbored rmpA. Sixteen isolates contained peg-344 (27.9%, 16/58). Only one strain was associated with iroB. Surprisingly, none strain harbored colibactin and rmpA2. The common key virulence genotype is iucA+peg-344+rmpA. For the serotype, KL64 was positive in the 27 strains (46.6%, 27/58) and KL47 was in 28 isolates (48.3%, 28/58). The other three strains presented with KL25.
All the ST11 Kp strains exhibited resistance against more than 3 classes of antimicrobial agents and presented with MDR, especially CR, phenotype. More specifically, all the ST11 strains were resistant to the TZP, CAZ, IPM, MEM, ETP and FEP. Additionally, only one isolate showed intermediary for the LVX and CSL, respectively. Six strains (10.3%, 6/58) were susceptive to the AMK. Fortunately, 60.3% (35/58) strains shown susceptive to the SXT, and the 28 isolates were associated with non-resistance phenotype for the MNO (Additional file 1: Table S1).
All the ST11 strains harbored the fosA before the Fosfomycin exposure. Only one Kp strains were not presented with blaKPC-2. Among the blaCTX-M-like positive strain, most of the strains (60.3%,35/58) were associated with blaCTX-M-65, distributed in the CR-hvKp (12 strains) and CR-cKp (23 strains). Strains that harbored the blaCTX-M-14 (4 strains) and blaCTX-M-3 (1 strain) were belonged to the cKp. Even worse is that the blaNDM-1 emerged in the hospital. Another common ESBLs, blaTEM-1B, existed in 53 isolates. Further, twenty-four strains carried tet(A) (Figure 1).
Combined with the virulence and AST, 28 strains were defined as CR-hvKp and 30 isolates were CR-cKp. The common genomic characteristics of the CR-hvKp presented with KL64+iucA+peg-344+blaKPC-2+blaTEM-1B, whereas the CR-cKp was frequently harbored KL47+blaKPC-2+blaTEM-1B+tet(A)+blaCTX-M-65.
All strains harbored the IncFII plasmid replicon and 98.3% (57/58) contained the ColRNAI plasmid replicon. Fifty strains (86.2%, 50/58) carried IncR plasmid replicons and 48.3% (28/58) were positive for the IncHI1B plasmid replicons, respectively. More than four types of replicon were present in 3/58 (5.2%) isolates (Figure 1).
Phylogenetic Relationships and Distribution of the CRKP
Totally, 1,325 hqSNPs were identified and were applied for phylogenetic analysis (Figure 1). Among all the ST11 CRKP strains, two distinguished clades were identified. Clade 1 contained 27 strains belonged to the CR-hvKp and KL64 serotype, most of which were collected from the Emergency department (14 isolates) and ICU (6 isolates). Clade 2 comprised 31 isolates, which contained four clusters: clade 2a, clade 2b, clade 2c and clade 2d, and could be separated into two large branches. Clade 2a, 2b and 2c belonged to the KL47 branch and clade 2d belonged to KL25 branch. Most of the strains were identified as CR-cKp, and only one strain might become CR-hvKp from CR-cKp during within-host evolution.
Transmission Route of the CR-hvKp and CR-cKp
Combined SNPs with epidemiological information, we reconstructed the potential transmission routes among these patients (Figure 2). It is estimated that the hvKp ancestor might have separated from an ancestor and then spread into Emergency department and ICU (Figure 2A). Briefly, the common ancestor of Clade 1 evolved into two main subclones (PEkp183 and PEkp017), which resulted the circulation within the Emergency department and then spread to the outpatient and other departments. Importantly, the PEkp125 strain isolated from Respiratory clinics and triggered the HCAI.
Most of the strains (34.5%, 20/58) in the Clade 2 were clustered within the Clade 2a (Figure 2B). The common ancestor of clade 2a has underwent slight change in SNPs during inter- and intra- host evolution, suggesting that MDR ST11 Kp strains is circulating within the ICU and Emergency department. More importantly, the MDR-cKp has transmitted into the branch of the hospital, alarming that enhancing surveillance is essential. Additionally, the PEkp099 resulted in the HCAI, suggesting that ST11 CR-cKp might successfully transmit into the Healthcare-associated institution. Although the tiny differences of SNPs were shown among PEkp050, PEkp182 and PEkp193 within the same host, the PEkp193 acquired the iucA+peg-344+peg-589+rmpA and subsequently conferred CR-hvKp.