Phenotypic and Genomic Characterization of Virulence Heterogeneity in Multidrug-Resistant ST11 Klebsiella pneumoniae During Inter-Host Transmission and Evolution

Prognostic models for estimating severity of disease and predicting 30-day mortality of Hypervirulent Klebsiella pneumoniae infections: a bicentric retrospective study

BACKGROUND

Hypervirulent Klebsiella pneumoniae (hvKP) is emerging globally and can cause various, severe infections in healthy individuals. However, the clinical manifestations of hvKP infections are nonspecific, and there is no gold standard for differentiating hvKP strains. Our objective was to develop prognostic models for estimating severity of disease and predicting 30-day all-cause mortality in patients with hvKP infections.

METHODS

We enrolled 116 patients diagnosed with hvKP infections and obtained their demographic and clinical data. Taking septic shock and acute respiratory distress syndrome (ARDS) as the primary outcomes for disease severity and 30-day all-cause mortality as the primary outcome for clinical prognosis, we explored the influencing factors and constructed prognostic models.

RESULTS

The results showed that increased Acute Physiologic and Chronic Health Evaluation (APACHE) II score [odds ratio (OR) = 1.146; 95% confidence interval (CI), 1.059-1.240], decreased albumin (ALB) level (OR = 0.867; 95% CI, 0.758-0.990), diabetes (OR = 9.591; 95% CI, 1.766-52.075) and high procalcitonin (PCT) level (OR = 1.051; 95%CI, 1.005-1.099) were independent risk factors for septic shock. And increased APACHE II score (OR = 1.254; 95% CI, 1.110-1.147), community-acquired pneumonia (CAP) (OR = 11.880; 95% CI, 2.524-55.923), and extrahepatic lesion involved (OR = 14.718; 95% CI, 1.005-215.502) were independent risk factors for ARDS. Prognostic models were constructed for disease severity with these independent risk factors, and the models were significantly correlated with continuous renal replacement therapy (CRRT) duration, vasopressor duration, mechanical ventilator duration and length of ICU stay. The 30-day all-cause mortality rate in our study was 28.4%. Younger age [hazard ratio (HR) = 0.947; 95% CI, 0.923-0.973)], increased APACHE II score (HR = 1.157; 95% CI, 1.110-1.207), and decreased ALB level (HR = 0.924; 95% CI, 0.869-0.983) were the independent risk factors for 30-day all-cause mortality. A prediction model for 30-day mortality was constructed, which had a good validation effect.

CONCLUSIONS

We developed validated models containing routine clinical parameters for estimating disease severity and predicting 30-day mortality in patients with hvKP infections and confirmed their calibration. The models may assist clinicians in assessing disease severity and estimating the 30-day mortality early.

Fusion plasmid enhanced the endemic extensively drug resistant Klebsiella pneumoniae clone ST147 harbored blaOXA-48 to acquire the hypervirulence and cause fatal infection

BACKGROUND

Klebsiella Pneumoniae (Kp) sequence type (ST) 147 has emerged globally and spread rapidly, particularly the extensively drug resistant (XDR) isolates. However, the infections caused by this subtype is rare reported in China for now. The clinical, microbiological and genomic characteristics are unclear.

METHODS

A systemic retrospective study was conducted in a Chinese tertiary hospital. Clinical information of the infection cases was collected, and whole-genome sequencing and phenotypic experiments were performed on the ST147 isolates. The resistance and virulence genes were identified, and the plasmids harboring these genes were further studied.

RESULTS

Six ST147 isolates from six patients among 720 available clincial Kp isolates were detected. Notably, two isolates, PEKP4035 and PEKP4265, represented both XDR and hypervirulence by acquiring bla_OXA-48, bla_CTX-M-15 and key virulence genes, iucA + rmpA2, representing no fitness cost and resulting fatal infection. Four of the six ST147 isolates presented with more nucleotide differences, whereas the PEKP4035 and PEKP4265 both isolated from the intensive care unit possessed 20 single nucleotide polymorphisms among one year, indicating the prolonged survive and transmission. Interestingly, the two isolates harbored the same fused plasmid composed of sul2 and iucA + rmpA2, which might be generated by recombination of a plasmid like KpvST101_OXA-48 with the pLVPK plasmid via IS26. Besides, two ~ 70 kb plasmids conferring multiple-drug resistance were also identified among the two isolates, which presented resistance genes including bla_OXA-48, bla_CTX-M-16, strA and strB. Interestingly, we reported that bla_CTX-M-15, a common resistance gene within ST147, has successfully transferred into the chromosome by ISEcp1.

CONCLUSIONS

XDR hypervirulent ST147 Kp is emerging, suggesting enhanced surveillance is essential.

Emergence of Extensively Drug-Resistant and Hypervirulent KL2-ST65 Klebsiella pneumoniae Harboring blaKPC-3 in Beijing, China

Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKp) has been emerging worldwide. However, the clinical, microbiological, and genomic characteristics of newly emerged MDR sequence type 65 (ST65) hvKp are unclear. We conducted active longitudinal genomic surveillance of K. pneumoniae in the hospital starting in 2017. Clinical characteristics, including demographic data, infection type, and outcomes, were collected. Whole-genome sequencing was performed to clarify phylogenetic and plasmid features, and phenotype determined by growth curves, plasmid transferability and stability, hypermucoviscosity, biofilm formation, and serum survival were analyzed to microbiologically characterize ST65 in depth. Ten ST65 (1.4%, 10/720) isolates were detected from 720 K. pneumoniae isolates in total. Nine patients (90%, 9/10) were older than 60 years and had multiple underlying diseases. All ST65 K. pneumoniae isolates harbored iucA, rmpA, rmpA2, iroB, and peg344 and were identified as hvKp. Surprisingly, two MDR-hvKp isolates that grew slowly were observed. Isolate PEKP4222 harbored a pLVPK-like plasmid and a conjunctive MDR plasmid. Isolate P1 harbored blaKPC-3 in a new plasmid, pP1-54, resulting in an extensively drug-resistant (XDR) phenotype; this isolate, which might have evolved from a strain harboring blaKPC-2, resulted in fatal infection. The pP1-54 plasmid could not be transferred to Escherichia coli by conjugation but could be stably inherited vertically. Interestingly, P1 also carried the pLVPK-like plasmid and acquired various antimicrobial resistance genes, and blaCTX-M-3 was detected in the IncB/O/K/Z plasmid. The convergence of XDR and hypervirulence within classical ST65 hvKp is emerging, highlighting the need for enhanced genomic surveillance. IMPORTANCE XDR-hvKp poses a great challenge to public health. ST65, a classical hvKp subtype, mostly presented with hypermucoviscosity, which restricts antimicrobial resistance acquisition. However, few studies have demonstrated the clinical, microbiological, and genomic characteristics of ST65, especially MDR-ST65 hvKp. Here, we first reported that ST65 hvKp acquired blaKPC-3 and then conferred the XDR-hvKp phenotype. Genomic context analysis concluded that the blaKPC-3 gene might have evolved from blaKPC-2. Additionally, the pLVPK-like plasmid seemed to acquire more resistance genes, and blaCTX-M-3 located in the IncB/O/K/Z plasmid was observed. The XDR-hvKp phenotype could be stably inherited vertically, indicating that strains harboring blaKPC-3 and pLVPK-like plasmids could persistently exist in hospital settings. These data suggest that genomic adaptation is rapid and that enhanced surveillance is essential.

Comparison of the therapeutic potential of bacteriophage KpV74 and phage-derived depolymerase (β-glucosidase) against Klebsiella pneumoniae capsular type K2

Bacteriophages and phage polysaccharide-degrading enzymes (depolymerases) are garnering attention as possible alternatives to antibiotics. Here, we describe the antimicrobial properties of bacteriophage KpV74 and phage depolymerase Dep_kpv74 specific to the hypervirulent Klebsiella pneumoniae of the K2 capsular type. The depolymerase Dep_kpv74 was identified as a specific glucosidase that cleaved the K2 type capsular polysaccharides of the K. pneumoniae by a hydrolytic mechanism. This depolymerase was effective against thigh soft tissue K. pneumoniae infection in mice without inducing adverse behavioral effects or toxicity. The depolymerase efficiency was similar to or greater than the bacteriophage efficiency. The phage KpV74 had a therapeutic effect only for treating the infection caused by the phage-propagating K. pneumoniae strain and was completely inactive against the infection caused by the K. pneumoniae strain that did not support phage multiplication. The depolymerase was effective in both cases. A mutant resistant to phage and depolymerase was isolated during the treatment of mice with bacteriophage. A confirmed one-base deletion in the flippase-coding wzx gene of this mutant is assumed to affect the polysaccharide capsule, abolishing the KpV74 phage adsorption and reducing the K. pneumoniae virulence.

An Alliance of Carbapenem-Resistant Klebsiella pneumoniae with Precise Capsular Serotypes and Clinical Determinants: A Disquietude in Hospital Setting

Carbapenemase-resistant Klebsiella pneumoniae (CRKP) is a genuine burden for physicians and researchers. We aimed at carbapenemase resistance and its relation with capsular serotyping in K. pneumoniae and studied some clinical determinants, which may influence the clinical infections. Initially, 61 K. pneumoniae isolates obtained from various clinical specimens were confirmed at the molecular level and then antimicrobial susceptibility test was performed followed by capsular serotyping performed by multiplex PCR. All isolates were subjected to the detection of carbapenemase genes including blaKPC, blaNDM-1, blaOXA-48, blaVIM, and blaIMP. Clinical and demographic data of all patients were reviewed including age, gender, underlying diseases, and the treatment obtained. Multidrug-resistance was a predominant feature in 77% K. pneumoniae strains. Presence of extended-spectrum beta-lactamase was detected phenotypically in 59% K. pneumoniae strains. Carbapenem resistance was noticed phenotypically in 24.6% isolates. blaOXA-48 and blaNDM-1 were the most frequent carbapenemase genes. blaNDM-1 positive isolates correlated with gentamicin, amikacin, imipenem, and meropenem resistance ( $p<0.05$ ). The nosocomial isolates mostly harbored blaOXA-48 gene ( $p<0.02$ ). Amongst all the K. pneumoniae isolates, 59% isolates could be typed and serotype K54 had the highest prevalence followed by K20 and K5. Correlation between the carbapenemase genes, serotype and type of infection showed that blaOXA-48 positive strains had a significant association with K20 serotype and urinary tract infections ( $p=0.2$ ) while, K20 serotype and blaKPC positive strains were significantly associated with wound infections (K20, $p=0.3$ and blaKPC, and $p=0.4$ ). Mucoid phenotype was not found related to presence of specific carbapenemase genes or serotypes except serotype K20 ( $p<0.001$ ). Patients with monotherapy had treatment failure in comparison to the combination therapy for blaKPC-associated infections. In conclusion, the present investigation exhibited the significant association between K20 serotype with blaOXA-48. The predominance of K54 reveals the possibility of endemicity in our hospital setting. K. pneumoniae isolated from wound specimens significantly harbors K20 serotype and blaKPC gene. Comprehensive clinical information and the distribution of antibiotic resistance genes, and serotypes may play important roles in the treatment process.

Hypervirulent carbapenem-resistant Klebsiella pneumoniae causing highly fatal meningitis in southeastern China

Klebsiella pneumoniae (K. pneumoniae) is one of the most common causes of bacterial meningitis worldwide. The purpose of this study was to investigate the clinical and microbiological characteristics of K. pneumoniae meningitis, as well as the association of antimicrobial resistance, virulence, and patient prognosis. The clinical data of patients with K. pneumoniae meningitis from 2014 to 2020 in a tertiary teaching hospital were retrospectively evaluated. Antimicrobial susceptibility profiles were performed by the agar dilution method and broth microdilution method. The isolates were detected for virulence-related genes, resistance genes, capsular serotypes, and molecular subtypes. A total of 36 individuals with K. pneumoniae meningitis were included in the study, accounting for 11.3% (36/318) of all cases of bacterial meningitis. Of the 36 available isolates, K1, K47, and K64 were tied for the most frequent serotype (7/36, 19.4%). MLST analysis classified the isolates into 14 distinct STs, with ST11 being the most common (14/36, 38.9%). Carbapenem resistance was found in 44.4% (16/36) of the isolates, while hypervirulent K. pneumoniae (HvKP) was found in 66.7% (24/36) of the isolates. The isolates of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) were then confirmed to be 36.1% (13/36). Importantly, individuals with meningitis caused by Hv-CRKP had a statistically significant higher mortality than the other patients (92.3%, 12/13 vs. 56.5%, 13/23; P < 0.05). The high percentage and fatality of K. pneumoniae-caused meningitis, particularly in Hv-CRKP strains, should be of significant concern. More effective surveillance and treatment solutions will be required in future to avoid the spread of these life-threatening infections over the world.

Epidemiological characteristics and molecular evolution mechanisms of carbapenem-resistant hypervirulent Klebsiella pneumoniae

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP), a type of Klebsiella pneumoniae (KP) that exhibits hypervirulence and carbapenem resistance phenotypes, can cause severe infections, both hospital- and community-acquired infections. CR-hvKP has brought great challenges to global public health and is associated with significant morbidity and mortality. There are many mechanisms responsible for the evolution of the hypervirulence and carbapenem resistance phenotypes, such as the horizontal transfer of the plasmid carrying the carbapenem resistance gene to hypervirulent Klebsiella pneumoniae (hvKP) or carbapenemase-producing Klebsiella pneumoniae (CRKP) acquiring a hypervirulence plasmid carrying a virulence-encoding gene. Notably, KP can evolve into CR-hvKP by acquiring a hybrid plasmid carrying both the carbapenem resistance and hypervirulence genes. In this review, we summarize the evolutionary mechanisms of resistance and plasmid-borne virulence as well as the prevalence of CR-hvKP.

Conjugation of a Hybrid Plasmid Encoding Hypervirulence and Carbapenem Resistance in Klebsiella pneumoniae of Sequence Type 592

Klebsiella pneumoniae simultaneously carrying genes encoding carbapenem resistance and hypervirulence causes fatal infections, representing a severe threat to human health. These carbapenem-resistant and hypervirulent K. pneumoniae (hvCRKP) strains are increasingly reported worldwide and have been found to belong to a variety of sequence types (STs). In this study, we report and characterized an hvCRKP strain of ST592, an uncommon ST, which caused a fatal infection in intensive care unit (ICU) in China and represents a novel type of hvCRKP. We demonstrated that this novel hvCRKP type emerged from the carbapenem-susceptible hypervirulent K. pneumoniae (hvKP) lineage of the K57 capsular type. K57 hvKP contains a pLVPK-like virulence plasmid and then acquired a conjugative bla_KPC–2-carrying plasmid to form hvCRKP. The pLVPK-like virulence plasmid contains no complete conjugation module but was able to be transferred by fusion with the conjugative bla_KPC–2-carrying plasmid during conjugation. This represents a new mechanism of simultaneous transfer genetic determinants of carbapenem resistance and virulence and highlights the undergoing expansion of hvCRKP, which requires rigorous monitoring and novel countermeasures to curb plasmid-mediated transmission.

The Role of Plasmid and Resistance Gene Acquisition in the Emergence of ST23 Multi-Drug Resistant, Hypervirulent Klebsiella pneumoniae

Multidrug-resistant (MDR) hypervirulent Klebsiella pneumoniae (hvKp) sequence type (ST) 23 (MDR-ST23-hvKp) is emerging in China. Despite its increasing importance, this pathogen has not yet been subject to detailed genomic interrogation. We identified 28 ST23 Kp isolated from three hospitals in China. The organisms were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). These novel genomic sequences were analyzed in combination with 218 publicly available genome sequences. We performed molecular serotyping and subtyping, assessed the composition of virulence-associated and antimicrobial resistance (AMR) genes, and determined mobile elements associated with horizontal gene transfer. Two MDR-ST23-hvKp were sequenced by long-read sequencing. The genetic characteristics of MDR and non-MDR isolates were compared. Among the 28 novel ST23 isolates, all were hvKp and 2/28 (7.1%) were MDR-hvKp. From the collection of 246 genomes, KL1 was the predominant serotype (224/246; 91.1%) and the siderophore combination of YbST46-CbST29-AbST1-SmST2 was dominant (101/246; 41.1%); 34/246 (13.8%) organisms belonged to MDR-ST23-hvKp. IncF and IncR plasmid replicons were significantly more prevalent in the MDR group (P < 0.05) than in the non-MDR group. IS26 was commonly involved in AMR acquisition. We observed that the acquisition of AMR genes within the ST23-hvKp was not associated with a loss of virulence genes. A 28-bp fusion site was highly conserved with two copies of the virulence-associated plasmid in ST23-hvKp, and we harbored by some of the IncFII plasmids of MDR-ST23-hvKp. Our data suggest that MDR-ST23-hvKp has undergone multiple independent genetic acquisition and recombination events within different sublineages. Notably, the acquisition of IncFII plasmids and/or IS26 contributed to the horizontal transfer of AMR genes within ST23-hvKp. Genomic surveillance is essential for further tracking of kMDR-ST23-hvKp. IMPORTANCE Hypervirulent Klebsiella pneumoniae (hvKp) has become the dominant pathotype in hospitals recently. The sequence type (ST) 23 hvKp, which are more commonly associated with the community-acquired infections previously, may have the capacity to acquire multidrug-resistant (MDR) phenotypes creating a new "superbug" (MDR-hvKp) in hospital. In the present study, we studied the associations of MDR and hypervirulence among ST23 K. pneumoniae from our strain collection and publicly accessible genome data. By comparative analysis of the carriage of resistance genes, virulence genes plasmid replicon types, and plasmid sequences, we found that IncFII plasmids were significantly more prevalent in MDR isolates and IS26 were commonly involved in resistance gene acquisition. We also discovered new MDR plasmids. These results provided an overview landscape of the genetic elements associated with MDR-ST23-hvKp based on currently accessible genome data and calling for further genomic surveillance and well-designed control studies of MDR-ST23-hvKp.

Shift in the Dominant Sequence Type of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infection from ST11 to ST15 at a Medical Center in Northeast China, 2015-2020

Objective

To investigate the clinical characteristics and molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infection at a medical center in northeast China, especially after coronavirus disease (COVID-19) pandemic.

Methods

Fifty-one patients were diagnosed with CRKP bloodstream infection between January 2015 and December 2020, among which 42 isolates were available for further study. Species identification and antibiotic susceptibilities were tested with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK 2 systems. Carbapenemase genes, virulence genes and MLST genes were detected by polymerase chain reaction. Moreover, the string test and serum killing assay were performed to evaluate the virulence of the CRKP isolates.

Results

During the six-year period, the detection rate of CRKP in bloodstream infection showed an increasing trend, with the intensive care unit, hematology and respiratory medicine wards mainly affected. Molecular epidemiology analyses showed that KPC-2 was the dominant carbapenemase gene. In addition, the dominant sequence type (ST) of CRKP shifted from ST11 to ST15 strains, which were all sensitive to amikacin in contrast to the ST11 stains. Furthermore, ST15 CRKP strains were positive for the KfuB virulence gene and more resistant to serum killing compared to the ST11 CRKP strains. Nonetheless, the mortality rate of patients infected with ST11 and ST15 CRKP did not show any significant differences.

Conclusion

A shift in the dominant sequence type of CRKP bloodstream infections from ST11 to ST15 was observed during the years 2015–2020. Compared to ST11, the ST15 CRKP strains showed amikacin sensitivity, positivity for KfuB gene, and serum resistance, which may indicate stronger virulence.

An Assessment of Siderophore Production, Mucoviscosity, and Mouse Infection Models for Defining the Virulence Spectrum of Hypervirulent Klebsiella pneumoniae

Hypervirulent Klebsiella pneumoniae (hvKp) bacteria are more virulent than classical K. pneumoniae (cKp) with resultant differences in clinical manifestations and management. It is unclear whether all hvKp isolates share a similar pathogenic potential. This report assessed the utility of siderophore production, mucoviscosity, and murine infection for defining the virulence spectrum of hvKp. Three strain cohorts were identified and defined based on the CD1 mouse subcutaneous (SQ) challenge model: (i) fully virulent hvKp strains (_fvhvKp), lethal at a challenge inoculum (CI) of ≤10³ CFU; (ii) partially virulent hvKp strains (_pvhvKp), lethal at a CI of >10³ to 10⁷ CFU; (iii) classical K. pneumoniae, not lethal at a CI of 10⁷ CFU. Quantitative siderophore and mucoviscosity assays differentiated _fvhvKp and _pvhvKp strains from cKp strains but were unable to differentiate between the _fvhvKP and _pvhvKP strain cohorts. However, SQ challenge of CD1 mice and intraperitoneal (IP) challenge of CD1 and BALB/c mice, but not C57BL/6 mice, were able to discriminate between an _fvhvKp and a _pvhvKp strain; SQ challenge of CD1 mice may have the greatest sensitivity. cKp was differentiated from hvKp both by SQ challenge of CD1 mice and IP challenge of all three mouse strains. These data identify a means to define the relative virulence of hvKP strains. It remains unclear whether the observed differences of hvKp virulence in mice translates to human infection. However, these data can be used to sort random collections of K. pneumoniae strains into _fvhvKp and _pvhvKp strain cohorts and assess for differences in clinical manifestations and outcomes.

IMPORTANCE The pathogenic potential of hvKp strains is primarily mediated by a large virulence plasmid. The minimal set of genes required for the full expression of the hypervirulent phenotype is undefined. A number of reports describe hvKp strains possessing only a portion of the virulence plasmid; the clinical consequences of this are unclear. Therefore, the goal of this report was to determine whether virulence among hvKp strains varied and, if so, how to best identify the relative virulence of hvKp isolates. Data demonstrate hvKp pathogenic potential varies in CD1 and BALB/c murine infection models. In contrast, measurements of siderophore production and mucoviscosity were unable to discriminate the differences in hvKp isolate virulence observed in mice. This information can be used in future studies to determine the mechanisms responsible for differences between fully virulent hvKp and partially virulent hvKp and whether the differences observed in mice translate to disease in humans.

Virulence evolution, molecular mechanisms of resistance and prevalence of ST11 carbapenem-resistant Klebsiella pneumoniae in China: A review over the last 10 years

Sequence type 11 (ST11) carbapenem-resistant Klebsiella pneumoniae (CRKP) has become the dominant clone in China. In this review, we trace the prevalence of ST11 CRKP in the China Antimicrobial Surveillance Network (CHINET), the key antimicrobial resistance mechanisms and virulence evolution. The recent emergence of ST11 carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) strains in China due to the acquisition of a pLVPK-like virulence plasmid, which may cause severe infections in relatively healthy individuals that are difficult to treat with current antibiotics, has attracted worldwide attention. There is a very close linkage among IncF plasmids, NTE_KPC and ST11 K. pneumoniae in China. Hybrid conjugative virulence plasmids are demonstrated to readily convert a ST11 CRKP strain to a CR-hvKP strain via conjugation. Understanding the molecular evolutionary mechanisms of resistance and virulence-bearing plasmids as well as the prevalence of ST11 CRKP in China allows improved tracking and control of such organisms.