An outbreak of extensively drug-resistant and hypervirulent Klebsiella pneumoniae in an intensive care unit of a teaching hospital in Southwest China

The wzc mutation mediates virulence changes in K1-type Klebsiella pneumoniae within the same patient

Hypervirulent Klebsiella pneumoniae (hvKp) is a major pathogen causing community-acquired infections, particularly severe diseases such as liver abscesses. Although extensive research has been conducted on the virulence mechanisms of hvKp and the genetic properties of resistance plasmids, studies on the adaptive evolution of clinical strains within the host are still limited. This study aimed to investigate the impact of genetic mutations on phenotypic changes in high-virulence K. pneumoniae within a host environment. We isolated three strains of K. pneumoniae from the same patient, two of which had identical genetic backgrounds but exhibited distinct phenotypic traits. Comparative genomic analysis was performed to identify genetic differences. A nucleotide mutation in the wzc gene was identified as a potential factor associated with changes in the mucoid phenotype. This mutation was verified using string tests and anti-centrifugal assays. Additionally, in vivo bioassays and animal infection models were conducted to further validate the findings. The comparative genomic analysis revealed a nucleotide mutation in the wzc gene, which was associated with changes in the mucoid phenotype of the strain. This was confirmed through string tests and anti-centrifugal assays. In vivo experiments and animal infection models suggested that hvKp adapts to the host by reducing capsular polysaccharide synthesis, thereby trading off some virulence for enhanced colonization capabilities. Our findings indicate that genetic mutations in hvKp can lead to significant phenotypic changes that facilitate adaptation within the host. The observed reduction in capsular polysaccharide synthesis appears to be a trade-off between virulence and colonization ability. This study provides insights into the adaptive evolution of hvKp and highlights the importance of considering intrahost genetic changes when studying the pathogenesis of hvKp. Future research should focus on further elucidating the mechanisms underlying these adaptations and their clinical implications.

Systematic review and meta-analysis on the carbapenem-resistant hypervirulent Klebsiella pneumoniae isolates

BACKGROUND

The global dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) poses a critical threat to public health. However, comprehensive data on the prevalence and resistance rates of CR-hvKp are limited. This systematic review and meta-analysis aim to estimate the pooled prevalence of carbapenem resistance among hvKp strains and assess the distribution of carbapenemase genes.

MATERIALS AND METHODS

A systematic search of ISI Web of Science, PubMed, and Google Scholar was conducted to identify studies reporting carbapenem resistance rates in hvKp strains. The pooled prevalence of carbapenem resistance and carbapenemase genes was calculated using event rates with 95% confidence intervals.

RESULTS

A total of 36 studies encompassing 1,098 hvKp strains were included. The pooled resistance rates were 49% for imipenem, 53.2% for meropenem, and 38.2% for ertapenem. Carbapenemase gene prevalence was 19.1% for blaVIM, 22.0% for blaNDM, 43.4% for blaOXA-48, and 58.8% for blaKPC.

CONCLUSION

The high prevalence of carbapenem resistance and the widespread distribution of carbapenemase genes among hvKp strains underscore their significant threat to global health. These findings highlight the urgent need for enhanced surveillance, rapid diagnostic tools, and stringent infection control measures to mitigate the spread of CR-hvKp. Future research should focus on understanding resistance mechanisms and developing targeted therapeutic strategies to address this critical challenge.

Hypervirulent Klebsiella pneumoniae have better clinical outcomes than classical Klebsiella pneumoniae for lower respiratory tract infection patients

BACKGROUND

The clinical outcomes and microbiological features of lower respiratory tract infections (LRTIs) caused by hypervirulent Klebsiella pneumoniae (hvKp) and classical Klebsiella pneumoniae (cKp) have not been well understood.

METHODS

This study collected 287 non-repetitive Klebsiella pneumoniae isolates from 287 LRTI patients. All these strains underwent annotation for resistance and virulence factors, with 141 strains undergoing mouse infection experiments to assess their virulence. The primary clinical outcomes of these patients were evaluated, including intensive care unit (ICU) admission and in-hospital mortality rates.

RESULTS

A total of 46 capsule serotypes were identified. Among these isolates subjected to mouse infection experiments, the proportions of strains exhibiting hypervirulent phenotypes were 92.6% (25/27), 92.1% (35/38), 80% (4/5), 25% (1/4), 10.5% (2/19), and 7.1% (1/14) for K2, K1, K20, K54, K47, and K25, respectively. Therefore, K1, K2, and K20 K. pneumoniae were defined as hvKp. In addition, the rates of ICU admission and in-hospital mortality for hvKp-infected patients were significantly lower than those of cKp-infected patients (51.4% vs. 65.9%, χ2 = 4.722, p = 0.03 and 8.6% vs. 29%, χ2 = 12.133, p < 0.001). Notably, among the cKp group, the cKp-ST11 subgroup had higher rates of ICU admission (77% vs. 58.5%, χ2 = 7.981, p = 0.005) and in-hospital mortality (44.8% vs. 18.5%, χ2 = 17.585, p < 0.001) than cKp-nonST11 subgroup.

CONCLUSIONS

These findings suggest that capsule serotype is a more accurate factor for the prediction of the virulence phenotype, while hvKp have better clinical outcomes than cKp for LRTI patients. Furthermore, the cKp-ST11 subgroup has the worst prognosis than cKp-nonST11 subgroup.

Multidrug-resistant ST11-KL64 hypervirulent Klebsiella pneumoniae with multiple bla- genes isolated from children's blood

Introduction

Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) poses an increasing public health risk due to its high treatment difficulty and associated mortality, especially in bone marrow transplant (BMT) patients. The emergence of strains with multiple resistance mechanisms further complicates the management of these infections.

Methods

We isolated and characterized a novel ST11-KL64 hv-CRKP strain from a pediatric bone marrow transplantation patient. Antimicrobial susceptibility testing was performed to determine resistance patterns. Comprehensive genomic analysis was conducted to identify plasmid types, virulence factors, and antimicrobial resistance genes, as well as potential resistance mechanisms associated with mutations and plasmid-mediated variants.

Results

The isolated hv-CRKP strain exhibited multidrug resistance to carbapenem, tigecycline, and polymyxin. Genomic analysis revealed that the IncHI1B/repB plasmid carried virulence factors (rmpA, ΔrmpA2, iucABCD, iutA), while IncFII/IncR and IncFII plasmids harbored resistance genes [bla C T X - M - 6 5 , bla T E M - 1 B , rmtB, bla S H V - 1 2 , bla K P C - 2 , qnrS1, bla L A P - 2 , sul2, dfrA14, tet(A), tet(R)]. The coexistence of bla C T X - M - 6 5 , bla T E M - 1 B , bla S H V - 1 2 , bla L A P - 2 ,and bla K P C - 2 in one hv-CRKP strain is exceptionally rare. Additionally, the Tet(A)-S251A variant in the conjugative plasmid pTET-4 may confer tigecycline resistance. Mutations in MgrB, PhoPQ, and PmrABCDK were identified as potential contributors to increased polymyxin resistance. Interestingly, plasmid-encoded restriction-modification systems and Retron regions were identified, which could potentially confer phage resistance.

Discussion

The combination of virulence and antimicrobial resistance factors in the ST11-KL64 hv-CRKP strain represents a significant challenge for treating immunocompromised pediatric patients. Particularly concerning is the resistance to polymyxin and tigecycline, which are often last-resort treatments for multidrug-resistant infections. The findings highlight the urgent need for effective surveillance, infection control measures, and novel therapeutic strategies to manage such hypervirulent and multidrug-resistant pathogens.

Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings

BACKGROUND

Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).

RESULTS

This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).

CONCLUSION

The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.

Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates

Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, _prmpA, peg-344) and resistance determinants (armA, bla_NDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.

Molecular epidemiology and clinical characteristics of the type VI secretion system in Klebsiella pneumoniae causing abscesses

Purpose

The type VI system (T6SS) has the potential to be a new virulence factor for hypervirulent Klebsiella pneumoniae (hvKp) strains. This study aimed to characterize the molecular and clinical features of T6SS-positive and T6SS-negative K. pneumoniae isolates that cause abscesses.

Patients and methods

A total of 169 non-duplicate K. pneumoniae strains were isolated from patients with abscesses in a tertiary hospital in China from January 2018 to June 2022, and clinical data were collected. For all isolates, capsular serotypes, T6SS genes, virulence, and drug resistance genes, antimicrobial susceptibility testing, and biofilm formation assays were assessed. Multilocus sequence typing was used to analyze the genotypes of hvKp. T6SS-positive hvKp, T6SS-negative hvKp, T6SS-positive cKP, and T6SS-negative cKP (n = 4 strains for each group) were chosen for the in vivo Galleria mellonella infection model and in vitro competition experiments to further explore the microbiological characteristics of T6SS-positive K. pneumoniae isolates.

Results

The positive detection rate for T6SS was 36.1%. The rates of hvKp, seven virulence genes, K1 capsular serotype, and ST23 in T6SS-positive strains were all higher than those in T6SS-negative strains (p < 0.05). Multivariate logistic regression analysis indicated that the carriage of aerobactin (OR 0.01) and wcaG (OR 33.53) were independent risk factors for T6SS-positive strains (p < 0.05). The T6SS-positive strains had a stronger biofilm-forming ability than T6SS-negative strains (p < 0.05). The T6SS-positive and T6SS-negative strains showed no significant differences in competitive ability (p = 0.06). In the in vivo G. mellonella infection model, the T6SS(+)/hvKP group had the worst prognosis. Except for cefazolin and tegacyclin, T6SS-positive isolates displayed a lower rate of antimicrobial resistance to other drugs (p < 0.05). The T6SS-positive isolates were more likely to be acquired from community infections (p < 0.05).

Conclusion

Klebsiella pneumoniae isolates causing abscesses have a high prevalence of T6SS genes. T6SS-positive K. pneumoniae isolates are associated with virulence, and the T6SS genes may be involved in the hvKp virulence mechanism.