Emergence of Colistin Resistance in Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae Under the Pressure of Tigecycline

Temporal Trends in the Management and Mortality Associated With Klebsiella pneumoniae Carbapenemase-Producing Enterobacterales: A Cohort Study

Introduction Klebsiella pneumoniae carbapenemase-producing Enterobacterales (KPC-CPE) are a significant cause of healthcare-associated infections, characterized by high-level resistance to beta-lactam antibiotics and limited therapeutic options. This study aimed to analyze the epidemiological trends, clinical management, and mortality associated with KPC-CPE infections over a decade, highlighting variations in incidence and treatment patterns during and after the COVID-19 pandemic. Methods A retrospective, single-center cohort study was conducted at a tertiary Portuguese hospital, analyzing data from August 2015 to June 2024. Patients with microbiologically confirmed KPC-CPE infections were included in this study. Epidemiological, clinical, and therapeutic data were extracted and analyzed using descriptive statistics and logistic regression to identify risk factors for mortality. Results Among 6,259 patients with KPC-CPE isolates, 483 (7.7%) developed infections. Infection rates peaked in 2016 and 2023, with a decline during the COVID-19 pandemic. The 30-day mortality rate was 28%, with bloodstream infections (BSIs) (odds ratio {OR}=1.64, p=0.028) and admission to the intensive care unit (ICU) significantly associated with increased mortality. Urinary tract infections (UTIs) were significantly more frequent in survivors (p=0.001). A shift from combination therapy to monotherapy, particularly with ceftazidime-avibactam (CZA), was observed, aligning with international guidelines. Patients who did not receive adequate antibiotic treatment had significantly higher mortality (OR=6.36, p<0.001). Monotherapy with aminoglycosides, ceftazidime-avibactam, tigecycline, co-trimoxazole (SXT), or fluoroquinolones was more common in survivors. Conversely, combination therapies involving high-dose meropenem (HD-MEM) or aminoglycosides were more common among non-survivors. Mortality was exceptionally high in 2019 and 2020, with no single explanatory factor identified. Conclusion Our study findings highlight the importance of rigorous infection control measures, the optimization of antimicrobial therapy, and the continuous surveillance of antimicrobial resistance. The growing reliance on monotherapy underscores the necessity of antimicrobial stewardship programs to prevent the development of resistance. Additional multicenter studies are needed to optimize therapeutic strategies and improve patient outcomes.

ESKAPE in China: epidemiology and characteristics of antibiotic resistance

The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.

Characterization of pKPN945B, a novel transferable IncR plasmid from hypervirulent carbapenem-resistant Klebsiella pneumoniae, harboring blaIMP-4 and qnrS1

Carbapenem-resistant Klebsiella pneumoniae producing metallo-β-lactamase poses a major public health threat worldwide. Imipenemase often coexists with other resistance genes leading to the formation of multidrug-resistant bacteria. In this study, we describe the microbiological and genomic characteristics of the hypervirulent carbapenem-resistant K. pneumoniae ST20-K23 strain KPN945 harboring blaIMP-4 and qnrS1. The minimum inhibitory concentration of KPN945 against antimicrobials was determined by the broth microdilution method. The virulence of KPN945 was evaluated through string test, serum killing resistance, and Galleria mellonella larvae infection models. The transferability of pKPN945B was assessed using a conjugation test. The genome sequence characteristics of KPN945 were analyzed through whole genome sequencing, and a phylogenetic tree was constructed to evaluate the prevalence of imipenemase. Our findings showed that KPN945 was non-susceptible to β-lactam antibiotics, highly resistant to serum killing, and highly lethal to G. mellonella larvae. The fusion plasmid pKPN945B carried by the isolate KPN945 belonged to the IncR incompatibility group and harbored multiple drug resistance genes such as blaIMP-4, blaCTX-M-14, qnrS1, and sul2. The most important point is that the IncR plasmid is a novel plasmid that arose by the accretion of parts from different plasmids, making it transferable and with a fitness cost. Globally, blaIMP-4 is the most prevalent imipenemase subtype, with the highest isolation rates in Asia, particularly China. The spread of blaIMP-4, especially the emergence of transferable plasmids, deserves our vigilance and prevention. Additionally, we should pay attention to the formation of hypervirulent K. pneumoniae mediated by non-virulent plasmids.

IMPORTANCE

Up to now, IncR replicons carrying blaIMP-4 have not been reported, and the IncR plasmids described in previous studies have been found to be non-transferrable to other bacteria through conjugation. Moreover, there have been no extensive phylogenetic analyses of strains carrying blaIMP in the published papers. The lack of data in these studies is noteworthy because blaIMP appears in the novel transferable fusion plasmid IncR. Although the IncR plasmid has no tra operon, it can still be transferred to Escherichia coli EC600 or Klebsiella pneumoniae ATCC13883 (RIFR) without high fitness cost, but it only affects the MIC of imipenem. blaIMP integrates with other resistance mechanisms leading to the formation of multidrug-resistant strains. Notably, the high prevalence of blaIMP-4 in Asia and the presence of blaIMP-4 on novel transferable IncR plasmids suggest the urgent need to monitor the emergence of such plasmids and control their spread.

Disruption of mgrB gene by ISkpn14 sourced from a blaKPC-2 carrying plasmid mediating polymyxin resistance against carbapenem-resistant Klebsiella pneumoniae during treatment: study on the underlying mechanisms

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections poses global challenges, with limited options available for targeted therapy. Polymyxin was been regarded as one of the most important last-resort antimicrobial agents. Many factors could accelerate the resistance evolution of polymyxin. Insertion sequence (IS) inserted into mgrB is the main polymyxin resistance mechanism in K. pneumoniae. In this study, two CRKPs (KP31157 and KP31311) were isolated from the urine of a patient, shifting from susceptible to resistant as the mgrB inserted by ISkpn14. We intended to explore the origin of the IS and underlying mechanisms resulting in polymyxin resistance.

METHODS

The within-host evolution relationship and molecular features of both CRKPs were determined by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). pKP31311_KPC-2 plasmid genome structures contained in the above two CRKPs were aligned with the homologic plasmids, retrieved from the NCBI genome database via comparative genomic analysis. The plasmids encoding ISkpn14 elements flanked by direct repeat (DR) or not were analyzed. The mRNA expression, plasmid curing and in vitro antibiotics inducing experiment were employed to understand the potential mechanism of polymyxin resistance.

RESULTS

Both strains, sharing homology, exhibited polymyxin resistance due to the insertion of ISkpn14 into the mgrB gene, influenced by minocycline exposure. Minocycline and tigecycline could accelerate polymyxin resistance (P < 0.05), validated by an in vitro induction experiment. The ISkpn14 without DR flanked expressed about 4 times higher than that with DR. The frequency of the mgrB insertion induced by polymyxin was significantly reduced (0 strain detected) after the blaKPC-2-carrying plasmid was eliminated.

CONCLUSIONS

This study provides direct experimental evidence that the ISkpn14 element causing mgrB inactivation and polymyxin resistance in K. pneumoniae originates from blaKPC-2-carrying plasmids. Minocycline exposure will accelerate the evolution of polymyxin resistance. Understanding the dynamics of IS transposition and its association with antibiotic exposure is crucial for developing effective strategies to reduce the emergence of polymyxin resistance in CRKP.

Characterization, Antibiotic Susceptibility, and Clonal Analysis of Carbapenem-Resistant Klebsiella pneumoniae From Different Clinical Cases

INTRODUCTION

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is recognized for its great ability to resist prescription drugs and its association with severe infections in humans.

OBJECTIVES

This study was designed to evaluate the characteristic resistance spectrum, to characterize the implicated carbapenem-resistant genes (CRGs), and to determine the extent of genetic diversity among Klebsiella pneumoniae isolates from human clinical cases in Duhok province.  Methodology: The VITEK-2 system was used to investigate the phenotypic antibiotic susceptibility of 23 K. pneumoniae isolated from distinct human clinical situations, multiplex PCR was used to assign the key common carbapenem-resistant genes (IMP, OXA48-like, bla-NDM, and KPC) in phenotypically carbapenem-resistant isolates, and the Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) assay was utilized to ascertain the clonal associations among those isolates.

RESULTS

Phenotypic resistance analysis revealed high resistance rates to various antibiotics, with all isolates exhibiting multidrug resistance (MDR). Coronavirus disease 2019 (COVID-19) patient isolates demonstrated significantly higher resistance compared to other sources. In addition, all isolates showed complete phenotypic resistance to carbapenems, PCR screening for CRGs identified blaOXA-48 as the predominant gene, present in all isolates. Genetic fingerprinting revealed diverse genotypes, with COVID-19 patient isolates exhibiting high similarity, contrasting with maximum diversity in non-COVID-19 clinical isolates.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Isolation and characterization of three novel lytic phages against K54 serotype carbapenem-resistant hypervirulent Klebsiella pneumoniae

The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) has driven us to explore alternative treatments for the limitation of antimicrobial agents. Lytic phages are considered a promising alternative treatment for CR-hvKP infection. In this study, we reported three novel lytic phages, vB_KpnA_SCNJ1-Z, vB_KpnS_SCNJ1-C, and vB_KpnM_SCNJ1-Y, against a CR-hvKP strain SCNJ1, and they possess genomes of double-stranded DNA with a size of 43,428 bp, 46,039 bp, and 50,360 bp, respectively. Phylogenetic analysis demonstrated that vB_KpnA_SCNJ1-Z belongs to the family Autographiviridae within the class Caudoviricetes, while vB_KpnS_SCNJ1-C and vB_KpnM_SCNJ1-Y are unclassified Caudoviricetes. The phages showed a narrow host range only lysing 1 of 50 tested clinical bacterial strains. The one-step growth curves and stability results showed that the phages displayed relatively short latency periods, with broad pH (pH 3-14) and thermal stabilities (20-60°C). The phages showed significant inhibition of the biofilm formation by SCNJ1 and strong antibacterial activity in vitro. In the mouse model, we demonstrated that administration of a single phage or phage cocktail significantly reduced bacteria loads in the lung, liver, and spleen, and effectively rescued mice from the infection of the SCNJ1 strain, with a survival rate of 70-80%. These findings suggested the three phages have great potential as an alternative therapy with favorable stability and strong antibacterial activity both in vivo and in vitro for the treatment of CR-hvKP infection.

Within-Host Resistance and Virulence Evolution of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST11 Under Antibiotic Pressure

Background

Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) has recently aroused an extremely severe health challenge and public concern. However, the underlying mechanisms of fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we report a hv-CRKP-associated fatal infection and reveal a reduction in virulence due to the acquisition of aminoglycoside resistance.

Methods

The bacterial identification, antimicrobial susceptibility, hypermucoviscosity, virulence factors, MLST and serotypes were profiled.The clonal homology and plasmid acquisition among hv-CRKP strains were detected by XbaI and S1-PFGE. The virulence potential of the strains was evaluated using Galleria mellonella larvae infection model, serum resistance assay, capsular polysaccharide quantification, and biofilm formation assay. Genomic variations were identified using whole-genome sequencing (WGS).

Results

Four K. pneumoniae carbapenemase (KPC)-producing CRKP strains were consecutively isolated from an 86-year-old patient with severe pneumonia. Whole-genome sequencing (WGS) showed that all four hv-CRKP strains belonged to the ST11-KL64 clone. PFGE analysis revealed that the four ST11-KL64 hv-CRKP strains could be grouped into the same PFGE type. Under the pressure of antibiotics, the antimicrobial resistance of the strains increased and the virulence potential decreased. Further sequencing, using the Nanopore platform, was performed on three representative isolates (WYKP586, WYKP589, and WYKP594). Genomic analysis showed that the plasmids of these three strains underwent a large number of breaks and recombination events under antibiotic pressure. We found that as aminoglycoside resistance emerged via acquisition of the rmtB gene, the hypermucoviscosity and virulence of the strains decreased because of internal mutations in the rmpA and rmpA2 genes.

Conclusion

This study shows that ST11-KL64 hv-CRKP can further evolve to acquire aminoglycoside resistance accompanied by decreased virulence to adapt to antibiotic pressure in the host.

Clonal Spread of Hospital-Acquired NDM-1-Producing Klebsiella pneumoniae and Escherichia coli in an Italian Neonatal Surgery Unit: A Retrospective Study

This article reports a rapid and unexpected spread of colonization cases of NDM-1 carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in a neonatal surgical unit (NSU) at Bambino Gesù Children's Hospital in Rome, Italy. Between the 16th of November 2020 and the 18th of January 2021, a total of 20 NDM-1 carbapenemase-producing K. pneumoniae (n = 8) and E. coli (n = 12) were isolated from 17 out of 230 stool samples collected from neonates admitted in the aforementioned ward and time period by an active surveillance culture program routinely in place to monitor the prevalence of colonization/infection with multidrug-resistant Gram-negative microorganisms. All strains were characterized by antimicrobial susceptibility testing, detection of resistance determinants, PCR-based replicon typing (PBRT) and multilocus-sequence typing (MLST). All isolates were highly resistant to most of the tested antibiotics, and molecular characterization revealed that all of them harbored the bla_NDM-1 gene. Overall, IncA/C was the most common Inc group (n = 20/20), followed by IncFIA (n = 17/20), IncFIIK (n = 14/20) and IncFII (n = 11/20). MLST analysis was performed on all 20 carbapenemase-producing Enterobacterales (CPE) strains, revealing three different Sequence Types (STs) among E. coli isolates, with the prevalence of ST131 (n = 10/12; 83%). Additionally, among the 8 K. pneumoniae strains we found 2 STs with the prevalence of ST37 (n = 7/8; 87.5%). Although patient results were positive for CPE colonization during their hospital stay, infection control interventions prevented their dissemination in the ward and no cases of infection were recorded in the same time period.

Determination of Mutational Timing of Colistin-Resistance Genes through Klebsiella pneumoniae Evolution

The emergence and dissemination of carbapenem-resistant Klebsiella pneumoniae (KP), one of the carbapenem-resistant Enterobacteriaceae (CRE), is now an emerging cause of antibiotic-resistant nosocomial infections associated with high rates of morbidity and mortality. Colistin, or polymyxin E, is a last-resort peptide antibiotic used to treat multidrug-resistant (MDR) Gram-negative bacterial infections including KP. Unfortunately, resistance to colistin is rising with increasing use in the clinical setting. Although clinical evidence links certain mutations to colistin resistance (COL-R) in KP, the origination and association of the mutations remain unclear. We hypothesize that the timing of COL-R mutations influences the development and progression of KP resistance to colistin. We performed planktonic and biofilm in vitro experimental evolutions of KP strain ATCC 43816 under increasing colistin concentrations to characterize the temporal regulation of critical COL-R mutations throughout COL-R progression. The resistance generation and mutation profiles of independently evolved bacterial populations with different lifestyles were compared. Genes with various functions theorize the timeline in which key mutations are generated and their roles in the progression of COL-R. Our results aim to advance the research and development of effective therapeutics to treat MDR bacterial infection as the dissemination of CRE continues to be a severe public health threat.

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.

Molecular and clinical characterization of hypervirulent Klebsiella pneumoniae isolates from individuals with urinary tract infections

Despite being a significant public health concern, hypervirulent Klebsiella pneumoniae (hvKP) has rarely been investigated in urinary tract infections (UTIs). To investigate the molecular and clinical characterization of hvKP in UTIs, we collected K. pneumoniae strains and clinical data from patients with UTIs. HvKP was confirmed by virulence-related genes and the Galleria mellonella model and sequenced by next-generation sequencing. Our data showed that 30/121 isolates were hvKP [17 carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP), 12 hvKP, and 1 extended-spectrum β-lactamase-producing hvKP]; these had higher resistance to most antimicrobials and were more likely to cause complicated UTIs (cUTIs). Notably, the mucoid phenotype-regulating genes _prmpA and _prmpA2 were truncated in 3 and 19 hvKP, respectively. Eight serotypes were detected and divided into three groups: K64 (n = 17), K1/K2 (n = 6), and others (n = 7). Furthermore, 16/17 K64 hvKP isolates were CR-hvKP but with a lower mortality rate of G. mellonella as the truncated _prmpA/_prmpA2 incurred high fitness cost to the isolates. In addition, all K64 isolates belonged to ST11 with the same cluster, and in two of these strains (KP88 and KP92) bla_KPC-2 gene was successfully transferred to EC600. Genetic environment analysis showed that IS26–tnpR–ISKpn27–bla_KPC−2–ISKpn6 may be the core structure in the horizontal transfer of bla_KPC-2. The highest mortality rate among the infected G. mellonella was observed in the K1/K2 group. In conclusion, hvKP had a higher resistance rate and was more likely to lead to cUTIs. Convergence of hypervirulence and carbapenem resistance in a transmissible ST11 clone of K64 K. pneumoniae was mediated by a plasmid in UTIs. Therefore, surveillance of hvKP in UTIs should be strengthened.