A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation

Klebsiella pneumoniae sensu stricto (KpI) is an opportunistic pathogen capable of residing as a commensal in both human and bovine intestinal tracts and can cause serious systemic infections in humans and severe clinical mastitis in dairy cattle. It is unclear what role zoonotic and anthroponotic transmission play in the dissemination of KpI. In this study, we use a comparative genomic approach to identify differences between KpI associated with disease in humans and cattle and aimed to identify any potential genetic barriers limiting transmission of KpI between these two hosts. A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. No obvious phylogenomic differentiation was observed between isolates from these hosts. However, subtle genetic differences exist between bovine and human KpI which likely reflect environmental adaptation to different host niches, including a higher representation of gene clusters encoding ferric citrate uptake transporters, as well as histidine, arginine, and lactose utilization pathways in bovine isolates. These gene clusters may be positively selected due to the unique metabolic environment of the mammary gland, where lactose, citrate-bound iron, and amino acids like histidine and arginine provide growth advantages for KpI during mastitis. Overall, our study identified no obvious genetic barriers to zoonotic transmission of KpI within the dairy environment and provides insight into the development of host-specific therapeutic options for KpI infections in humans and bovine.

Epidemiological and genomic insights of mcr-1-positive colistin-resistant Klebsiella pneumoniae species complex strains from wastewater treatment plants in Shanghai

The emergence of mcr-1-positive Klebsiella pneumoniae species complex (MP-KpSC) poses a significant threat to public health due to its resistance to last-resort antibiotics like colistin. This study aimed to investigate the prevalence, genomic characteristics, and transmission features of MP-KpSC in wastewater treatment plants (WWTPs) in Shanghai, China. A total of 13 (0.36 %) MP-KpSC isolates were identified, including 12 K. pneumoniae and 1 K. quasipneumoniae subsp. similipneumoniae (Kqps). Nine multidrug-resistant (MDR) MP-KpSC and 3 extensively drug-resistant (XDR) MP-KpSC strains were identified. Twenty-two resistance determinants were present in over 30 % of the strains, with the most prevalent being mcr-1 (100 %), floR (84.62 %), mphA (69.23 %), and tet(A) (69.23 %). MP-KpSC exhibited 11 sequence types, 4 plasmid types, 6 mcr-1-flanked regions, 4 clonal groups, and diverse serotypes. In 53.85 % of strains, transposons were identified within the mcr-1-flanked regions. One strain contained both mcr-8.2 and mcr-1 gene. Notably, the mcr-1 gene was identified for the first time in Kqps and was located on the conjugative IncP1 plasmid, with ISApl1 elements upstream of it. Worryingly, two carbapenem- and colistin-resistant XDR MP-KpSC stains, and three possible hypervirulence (hv) were found in MDR MP-KpSC strains. Moreover, multiple virulence genes and mcr-1, on the same contig with IS679 insert element. The evolutionary trajectories of these strains among WWTPs-human-animals were unveiled in Shanghai. The study reveals that WWTPs serve as critical environmental reservoirs for MP-KpSC, highlighting the potential transmission risks posed by XDR and hv strains to both humans and aquatic ecosystems. These findings advocate for the implementation of active surveillance targeting WWTPs to curb the spread of MP-KpSC.

Molecular epidemiology and clinical features of Klebsiella variicola bloodstream infection compared with infection with other Klebsiella pneumoniae species complex strains

Klebsiella variicola is an emerging pathogen within the Klebsiella pneumoniae species complex, and its clinical and microbiological characteristics remain poorly understood. This retrospective case-control study analyzed 252 patients with bloodstream infections caused by K. pneumoniae species complex, including 60 with K. variicola infection, to elucidate these characteristics. Our study showed no significant differences in clinical outcomes, such as 30-day mortality, between K. variicola and K. pneumoniae. However, a significant difference was found in the rate of harboring [peg-344, iucA, and rmpA] genes, which are associated with virulence in K. pneumoniae, suggesting that K. variicola may be generally less virulent. Notably, we identified two patients with community-acquired liver abscess caused by hypervirulent K. variicola, representing the first genetically analyzed case of this phenomenon in Japan and highlighting the potential virulence of this species. While there have been several reports on K. variicola carrying hypervirulence genes, this is the first report in Japan, to our knowledge, to genetically characterize a hypervirulent K. variicola isolated from a patient with disseminated liver abscesses using whole-genome sequencing. Multilocus sequence typing revealed high diversity among K. variicola isolates, with 49 distinct sequence types identified, 30 of which were newly registered, highlighting the genetic heterogeneity of this pathogen. No significant clinical differences were observed between K. variicola and other Klebsiella spp. The emergence of hypervirulent K. variicola strains with the potential to cause severe complications warrants further surveillance and research.

IMPORTANCE

Klebsiella variicola is increasingly recognized as an emerging pathogen commonly found in the environment and human gut. However, its clinical and microbiological characteristics remain poorly understood. This study provides a comprehensive analysis of K. variicola bloodstream infections (BSIs), comparing clinical and genetic features with the closely related K. pneumoniae. We identified significant differences in the prevalence of virulence genes between the two species. Notably, we observed K. variicola causing disseminated liver abscesses, similar to hypervirulent K. pneumoniae strains. These findings have important implications for accurate species identification, informing treatment strategies, and improving patient outcomes in the face of this emerging infectious threat.

De novo virulence feature discovery and risk assessment in Klebsiella pneumoniae based on microbial genome vectorization

Bacterial pathogenicity has traditionally focused on gene-level content with experimentally confirmed functional properties. Hence, significant inferences are made based on similarity to known pathotypes and DNA-based genomic subtyping for risk. Herein, we achieved de novo prediction of human virulence in Klebsiella pneumoniae by expanding known virulence genes with spatially proximal gene discoveries linked by functional domain architectures across all prokaryotes. This approach identified gene ontology functions not typically associated with virulence sensu stricto. By leveraging machine learning models with these expanded discoveries, public genomes were assessed for virulence prediction using categorizations derived from isolation sources captured in available metadata. Performance for de novo strain-level virulence prediction achieved 0.81 F1-Score. Virulence predictions using expanded "discovered" functional genetic content were superior to that restricted to extant virulence database content. Additionally, this approach highlighted the incongruence in relying on traditional phylogenetic subtyping for categorical inferences. Our approach represents an improved deconstruction of genome-scale datasets for functional predictions and risk assessment intended to advance public health surveillance of emerging pathogens.

Weberviruses are gut-associated phages that infect Klebsiella spp

Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life, and associated depolymerases. In this study, we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome, and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n = 258 from isolates, n = 65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n = 330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%), and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.

Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis

BACKGROUND

Antimicrobial resistance in Enterobacterales represents a substantial threat in modern clinical practice and the collection of data on the efficacy of new molecules is of paramount importance. Our study aimed to analyse the in vitro activity of imipenem/cilastatin/relebactam (IMI/REL) against KPC-producing Klebsiella pneumoniae (KPC-Kp) and investigate the genetic determinants of resistance to this agent.

METHODS

A total of 603 KPC-Kp strains, which were randomly collected during a multicentre study in northern Italy in the period 2016-2018, were analysed retrospectively. Antibiotic susceptibility testing was performed using a commercial broth microdilution. IMI-REL-resistant KPC-Kp strains were further analysed by whole genome sequencing to identify resistance determinants.

RESULTS

Ninety-eight percent of KPC-Kp (591/603) showed in vitro susceptibility to IMI/REL, with a minimum inhibitory concentration below the EUCAST cut-off. Different mutations in OmpK36 were found in all 12 IMI/REL-resistant strains, which belonged to MLST STs 258 (3 isolates), 307 (8 isolates) and 512 (1 isolate), but no clonal relatedness was detected by the minimum spanning tree analysis, except for 2 strains isolated in the same hospital. Equal distribution of blaKPC-2 (6/12) and blaKPC-3 (6/12) was found, and in 11 isolates the presence of genetic variants associated with the production of beta-lactamases was also identified. KPC-Kp resistant to IMI/REL retained susceptibility to meropenem/vaborbactam (MVB, 12/12, 100%) and ceftazidime/avibactam (CZA, 11/12, 91.7%). Only one strain of 603 was resistant to either MVB and CZA but susceptible to IMI/REL with a MIC of 2 mg/L; 4/603 (0.7%) were resistant to CZA but susceptible to IMI/REL and MVB.

CONCLUSIONS

IMI/REL showed good in vitro activity against the KPC-Kp strains analysed. All the IMI/REL-resistant strains displayed a mutation in porin OmpK36 and produced carbapenemases, with KPC-2 and KPC-3 being equally distributed. MVB and CZA maintained good activity against IMI/REL resistant isolates.

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of healthcare-associated infections in hospitals, which are frequently antimicrobial resistant (AMR). Exacerbating the public health threat posed by K. pneumoniae, some strains also harbour additional hypervirulence determinants typically acquired via mobile genetic elements such as the well-characterised large virulence plasmid KpVP-1. The rmpADC locus is considered a key virulence feature of K. pneumoniae and is associated with upregulated capsule expression and the hypermucoid phenotype, which can enhance virulence by contributing to serum resistance. Typically such strains have been susceptible to all antimicrobials besides ampicillin; however, the recent emergence of AMR hypermucoid strains is concerning.

METHODS

Here, we investigate the genetic diversity, evolution, mobilisation and prevalence of rmpADC, in a dataset of 14,000 genomes from isolates of the Klebsiella pneumoniae species complex, and describe the RmST virulence typing scheme for tracking rmpADC variants for the purposes of genomic surveillance. Additionally, we examine the functionality of representatives for variants of rmpADC introduced into a mutant strain lacking its native rmpADC locus.

RESULTS

The rmpADC locus was detected in 7% of the dataset, mostly from genomes of K. pneumoniae and a very small number of K. variicola and K. quasipneumoniae. Sequence variants of rmpADC grouped into five distinct lineages (rmp1, rmp2, rmp2A, rmp3 and rmp4) that corresponded to unique mobile elements, and were differentially distributed across different populations (i.e. clonal groups) of K. pneumoniae. All variants were demonstrated to produce enhanced capsule production and hypermucoviscosity.

CONCLUSIONS

These results provide an overview of the diversity and evolution of a prominent K. pneumoniae virulence factor and support the idea that screening for rmpADC in K. pneumoniae isolates and genomes is valuable to monitor the emergence and spread of hypermucoid K. pneumoniae, including AMR strains.

KpnK48 clone driving hypervirulent carbapenem-resistant Escherichia coli epidemics: Insights into its evolutionary trajectory similar to Klebsiella pneumoniae

AIMS

Hypervirulent and carbapenem-resistant pathogens posed a significant and growing threat to global public health. This study focused on the rapid spread of a hypervirulent carbapenem-resistant E. coli (hv-CREC) subclone and its genomic resembles with hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP), driven by recombination impacting both chromosomal and plasmid gene content.

METHODS

A multicenter molecular epidemiological study was conducted on 653 CREC clinical isolates collected across China (2013-2022), integrated with public genomic data. Pangenome-wide and phylogeographical analyses were performed to uncover recombination events, define the epidemic clone, and trace its evolutionary history. Growth advantage and virulence were evaluated through competition assays and Galleria mellonella infection models.

RESULTS

Sequence types (ST) 167, ST410, ST617, and ST361 collectively accounted for 53.8 % (351/653) of the CREC isolates, with ST167 showing a sharp increase in prevalence after 2017. Among these, subclone named KpnK48 emerged as the primary driver of the increase in ST167 CREC prevalence. Traced to a European origin, KpnK48 rapidly expanded globally, particularly in China. The remarkable success of KpnK48 could plausibly be attributed to enhanced survival and virulence, driven by the acquisition of a ∼492 kb recombinant genomic region which mirrored the genomic architecture underlying the hv-CRKP ST11-K64 clone, reflecting a Klebsiella-like evolutionary path. Additionally, plasmid shift in KpnK48 clone from the prevalent NDM-IncX3 plasmid to Klebsiella-common NDM-IncF plasmid expanded its resistance spectrum and virulence gene repertoire, likely further amplifying its pathogenicity and success.

CONCLUSIONS

The KpnK48 subclone combined the features of hypervirulence and carbapenem resistance, bridging genomic traits of E. coli and K. pneumoniae, signifying a broader evolutionary trend with profound global health implications.

Emergence and characterization of IncFII/IncR plasmids with multiple 5,692 bp- bla KPC-2-bearing tandem repeats in ceftazidime/avibactam non-susceptible Klebsiella pneumoniae strains

Ceftazidime/avibactam (CAZ/AVI) is widely recognized as an effective treatment for infections caused by KPC-producing Klebsiella pneumoniae (KPC-Kp). However, the prevalence of CAZ/AVI resistance among KPC-Kp isolates has increased rapidly in recent years. In this study, high-level carbapenem resistance and enhanced CAZ/AVI resistance were observed in two hypervirulent carbapenem-resistant K. pneumoniae isolates, KP1878 and KP3034, following prolonged carbapenem use. Virulence phenotypes were confirmed using the string test and a Galleria mellonella larvae infection model. Real-time quantitative PCR revealed that the relative expression of bla KPC-2 in KP1878 and KP3034 was 2.4-fold and 11.6-fold higher, respectively, than that in the CAZ/AVI-susceptible KPC-Kp strain KP1880. Whole-genome sequencing showed that the bla KPC-2 gene resided within an identical 5,692-bp ΔklcA-korC-ΔISKpn6-bla KPC-2-ISKpn8-ΔtnpR-IS26 tandem repeat, which was replicated twice and four times in plasmids pKPC1878 and pKPC3034, respectively. Compared with KP1880, the β-lactamase hydrolysis activities of crude cell lysates derived from KP1878 and KP3034 were significantly higher in their ability to hydrolyze meropenem, ceftazidime, and nitrocefin. S1-nuclease-digested pulsed-field gel electrophoresis, along with Southern blot and restriction fragment length polymorphism fingerprinting, identified plasmid profiles but revealed one or more 5.6-kilobase variations in the regions hybridized with the KPC-specific probe. Further comparative genomic analysis suggested that a potential homologous recombination event occurred between the bla KPC-2-carrying plasmid and the pLVPK-like virulence plasmid of KP3034, leading to the generation of a cointegrated plasmid that combined both virulence and CAZ/AVI resistance.

Essentiality of the virulence plasmid-encoded factors in disease pathogenesis of the major lineage of hypervirulent Klebsiella pneumoniae varies in different infection niches

BACKGROUND

Hypervirulent Klebsiella pneumoniae (HvKp) can metastasise to extra-intestinal sites to cause disseminated disease such as pyogenic liver abscesses. HvKp harbours a large virulence plasmid (KpVP) that contributes to pathogenicity. We previously identified a crucial gene region that confers virulence in SGH10 (ST23, K1 capsule), spanning genes encoding the siderophores aerobactin and salmochelin, as well as the regulator of mucoidy phenotype A (iuc-rmp-iro).

METHODS

SGH10 isogenic mutants of aerobactin, rmpA, and salmochelin were generated and tested in vitro for their siderophore production, hypermucoviscosity and growth. We investigated the essentiality of these factors in different murine infection or colonisation models.

FINDINGS

In a lung pneumonia model, capsule modulation by rmpA was the primary driver of high bacterial burden in the lung. In a systemic infection setting, rmpA was still the primary driver, followed by a significant contribution by salmochelin, that conferred virulence. However, the role of aerobactin was more significant in hvKp persistence in the gut. We further examined a large collection of Kp genomes and observed that the iro loci is often co-inherited with iuc in KpVP-1, suggesting the evolutionary importance of expressing both siderophores in these lineages.

INTERPRETATION

HvKp typically colonises the intestinal niche, however, the acquisition of the KpVP plasmid has enabled it to thrive outside the gut and cause metastatic infections. While the iuc-rmp-iro region is pivotal in bestowing virulence, the encoded factors contribute differently to the success of the pathogen in various infection sites, where the microenvironment, nutrient availability and immune response can vary. Thus, our study demonstrates that possessing the iuc-rmp-iro gene region can be an evolutionary advantage by allowing for flexibility in modulating siderophore and capsule expression in order for K. pneumoniae to thrive in distinct host niches.

FUNDING

This work is funded by the National Research FoundationMOH-000925-00 to YH Gan and OFYIRG22jul-0042 by the National Medical Research Council (NMRC) to THT.

Molecular epidemiology and emergence of sequence type 25 hypervirulent Klebsiella pneumoniae in pigs in the Netherlands (2013-2020): a global comparative analysis with human and pig isolates

Klebsiella pneumoniae (Kp), a ubiquitous pathogen found in diverse ecological niches, poses a threat to human and animal health. Hypervirulent Kp (hvKp) is concerning for its acquisition of virulence and antimicrobial resistance genes through plasmids. This study investigates hvKp as a cause of septicaemia in piglets in the Netherlands and examines the role of plasmids in virulence and host association. We collected 41 Kp isolates cultured from necropsies submitted from 15 different farms (2013-2020) and sequenced them using long-read sequencing. We identified sequence type (ST) 25 as the dominant Kp (67%, 10/15 farms) associated with septicaemia in pigs in the Netherlands. ST25 isolates displayed a hypervirulent profile, including the K2 hyper-capsule type and carried an iuc3 virulence plasmid. Further analysis revealed two ST25 clonal groups: CG25 and CG3804, a novel porcine clone. Multidrug resistance was identified in CG25 isolates from five pig farms. There was one colistin-resistant isolate carrying mcr-1 on a plasmid. Comparative genomic analysis was performed by including a large dataset of related publicly available Kp genomes from ST25 humans (n=230) and pigs (n=12) of all STs for phylogenetic and plasmid analysis. Pangenomic analysis revealed significantly higher iuc3 prevalence in global CG25 pig isolates (98%, 40/41) compared to humans (10%, 24/234) correlating with their enhanced virulence (scores 3-4 vs 0-1). The study highlights ST25 hvKp causing septicaemia in piglets in the Netherlands for the first time. Aerobactin lineage iuc3 on a plasmid is associated with infections in pigs and is responsible for an increased virulence score.

Rapid emergence, transmission, and evolution of KPC and NDM coproducing carbapenem-resistant Klebsiella pneumoniae

Due to the limited treatment options, the widespread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a serious clinical challenge. The emergence of Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM) coproducing CRKP (KPC-NDM-CRKP) further aggravates this issue. In this study, we identified 15 KPC-2-NDM-5-CRKPs as being responsible for an outbreak that involved 10 patients from October 2020 to May 2021. The outbreak was sustained by ST11-KL47-OL101 KPC-2-NDM-5-CRKPs, which exhibited non-susceptible to all antimicrobials available in mainland China. Of these strains, we characterized a conjugative hybrid plasmid co-harboring blaKPC-2 and blaNDM-5 with high stability. Plasmid comparison and phylogenetic analysis were performed to investigate the origin of the hybrid plasmid and its fusion mechanism. It was speculated that the hybrid plasmid might originate from Klebsiella pneumoniae subsp. pneumoniae strain kpn-hnqyy plasmids unnamed1 (encoding NDM-5) and unnamed2 (encoding KPC-2). The fusion of these two plasmids was presumably mediated by IS26. Global genomic surveillance raised an alarm about the increased prevalence of KPC-NDM-CRKPs. Phylogenetic evaluation was carried out with a total of 327 KPC-NDM-CRKP genomes to provide a global perspective on such strains, and potential transmission events in other global regions were also observed during the COVID-19 period. The outbreak of such strains in the real world and the co-transfer of blaKPC and blaNDM would exacerbate the dispersal of KPC-NDM-CRKPs, which poses a severe threat to public health.

Whole Genome Sequencing Analysis of Klebsiella pneumoniae Isolates from Health Care-Associated Bacteremia of Urinary Origin in Spain: Findings from the Multicenter ITUBRAS-2 Cohort Study

Background

The objective of this study was to assess the microbiological and clinical features of Klebsiella pneumoniae health care-associated bacteremia of urinary origin (HCA-BUO) in Spain, with a focus on third-generation cephalosporin-(3GCR-Kp) and carbapenem-resistant K pneumoniae (CR-Kp) isolates.

Methods

A total of 96 (21.4%, 96/449) K pneumoniae blood isolates were prospectively collected from patients with HCA-BUO (n = 443) from 12 tertiary care hospitals in Spain (2017-2019). Antimicrobial susceptibility was determined (standard broth microdilution), and extended-spectrum β-lactamase, AmpC, and carbapenemase production was screened. A subset of 55 K pneumoniae isolates was analyzed by whole genome sequencing (Illumina) to determine population structure, resistome, and virulome. Additionally, 13 of these isolates were subjected to long-read sequencing (Nanopore) for plasmid characterization. Patients' baseline and clinical characteristics were reviewed.

Results

3GCR-Kp prevalence was 43.8% (42/96), mostly associated with extended-spectrum β-lactamase production (34/96, 35.4%; mainly CTX-M-15, 32/34, 94.1%) and the dissemination of sequence type (ST)-307 (15/34, 44.1%) and other globally spread multidrug-resistant high-risk clones. CR-Kp prevalence was 9.4% (9/96); all isolates belonged to different STs and were mostly associated with carbapenemase production (6/9, 66.7%; mainly OXA-48-like, n = 3). Additionally, 3GCR-Kp and CR-Kp isolates showed higher content of other antibiotic resistance genes. Altogether, these episodes were associated with prior antibiotic use and receipt of inadequate empirical treatment.

Conclusions

There is a high prevalence of 3GCR and CR-Kp causing HCA-BUO in Spain, mainly driven by the dissemination of ST307/CTX-M-15 and other globally spread multidrug-resistant high-risk clones, challenging the selection of empirical and targeted treatments for these infections.

Revisiting therapeutic options against resistant klebsiella pneumoniae infection: Phage therapy is key

Multi-drug resistant and carbapenem-resistant hypervirulent Klebsiella pneumoniae strains are spreading globally at an alarming rate, emerging as one of the most serious threats to global public health. The formidable challenges posed by the current arsenal of antimicrobials highlight the urgent need for novel strategies to combat K. pneumoniae infections. This review begins with a comprehensive analysis of the global dissemination of virulence factors and critical resistance profiles in K. pneumoniae, followed by an evaluation of the accessibility of novel therapeutic approaches for treating K. pneumoniae in clinical settings. Among these, phage therapy stands out for its considerable potential in addressing life-threatening K. pneumoniae infections. We critically examine the existing preclinical and clinical evidence supporting phage therapy, identifying key limitations that impede its broader clinical adoption. Additionally, we rigorously explore the role of genetic engineering in expanding the host range of K. pneumoniae phages, and discuss the future trajectory of this technology. In light of the 'Bad Bugs, No Drugs' era, we advocate leveraging artificial intelligence and deep learning to optimize and expand the application of phage therapy, representing a crucial advancement in the fight against the escalating threat of K. pneumoniae infections.

Carbapenem-Resistant, Virulence Plasmid-Harboring Klebsiella pneumoniae, United States

Carbapenem-resistant and virulence plasmid-harboring Klebsiella pneumoniae (pVir-CRKP) has emerged and spread globally, yet clinical investigations from the United States remain limited. We conducted a genomic analysis of 884 unique carbapenem-resistant K. pneumoniae isolates from a multicenter US cohort and identified 6 pVir-CRKP isolates, including 2 sequence type (ST) 23, 2 ST893, and 2 ST11 isolates. Patients infected with pVir-CRKP experienced high Pitt bacteremia scores and a 33% 30-day mortality rate. The pVir-CRKP isolates exhibited significant sequence variation in virulence genes and plasmids, along with differences in mucoviscosity, capsule production, survival in normal human serum, resistance to killing by human polymorphonuclear neutrophils, and in vivo pathogenicity. Phylogenetic analyses showed that most pVir-CRKP isolates were genetically similar to strains reported from other global regions. The emergence of pVir-CRKP with higher virulence potential and carbapenem resistance in the United States than the predominant carbapenem-resistant K. pneumoniae clone underscores the need for active global surveillance.

Emergence and evolution of rare ST592 bla NDM-1-positive carbapenem-resistant hypervirulent Klebsiella pneumoniae in China

Objectives

This study aimed to characterize the genomes of two rare ST592 Klebsiella pneumoniae isolates and to explore their evolution into carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKp).

Methods

The minimum inhibitory concentrations (MICs) were determined using a VITEK 2 compact system. Conjugation experiments were conducted using film matings. Whole-genome sequencing (WGS) was performed using the Illumina and Nanopore platforms. The antimicrobial resistance determinants were identified using the ABRicate program in the ResFinder database. Insertion sequences were identified using ISFinder and the bacterial virulence factors identified using the Virulence Factor Database (VFDB). The K and O loci were examined using Kleborate. Multilocus sequence typing (MLST) and replicon type identification were performed by the Center for Genomic Epidemiology. Conjugation-related elements were predicted using oriTfinder. The plasmid structure was visualized using Circos, and a possible evolutionary model was constructed using BioRender.

Results

Isolates KPZM6 and KPZM16 were identified as ST592 and KL57, respectively, and were collected from the same department. The antimicrobial susceptibility testing data revealed that KPZM16 possesses an extensively drug-resistant (XDR) profile, whereas KPZM6 is a susceptible K. pneumoniae. The hybrid assembly showed that both KPZM6 and KPZM16 have one pLVPK-like virulence plasmid carrying the rmpA, rmpA2, and iucABCD-iutA gene clusters. However, strain KPZM16 harbors one IncN plasmid carrying the carbapenem resistance genes bla NDM-1, dfrA14, and qnrS1. The results of the conjugation experiments demonstrated that the plasmid could be transferred to the recipient strain. It is possible that the NDM-1-producing plasmid was transferred from KPZM6 to KPZM16 via conjugation, leading to the formation of CR-hvKp.

Conclusions

This is the first study in which complete genomic characterization of the rare NDM-1-producing ST592 K. pneumoniae clinical isolate was performed. This study provides a possible evolutionary hypothesis for the formation of CR-hvKp via conjugation. Early detection is recommended to avoid the extensive spread of this clone.

Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China

The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.

O-antigen polysaccharides in Klebsiella pneumoniae: structures and molecular basis for antigenic diversity

SUMMARYKlebsiella pneumoniae is a gram-negative species, whose isolates are found in the environment and as commensals in the human gastrointestinal tract. This bacterium is among the leading causes of a range of nosocomial and community-acquired infections, particularly in immunocompromised individuals, where it can give rise to pneumonia, urinary tract infections, septicemia, and liver abscesses. Treatment of K. pneumoniae infections is compromised by the emergence of isolates producing carbapenemase and extended-spectrum β-lactamase enzymes, making it a high priority for new therapeutic approaches including vaccination and immunoprophylaxis. One potential target for these strategies is the O-antigen polysaccharide component of lipopolysaccharides, which are important virulence determinants for K. pneumoniae. Consideration of immunotherapeutic opportunities requires a comprehensive and fundamental understanding of O-polysaccharide structures, distribution of particular O serotypes in clinical isolates, and the potential for antigenic diversification. The number of recognized K. pneumoniae O-polysaccharide antigens has varied over time, complicated by the observation that some examples share similar structural (and potentially antigenically cross-reactive) elements, and by the existence of genetic loci for which corresponding O-polysaccharide structures have yet to be determined. Here, we provide a comprehensive integration of the current carbohydrate structures and genetic information, together with a proposal for an updated classification system for K. pneumoniae O-antigens, that is being implemented in Kaptive for molecular serotyping. The accumulated insight into O-polysaccharide assembly pathways is used to describe the molecular basis for O-antigen diversity in K. pneumoniae.

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii

The proliferation of multi-drug resistant (MDR) bacteria is driven by the global spread of epidemic lineages that accumulate antimicrobial resistance genes (ARGs). Acinetobacter baumannii, a leading cause of nosocomial infections, displays resistance to most frontline antimicrobials and represents a significant challenge to public health. In this study, we conduct a comprehensive genomic analysis of over 15,000 A. baumannii genomes to identify a predominant epidemic super-lineage (ESL) accounting for approximately 70% of global isolates. Through hierarchical classification of the ESL into distinct lineages, clusters, and clades, we identified a stepwise evolutionary trajectory responsible for the worldwide expansion and transmission of A. baumannii over the last eight decades. We observed the rise and global spread of a previously unrecognized Clade 2.5.6, which emerged in East Asia in 2006. The epidemic of the clade is linked to the ongoing acquisition of ARGs and virulence factors facilitated by genetic recombination. Our results highlight the necessity for One Health-oriented research and interventions to address the spread of this MDR pathogen.

Global molecular epidemiology of the incomplete CirA protein related to cefiderocol resistance in Klebsiella pneumoniae: a genome-based study

CirA is an iron transporter comprising 657 amino acids in Klebsiella pneumoniae, and incomplete CirA alone leads to reduced susceptibility to cefiderocol. We performed a genome-based analysis to study the prevalence of incomplete CirA in K. pneumoniae through analyzing all genomes of this species (n = 55,517, as of 26 October 2023) available in NCBI. We detected incomplete CirA in 633 (1.27%) genomes with the corresponding strains collected since 1911, across 44 countries on six continents, and mostly (n = 563, 88.94%) from humans. Notably, 77 (12.16%) genomes had incomplete CirA in combination with β-lactamases (NDM-1, NDM-5, NDM-7, or KPC-3 plus SHV-11) known to confer cefiderocol resistance. We identified 189 variants of incomplete CirA, including two particularly common ones, a 362-amino-acid remnant due to frameshift by a deletion at cirA nucleotide position 1,083 (116/633, 18.33%) and a 562-amino-acid remnant due to premature stop resulting from a mutation at nucleotide position 1,684 (71/633, 11.22%). The 362-amino-acid remnant was mainly found in ST26 (39/116), ST34 (36/116), and ST359 (31/116) strains. The 562-amino-acid remnant was almost exclusive to ST86 (69/71), particularly related to the hypervirulent capsule type K2. Clonal outbreaks (ST26 in USA, ST34 in UK, and ST86 in Vietnam) and cross-border transmission (ST34 in UK and Portugal) were observed. However, this study has limitations, as the analyzed publicly available K. pneumoniae assemblies are biased, and only mutations resulting in incomplete CirA were considered. In conclusion, K. pneumoniae with incomplete CirA is a global concern, highlighting the urgent need for heightened vigilance and further studies.IMPORTANCECefiderocol is a critically important antimicrobial agent against multidrug-resistant organisms including carbapenem-resistant Klebsiella pneumoniae. We performed a genome-mining study and found incomplete CirA (an iron transporter), which is related to cefiderocol resistance, in a small proportion (1.27%) of publicly available K. pneumoniae genomes. However, K. pneumoniae strains with incomplete CirA are globally distributed and have been present for over a century, well before the clinical use of cefiderocol. One hundred eighty-nine incomplete CirA variants were identified, suggesting multifactorial causes. Almost all publicly available genomes of ST26, ST34, and ST86 K. pneumoniae strains with incomplete CirA have a wide geographic distribution, pointing to the potential existence of particular lineages prone to develop resistance to cefiderocol. Clonal outbreaks and cross-border transmission of strains with incomplete CirA were detected. Incomplete CirA was associated with the hypervirulent K2-ST86 lineage or high-risk multidrug resistance ST16 clone, posing an increased threat or challenge to treatment and infection control.

Characterization of a multidrug-resistant hypovirulent ST1859-KL35 klebsiella quasipneumoniae subsp. similipneumoniae strain co-harboring tmexCD2-toprJ2 and blaKPC-2

OBJECTIVES

The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24).

METHODS

Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships.

RESULTS

KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1), an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination.

CONCLUSIONS

KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.

Complete genome sequences of Klebsiella pneumoniae, Klebsiella quasipneumoniae, and Klebsiella variicola clinical isolates from an epidemiology study

An epidemiology study of Klebsiella spp. causing infections was carried out. In the study, K. pneumoniae was identified with a prevalence of 94.6%, K. quasipneumoniae with 3.8%, and K. variicola with 1.6%. Here, we report the draft genome sequence of four selected Klebsiella pneumoniae species complex (KpSC) clinical isolates obtained from different sources.

Increasing polymyxin resistance in clinical carbapenem-resistant Klebsiella pneumoniae strains in China between 2000 and 2023

BACKGROUND

Development of polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a severe challenge to public health. Here we aimed to perform a retrospective study of prevalence and molecular characteristics of polymyxin-resistant CRKP strains.

METHODS

4455 clinical CRKP strains from 18 provinces in China during 2000 to 2023 were collected. Polymyxin-resistant CRKP strains were subjected to antimicrobial susceptibility testing, whole genome sequencing and bioinformatic analysis. Molecular mechanisms underlying the polymyxin resistance in CRKP were analyzed.

RESULTS

Here we show that polymyxin-resistant CRKP emerge initially in 2014, prevalence of such strains then increase steadily over the years, reaching a rate of 9.86% in 2023. In total, 112 polymyxin-resistant CRKP isolates are identified. Antimicrobial susceptibility tests show that all polymyxin-resistant CRKP are resistant to commonly used antibiotics, yet most isolates remain susceptible only to ceftazidime-avibactam and tigecycline. Predominant polymyxin resistance mechanism in CRKP is mutations in mgrB (59/112), which commonly involves disruption of mgrB by insertion of elements such as ISKpn26 (20/59), IS903B (14/59), and ISKpn14 (9/59). Phylogenetic analysis reveals frequent clonal dissemination of polymyxin-resistant CRKP within the same hospital and even among different hospitals in neighboring provinces. pLVPK-like virulence plasmids are detected in 46 isolates, such strains are therefore categorized as polymyxin and carbapenem-resistant hypervirulent K. pneumoniae which may cause infections with high mortality.

CONCLUSIONS

Our results highlight frequent clonal transmission of polymyxin-resistant CRKP within hospitals. Continuous surveillance of polymyxin resistance among CRKP should be implemented to prevent further dissemination of such strains in clinical settings in China.

Adaptive attenuation of virulence mediated by Wzc mutation in ST11-KL47 Carbapenem-resistant Klebsiella pneumonia

Introduction

The impact of the hypermucoviscosity (HMV) phenotype in ST11-KL47 carbapenem-resistant Klebsiella pneumoniae (CRKp) pathogenicity warrants investigation for public health risk assessment.

Methods

We analyzed 230 clinical ST11-KL47 CRKp to identify the key factor in mucoviscosity acquisition via comparative genomic analysis. Sedimentation value served as the objective index to quantify HMV. The virulence in vivo was assessed using Galleria mellonella and mouse infection models. We employed genome engineering, capsular polysaccharides (CPS) quantification, and visualization to explore the role of Wzc mutation in CPS biosynthesis and HMV. The biological impact of Wzc-mediated HMV was investigated through competitive growth analysis, biofilm formation, serum resistance, anti-phagocytic ability, and adhesion assays. Transcriptomic analysis and scanning electron microscopy (SEM) were utilized to explore the relationship between polysaccharide composition, physical distribution, and changes in virulence.

Results

The Wzc mutations are identified as the key to mucoviscosity acquisition. Unexpectedly, Wzc-mediated HMV CRKp exhibits reduced pathogenicity versus non-mucoviscosity (NMV) strains in different animal models, with competitive disadvantage, decreased biofilm formation, serum resistance, and adhesion, yet higher anti-phagocytic ability in vitro. CPS extraction and visualization of genome-engineered strains verify the Wzc mutations mediate HMV by standardizing CPS chain length and overproducing cell-free extracellular polysaccharides (cell-free EPS). Transcriptomic results, lipopolysaccharides (LPS) quantification, and SEM collectively indicate a downregulation of LPS synthesis and the masking of LPS in HMV strains.

Discussion

These findings demonstrate that the Wzc-induced HMV attenuates ST11-KL47 CRKp virulence by modifying the exopolysaccharide composition and physical distribution.

Double carbapenemases in Klebsiella pneumoniae blood isolates: dissemination in a single medical center via multiple plasmids and a variety of highly efficient clones

Acquisition of multiple carbapenemase genes by Klebsiella pneumoniae (Kp) is an emerging public health threat. Here, we aim to elucidate the population structure of Kp blood isolates carrying two different carbapenemase genes and identify the mechanism facilitating their dissemination. The study was conducted in a tertiary healthcare center between 2014 and 2022. Twenty-four patients with bacteremia caused by Kp carrying two different carbapenemase genes were identified. All 24 blood isolates were analyzed by short-read genome sequences supplemented by long reads in a selected number of isolates. All isolates carried blaKPC (23 blaKPC-2, 1 blaKPC-3) and blaVIM-1 genes, along with a variety of antimicrobial resistance determinants. The isolates were clustered in six clonal lineages (ST39, ST147, ST323, ST258, ST3035, and ST340). Long-read genome sequences demonstrated that each carbapenemase gene was located in a separate group of plasmids: the blaKPC-2 on a fusion of IncFIB(pQil) and IncFII(K) plasmids, the blaKPC-3 on IncX3, the blaVIM-1 on IncC, or a fusion of the IncFIB(pNDM-Mar) and IncHI1B(pNDM-MAR) plasmids. Comparison of plasmid content of eight isolates carrying a single carbapenemase gene from a previous study with eight isolates carrying two carbapenemase genes from the present study, matched by clonal lineages, revealed that the second carbapenemase gene was acquired by addition of another plasmid. Identical plasmids were found within the same lineage and across lineages. These findings suggest that dissemination of carbapenemase genes in our hospital setting was driven by multiple plasmids across a variety of highly efficient clones.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.

Clinical and genomic characterization of Klebsiella pneumoniae infections in Dhaka, Bangladesh

BACKGROUND

Klebsiella pneumoniae (Kpn), a WHO priority pathogen with high rates of antimicrobial resistance (AMR), has emerged as a leading cause of hospital acquired pneumonia and neonatal sepsis.

OBJECTIVE

We aimed to define the clinical characteristics of a cohort of patients with Kpn infection in Dhaka, Bangladesh and to perform phenotypic and genetic characterization of the associated isolates.

METHODS

We retrospectively extracted clinical data about patients at Dhaka Medical College Hospital from whom Klebsiella spp was isolated from a clinical specimen collected between February and September 2022. We used standard microbiologic techniques to evaluate AMR and whole-genome sequencing (WGS) to assess dominant lineages, common capsular (K) and O-polysaccharide (O) antigen types, and AMR and virulence genes.

RESULTS

Ninety-eight patients were included, with diagnoses of pneumonia (38/98, 39 %), wound infection (29/98, 31 %), urinary tract infection (29/98, 31 %) and bacteremia (2/98, 2 %). We tested isolates for susceptibility to eight classes of antibiotics. Of the 98 isolates, 41 % were multidrug resistant (MDR), 15 % were extensively drug resistant (XDR), and 16 % were pan-drug resistant (PDR). Three isolates (3 %) were resistant to polymyxin B. Outcome data were available for 46 patients; 4 patients (8 %) died from infections caused by PDR (n = 2), XDR (n = 1), and MDR isolates (n = 1). WGS revealed a high degree of genomic diversity, with multiple sequence types (STs), O-types and K-types represented; ST16:K81:OL101 and ST43:K30:O1 were the most prevalent.

CONCLUSION

Our findings suggest alarming levels of AMR among Kpn isolates in Bangladesh and a critical need for improved treatment modalities and vaccine development.

Multiple regional outbreaks caused by global and local VIM-producing Klebsiella pneumoniae clones in Poland, 2006-2019

PURPOSE

This study was aimed at comprehensive genomic analysis of VIM-type carbapenemase-producing Klebsiella pneumoniae species complex (KpSC) in Poland.

METHODS

All non-duplicate 214 VIM-producing KpSC isolates reported in Poland in 2006-2019 were short-read sequenced and re-identified by the average nucleotide identity scoring. Their clonality/phylogeny was assessed by cgMLST and SNP in comparison with genomes from international databases. Serotypes, VIM-encoding integrons, resistomes, virulomes and plasmid replicons were identified by various bioinformatic tools. Structures of plasmids and genomic islands with VIM integrons were analysed for representative long-read sequenced isolates.

RESULTS

The KpSC isolates were the second most prevalent VIM-positive Enterobacterales (23.1%) in Poland in 2006-2019, following Enterobacter spp. (40.1%). Their significance emerged in 2014 and then grew consequently, owing to eight regional outbreaks of K. pneumoniae sequence types (STs) ST437, ST147, ST15, ST277 and ST392. These carried different VIM integrons, mainly In238 and In916 types, located on IncFIB + IncHI2 (pNDM-MAR)-, IncA- or IncM-like plasmids, or clc-type integrative and conjugative elements. Despite relatedness of the outbreak clusters to isolates from other countries, e.g. Greece, Spain, Slovakia or Germany, most of them have apparently emerged on site by horizontal acquisition of resistance determinants from other species, including Enterobacter spp. and Pseudomonas spp.

CONCLUSIONS

This work shows dynamic epidemiology of VIM-producing organisms, driven by a mix of circulation of different VIM-encoding elements, and parallel clonal spread of multiple organisms.

Genomically defined hypervirulent Klebsiella pneumoniae contributed to early-onset increased mortality

The presence of all five of the virulence-associated genes iucA, iroB, peg-344, rmpA, and rmpA2 is presently the most accurate genomic means for predicting hypervirulent Klebsiella pneumoniae (hvKp-p). With this longitudinal cohort study, we firstly provide novel insights into the clinical and genomic characteristics of hvKp-p in high-risk regions. Through propensity score matching, we show that hvKp-p is less likely to acquire antimicrobial resistance but develops more severe disease and result in increased mortality. HvKp-p are predominantly isolated from hospital settings and caused pneumonia in majority of the cases. ST23 and KL1 are the most common types in the hvKp-p cohort. Community-acquired and healthcare-associated infections are also identified as independent risk factors for hvKp-p. This genomic definition, albeit imperfect, offers a practical and efficient alternative to murine models, allowing for early identification and timely intervention in clinical settings.

Characterization of carbapenem-resistant Klebsiella pneumoniae from blood cultures in Gaza Strip hospitals, Palestine

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a difficult to treat organism owing to limited therapeutic options. So far, little is known about the molecular characteristics of CRKP in Palestine.

OBJECTIVES

The aim of this study was to investigate the antimicrobial resistance patterns, multilocus sequence types (ST) and resistance genes among clinical K. pneumoniae isolates from hospitalized patients in Gaza Strip, Palestine.

METHODS

K. pneumoniae from blood cultures (n = 55) were collected at two hospitals in Gaza Strip (2023) and identified by MALDI-TOF-MS. Antimicrobial susceptibility testing was done using VITEK-2 automated systems. Carbapenemases were phenotypically detected. Whole genome sequencing (WGS) of all CRKP isolates was performed to assess determinants for carbapenem resistance and genotypes.

RESULTS

Of all K. pneumoniae isolates, 40 % (n = 22/55) were CRKP. Among CRKP, cefiderocol showed the least resistance (46 %, n = 10/22) while ceftazidime/avibactam showed a synergistic effect with aztreonam (36 %, n = 8/22). The majority (86 %, n = 19/22) of CRKP carried metallo-β-lactamases, and only 9 % (n = 2/22) encoded OXA-48 carbapenemase. WGS of CRKP revealed that the predominant genotype is multilocus sequence type ST147 harboring blaNDM-5 and blaCTX-M-15.

CONCLUSION

The proportion of CRKP among all K. pneumoniae from bloodstream infection in Gaza Strip is high (40 %) and mainly associated with the blaNDM-5-positive high-risk clone ST147.

Virulence determinants in Klebsiella pneumoniae associated with septicaemia outbreaks in neonatal pigs

Klebsiella pneumoniae is recognized as an opportunistic pathogen in pigs causing pneumonia, mastitis and diarrhoea, but can also cause mortalities due to septicaemia and meningitis in previously healthy piglets. This study aimed to identify virulence genes present in K. pneumoniae that caused outbreaks of septicaemia in neonatal pigs. The genomes of thirty-eight Australian K. pneumoniae isolates from pigs with septicaemia, meningitis, myocarditis, pneumonia, enteritis and healthy cohorts were sequenced. The presence of antimicrobial resistance, siderophore and enhanced capsule production genes were identified by sequence analysis and verified by either PCR or phenotypic tests. An additional 52 international K. pneumoniae genomes from healthy and clinically affected pigs (28), humans (16), birds (3), one rodent and environmental isolates (4) were included in a pangenome analysis. Porcine septicaemic K. pneumoniae genomes from the UK and Australia clustered together and had higher virulence scores than all other clinical and non-clinical isolates. Septicaemic isolates were predominantly ST25, had enhanced capsule polysaccharide production with K2 capsule type and contained genes for the siderophores aerobactin, salmochelin and yersiniabactin. Septicaemic K. pneumoniae were more likely to have genes encoding the assembly of LPS, fimbriae and adhesins, and enzymes needed for the integration of mobile genetic elements. No single virulence gene was solely associated with isolates causing septicaemia. These findings indicate that there may be genotypes associated with clinical disease outcomes for K. pneumoniae. In the absence of some virulence genes, K. pneumoniae was still able to cause significant disease if the pig's immune system was immature or compromised.

Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.

An Unusual 'Gift' from Humans: Third-Generation Cephalosporin-Resistant Enterobacterales in migratory birds along the East Asian-Australasian Flyway

Migratory birds play a pivotal role in the global dissemination of antimicrobial resistance genes (ARGs), with shorebirds relying on coastal wetlands during their long-distance migrations, environments often contaminated and conducive to ARG transmission. However, systematic investigations into antimicrobial resistance (AMR) in shorebirds remain scarce. During spring and autumn of 2023, we collected 893 throat and cloacal swabs from 480 shorebirds, representing 28 species, at Chongming Dongtan, a critical stopover along the East Asian-Australasian Flyway. Our analysis identified six strains, including four extra-intestinal pathogenic E. coli (ExPEC) and two K. pneumoniae, that exhibited resistance to third-generation cephalosporins, with three ExPEC strains exhibiting significant virulence in Galleria mellonella infection assays. We identified two conjugative plasmids: E042113F_p1, carrying the blaCMY-2 gene in E. coli, and M50_p2, carrying the blaKPC-2 gene in a hypervirulent K. pneumoniae with a virulence plasmid harboring the aerobactin system. Bioinformatic and experimental analyses confirmed that these plasmids could transfer without any fitness cost, remaining stable for at least 30 passages. Surprisingly, genomic tracing revealed that among the plasmids similar to E042113F_p1 (blaCMY-2), the earliest was identified in a Chinese swallow in 2015, with subsequent detections in wild birds from Mongolia (2017), Russia (2018), and Australia (2019). Notably, these E04-CMY-like/M50-KPC-like plasmids predominantly originated from human sources, underscoring the pivotal role of human activity in the cross-species transmission of AMR. This human-mediated transmission of resistance elements into wildlife posed a substantial risk for amplifying and disseminating AMR through long-range migratory bird movements, highlighting the urgent need for international collaboration under a One Health framework. Integrated surveillance, environmental management, and stringent antibiotic stewardship are critical to mitigating the risks posed by migratory birds in amplifying and spreading AMR across ecosystems.

Global emergence of Carbapenem-resistant Hypervirulent Klebsiella pneumoniae driven by an IncFIIK34 KPC-2 plasmid

BACKGROUND

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) has been increasingly reported worldwide, posing a severe challenge to public health; however, the mechanisms driving its emergence and global dissemination remain unclear.

METHODS

We analysed CR-hvKp strains derived from canonical hvKp backgrounds, and acquired a carbapenemase-encoding gene. These strains were identified from 485 CRKp isolates in the CRACKLE-2 China cohort, 259 CRKp isolates from a multi-centre study, and 67,631 K. pneumoniae genomes available in GenBank. Clinical isolates harbouring the IncFIIK34 KPC-2 plasmid were selected for genome sequencing, RNA-Seq, conjugation assays, in vivo, ex vivo, and in vitro phenotypic characterisation.

FINDINGS

Analysis of clinical CR-hvKp isolates and the 414 genomes from 24 countries available in GenBank identified an IncFIIK34 KPC-2 plasmid as the prevalent KPC plasmid (detected in 25%, 45/178 of KPC-producing CR-hvKp). Compared with the epidemic IncFIIK2 KPC-2 plasmid, the IncFIIK34 KPC-2 plasmid exhibited a 100- to 1000-fold increase in conjugation frequency (10-4-10-5 vs. 10-7) and an in vitro growth advantage under meropenem challenge-likely due to the overexpression of conjugation-related genes and an increased blaKPC copy number and expression. CR-hvKp isolates and hvKp transconjugants carrying this plasmid often exhibited reduced mucoviscosity, while retaining hypervirulence in both murine models and human neutrophil assays.

INTERPRETATION

The IncFIIK34 plasmid may be a key factor driving the global dissemination of CR-hvKp, underscoring the urgent need for enhanced molecular surveillance of this emerging pathogen.

FUNDING

National Natural Science Foundation of China and National Institutes of Health.

Global dissemination of Klebsiella pneumoniae in surface waters: Genomic insights into drug resistance, virulence, and clinical relevance

The aquatic environment is a major pathway for the spread of antibiotic resistance (AR) among microorganisms. Among these, Klebsiella pneumoniae reveals high genome plasticity, adaptability, and the ability to colonize humans, animals, and the natural environment, awarding it a significant role in the spread of AR. This work presents an in-depth analysis of the whole sequences of 149 K. pneumoniae genomes isolated from surface waters available in databases. The sequences were obtained from 20 countries in five continents. The analyses showed a high genomic diversity of isolates, classifying them into 94 unique sequence types. The isolates carried numerous virulence and drug resistance determinants in their genomes, including genes for carbapenem and colistin resistance. The critical resistance genes were located on plasmids, indicating their high mobility and ease of access in water environments. Sublineage 258 members, in particular ST11, have been identified as important carriers of both important drug resistance determinants and key virulence factors, thus posing a substantial threat to human health. Our analysis revealed the direct transmission of drug-resistant and virulent clinical strains to the natural environment, highlighting the role of K. pneumoniae in the dissemination of drug resistance within the "One Health" framework. Surface waters represent an environment conducive to the spread and evolution of drug resistance, and K. pneumoniae plays a significant role in this process by providing clinically-significant antibiotic resistance genes to environmental recipients.

Characterization of a novel KPC-2 variant, KPC-228, conferring resistance to ceftazidime-avibactam in an ST11-KL64 hypervirulent Klebsiella pneumoniae

BACKGROUND

With the widespread clinical use of ceftazidime-avibactam (CZA), reports of resistance have increased continuously, posing immense threats to public health worldwide. In this study, we explored the underlying mechanisms leading to the development of CZA resistance in an ST11-KL64 hypervirulent Klebsiella pneumoniae CRE146 that harbored the blaKPC-228 gene.

METHODS

Twelve carbapenem-resistant Klebsiella pneumoniae (CRKP) strains were isolated from the same patient, including K. pneumoniae CRE146. Whole-genome sequencing (WGS), phylogenetic analysis, blaKPC gene cloning and pACYC-KPC construction assays were conducted to further explore the molecular mechanisms of CZA resistance. Quantitative siderophore production assay, string test, capsule quantification and Galleria mellonella in vivo infection model were applied to verify the level of pathogenicity of K. pneumoniae CRE146.

RESULTS

This strain carried key virulence factors, iutA-iucABCD operon and rmpA gene. Compared to the wild-type KPC-2 carbapenemase, the novel KPC-228 enzyme exhibited a deletion of four amino acids in the Ω-loop (del_167-170_ELNS). In addition, the emergence of CZA resistance appeared to be associated with drug exposure, and we observed the in vivo evolution of wild-type KPC-2 to KPC-228 and then the reversion to its original wild-type KPC-2. The blaKPC-228 gene was located within the double IS26 flanking the ISKpn6-blaKPC-228-ISKpn27 core structure and carried on an IncFII/IncR-type plasmid. Notably, CRE146 exhibited high-level resistance to CZA (64/4 mg/L) but increased susceptibility to meropenem (1 mg/L) and imipenem (0.5 mg/L) respectively. PACYC-KPC plasmids were constructed and expressed in K. pneumoniae ATCC13883. Compared to K. pneumoniae ATCC13883 harboring blaKPC-2, K. pneumoniae ATCC13883 harboring blaKPC-228 exhibited a high-level resistance to CZA (32/4 mg/L) and increased susceptibility to meropenem (1 mg/L) and imipenem (0.5 mg/L). Interestingly, K. pneumoniae ATCC13883 harboring blaKPC-228 showed a significant decrease in their resistance to all β-lactamases tested except CZA and ceftazidime.

CONCLUSIONS

In conclusion, we reported a novel KPC variant, KPC-228, in a clinical ST11-KL64 hypervirulent K. pneumoniae strain, which conferred CZA resistance, possibly through enhancing ceftazidime affinity and reducing avibactam binding. The blaKPC-228 can mutate back to blaKPC-2 under carbapenem pressure, which was very detrimental to clinical treatment. This strain carried both resistance and virulence genes, posing a major challenge in clinical management.

The results of polymerase chain reaction and MALDI-TOF mass spectrometry versus phenotypic distinction between Klebsiella pneumoniae and Klebsiella oxytoca

Introduction

Klebsiella pneumoniae and K. oxytoca are members of Enterobacteriaceae. They are Gram-negative, non-motile rods that are ubiquitous in the environment and part of the human intestinal microbiota. These opportunistic pathogens may cause pneumonia and urinary tract infections. Klebsiella species are genetically and biochemically similar; therefore, it is important to find reliable methods for their differentiation.

Methods

This study presents the results of biochemical assays, PCR, and MALDI-TOF mass spectrometry (MS) performed on 35 Klebsiella isolates obtained from the urine of patients from central Poland.

Results

Among biochemical methods, the indole test demonstrated the highest discriminatory power, whereas the determination of growth at 10°C was the least effective. For all strains biochemically identified as K. pneumoniae, a 108-bp amplicon was detected, indicating the presence of the rpoB gene in their genome. Only 12 K. oxytoca isolates produced a product of the pehX gene. All tested strains were analyzed using the MALDI-TOF Biotyper, which confirmed, with high-quality scores, their identification based on api 20E and indole tests. Strain 0.011 was identified as Raoultella ornithinolytica.

Conclusion

MALDI-TOF MS analysis proved to be the most reliable method for identifying K. oxytoca and K. pneumoniae, with the potential for phylogroup differentiation.

Surveillance and Genomic Characterisation of Colistin-Resistant Gram-Negative Bacteria in the Drains of High-Risk Hospital Units

OBJECTIVE

The health care water environment, including sinks and drainage systems, can be a long-term reservoir of nosocomial pathogens. In this study, we aimed to investigate the presence of colistin-resistant Gram-negative (ColR-GN) bacteria in humid compartments of high-risk hospital units at the University Medical Center Groningen, The Netherlands.

METHODS

Environmental sampling was conducted in sink and shower drains of high-risk hospital units, and colistin MICs were determined using broth microdilution. Whole-genome sequencing was performed to investigate the presence of mobile colistin resistance (mcr) genes, chromosomal point mutations and gene alterations linked to colistin resistance.

RESULTS

ColR-GN bacteria were detected in all investigated units, with Enterobacter spp. being the most abundant genus. Twelve isolates exhibited colistin resistance (MIC >2 mg/L), including Enterobacter cloacae complex (n = 11) and Klebsiella pneumoniae (n = 1). Chromosomal mutations in genes involved in lipopolysaccharide structure modifications were the main mechanisms contributing to colistin resistance in Enterobacter spp. and Klebsiella spp. (91.6%, 11/12). Additionally, two Enterobacter kobei isolates harboured mobile colistin resistance genes, mcr-4.3 and mcr-9.1.

CONCLUSIONS

The presence and persistence of bacterial ColR-GN clones in the sink and shower drains of high-risk hospital units highlights the importance of monitoring such environments for antibiotic-resistant bacteria to identify reservoirs and prevent further spread.

Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies

Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient sequence data for effective downstream analysis. CRISPR-Cas9 enrichment is designed to improve the yield of low abundance sequences but has not been thoroughly explored with Oxford Nanopore Technologies (ONT) for use in clinical bacterial epidemiology. We designed CRISPR-Cas9 guide RNAs to enrich the human pathogen Klebsiella pneumoniae, by targeting multi-locus sequence type (MLST) and transfer RNA (tRNA) genes, as well as common antimicrobial resistance (AMR) genes and the resistance-associated integron gene intI1. We validated enrichment performance in 20 K. pneumoniae isolates, finding that guides generated successful enrichment across all conserved sites except for one AMR gene in two isolates. Enrichment of MLST genes led to a correct allele call in all seven loci for 8 out of 10 isolates that had depth of 30× or more in these regions. We then compared enriched and unenriched sequencing of three human fecal samples spiked with K. pneumoniae at varying abundance. Enriched sequencing generated 56× and 11.3× the number of AMR and MLST reads, respectively, compared to unenriched sequencing, and required approximately one-third of the computational storage space. Targeting the intI1 gene often led to detection of 10-20 proximal resistance genes due to the long reads produced by ONT sequencing. We demonstrated that CRISPR-Cas9 enrichment combined with ONT sequencing enabled improved genomic characterization outcomes over unenriched sequencing of patient samples. This method could be used to inform infection control strategies by identifying patients colonized with high-risk strains.

IMPORTANCE

Understanding bacteria in complex samples can be challenging due to their low abundance, which often results in insufficient data for analysis. To improve the detection of harmful bacteria, we implemented a technique aimed at increasing the amount of data from target pathogens when combined with modern DNA sequencing technologies. Our technique uses CRISPR-Cas9 to target specific gene sequences in the bacterial pathogen Klebsiella pneumoniae and improve recovery from human stool samples. We found our enrichment method to significantly outperform traditional methods, generating far more data originating from our target genes. Additionally, we developed new computational techniques to further enhance the analysis, providing a thorough method for characterizing pathogens from complex biological samples.

Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh

Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.

Enhanced invasion and survival of antibiotic- resistant Klebsiella pneumoniae pathotypes in host cells and strain-specific replication in blood

Background

Klebsiella pneumoniae is one of the most important opportunistic pathogens causing healthcare-associated and community-acquired infections worldwide. In recent years, the increase in antibiotic resistance and infections caused by hypervirulent K. pneumoniae poses great public health concerns. In this study, host-pathogen interactions of different K. pneumoniae strains of human and animal origins were analyzed in microbiological, cell-biological and immunological experiments.

Methods

In vitro infection experiments using representatives of different K. pneumoniae pathotypes and various epithelial and macrophage cell lines were executed analyzing adhesion, invasion and intracellular replication. Experimental conditions involved normoxia and hypoxia. Furthermore, survival and growth of further K. pneumoniae isolates expressing defined siderophores in blood (platelet concentrates, serum) was investigated. All experiments were done in triplicate and statistically significant differences were determined.

Results

Significant differences in adhesion and invasion capability, phagocytosis resistance and intracellular replication were measured between different K. pneumoniae pathotypes. Especially, ESBL-producing K. pneumoniae isolates demonstrated increased invasion in host cell lines and survival in macrophages. A strong cytotoxic effect on intestinal cells was observed for hypervirulent K. pneumoniae. The results from our investigations of the growth behavior of K. pneumoniae in platelets and serum showed that siderophores and/or an enlarged capsule are not essential factors for the proliferation of (hypervirulent) K. pneumoniae strains in blood components.

Conclusion

Our in vitro experiments revealed new insights into the host-pathogen interactions of K. pneumoniae strains representing different pathovars and clonal lineages in different infectious contexts and hosts. While a clear limitation of our study is the limited strain set used for both infection and as potential host, the results are a further step for a better understanding of the pathogenicity of K. pneumoniae and its properties essential for different stages of colonization and infection. When developed further, these results may offer novel approaches for future therapeutics including novel "anti-virulence strategies".

Molecular epidemiology and genetic dynamics of carbapenem-resistant hypervirulent Klebsiella pneumoniae in China

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CRhvKP) poses a significant global health threat due to its enhanced virulence and resistance. This study analyzed 5,036 publicly available K. pneumoniae genomes from China (2005-2023), identifying 1,538 CRhvKP genomes, accounting for 44.6% of carbapenem-resistant isolates and 69.5% of hypervirulent isolates. Predominant carbapenemases included bla KPC (92.1%), with an increasing prevalence of bla NDM and bla OXA-48-like genes. Most isolates (93.6%) carried both aerobactin and yersiniabactin genes. The genetic background showed high diversity, characterized by 36 sequence types (STs) and 22 capsule types, with high-risk endemic STs such as ST11, ST15, and ST23 being predominant. ST23 demonstrated enhanced virulence, whereas ST11 carried more resistance genes but showed minimal presence of iroBCDN genes. A core genome MLST analysis revealed that 89.0% of CRhvKP isolates clustered into 131 clonal groups, indicating widespread dissemination, particularly in eastern China. CR and hv plasmids, primarily IncF, IncH, and IncR types, showed distinct community structures, with CR plasmids demonstrating higher mobility and diversity. Crucially, we identified 40 CR-hv convergent plasmids across five STs, likely resulting from plasmid fusions, which have become increasingly prevalent in eastern China over the last decade. Furthermore, chromosomal integration of hv genes and bla KPC-2 was detected, underscoring the stable inheritance of these traits. Class 1 Integrons were present in 84.5% of CRhvKP strains, most notably in ST11 and least in ST23. These integrons harbored genes that confer resistance to various antibiotics, including bla IMP and bla VIM, with their content varying across different STs. This study highlights the genetic complexity, rapid dissemination, and increasing prevalence of CRhvKP in China, emphasizing the urgent need for enhanced genomic surveillance and targeted interventions to mitigate the threat posed by these multidrug-resistant and hypervirulent strains.

Establishment and Application of Duplex Recombinase-Aided Amplification Combined with Lateral Flow Dipsticks for Rapid and Simultaneous Visual Detection of Klebsiella pneumoniae and Staphylococcus aureus in Milk

Staphylococcus aureus and Klebsiella pneumoniae are significant and prevalent pathogens associated with bovine mastitis on dairy farms worldwide, resulting in severe infections in both dairy cows and, subsequently, human beings. Fast and dependable pathogen diagnostics are essential to minimize the effects of cow mastitis and human infections. The aim of this research was to develop a duplex recombinase-aided amplification (RAA) combined with the lateral flow dipstick (LFD) method, which was used for rapid, simultaneous detection of S. aureus and K. pneumoniae. The SKII culture medium for S. aureus and K. pneumoniae cocultivation was developed in this study. By optimizing the duplex RAA-LFD reaction conditions in terms of primer concentration, amplification temperature, and reaction time, the duplex RAA-LFD assay could successfully detect S. aureus and K. pneumoniae when the reaction was conducted at 39 °C for 20 min. The duplex RAA-LFD method demonstrated good specificity, exhibiting no cross-reactivity with other pathogens. In addition, the detection limit of the duplex RAA-LFD for S. aureus and K. pneumoniae was 60 fg of genomic DNA and 1.78 × 103 and 2.46 × 103 CFU/mL of bacteria in pure culture. Moreover, the duplex RAA-LFD technique is capable of identifying S. aureus and K. pneumoniae in artificially spiked milk samples even at very low initial concentrations of 1.78 × 101 and 2.46 × 100 CFU/mL, respectively, after 6 h of enrichment. The result of the actual samples showed that the total concordance rate of the duplex RAA-LFD method with the biochemical identification method and PCR method could reach 92.98~98.25% with high consistency. The results of this study indicated that the duplex RAA-LFD assay, which is a precise, sensitive, and simple field testing technique, can be used to identify S. aureus and K. pneumoniae and is expected to be used for disease diagnosis.

Phage-mediated virulence loss and antimicrobial susceptibility in carbapenem-resistant Klebsiella pneumoniae

Bacteriophages, known for their ability to kill bacteria, are hampered in their effectiveness because bacteria are able to rapidly develop resistance, thereby posing a significant challenge for the efficacy of phage therapy. The impact of evolutionary trajectories on the long-term success of phage therapy remains largely unclear. Herein, we conducted evolutionary experiments, genomic analysis, and CRISPR-mediated gene editing, to illustrate the evolutionary trajectory occurring between phages and their hosts. Our results illustrate the ongoing "arms race" between a lytic phage and its host, a carbapenem-resistant Klebsiella pneumoniae clinical strain Kp2092, suggesting their respective evolutionary adaptations that shape the efficacy of phage therapy. Specifically, Kp2092 rapidly developed resistance to phages through mutations in a key phage receptor (galU) and bacterial membrane defenses such as LPS synthesis, however, this evolution coincides with unexpected benefits. Evolved bacterial clones not only exhibited increased sensitivity to clinically important antibiotics but also displayed a loss of virulence in an in-vivo model. In contrast, phages evolved under the selection pressure against Kp2092 mutants and exhibited enhanced bacterial killing potency, targeting mutations in phage tail proteins gp12 and gp17. These parallel evolutionary trajectories suggest a common genetic mechanism driving adaptation, ultimately favoring the efficacy of phage therapy. Overall, our findings highlight the potential of phages not only as agents for combating bacterial resistance, but also a driver of evolution outcomes that could lead to more favorable clinical outcomes in the treatment of multidrug resistance pathogens.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae represents one of the leading pathogens for infectious diseases. With traditional antibiotics often being ineffective, phage therapy has emerged as a promising alternative. However, phage predation imposes a strong evolutionary pressure on the rapid evolution of bacteria, challenging treatment efficacy. Our findings illustrate how co-evolution enhances phage lytic capabilities through accumulated mutations in the tail proteins gp12 and gp17, while simultaneously reducing bacterial virulence and antibiotic resistance. These insights advance our understanding of phage-host interactions in clinical settings, potentially inspiring new approaches akin to an "arms race" model to combat multidrug-resistant crises effectively.

Detection of CRISPR‒Cas and type I R-M systems in Klebsiella pneumoniae of human and animal origins and their relationship to antibiotic resistance and virulence

The clustered regularly interspaced short palindromic repeats (CRISPR)‒CRISPR-associated protein (Cas) and restriction‒modification (R-M) systems are important immune systems in bacteria. Information about the distributions of these two systems in Klebsiella pneumoniae from different hosts and their mutual effect on antibiotic resistance and virulence is still limited. In this study, the whole genomes of 520 strains of K. pneumoniae from GenBank, including 325 from humans and 195 from animals, were collected for CRISPR‒Cas systems and type I R-M systems, virulence genes, antibiotic resistance genes, and multilocus sequence typing detection. The results showed that host origin had no obvious influence on the distributions of the two systems (CRISPR‒Cas systems in 29.8% and 24.1%, type I R-M systems in 9.8% and 11.8% of human-origin and animal-origin strains, respectively) in K. pneumoniae. Identical spacer sequences from different hosts demonstrated there was a risk of human-animal transmission. All virulence genes (yersiniabactin, colibactin, aerobactin, salmochelin, rmpADC, and rmpA2) detection rates were higher when only the CRISPR‒Cas systems were present but were all reduced when coexisting with type I R-M systems. However, a lower prevalence of most antibiotic-resistance genes was found when the CRISPR‒Cas systems were alone, and when type I R-M systems were coexisting, some of the antibiotic resistance gene incidence rates were even lower (quinolones, macrolides, tetracyclines and carbapenems), and some of them were higher instead (aminoglycosides, clindamycins, rifampicin-associated, sulfonamides, methotrexates, beta-lactamases and ultrabroad-spectrum beta-lactamases). The synergistic and opposed effects of the two systems on virulence and antibiotic-resistance genes need further study.IMPORTANCEK. pneumoniae is an important opportunistic pathogen responsible for both human and animal infections, and the emergence of hypervirulent and multidrug-resistant K. pneumoniae has made it difficult to control this pathogen worldwide. Here, we find that CRISPR‒Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, have synergistic and opposed effects on virulence and antibiotic resistance genes in K. pneumoniae. Moreover, this study provides insights into the distributions of the two systems in K. pneumoniae from different hosts, and there is no significant difference in the prevalence of the two systems among K. pneumoniae spp. In addition, this study also characterizes the CRISPR arrays of K. pneumoniae from different hosts, suggesting that the strains sharing the same spacer sequences have the potential to spread between humans and animals.

Emerging carbapenem-resistant Klebsiella pneumoniae in a tertiary care hospital in Lima, Peru

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant public health threat, particularly in low- and middle-income countries (LMICs) with limited surveillance and treatment options. This study examines the genetic diversity, resistance patterns, and transmission dynamics of 66 CRKP isolates recovered over 5 years (2015-2019) after the first case of CRKP was identified at a tertiary care hospital in Lima, Peru. Our findings reveal a shift from blaKPC-2 to blaNDM-1 as the dominant carbapenemase gene after 2017. Lineage ST45 was the most prevalent and persisted for multiple years, followed by high-risk clones ST11 and ST147. The blaNDM-1 gene was carried almost exclusively by a Tn125-like transposon, similar to the one reported in previous studies from two Peruvian hospitals. Long-read sequencing revealed nearly identical blaNDM-carrying plasmids across the four assessed lineages. A comparative analysis of 1,023 South American CRKP genomes confirmed a unique pattern in Peru, where blaNDM-1 (81.4%) outpaced blaKPC-2, which remained dominant (59.4%) elsewhere. In addition, emerging clones ST45 and ST348 found in Peru were rarely found elsewhere in South America, suggesting potential regional adaptation. In conclusion, our study provides a comprehensive picture of the intra-hospital dynamics of these emerging pathogens and provides a framework for studying their genomic diversity in the understudied South American region.IMPORTANCEThis study provides novel insights into the transmission and genetic diversity of carbapenem-resistant Klebsiella pneumoniae, a bacteria responsible for severe infections, with limited treatment options. By examining isolates recovered over 5 years at a major hospital in Lima, Peru, we demonstrated a shift from one type of resistance gene, blaKPC, to another, blaNDM, which is more challenging to treat. Our findings reveal that specific bacterial lineages carrying the blaNDM gene in a specific plasmid are emerging in Peru, including well-known high-risk strains and others rarely found elsewhere in South America. This pattern highlights an urgent need for targeted surveillance and infection control as these strains pose a significant challenge to healthcare systems. Our study provides crucial data on Klebsiella pneumoniae in Peru, contributing to broader efforts to monitor and control antibiotic-resistant infections in South America and globally.

Emergence of mcr-8.1-bearing MDR-hypervirulent Klebsiella pneumoniae ST307

We report for the first time whole-genome sequencing of four multidrug-resistant sequence type (ST) 307 Klebsiella pneumoniae recovered from patients in two hospitals in Armenia. Comparative genomic analysis revealed that the isolates were closely related, with a maximum of 39 single nucleotide polymorphism (SNP) differences in the core genome. All Armenian isolates carried the integrative and conjugative element ICEKp4, which bears the yersiniabactin locus, and shared a common evolutionary origin, diverging around 2005 (95% CI: 1999 to 2011). Antibiotic susceptibility testing showed resistance to several antibiotics, including ampicillin, amoxicillin-clavulanic acid, cefepime, ceftazidime, norfloxacin, levofloxacin, and chloramphenicol. Specifically, isolates designated as ARM03 and ARM06 were resistant to piperacillin-tazobactam, ARM04 and ARM05 had intermediate resistance to both piperacillin-tazobactam and imipenem, and ARM03 showed intermediate resistance to amikacin. We further identified antimicrobial resistance (AMR) genes in four Armenian isolates, including blaOXA-1, blaTEM-1D, blaSHV-28, dfrA14, tet(A), sul2, qnrB1, aac(6´)-Ib-cr, strA, strB and the extended-spectrum β-lactamase gene blaCTX-M-15. Additionally, ARM03 and ARM06 also obtained dfrA5, sul1, sul3, cmlA1, mphA, aph3-Ia and the unique colistin resistance gene mcr-8.1, which was absent in all other publicly available ST307 isolates. These two isolates also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 had rmpA fragment). ARM04 and ARM05, as well as ARM03 and ARM06, had nearly identical AMR and virulence genes, along with similar plasmid replicon profiles, respectively. Our findings suggest that a transmission event occurred between the two hospitals in Armenia, likely facilitated by patients or community members, during which K. pneumoniae ST307 isolates acquired plasmids carrying AMR and virulence genes.IMPORTANCEMultidrug-resistant (MDR) Klebsiella pneumoniae sequence type (ST) 307 has emerged as a high-risk clone associated with hospital- and community-acquired infections, posing a major threat to global public health. We report in-depth comparative genomics analyses of K. pneumoniae ST307 isolates recovered from patients in Armenia. The unique colistin resistance gene mcr-8.1 identified in ARM03 and ARM06 was absent in all other ST307 isolates obtained from the publicly available data sets. ARM03 and ARM06 also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 possessed incomplete rmpA fragment). Our findings suggest that a transmission event has occurred between two hospitals in Armenia either through patients or community members. In addition, the Armenian isolates obtained plasmids carrying virulence and AMR genes during the transmission event. Our study emphasises the importance of genomic surveillance of this emerging MDR-hypervirulent pathogen to provide early interventions.

Carbapenemase-Producing Enterobacterales from Patients Arriving from Ukraine in Poland, March 2022-February 2023

INTRODUCTION

Despite a scarcity of data, before 2022 Ukraine was already considered a high-prevalence country for carbapenemase-producing Enterobacterales (CPE), and the situation has dramatically worsened during the full-scale war with Russia. The aim of this study was to analyse CPEs isolated in Poland from victims of war in Ukraine.

METHODS

The study included 65 CPE isolates from March 2022 till February 2023, recovered in 36 Polish medical centres from 57 patients arriving from Ukraine, differing largely by age and reason for hospitalisation. All isolates were sequenced by MiSeq and ten Klebsiella pneumoniae isolates also by MinION. Taxonomy, clonality and resistomes were analysed for all CPEs, whereas phylogeny, serotypes, virulomes and plasmids were characterised for K. pneumoniae, and partially for Escherichia coli ST131, using various bioinformatic tools.

RESULTS

Multifactorial diversity of the isolates reflected the patients' clinical-epidemiological heterogeneity. The CPEs represented six species. Klebsiella pneumoniae was the most prevalent with 50 isolates and 15 sequence types (STs), mainly ST395, ST307, ST11, ST147 and ST23, producing NDM (-1/-5), OXA-48 (-48/-1242) or KPC (-2/-3)-like carbapenemases. Each of the STs produced groups of loosely related isolates, clusters of close relatives and/or unique isolates, correlating with K serotypes and carbapenemases. Many of these, especially NDM-1- and/or OXA-48-producing ST395 and ST307, were related to Russian organisms. Others, for example, NDM-1-producing ST11, clustered with those from Poland. Numerous K. pneumoniae isolates had specific virulence genes, including aerobactin iuc, largely due to spread of pNDM-MAR plasmids, showing both resistance and virulence. Two E. coli ST131 isolates belonged to clades B or C1 and produced KPC-3 or NDM-1, respectively.

CONCLUSIONS

Together with similar studies from Germany and The Netherlands, this work has documented broad dissemination of CPE in Ukraine, driven by a number of specific K. pneumoniae lineages circulating over a large territory of Eastern Europe.

In vitro antimicrobial activity of six novel β-lactam and β-lactamase inhibitor combinations and cefiderocol against NDM-producing Enterobacterales in China

INTRODUCTION

To date, the global prevalence of New Delhi metallo-β-lactamase (NDM) in carbapenem-resistant Enterobacterales (CRE) has been of concern, which is not inhibited by classical β-lactamase inhibitors (BLIs). In this study, we investigated the newly developed antimicrobial agents or inhibitors against NDM-producing Enterobacterales (NPEs).

METHODS

The in vitro activities of cefiderocol, cefepime/taniborbactam, meropenem/taniborbactam, cefepime/zidebactam, meropenem/nacubactam, aztreonam/nacubactam and aztreonam/avibactam were analyzed in 204 NPE strains collected in China. The potential resistance mechanisms were identified by whole genome sequencing.

RESULTS

Of 204 NPE strains, 18.1% (37/204) were resistant to cefiderocol, in which cirA deleterious alteration, PBP3 insertion and NDM production were taken as potential resistance mechanisms; 28.9% (59/204) were resistant to cefepime/zidebactam, involving K. pneumoniae with ompK35 deleterious alteration; 22.5% (46/204) were resistant to cefepime/taniborbactam, in which YRIN or YRIK inserted in PBP3 and altered ompC are more frequently detected in the resistant E. coli isolates; 27.9% (57/204) were resistant to meropenem/taniborbactam. Aztreonam/avibactam and aztreonam/nacubactam exhibited excellent activity against NPE. However, meropenem/nacubactam had the lowest activity, with only 49.0% (100/204) of all isolates having MICs of <4/4 mg/L.

CONCLUSIONS

Aztreonam/avibactam and aztreonam/nacubactam showed the highest activity against NPE. The potential resistance mechanisms of novel antimicrobial agents against NPE should be under active surveillance.

The pivotal role of IncFIB(Mar) plasmid in the emergence and spread of hypervirulent carbapenem-resistant Klebsiella pneumoniae

The hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) poses a substantial challenge to the global health care. However, the mechanism behind its evolution and transmission remain elusive. Here, four virulence plasmid types were identified from 310 hv-CRKP isolates collected nationwide during 2017-2018, based on their aerobactin (iuc locus) lineage and IncFIB replicons. Notably, pIUC1-IncFIB(K)37 and pIUC1-IncFIB(Mar), representing two epidemic virulence plasmids in Asia and Europe, respectively, accounted for >90% of the hv-CRKP episodes. Analysis of 494 K. pneumoniae isolates (376 from 2010-2013; 118 from 2017-2018) and 2578 public K. pneumoniae genomes indicated the notable role of IncFIB(Mar) plasmids in the hv-CRKP emergence and spread. Conjugation assays showed the helper IncFIB(Mar) plasmid could efficiently transfer into a hypervirulent strain and uniquely retromobilize with pIUC1-IncFIB(K)37 back into CRKP. Thereafter, the IncFIB(Mar) plasmid either lost rapidly or recombined with pIUC1-IncFIB(K)37, generating the hybrid pIUC1-IncFIB(Mar) plasmid. Our findings elucidated formation, evolution, and dissemination trajectories of the two major hv-CRKP strains in different regions.