Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395

Genomic analysis of carbapenemase-encoding plasmids and antibiotic resistance in carbapenem-resistant Klebsiella pneumoniae isolates from Vietnam, 2021

Carbapenem resistance in gram-negative rods is increasing in low- and middle-income countries. We conducted a single-center study to identify carbapenemase-encoding plasmids in carbapenem-resistant Klebsiella pneumoniae isolates causing human infections in Vietnam. The secondary objective was to investigate the prevalence of multidrug-resistant (MDR) and hypervirulent K. pneumoniae in this setting. Our genomic analysis study characterized 105 of 245 clinical K. pneumoniae isolates at the 108 Military Hospital in Hanoi, Vietnam, collected from intensive care unit and regular wards between 1 January 2021 and 31 December 2021. All isolates were characterized using long- and short-read sequencing, followed by hybrid assembly. Comprehensive genomic analysis was performed to identify carbapenemase-encoding plasmids, complemented by extended antibiotic susceptibility testing for commonly used and novel antibiotics. We observed a high prevalence of NDM-4-related carbapenem resistance (30.5%, 32/105) mostly carried by a specific 83-kb IncFII plasmid co-carrying the blaTEM-1 (46.9%, 15/32). The genomic content of the blaNDM-4-harboring plasmids is highly variable. While blaOXA-181 and blaOXA-48 were predominantly located on an IncX3 and an IncL plasmid, respectively, the majority of plasmids harboring blaKPC-2 were not related to any named Inc-type. All isolates exhibited the MDR phenotype; however, the majority remained susceptible to the siderophore-cephalosporin cefiderocol (79%, 83/105). All isolates were susceptible to aztreonam/avibactam. In addition, we identified a hypervirulent, carbapenem-resistant K. pneumoniae ST23 strain, confirmed through both in vitro and in vivo experiments. Our study provides insights into plasmids harboring the carbapenemases New Delhi metallo-β-lactamase, oxacillinase-48 like, and K. pneumoniae carbapenemase-2 circulating in Vietnam.IMPORTANCECarbapenem resistance in Klebsiella pneumoniae is a major public health threat, especially in low- and middle-income countries. This study examined resistant strains from a hospital in Vietnam to understand how they spread and which antibiotics might still work. We found that a significant number of these bacteria carried resistance genes on different types of plasmids. Despite their resistance to many antibiotics, most strains remained susceptible to newer substances like cefiderocol and aztreonam/avibactam. Alarmingly, we also identified a hypervirulent strain that is carbapenem resistant, potentially posing an even greater risk to patients. This research provides insight into the epidemiology of the carbapenemase gene-harboring plasmids in a Vietnamese hospital. Understanding these resistance patterns can help guide antibiotic use and policy decisions to combat the growing threat of multidrug-resistant infections in Vietnam.

Transmission dynamics of multidrug resistant Klebsiella pneumoniae from an Indian hospital

OBJECT

The dissemination of Klebsiella pneumoniae is becoming a major concern, as this organism is responsible for a significant proportion of hospital acquired infections. Due to complexity of this organism adequate knowledge on the epidemiology and infection control practices associated with the dissemination is highly required. Therefore, this study designed to include consecutive samples from environment and patients to assess the similarity pattern among isolates from different sources.

METHODOLOGY

We included patients with hospital acquired infections with K. pneumonaie and environment isolates. To obtain the complete sequence forty-eight isolates were sequenced on Illumina MiSeq 250 2 × 250 bp paired end (Illumina, USA) and Nanopore (Oxford). These includes 30 BSI cases, 13 environment and 5 from water. Assembly of good quality reads were prepared using Unicycler. AMR gene detection was done using Resfinder of Abricate and sequence similarity was observed by SNP based phylogenetic analysis.

RESULTS

The most common sequence type of organism among all was ST 231 and ST 395. ST 29 was common between water and clinical isolates. Average (range) number of AMR genes present in clinical isolates were 16 (3-24). The antimicrobial genes belong to 41 classes and fosA was highly prevalent. The frequency of blaNDM was present 55.4 % (27/48) and blaOXA in 61.6 % (30/48). The strain ST 395 and ST 16 carried highest no. of replicons n = 10 and n = 9. The predominant plasmid replicon Col440I (N = 58) followed by IncFII_1_pKP91 (N = 34) and ColRNAI (N = 29). The phylogenetic analysis showed high similarity between clinical and environmental samples.

CONCLUSION

This study concludes that environment play essential role in disseminating the infectious strains of organism resulting in increased rates of hospital acquired infections. Therefore, there is an imperative necessity for implementing infection control practices to prevent the spread of infectious diseases.

The Klebsiella pneumoniae tellurium resistance gene terC contributes to both tellurite and zinc resistance

Klebsiella pneumoniae is widely recognized as a pathogen responsible for hospital-acquired infections and community-acquired invasive infections. It has rapidly become a significant global public health threat due to the emergence of hypervirulent and multidrug-resistant strains, which have increased the challenges associated with treating life-threatening infections. Tellurium resistance genes are widespread on virulence plasmids in K. pneumoniae isolates. However, the core function of the ter operon (terZABCDEF) in K. pneumoniae remains unclear. In this study, the multidrug-resistant K. pneumoniae P1927 strain was isolated from the sputum of a hospitalized pneumonia patient. The ter operon, along with antimicrobial resistance and virulence genes, was identified on a large hybrid plasmid in K. pneumoniae P1927. We generated a terC deletion mutant and demonstrated that this mutant exhibited reduced virulence in a Galleria mellonella larva infection model. Further physiological functional analysis revealed that terC is not only important for Te(IV) resistance but also for resistance to Zn(II), Mn(II), and phage infection. All genes of the ter operon were highly inducible by Zn(II), which is a stronger inducer than Te(IV), and the terBCDE genes were also induced by Mn(II). Collectively, our study demonstrates novel physiological functions of TerC in Zn(II) resistance and virulence in K. pneumoniae.IMPORTANCEKlebsiella pneumoniae has rapidly become a global threat to public health. Although the ter operon is widely identified in clinical isolates, its physiological function remains unclear. It has been proposed that proteins encoded by the ter operon form a multi-site metal-binding complex, but its exact function is still unknown. TerC, a central component of the tellurium resistance determinant, was previously shown to interact with outer membrane proteins OmpA and KpsD in Escherichia coli, suggesting potential changes in outer membrane structure and properties. Here, we report that TerC confers resistance to Zn(II), Mn(II), and phage infection, and Zn(II) was shown to be a strong inducer of the ter operon. Furthermore, TerC was identified as a novel virulence factor. Taken together, our results expand our understanding of the physiological functions encoded by the ter operon and its role in the virulence of K. pneumoniae, providing deeper insights into the link between heavy metal(loid) resistance determinants and virulence in pathogenic bacteria.

New insights and perspectives on the virulence of hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae, a Gram-negative bacterium, comprises strains with diverse virulence potentials, ranging from classical to hypervirulent variants. Understanding the genetic basis underlying the virulence disparities between hypervirulent (hvKp) and classical K. pneumoniae (cKp) strains is crucial. hvKp strains are characterized by hypermucoviscosity, attributed to the presence of specific virulence genes and the production of molecules that aid in their ability to survive, evade host immune defenses, and cause infection. In contrast, classical strains exhibit a broader array of antimicrobial resistance determinants, conferring resistance to multiple antibiotics. Although current definitions of hvKp incorporate clinical features, phenotypes, and genotypes, identifying hvKp strains in clinical settings remains challenging. Genomic studies have been pivotal and have helped to identify distinct genetic profiles in hvKp strains, including unique virulence plasmids and chromosomal variations, underscoring the genetic diversity within K. pneumoniae populations. This review examines the virulence and genetic determinants associated with hvKp. The presence of genes defining hypervirulence, alongside considerations of their utility as biomarkers and targets for therapeutic strategies, is discussed, while also providing insight into biofilm formation by hvKp and key questions that need urgent responses in understanding hvKp.

Development of a lytic bacteriophage BPK01 impregnated biopolymer (chitosan) hydrogel for combating high-risk strains of carbapenem resistant Klebsiella pneumoniae (CRKP) pathogens- in vitro and in vivo evaluation

Alternative strategies are urgently required to combat the rise of high-risk carbapenem-resistant Klebsiella pneumoniae (CRKP), including blaNDM-positive strains that produce carbapenemase enzymes, which deactivate beta-lactam antibiotics and result in poor treatment outcomes. In this study, we isolated a bacteriophage BPK01, targeting a high-risk strain of Klebsiella pneumoniae (carbapenem-resistant, blaNDM-positive, ST147, capsular type K64, biofilm former). BPK01 demonstrated strong lytic activity (84%) against a panel of genetically characterized CRKP strains (n = 59) from clinical specimens, including pus, urine, sputum, blood, and tracheal aspirates. BPK01 was classified as a Caudoviricetes phage, exhibiting a burst size of 220 virions and a short latent period of 10 min. It demonstrated stability across a range of conditions (temperature, pH, and organic solvents) and effectively disrupted biofilms on silicone catheters. In vivo, BPK01 improved survival rates in the Galleria mellonella infection model and reduced bacterial burden in a murine bacteremia model, underscoring its therapeutic potential. Subsequently, we developed a hydrogel by incorporating BPK01 into a chitosan biopolymer, which demonstrated efficient lytic activity (spot assay, scanning electron microscopy, time kill assay) against CRKP pathogens, stability of biological activity for 6 months of storage, and controlled release kinetics, with the mathematical model Korsmeyer - Peppas being the best fit (R2 = 0.9962). The hydrogel expedited the healing of CRKP-infected lesions in a murine model, suggesting its potential as an effective topical treatment. This study highlights BPK01 as a promising biotherapeutic candidate for treating CRKP infection, with the phage hydrogel offering an ecofriendly and sustainable solution for treating infected lesions. Further research could expand its use in phage cocktails and other formulations for broader CRKP infection management.

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.

Molecular Epidemiology and In-Depth Characterization of Klebsiella pneumoniae Clinical Isolates from Armenia

The global dissemination of Klebsiella pneumoniae pathotypes with multidrug-resistant (MDR) and hypervirulent traits poses a threat to public health. The situation in Armenia is unclear, and we performed a comprehensive characterisation of 48 clinical isolates of K. pneumoniae, collected from 2018 to 2024. The majority of the isolates (64.58%) were extensively drug-resistant (XDR) and MDR. Genomic analysis of 21 isolates revealed the presence of international high-risk MDR clones (ST395, ST15, and ST307). The ST395 strains were isolated from children and resisted the first-line drugs such as beta-lactams. These isolates harboured a range of virulence determinants, from capsule polysaccharides to siderophores to regulators of the mucoid phenotype. The ST395 strains are enriched by ICEs, plasmids, and prophages, on which antimicrobial resistance (AMR) and virulence genes are located and which may lead to the convergence of MDR and hypervirulent traits. There is a widespread non-specific AMR mechanism among our K. pneumoniae strains. These are mutations in the porin genes, which reduce permeability to antimicrobials, and mutations in the regulators of efflux pumps, which lead to overexpression of drug efflux pumps such as AcrAB. These mechanisms may contribute to the elevated MICs and confer AMR to strains with no specific AMR genes.

Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Klebsiella pneumoniae

BACKGROUND

The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the 'global clones of high risk'. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is more and more often used for these purposes, including the epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations.

DESCRIPTION

In this database, we provide the results of a thorough genomic analysis of 61,857 genomes of a highly dangerous bacterial pathogen Klebsiella pneumoniae. Important isolate typing information including multilocus sequence typing (MLST) types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, the presence of CRISPR-Cas systems, and cgMLST profiles are given, and the information regarding the presence of AMR, virulence genes and plasmid replicons within the genomes is provided.

CONCLUSION

This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.11069018 . The database will facilitate selection of the proper reference isolate sets for any types of genome-based investigations. It will be helpful for investigations in the field of K. pneumoniae genomic epidemiology, as well as antimicrobial resistance analysis and the development of prevention measures against this important pathogen.

Sequencing Analysis of Invasive Carbapenem-Resistant Klebsiella pneumoniae Isolates Secondary to Gastrointestinal Colonization

Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient's management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and immunocompromised patients. We described a six-month routine screening protocol from the Policlinico of Catania (Italy), while blood samples were collected from the same patients only in cases of a systemic infection suspicion. All the patients who had dissemination episodes were furtherly investigated through next-generation sequencing, analyzing both colonizing and disseminating strains. This study documents emerging invasive sequence types such as ST101, ST307, and ST395, mainly revealing blaNDM or blaKPC genes, along with siderophores and hyperproduction capsule markers as virulence factors. Most of the detected factors are presumably related to a specific plasmid content, which are extremely varied and rich. In conclusion, active surveillance through sequencing is essential to enhance awareness of local epidemiology within high-risk multi-drug resistance areas. A random sequencing analysis on the most warning microorganisms could enhance sequence typing (ST) awareness within specific settings, allowing for better prevention control strategies on their eventual persistence or diffusion.

High-Risk Lineages of Hybrid Plasmids Carrying Virulence and Carbapenemase Genes

Background/Objectives: Carbapenem-resistant Enterobacterales (CRE) are a global health threat due to their high morbidity and mortality rates and limited treatment options. This study examines the plasmid-mediated transmission of virulence and antibiotic resistance determinants in carbapenem-resistant Klebsiella pneumoniae (Kpn) and Escherichia coli (E. coli) isolated from Russian hospitals. Methods: We performed short- and long-read whole-genome sequencing of 53 clinical isolates (48 Kpn and 5 E. coli) attributed to 15 genetic lineages and collected from 21 hospitals across nine Russian cities between 2016 and 2022. Results: The plasmid analysis identified 18 clusters that showed high concordance with replicon typing, with all clusters having a major replicon type. The majority of plasmids in the IncHI1B(pNDM-MAR)/IncFIB(pNDM-Mar)-like cluster (79.16%) carried both antibiotic resistance genes (e.g., blaNDM-1 and blaOXA-48) and virulence factors (VFs) such as siderophore genes. We hypothesized that hybrid plasmids could play a critical role in the dissemination of antibiotic resistance genes and VFs. Comparative analyses with global plasmid databases revealed high-risk lineages of hybrid plasmids that are predominantly spread throughout Russia at present. Conclusions: Our findings underscore the importance of monitoring plasmid backbones for clinical management, surveillance, and infection control activities.

Cell-free supernatant of Lactobacillus gasseri 1A-TV shows a promising activity to eradicate carbapenem-resistant Klebsiella pneumoniae colonization

Background

The use of beneficial bacteria like Lactobacillus spp. is a potential innovative approach to fight antibiotic-resistant pathogens. Klebsiella pneumoniae is one of the most concerning multi drug-resistant (MDR) pathogens, and its ability to colonize the human gut is considered to be the main reason for recurrent infections in critically ill patients.

Methods

In this study, Lactobacillus gasseri 1A-TV, already described for its probiotic activity, was characterized at the genomic level. Moreover, its cell-free supernatant (CFS) was tested for antimicrobial activity against extended-spectrum β-lactamase (ESBL)- and carbapenemase (KPC)-producing K. pneumoniae clinical isolates.

Results

Whole-genome sequencing showed that the L. gasseri 1A-TV genome was of 2,018,898 bp in size with 34.9% GC content, containing 1,937 putative protein coding sequences, 55 tRNA, and 4 rRNA detected by RAST and classified in 20 functional groups by Cluster of Orthologous Genes (COG). BAGEL4 (BActeriocin GEnome minimal tooL) and the antiSMASH 7.0 pipeline identified two bacteriocin biosynthetic gene clusters (BBGCs), namely, BBGC1 that comprises two class IIc bacteriocins including gassericin A-like bacteriocin, and BBGC2 carrying the class III bacteriocin helveticin J. Strikingly, 1A-TV CFS inhibited the growth of all K. pneumoniae isolates only after 8 h of incubation, showing a bactericidal effect at 24 h and interfering, even at lower concentrations, with the biofilm production of biofilm-producer strains independently of a bactericidal effect. NMR analysis of CFS identified and quantified several metabolites involved in carbohydrate metabolism and amino acid metabolism, and organic acids like ethanol, lactate, acetate, and succinate. Finally, in vitro assays of 1A-TV showed significant co-aggregation effects against carbapenem-resistant K. pneumoniae, namely, strains 1, 2, 3, and 7.

Conclusions

Our findings highlight the antimicrobial activity of 1A-TV as a probiotic candidate or its CFS as a natural bioproduct active against MDR K. pneumoniae strains, underlining the importance of novel therapeutic strategies for prevention and control of ESBL- and carbapenemase-producing K. pneumoniae colonization.

Synergy of bacteriophage depolymerase with host immunity rescues sepsis mice infected with hypervirulent Klebsiella pneumoniae of capsule type K2

The hypervirulent Klebsiella pneumoniae (hvKp) with K1 and K2 capsular types causes liver abscess, pneumonia, sepsis, and invasive infections with high lethality. The presence of capsular polysaccharide (CPS) resists phagocytic engulfment and contributes to excessive inflammatory responses. Bacteriophage depolymerases can specifically target bacterial CPS, neutralizing its defense. Based on our previous research, we expressed and purified a bacteriophage depolymerase (Dep1979) targeting hvKp with capsule type K2. Interestingly, although Dep1979 lacked direct bactericidal activity in vitro, it exhibited potent antibacterial activity in vivo. Low-dose Dep1979 (0.1 mg/kg) improved the 7-day survival of immunocompetent mice to 100%. Even at 0.01 mg/kg, mice achieved 100% survival at 5 days, although efficacy sharply declined at doses as low as 0.001 mg/kg. Following Dep1979 treatment, reduced expression of inflammatory factors and no apparent tissue damage were observed. However, therapeutic efficacy significantly diminished in immunosuppressed mice. These findings underscore the critical role of Dep1979 in disarming CPS, which synergizes with host immunity to enhance antibacterial activity against hvKp.

An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic

BACKGROUND

Klebsiella pneumoniae (Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus.

METHODS

To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic.

FINDINGS

The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %).

INTERPRETATION

The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.

Characterization of four novel bacteriophages targeting multi-drug resistant Klebsiella pneumoniae strains of sequence type 147 and 307

The global dissemination of multi-drug resistant (MDR) pathogenic bacteria requires the rapid research and development of alternative therapies that can support or replace conventional antibiotics. Among MDR pathogens, carbapenem-resistant Klebsiella pneumoniae (CR-Kp) are of particular concern due to their extensive resistance profiles, global dissemination in hospital environments, and their major role in some life-threatening infections. Phages, or some of their components, are recognized as one of the potential alternatives that might be helpful to treat bacterial infections. In this study, we have isolated and characterized four lytic bacteriophages targeting K. pneumoniae strains of Sequence Type (ST) 307 or ST147, two predominant high-risk clones of CR-Kp. Phages, designated vB_KpS_GP-1, vB_KpP_GP-2, vB_KpP_GP-4, and vB_KpP_GP-5, were isolated from sewage wastewater samples. The vB_KpS_GP-1 phage was a siphovirus unable to establish lysogeny with its host, while the other three were podoviruses. While 85.7% of K. pneumoniae strains of ST307 were selectively lysed by the phages vB_KpS_GP-1 or vB_KpP_GP-5, the other two phages were able to lyse all the tested strains of ST147 (n = 12). Phages were stable over a broad pH and temperature range and were characterized by burst sizes of 10-100 plaque forming units and latency periods of 10-50 minutes. Genome sequencing confirmed the absence of antibiotic resistance genes, virulence factors or toxins and revealed that two phages were likely members of new genera. Given their strictly lytic nature and high selectivity towards two of the major high-risk clones of K. pneumoniae, cocktails of these phages could represent promising candidates for further evaluation in in vivo experimental models of K. pneumoniae infection.

Whole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador

BACKGROUND

Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador.

RESULTS

The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador.

CONCLUSIONS

Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.

Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness

The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.

In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion

Non-carbapenemase-producing carbapenem-resistant Enterobacterales (non-CP CRE) may be associated with a grave outcome. The common underlying mechanism is beta-lactamases and mutations in outer membrane porins. We report a case of a deep-seated infection caused by Klebsiella pneumoniae ST395 not amenable to source control, involving recurrent bloodstream infection, resulting in in vivo selection of carbapenem resistance under therapy. Three consecutive K. pneumoniae blood isolates were studied using short- and long-read sequencing. The genomes were subject to resistome and virulome, phylogenetic, and plasmid analyses. ompK36 porins were analyzed at the nucleotide and amino acid levels. Genomes were compared to 297 public ST395 K. pneumoniae genomes using cgMLST, resistome, and porin analyses and the EuSCAPE project. Relevant ompK36 and micF sequences were extracted and analyzed as above. The three sequential K. pneumoniae blood isolates belonged to the same clone. Subsequent CR isolates revealed a new large deletion of the ompK36 gene also involving the upstream region (deletion of micF). Comparison with public ST395 genomes revealed the study isolates belonged to clade B, representing a separate clone. N-terminal large ompK36 truncations were uncommon in both public data sets. In vivo selection of non-CP CRE K. pneumoniae could have substantial clinical implications. Such selection should be scrutinized through repeated cultures and frequent susceptibility testing during antimicrobial treatment, especially in the context of persistent or recurrent bloodstream infections and when adequate source control cannot be achieved. The occurrence of an unusually large deletion involving the ompK36 locus and upstream micF should be further studied.

Genomic Profile of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from a Urine Specimen

Klebsiella pneumoniae is an opportunistic pathogen mostly found in health care-associated infections but can also be associated with community-acquired infections and is in critical need of new antimicrobial agents for strains resistant to carbapenems. The prevalence of carbapenemase-encoding genes varies among studies. Multidrug-resistant K. pneumoniae strains can harbor several antimicrobial-resistant determinants and mobile genetic elements (MGEs), along with virulence genetic determinants in community settings. We aim to determine the genetic profile of a multidrug-resistant K. pneumoniae strain isolated from a patient with community-acquired UTI. We isolated a K. pneumoniae strain UABC-Str0120, from a urine sample of community-acquired urinary tract infection. Antimicrobial susceptibility tests and Whole-genome sequencing (WGS) were performed. The phylogenetic relationship was inferred by SNPs calling and filtering. UABC-Str0120 showed resistance toward β-lactams, combinations with β-lactamase inhibitors, and carbapenems. WGS revealed the presence of genes conferring resistance to aminoglycosides, β-lactams, carbapenems, quinolones, sulfonamides, phosphonates, phenicols, and quaternary ammonium compounds, 77 subsystems of virulence genes were identified, and an uncommon sequence type ST5889 was also determined. The sequenced strain harbors several MGEs. The UABC-Str0120 recovered from a urine sample harbors several virulence and antimicrobial resistance determinants, which assembles an endangering combination for an immunocompromised or a seemly healthy host, given its presence in a community setting.

Phenotypic and genomic analysis of bacteria from war wounds in Dnipro, Ukraine

Objectives

To better understand the source and potential transmission routes of antibiotic-resistant bacteria infecting injured service members in Ukraine.

Methods

Phenotypic and genomic characterizations were performed on 11 Gram-negative pathogens cultured from war wounds at an intermediate evacuation hospital in Dnipro.

Results

The analysis revealed both susceptible and extensively drug-resistant strains present in cultures, including high-risk global clones carrying carbapenemases.

Conclusions

Globally distributed carbapenemase-producing lineages are being acquired early in the medical evacuation process.

Emergence of OXA-48-producing Klebsiella pneumoniae in Lithuania, 2023: a multi-cluster, multi-hospital outbreak

In 2023, an increase of OXA-48-producing Klebsiella pneumoniae was noticed by the Lithuanian National Public Health Surveillance Laboratory. Whole genome sequencing (WGS) of 106 OXA-48-producing K. pneumoniae isolates revealed three distinct clusters of carbapenemase-producing K. pneumoniae high-risk clones, including sequence type (ST) 45 (n = 35 isolates), ST392 (n = 32) and ST395 (n = 28), involving six, six and nine hospitals in different regions, respectively. These results enabled targeted investigation and control, and underscore the value of national WGS-based surveillance for antimicrobial resistance.

Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany

BACKGROUND

Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany.

METHODS

A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared.

RESULTS

WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains.

CONCLUSIONS

Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.

The molecular detection of carbapenem markers with a two-levels amplification screening protocol: epidemiological and resistome insights

Objectives

Carbapenem-resistance is a challenging healthcare concern and require specific stewardship programs. Monitoring workflows include the identification from surveillance samples, such as rectal swabs. Although culture assays represent the gold standard, data report a significant effectiveness in detecting carbapenemases genes directly from rectal swabs. The aim of this study was to evaluate the REALQUALITY Carba-Screen kit (AB ANALITICA, Padova, Italy) in detecting carbapenemases genes directly from rectal swabs, also comparing its effectiveness to culture assays results. A next-generation sequencing (NGS) was performed to investigate the positive samples about resistance markers and sequence type (ST).

Methods

A number of 136 rectal swabs were collected from the University Hospital Policlinico of Catania critical wards. The samples simultaneously underwent culture and molecular assays (REALQUALITY Carba-Screen kit). The molecular method included two-steps. The first step (1 h and 6 min) rapidly excluded negative samples, while the second one (1 h and 6 min) included only positive samples for a resistance confirmation. All the positive culture samples underwent NGS analysis.

Results

Statistical evaluations demonstrated high sensitivity (100%) and detection rates (92.6%) for the REALQUALITY Carba-Screen kit, which mostly correlated to the standard workflow. All the culture positive results matched the positive molecular results, which were mainly confirmed by the NGS resistome analysis. The identified ST appeared to be diversified and different from the clinically significative strains of the same setting, furnishing interesting epidemiological evidence.

Conclusion

The molecular detection allowed a coordinate approach in a high-prevalence multi-drug-resistance area. The rapid identification with a multi-step procedure accelerated the infection control procedures, while the preliminary negative results reduced the overtreatment episodes. The molecular method efficacy was confirmed through the NGS. In conclusion, the molecular screening could initially lead to a more conservative approach, which may be reevaluated after a culture result about the microorganisms' identification and susceptibility profile.

Should multidrug resistant Klebsiella pneumoniae strains displaying hypervirulent traits be reclassified as either ultravirulent or supervirulent?

Historically, Klebsiella pneumoniae isolates were described either as hypervirulent or classical. While hypervirulent strains display a precise phenotype (thicker capsule, hypermucoviscosity, absence of antibiotic resistance markers, several siderophores, etc.), classical strains can relate to all other K. pneumoniae strains, including virulent multidrug-resistant clinical isolates. Recently, many surveillance studies reported virulent K. pneumoniae nosocomial strains resistant to all antibiotic classes which also contain genetic markers associated with hypervirulence. Due to their higher virulence and clinical importance, here it is proposed reclassify them as ultravirulent and as supervirulent, to distinguish them from each other and from those with either hypervirulent or virulent phenotypes.

Phenotypic and molecular characterization of beta-lactam resistant Multidrug-resistant Enterobacterales isolated from patients attending six hospitals in Northern Nigeria

Infections caused by multi-drug resistant Enterobacterales (MDR-E) are difficult to treat and cause significant mortality, especially in developing countries. This study characterized the phenotypic and genotypic profiles of 49 randomly selected beta-lactam resistant MDR-E previously isolated from patients being managed in hospitals in Nigeria using whole genome sequencing. The study isolates exhibited 85.5% resistance to 3rd generation cephalosporins and 65.3% resistance to carbapenems. The bla_TEM-1B (29, 59.2%)_, bla_CTX-M-15 (38, 77.6%)_, and bla_NDM-1 (17, 51.5%) were the most common penicillinase, ESBL, and carbapenem resistant genes across isolates, respectively. Seventeen (45%) of bla_CTX-M-15 was carried on the insertion sequence ISEc9 while bla_NDM-1 (11, 64.7%) were associated with ISEc33. None of the 21 plasmids detected were associated with β-lactamase genes. Higher resistance rates were found in E. coli ST-88 (n = 2) and the high-risk ST-692 (n = 2). For Klebsiella species, the high-risk clones ST-476 (n = 8) and ST-147 (n = 3) predominated and had higher phenotypic resistance rates and higher number of AMR genes. The mechanisms and pattern of antibiotic resistance differ from patterns previously described with isolates harbouring a wide range of AMRGs. The detection of several chromosomally mediated carbapenemases in our study also represents a significant finding that warrants further investigation to better understand its' implications for clinical practice and public health. The selected MDR-Es were found to be pan-susceptible to tigecycline and had very low resistance to fosfomycin, suggesting a potential for these as empiric treatments. A surveillance approach incorporating both conventional laboratory techniques and modern molecular techniques is essential for the comprehensive characterization of the emergence and dissemination of antimicrobial resistance in Enterobacterales infections within Nigeria.