Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

Virulence characteristics and antibiotic resistance analysis of Klebsiella pneumoniae isolated from pig farms in Xinjiang, China: revealing potential zoonotic risks

BACKGROUND

This study aimed to analyze the antimicrobial resistance and pathogenicity of Klebsiella pneumoniae(K. pneumoniae) isolates from pigs, evaluate their potential threat to pig farming and public health, and provide a theoretical basis for controlling K. pneumoniae infections in pig farms.

METHODS

Nasal swabs collected from pigs were subjected to bacterial isolation, biochemical identification, species-specific PCR, and 16S rRNA sequencing to identify K. pneumoniae. Serotyping and multilocus sequence typing (MLST) were conducted using the wzi and MLST methods, respectively. Biofilm formation was assessed using crystal violet staining. Antimicrobial susceptibility was evaluated via the Kirby-Bauer disk diffusion method, and resistance and virulence genes were identified using PCR. Pathogenicity was determined through string testing and mouse infection models.

RESULTS

21 strains of K. pneumoniae were isolated and identified from 50 swabs of pig nasal cavities. The isolates were classified into serotypes wzi 19 and wzi 81 and sequence types ST37 and ST967. Ten isolates exhibited strong biofilm-forming ability, while 11 showed moderate biofilm production. Antimicrobial susceptibility testing revealed resistance to β-lactams, aminoglycosides, quinolones, tetracyclines, sulfonamides, aminoalcohols, and glycopeptides, with sensitivity restricted to imipenem and polymyxins. Ten resistance genes and eight virulence genes were detected. Pathogenicity testing in mice revealed a moderate virulence level, with a median lethal dose (LD50) of 4.0 × 10⁶ CFU/mL. Infected mice exhibited significant lesions in the liver, lungs, and small intestine.

CONCLUSION

These findings highlight a potential risk to pig farming and public health, emphasizing the need for effective control measures against K. pneumoniae infections in pig farms.

Whole genome sequencing based prediction of antimicrobial resistance evolution among the predominant bacterial pathogens of diabetic foot ulcer

Emerging antibiotic resistance among bacterial pathogens of diabetic foot ulcers (DFUs) cause a significant threat to the human health. In the study, deep ulcer swabs were collected from 70 diabetic patients with foot ulcer. Among the 187 bacterial strains purified from the same, major representations were identified to be from Klebsiella pneumoniae and Staphylococcus spp. Here, polymicrobial infection (87.14%) was found to be more prevalent than monomicrobial (12.86%). From the antibiotic susceptibility test results, 34 bacterial isolates were identified as MDR pathogens with resistance to β-lactam and carbapenem classes of antibiotics. Furthermore, molecular screening has revealed the presence of antibiotic resistance gene such as blaSHV,blaCTX-M, blaTEM,blaOXA-48, NDM-1, mecA and blaZ genes among the isolates studied. Biofilm analysis has further revealed 31 strains to have strong and 3 with moderate biofilm production property. Among the MDR strains, K. pneumoniae (DFU2.2) and methicillin-resistant S. aureus (MRSA) (DFU24.3) were subjected to the whole-genome sequencing (WGS) based analysis due to their significant role in the chronicity of DFUs. The resistome prediction from the WGS data of DFU2.2 has revealed it to have the presence of a novel extended β-lactamase gene blaSHV-106 which has not been reported previously from India. Pan-genome analysis of DFU2.2 and DFU24.3 has also provided detailed insight into the genetic diversity, evolution, and pathogenic potential of the selected strains. The findings of this study hence suggest the emerging AMR to be one of the major risk factors challenging the therapeutic response of DFUs, the incidence of which is alarmingly high.

Clonal and Plasmid-Mediated Dissemination of β-Lactamases Producing Klebsiella spp. Among Environment and Humans in an Intensive Vegetable Cultivation Area in Eastern China

Background: Emergence and the rising prevalence of extended-spectrum β-lactamases (ESBLs) producing multidrug-resistant Klebsiella spp. is a global concern. Methods: 391 samples were collected from environmental and people in an intensive vegetable cultivation area in eastern China in June 2019. ESBLs-producing Klebsiella spp. were obtained by PCR and strain identification. The resistance genotype and phenotype of the strain were determined by PCR and drug susceptibility test. The number and size of plasmids were determined by pulsed-field gel electrophoresis assays of plasmids. The plasmid of blaCTX-M was determined by DNA imprinting hybridization, and the transferability of plasmid was understood by plasmid conjugation experiment. Whole-genome sequencing analysis (WGS) was used to obtain other antimicrobial resistance genes, virulence factors, mobile elements, and genetic environment. Results: Seventeen ESBL-producing Klebsiella spp. were multi-drug resistant. Sixteen ESBLs-producing Klebsiella spp. carried the blaCTX-M, and the size of the plasmid containing the blaCTX-M anged from ∼33.3 kb to ∼244.4 kb. Thirteen ESBLs-producing Klebsiella spp. carried the blaCTX-M were successfully transferred to the recipient bacterium through plasmid mediation. Single nucleotide polymorphism analysis showed clonal transmission between river water (J4-J8) and river sediment (J9), in river water (J3) and human feces (J12). WGS showed that all blaCTX-M were associated with the mobile element Tn3 and/or IS1380 family. All strains carried virulence factors related to adhesion, colonization, and pathogenicity. Conclusion: This study reminds us that antibiotic-resistant bacteria (ARB) from vegetable cultivation environments can spread to human. It is vital to enhance surveillance of the vegetable cultivation area and high vigilance for the risk of ARB movement from the vegetable plantation environment to humans.

Mobile genetic elements in Klebsiella pneumoniae

Klebsiella pneumoniae is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant K. pneumoniae has posed great challenges in clinical anti-infective therapy. In the K. pneumoniae genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in K. pneumoniae, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.

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.

Role of endosomal toll-like receptors in immune sensing of Klebsiella pneumoniae

Klebsiella pneumoniae is the causative agent of a wide range of antibiotic-resistant infections, including nosocomial pneumonia and neonatal sepsis. We investigate here the mechanisms underlying innate immune recognition of this pathogen by focusing on the role of endosomal Toll-like receptors (TLRs), which sense prokaryotic nucleic acids, in comparison with TLR4, which recognizes the cell-wall lipopolysaccharide component. Lack of functional endosomal TLRs made mice more susceptible to pulmonary infection by K. pneumoniae, in association with reduced production of proinflammatory and chemotactic cytokines and reduced neutrophil recruitment to the lung. This phenotype was as severe as that of TLR4-deficient mice and only moderately milder than that of mice lacking the TLR adaptor MyD88. Notably, macrophages lacking at the same time TLR7, 9 and 13 were more defective than those lacking only TLR9 in their ability to produce proinflammatory cytokines, suggesting a role for the RNA sensing TLR7 and 13 receptors in K. pneumoniae recognition. Collectively, our results unveil the presence of an integrated system of DNA and RNA sensing TLRs that cooperates with TLR4 in immune detection and clearance of K. pneumoniae. These data may be useful to devise alternative therapeutic approaches aimed at stimulating responses against antibiotic-resistant K. pneumoniae strains.

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.

A Comprehensive Overview of Klebsiella Pneumoniae: Resistance Dynamics, Clinical Manifestations, and Therapeutic Options

Klebsiella pneumoniae (Kp) is a notable pathogen responsible for various infections. The emergence of hypervirulent and carbapenem-resistant strains has raised global concern. Many novel approaches were developed to combat the current severe situation of antibiotic resistance, and clinical guidelines have also provided corresponding recommendations. This review highlights the critical aspects of Kp, including classification, virulence factors, systemic dissemination, drug resistance progression and the new therapeutic strategies to combat this evolving threat.

Genomic relatedness of colonizing and invasive disease Klebsiella pneumoniae isolates in South African infants

Klebsiella pneumoniae (KPn) colonizes multiple anatomical sites and is a leading cause of invasive disease and death in African children; however, there is no comparative genomic analysis between colonizing and invasive strains. This study investigated the genomic relatedness of KPn colonizing and invasive isolates in South African infants; and evaluated the relative invasiveness of KPn isolates based on sequence types (ST), capsular (KL), and lipopolysaccharide (O) loci by calculating case-carrier ratios (CCRs). There was less genomic diversity amongst invasive (22 ST, 17 K-loci) than colonizing isolates (31 ST, 29 K-loci), with invasive isolates being 8.59-fold and 3.49-fold more likely to harbour genes encoding for multi-drug resistance and yersiniabactin production compared with colonizing isolates. The CCRs for KL102 and O1/O2v2 were > 1, and < 1 for KL8, ST1414, and O1O2v1. Identifying high-risk strains, including KL102 and O1O2v2, that may have a higher potential to cause invasive disease, could enhance risk assessment and management strategies in vulnerable populations.

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.

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".

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.

Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence

Background

Targeted next-generation sequencing (tNGS) is a high-throughput and cost-effective diagnostic alternative for pneumonia, with the ability to simultaneously detect pathogens, antimicrobial resistance genes, and virulence genes. We aimed to explore the applicability of tNGS in the co-detection of the responsible pathogens, antimicrobial resistance (AMR) genes, and virulence genes in patients with pneumonia.

Methods

A prospective study was conducted among patients with suspected pneumonia at Ruijin Hospital from March 1 to May 31, 2023. Bronchoalveolar lavage fluid (BALF) or sputum samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and conventional microbiological tests (CMTs).

Results

In total, 67 BALF and 11 sputum samples from 78 patients were included in the analyses. According to the composite reference standards, the accuracy of tNGS in the detection of responsible pathogens was 0.852 (95% confidence interval 0.786-0.918), which resembled that of mNGS and remarkably exceeded that of CMTs. In addition, 81 AMR genes associated with responsible pathogens were reported, and 75.8% (25/33) priority drug-resistant pathogens could be directly identified. A total of 144 virulence genes were detected for four common pathogens. And patients with virulence genes detected were of higher proportions of severe pneumonia (95.0% vs 42.9%, P = 0.009), acute respiratory distress syndrome (55.0% vs 0%, P = 0.022), and neutrophils (82.3% vs 62.2%, P = 0.026) than those not.

Conclusion

In patients with pneumonia, tNGS could detect the responsible pathogens, AMR genes, and virulence genes simultaneously, serving as an efficient and cost-effective tool for the diagnosis, treatment, and severity indication of pneumonia.

Prevalence and molecular characteristics of colistin-resistant isolates among carbapenem-resistant Klebsiella pneumoniae in Central South China: a multicenter study

BACKGROUND

The emergence of colistin resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant public health concern, as colistin has been the last resort for treating such infections. This study aimed to investigate the prevalence and molecular characteristics of colistin-resistant CRKP isolates in Central South China.

METHODS

CRKP isolates from twelve hospitals in Central South China were screened for colistin resistance using broth microdilution. The epidemiological characteristics, virulome, resistome, plasmid replicons and two-component systems associated with colistin resistance of colistin-resistant isolates were explored by whole-genome sequencing. The mgrB gene and the relative expression of the pmrC and pmrK genes were analyzed by polymerase chain reaction (PCR) and real-time quantitative PCR, respectively. The bacterial virulence was evaluated through a Galleria mellonella larvae infection model.

RESULTS

Of the 429 nonduplicate CRKP isolates, 26 (6.1%) were colistin-resistant and they included eight clonal clusters. Six distinct sequence type (ST)-capsule loci (KL) types were identified: ST11-KL64, ST11-KL47, ST963-KL16, ST307-KL102, ST751-KL64 and ST5254-KL47. 88.5% (23/26) of them were found to carry at least one carbapenemase gene, including blaKPC-2 (65.4%, 17/26) and blaNDM-1 (7.7%, 2/26), as well as coharbouring blaKPC-2 and blaNDM-1 (15.4%, 4/26). Diverse mutations of colistin resistance-related genes were observed, with mgrB inactivation by insertions and the T157P deleterious mutation in pmrB being detected in 57.7% and 42.3% of the colistin-resistant isolates, respectively. In addition, a novel deleterious mutation, R248P, in the crrB gene was found in two ST11 isolates. 88.5% of the 26 isolates presented an increase in pmrK transcription, and 69.2% of them had an overexpression of the pmrC gene. All the 16 ST11-KL64 isolates and one ST751-KL64 isolate (65.4%, 17/26) carried at least two hypervirulence biomarkers and showed high virulence in vivo.

CONCLUSIONS

This study highlights the presence of different colistin resistance mechanisms in isolates belonging to the same clone and identified multiple clonal transmission clusters in colistin resistant isolates, including the globally high-risk ST11 and ST307 clones, of which a significant proportion exhibited high virulence. Consequently, it is crucial to enforce measures to prevent the ongoing spread of colistin resistance.

Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in Gauteng South Africa

Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient's urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.

Genetic characteristics of clinical carbapenem-resistant Klebsiella pneumoniae: epidemic ST11 KPC-2-producing strains and non-negligible NDM-5-producing strains with diverse STs

Klebsiella pneumoniae is among the most important Gram-negative pathogens that can cause serious nosocomial infections. The emergence and prevalence of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) pose a significant challenge to public health. In this study, we characterized thirty carbapenem-resistant K. pneumoniae (CRKP) strains from a tertiary care hospital in Sichuan province, China, by whole-genome sequencing and genome analysis. These strains were all highly resistant to carbapenem but remained susceptible to tigecycline. Of the 30 tested CRKP strains, 23 were positive for blaKPC-2 and seven for blaNDM-5. These blaKPC-2-positive strains all belonged to ST11, while blaNDM-5-positive strains belonged to five distinct STs. Phylogenetic analysis revealed a predominant intra-hospital transmission of ST11-KL64 in KPC-2-producing CRKP, and that both clonal and horizontal transmission of blaNDM-5 have occurred among NDM-5-producing CRKP strains in this hospital. Hypervirulence genes were commonly detected in the CRKP. The prevalent pLVKP-like plasmid and ICEKp seem to have contributed largely to the transmission of virulence genes in them. blaNDM-5 was located on highly similar IncX3 plasmids in the collected strains, and its truncated vision was highlighted. blaKPC-2 was primarily carried by IncFII/IncR plasmids in our collection. At least two IncFII/IncR plasmid subtypes were identified, exhibiting high similarity to many previously reported blaKPC-2-bearing plasmids from different parts of China. The findings provide an expanded knowledge of the genetic characteristics of CRKP, the transmission pattern of carbapenem-resistance genes, and also the convergence of Hv-CRKP.

Identification of potential flavonoid compounds as antibacterial therapeutics against Klebsiella pneumoniae infection using structure-based virtual screening and molecular dynamics simulation

Klebsiella pneumoniae, which is among the top three pathogens on WHO's priority list, is one of the gram-negative bacteria that doctors and researchers around the world have fought for decades. Capsular polysaccharide (CPS) protein is extensively recognized as an important K. pneumoniae virulence factor. Thus, CPS has become the most characterized target for the discovery of novel drug candidates. The ineffectiveness of currently existing antibiotics urges the search for potent antimicrobial compounds. Flavonoids are a group of plant metabolites that have antibacterial potential and can enhance the present medications to elicit improved results against diverse diseases without adverse reactions. Henceforth, the present study aims to illustrate the inhibitory potential of flavonoids with varying pharmacological properties, targeting the CPS protein of K. pneumoniae by in silico approaches. The flavonoid compounds (n = 169) were retrieved from the PubChem database and screened using the structure-based virtual screening approach. Compounds with the highest binding score were estimated through their pharmacokinetic effects by ADMET descriptors. Finally, four potential inhibitors with PubChem CID: (4301534, 5213, 5481948, and 637080) were selected after molecular docking and drug-likeness analysis. All four lead compounds were employed for the MDS analysis of a 100 ns time period. Various studies were undertaken to assess the stability of the protein-ligand complexes. The binding free energy was computed using MM-PBSA, and the outcomes indicated that the molecules are having stable interactions with the binding site of the target protein. The results revealed that all four compounds can be employed as potential therapeutics against K. pneumoniae.

Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis

Klebsiella pneumoniae is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of K. pneumoniae is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical K. pneumoniae strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of K. pneumoniae strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (rmpA, iucA, iutA, irp2, fyuA, ybtS, iroN, allS and clbA) compared to the major group. Pathogenicity was assessed using Galleria mellonella larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the G. mellonella infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.

Phylogenetics and Mobilization of Genomic Traits of Cephalosporin-Resistant Escherichia coli Originated from Retail Meat

Contaminations with cephalosporin-resistant Escherichia coli across the food chain may pose a significant threat to public health because those antimicrobials are critically important in human medicine. The impact of the presented data is especially significant concerning Poland's role as one of the leading food producers in the EU. This work aimed to characterize the genomic contents of cephalosporin-resistant Escherichia coli (n = 36) isolated from retail meat to expand the official AMR monitoring reported by EFSA. The ESBL mechanism was predominant (via blaCTX-M-1 and blaSHV-12), with the AmpC-type represented by the blaCMY-2 variant. The strains harbored multiple resistance genes, mainly conferring resistance to aminoglycosides, sulfonamides, trimethoprim, tetracyclines. In some isolates, virulence factors-including intimin (eae) and its receptor (tir) were detected, indicating significant pathogenic potential. Resistance genes showed a link with IncI1 and IncB/O/K/Z plasmids. Cephalosporinases were particularly linked to ISEc9/ISEc1 (blaCTX-M-1 and blaCMY-2). The association of virulence with mobile elements was less common-mostly with IncF plasmids. The analysis of E. coli isolated from retail meat indicates accumulation of ARGs and their association with various mobile genetic elements, thus increasing the potential for the transmission of resistance across the food chain.

Correlation between Antibiotics-Resistance, Virulence Genes and Genotypes among Klebsiella pneumoniae Clinical Strains Isolated in Guangzhou, China

Klebsiella pneumoniae is an important opportunistic pathogen causing community-acquired and hospital-acquired infections. This aim of this study was to analysis the antibiotic-resistance phenotypes, carbapenemase genes, virulence genes, and genotypes the 62 K. pneumoniae clinical isolates, and to explore the correlations between these isolates. The antimicrobial susceptibility profiles were determined using the BD Phoenix-100 system. Carbapenemase and virulence genes were detected using multiplex PCR. Out of the 62 K. pneumoniae clinical isolates, 79.0% were exhibited resistance to antibiotics, with 69.4% displaying multi-drug resistance. The rate of antibiotic-resistance was highest for penicillin (71.0%), followed by cephalosporins (66.1%), and lowest for carbapenems (29.0%). The detection rates of carbapenemase genes were as follows: KPC (56.5%), VIM (35.5%), and NDM (1.61%). Additionally, seven virulence genes were detected with the highest prevalence rates, of which entB and mrkD were at the top of the carrier rates with 95.2% each. The study classified 62 isolates into 13 clusters and 46 genotypes using ERIC-PCR. Cluster A6 exhibited the highest genetic diversity, comprising 20 strains and 13 genotypes. The statistical analysis revealed a strong correlation between MDR and resistance to penicillin and cephalosporin. Furthermore, genes related to siderophores were closely associated with mrkD. Genotypes identified by ERIC-PCR showed a negative correlation with allS. The study revealed a negative correlation between antibiotic resistance and genes kfu, ybtS, iutA, rmpA, and allS. Conversely, a positive correlation was observed between antibiotic resistance and genes entB and mrkD. The correlations identified in this study provide insights into the occurrence of hospital-acquired infections. The findings of this study may guide the prevention and control of K. pneumoniae outbreaks by utilizing appropriate medication.

A unique combination of natural fatty acids from Hermetia illucens fly larvae fat effectively combats virulence factors and biofilms of MDR hypervirulent mucoviscus Klebsiella pneumoniae strains by increasing Lewis acid-base/van der Waals interactions in bacterial wall membranes

Introduction

Hypervirulent Klebsiella pneumoniae (hvKp) and carbapenem-resistant K. pneumoniae (CR-Kp) are rapidly emerging as opportunistic pathogens that have a global impact leading to a significant increase in mortality rates among clinical patients. Anti-virulence strategies that target bacterial behavior, such as adhesion and biofilm formation, have been proposed as alternatives to biocidal antibiotic treatments to reduce the rapid emergence of bacterial resistance. The main objective of this study was to examine the efficacy of fatty acid-enriched extract (AWME3) derived from the fat of Black Soldier Fly larvae (Hermetia illucens) in fighting against biofilms of multi-drug resistant (MDR) and highly virulent Klebsiella pneumoniae (hvKp) pathogens. Additionally, the study also aimed to investigate the potential mechanisms underlying this effect.

Methods

Crystal violet (CV) and ethidium bromide (EtBr) assays show how AWME3 affects the formation of mixed and mature biofilms by the KP ATCC BAA-2473, KPi1627, and KPM9 strains. AWME3 has shown exceptional efficacy in combating the hypermucoviscosity (HMV) virulent factors of KPi1627 and KPM9 strains when tested using the string assay. The rudimentary motility of MDR KPM9 and KP ATCC BAA-2473 strains was detected through swimming, swarming, and twitching assays. The cell wall membrane disturbances induced by AWME3 were detected by light and scanning electron microscopy and further validated by an increase in the bacterial cell wall permeability and Lewis acid-base/van der Waals characteristics of K. pneumoniae strains tested by MATS (microbial adhesion to solvents) method.

Results

After being exposed to 0.5 MIC (0.125 mg/ml) of AWME3, a significant reduction in the rudimentary motility of MDR KPM9 and KP ATCC BAA-2473 strains, whereas the treated bacterial strains exhibited motility between 4.23 ± 0.25 and 4.47 ± 0.25 mm, while the non-treated control groups showed significantly higher motility ranging from 8.5 ± 0.5 to 10.5 ± 0.5 mm.

Conclusion

In conclusion, this study demonstrates the exceptional capability of the natural AWME3 extract enriched with a unique combination of fatty acids to effectively eliminate the biofilms formed by the highly drug-resistant and highly virulent K. pneumoniae (hvKp) pathogens. Our results highlight the opportunity to control and minimize the rapid emergence of bacterial resistance through the treatment using AWME3 of biofilm-associated infections caused by hvKp and CRKp pathogens.

Hypervirulent Klebsiella pneumoniae in a South African tertiary hospital-Clinical profile, genetic determinants, and virulence in Caenorhabditis elegans

Introduction

A distinct strain of Klebsiella pneumoniae (K. pneumoniae) referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in K. pneumoniae isolates from one of the largest tertiary hospitals in a South African province.

Methods

A total of 74 K. pneumoniae isolates were received from Pelonomi Tertiary Hospital National Health Laboratory Service (NHLS), Bloemfontein. Virulence-associated genes (rmpA, capsule serotype K1/K2, iroB and irp2) were screened using Polymerase Chain Reaction (PCR). The iutA (aerobactin transporter) gene was used as a primary biomarker of hvKp. The extracted DNAs were sequenced using the next-generation sequencing pipeline and the curated sequences were used for phylogeny analyses using appropriate bioinformatic tools. The virulence of hvKp vs. classical Klebsiella pneumoniae (cKp) was investigated using the Caenorhabditis elegans nematode model.

Results

Nine (12.2%) isolates were identified as hvKp. Moreover, hvKp was significantly (p < 0.05) more virulent in vivo in Caenorhabditis elegans relative to cKp. The virulence-associated genes [rmpA, iroB, hypermucoviscous phenotype (hmv) phenotype and capsule K1/K2] were significantly (p < 0.05) associated with hvKp. A homology search of the curated sequences revealed a high percentage of identity between 99.8 and 100% with other homologous iutA gene sequences of other hvKp in the GenBank.

Conclusion

Findings from this study confirm the presence of hvKp in a large tertiary hospital in central South Africa. However, the low prevalence and mild to moderate clinical presentation of infected patients suggest a marginal threat to public health. Further studies in different settings are required to establish the true potential impact of hvKp in developing countries.

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.

Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Extensively drug-resistant (XDR) Klebsiella pneumoniae inflict a notable burden on healthcare worldwide. Of specific concern are strains producing carbapenem-hydrolyzing enzymes, as the therapeutic options for these strains are still very limited. Specific sequence types of K. pneumoniae have been noted for their epidemic occurrence globally, but the mechanisms behind the success of specific clones remain unclear. Herein, we have characterized 20 high-risk clones (HiRCs) and 10 non-HiRCs of XDR K. pneumoniae, exploring factors connected to the epidemiological success of some clones. Isolates were subjected to core genome multilocus sequence typing analysis to determine the clonal relationships of the isolates and subsequently characterized with regard to features known to be linked to overall bacterial fitness and virulence. The genomes were analyzed in silico for capsule types, O antigens, virulence factors, antimicrobial resistance genes, prophages, and CRISPR-Cas loci. In vitro growth experiments were conducted to retrieve proxies for absolute and relative fitness for 11 HiRC and 9 non-HiRC isolates selected based on the clonal groups they belonged to, and infections in a Galleria mellonella insect model were used to evaluate the virulence of the isolates in vivo. This study did not find evidence that virulence factors, prophages, CRISPR-Cas loci, or fitness measured in vitro alone would contribute to the global epidemiological success of specific clones of carbapenemase-producing XDR K. pneumoniae. However, this study did find the HiRC group to be more virulent than the non-HiRC group when measured in vivo in a model with G. mellonella. This suggests that the virulence and epidemiological success of certain clones of K. pneumoniae cannot be explained by individual traits investigated in this study and thus warrant further experiments in the future.IMPORTANCEHerein, we explored potential explanations for the successfulness of some epidemic or high-risk clones of carbapenemase-producing Klebsiella pneumoniae. We found differences in mortality in a larva model but found no clear genomic differences in known virulence markers. Most of the research on virulence in K. pneumoniae has been focused on hypervirulent strains, but here, we try to understand differences within the group of highly resistant strains. The results from the larva virulence model could be used to design experiments in higher animals. Moreover, the data could provide further support to a differentiated infection control approach against extensively drug-resistant strains, based on their classification as high-risk clones.

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.

Comparative genomic analysis of strong biofilm-forming Klebsiella pneumoniae isolates uncovers novel ISEcp1-mediated chromosomal integration of a full plasmid-like sequence

BACKGROUND

The goal of the current study was to elucidate the genomic background of biofilm formation in Klebsiella pneumoniae.

METHODS

Clinical isolates were screened for biofilm formation using the crystal violet assay. Antimicrobial resistance (AMR) profiles were assessed by disk diffusion and broth microdilution tests. Biofilm formation was correlated to virulence and resistance genes screened by PCR. Draft genomes of three isolates that form strong biofilm were generated by Illumina sequencing.

RESULTS

Only the siderophore-coding gene iutA was significantly associated with more pronounced biofilm formation. ST1399-KL43-O1/O2v1 and ST11-KL15-O4 were assigned to the multidrug-resistant strain K21 and the extensively drug-resistant strain K237, respectively. ST1999-KL38-O12 was assigned to K57. Correlated with CRISPR/Cas distribution, more plasmid replicons and prophage sequences were identified in K21 and K237 compared to K57. The acquired AMR genes (blaOXA-48, rmtF, aac(6')-Ib and qnrB) and (blaNDM-1, blaCTX-M, aph(3')-VI, qnrS, and aac(6')-Ib-cr) were found in K237 and K21, respectively. The latter showed a novel ISEcp1-mediated chromosomal integration of replicon type IncM1 plasmid-like structure harboring blaCTX-M-14 and aph(3')-VI that uniquely interrupted rcsC. The plasmid-mediated heavy metal resistance genes merACDEPRT and arsABCDR were spotted in K21, which also exclusively carried the acquired virulence genes mrkABCDF and the hypervirulence-associated genes iucABCD-iutA, and rmpA/A2. Pangenome analysis revealed NTUH-K2044 accessory genes most frequently shared with K21.

CONCLUSIONS

While less virulent to Galleria mellonella than ST1999 (K57), the strong biofilm former, multidrug-resistant, NDM-producer K. pneumoniae K21 (ST1399-KL43-O1/O2v1) carries a novel chromosomally integrated plasmid-like structure and hypervirulence-associated genes and represents a serious threat to countries in the area.

Distribution patterns and influential factors of pathogenic bacteria in freshwater aquaculture sediments

Pathogenic bacteria, the major causative agents of aquaculture diseases, are a serious impediment to the aquaculture industry. However, the bioinformatics of pathogenic bacteria and virulence factors (VFs) in sediments, an important component of freshwater aquaculture ecosystems, are not well characterized. In this study, 20 sediment samples were collected from fish pond sediments (FPS), shrimp field sediments (SFS), fish pond sediment control (FPSC), and shrimp field sediment control (SFSC). Molecular biological information was obtained on a total of 173 pathogenic bacteria, 1093 virulence factors (VFs), and 8475 mobile genetic elements (MGEs) from these samples. The results indicated that (1) aquaculture patterns and sediment characteristics can affect the distribution of pathogenic bacteria. According to the results of the Kruskal-Wallis H test, except for Mycobacterium gilvum, there were significant differences (P < 0.05) among the four sediment types in the average abundance of major pathogenic bacteria (top 30 in abundance), and the average abundance of major pathogenic bacteria in the four sediment types followed the following pattern: FPS > SFS > FPSC > SFSC. (2) Pathogenic bacteria are able to implement a variety of complex pathogenic mechanisms such as adhesion, invasion, immune evasion, and metabolic regulation in the host because they carry a variety of VFs such as type IV pili, HSI-I, Alginate, Colibactin, and Capsule. According to the primary classification of the Virulence Factor Database (VFDB), the abundance of VFs in all four types of sediments showed the following pattern: offensive VFs > non-specific VFs > defensive VFs > regulation of virulence-related genes. (3) Total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), nitrite, and nitrate were mostly only weakly positively correlated with the major pathogenic bacteria and could promote the growth of pathogenic bacteria to some extent, whereas ammonia was significantly positively correlated with most of the major pathogenic bacteria and could play an important role in promoting the growth and reproduction of pathogenic bacteria. (4) Meanwhile, there was also a significant positive correlation between CAZyme genes and major pathogenic bacteria (0.62 ≤ R ≤ 0.89, P < 0.05). This suggests that these pathogenic bacteria could be the main carriers of CAZyme genes and, to some extent, gained a higher level of metabolic activity by degrading organic matter in the sediments to maintain their competitive advantage. (5) Worryingly, the results of correlation analyses indicated that MGEs in aquaculture sediments could play an important role in the spread of VFs (R = 0.82, P < 0.01), and in particular, plasmids (R = 0.75, P < 0.01) and integrative and conjugative elements (ICEs, R = 0.65, P < 0.05) could be these major vectors of VFs. The results of this study contribute to a comprehensive understanding of the health of freshwater aquaculture sediments and provide a scientific basis for aquaculture management and conservation.

Extensively Drug-Resistant Klebsiella pneumoniae Associated with Complicated Urinary Tract Infection in Northern India

Klebsiella pneumoniae (Kp), which is associated with hospital-acquired infections, is extensively drug-resistant (XDR), making treatment difficult. Understanding the genetic epidemiology of XDR-Kp can help determine its potential to be hypervirulent (hv) through the presence of siderophores. We characterized the genomes of 18 colistin-resistant XDR-Kp isolated from 14 patients with complicated tract infection at an Indian healthcare facility. The 18 organisms comprised the following sequence types (STs): ST14 (n = 9), ST147 (n = 5), ST231 (n = 2), ST2096 (n = 1), and ST25 (n = 1). Many patients in each ward were infected with the same ST, suggesting a common source of infection. Some patients had recurrent infections with multiple STs circulating in the ward, providing evidence of hospital transmission. β-lactamase genes (blaCTX-M-1, blaSHV, and blaampH) were present in all isolates. blaNDM-1 was present in 15 isolates, blaOXA-1 in 16 isolates, blaTEM-1D in 13 isolates, and blaOXA-48 in 3 isolates. Disruption of mgrB by various insertion sequences was responsible for colistin resistance in 6 isolates. The most common K-type among isolates was K2 (n = 10). One XDR convergent hvKp ST2096 mutation (iuc+ybt+blaOXA-1+blaOXA-48) was associated with prolonged hospitalization. Convergent XDR-hvKp has outbreak potential, warranting effective antimicrobial stewardship and infection control.

Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem

The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.

Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station

IMPORTANCE

The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.

Clinical Characteristics and Molecular Epidemiology of ST23 Klebsiella pneumoniae in China

Purpose

In clinical settings, CG23 Klebsiella pneumoniae (Kp) is the most virulent clonal group of Kp. Continuous fusions of hypervirulent (Hv) and highly resistant strains have been reported; however, few studies have analysed the molecular epidemiology and clinical characteristics of CG23 strains, especially MDR-sequence type ST23 strains. In this study, we investigated the molecular characteristics of ST23 Kp and analysed the clinical characteristics of ST23 Kp infections in a large teaching hospital of the third class in China.

Methods

ST23 Kp isolates were screened using whole-genome sequencing data from a large single centre. We compared the clinical characteristics of ST23 strains isolated from community-acquired infections (CAI) and hospital acquired infection (HAI). In addition, the infection characteristics of MDR and poor-prognosis isolates were investigated. We analysed genetic characteristics of ST23 Kp and further investigated the evolutionary relationship based on single-nucleotide polymorphism phylogenetic trees.

Results

We detected 184 ST23 strains between 2013 and July of 2018. There were no significant differences between the isolation rates of pulmonary, bloodstream, urinary tract, and cutaneous soft tissue infections in the community and hospitals, except for abscess infections. MDR strains primarily cause pulmonary infections and abscesses; infections with a poor prognosis are typically bloodstream and pulmonary infections. Fourteen MDR strains producing extended-spectrum or class C beta-lactamases, resulting in resistance to third-generation cephalosporins. In 3.8% of ST23 Kp strains, the clb locus was absent. The phylogenetic tree revealed that the isolates were primarily divided into three clades, and based on clinical data, it is inferred that three clonal transmission events have occurred, mainly in ICU causing lung infection.

Conclusion

This study demonstrates that virulence and drug-resistance fusion events of ST23 strains occur gradually, and that the hypervirulent clones facilitate the widespread dissemination of CAI and HAI, particularly pulmonary. Monitoring genomics and developing antivirulence strategies are essential.

Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan

Carbapenem-resistant ST11_KL64 Klebsiella pneumoniae emerged as a significant public health concern in Taiwan, peaking between 2013 and 2015, with the majority of isolates exhibiting OXA-48 as the sole carbapenemase. In this study, we employed whole-genome sequencing to investigate the molecular underpinnings of ST11_KL64 isolates collected from 2013 to 2021. Phylogenomic analysis revealed a notable genetic divergence between the ST11_KL64 strains in Taiwan and those in China, suggesting an independent evolutionary trajectory. Our findings indicated that the ST11_KL64_Taiwan lineage originated from the ST11_KL64 lineage in Brazil, with recombination events leading to the integration of ICEKp11 and a 27-kb fragment at the tRNAASN sites, shaping its unique genomic landscape. To further elucidate this unique sublineage, we examined the plasmid contents. In contrast to ST11_KL64_Brazil strains, which predominantly carried blaKPC-2, ST11_KL64_Taiwan strains exhibited the acquisition of an epidemic blaOXA-48-carrying IncL plasmid. Additionally, ST11_KL64_Taiwan strains consistently harbored a multi-drug resistance IncC plasmid, along with a collection of gene clusters that conferred resistance to heavy metals and the phage shock protein system via various Inc-type plasmids. Although few, there were still rare ST11_KL64_Taiwan strains that have evolved into hypervirulent CRKP through the horizontal acquisition of pLVPK variants. Comprehensive characterization of the high-risk ST11_KL64 lineage in Taiwan not only sheds light on its epidemic success but also provides essential data for ongoing surveillance efforts aimed at tracking the spread and evolution of ST11_KL64 across different geographical regions. Understanding the molecular underpinnings of CRKP evolution is crucial for developing effective strategies to combat its emergence and dissemination.

Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence

Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.

Country-wide expansion of a VIM-1 carbapenemase-producing Klebsiella oxytoca ST145 lineage in Poland, 2009-2019

PURPOSE

To elucidate the role of the Klebsiella oxytoca species complex (KoSC) in epidemiology of VIM-type MBL-producing Enterobacterales in Poland.

METHODS

The study comprised all 106 VIM-positive KoSC isolates collected by the Polish National Reference Centre for Susceptibility Testing during 2009-2019 from 60 institutions in 35 towns. All isolates were sequenced by Illumina MiSeq, followed by MinION sequencing of selected organisms. Genomes were subjected to bioinformatic analysis, addressing taxonomy, clonality, phylogeny and structural characterisation of key resistance determinants within their chromosomal and plasmidic loci.

RESULTS

Among five species identified, K. oxytoca was predominant (n = 92), followed by Klebsiella michiganensis (n = 11). MLST distinguished 18 STs, with the most prevalent Klebsiella oxytoca ST145 (n = 83). The clone segregated a lineage with the In237-like integron [blaVIM-1-aacA4 genes; n = 78], recorded in 28 cities almost all over the country. The integron was located in a ~ 49-50 kb chromosomal mosaic region with multiple other resistance genes, linked to a ~ 51 kb phage-like element. The organism might have originated from Greece, and its evolution in Poland included several events of chromosomal ~ 54-258 kb deletions, comprising the natural β-lactamase blaOXY gene. A group of other isolates of various species and clones (n = 12) carried the integron In916 on self-transmissible IncA-type plasmids, effectively spreading in Italy, France and Poland.

CONCLUSION

KoSC has been one of the major VIM producers in Poland, owing largely to clonal expansion of the specific K. oxytoca-In237-like lineage. Its apparently enhanced epidemic potential may create a danger on international scale.

A novel virulence plasmid encoding yersiniabactin, salmochelin, and RmpADC from hypervirulent Klebsiella pneumoniae of distinct genetic backgrounds

Hypervirulent Klebsiella pneumoniae (hvKP) is increasingly reported worldwide as a major clinical and public health threat. The virulence of hvKP is attributed largely to the carriage of virulence plasmids (KpVPs). To date, two dominant types of KpVP have been identified, namely, KpVP-1 and KpVP-2. In this study, we reported two hvKP strains from bloodstream infections that carry highly identical virulence plasmids that exhibited <40% coverage compared with KpVP-1 and KpVP-2. This novel virulence plasmid was designated KpVP-3. The two hvKP have different genetic backgrounds, which belonged to ST29-K54 and ST111-K63, respectively. They were both positive for the string test, highly virulent on the Galleria mellonella infection model, and possess high-level macrophage-killing resistance in vitro. Apart from the intrinsic non-susceptibility to ampicillin, both strains were susceptible to commonly used antibiotics. The virulence plasmid carried virulence genes rmpADC, iroBCDN (iro1), and the ybt locus (ybt4) which was not present on either KpVP-1 or KpVP-2. It did not carry antimicrobial resistance genes but carried an incomplete conjugation machinery containing only the traH and traF genes. The KpVP-3 plasmid was stably maintained in both hvKP strains and could not be eliminated with SDS treatment or by serial passage on stress-free agar plates. KpVP-3 was non-self-transmissible under experimental conditions. Data mining suggested KpVP-3-type plasmids have emerged in different countries including China, Australia, and the USA. The emergence of this novel virulence plasmid might pose a potential threat to public health. Heightened efforts are required to study its dissemination mechanism.

Genotypic Evolution of Klebsiella pneumoniae Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy

In February 2022, a critically ill patient colonized with a carbapenem-resistant K. pneumoniae producing KPC-3 and VIM-1 carbapenemases was hospitalized for SARS-CoV-2 in the intensive care unit of Policlinico Umberto I hospital in Rome, Italy. During 95 days of hospitalization, ceftazidime/avibactam, meropenem/vaborbactam, and cefiderocol were administered consecutively to treat 3 respiratory tract infections sustained by different bacterial agents. Those therapies altered the resistome of K. pneumoniae sequence type 512 colonizing or infecting the patient during the hospitalization period. In vivo evolution of the K. pneumoniae sequence type 512 resistome occurred through plasmid loss, outer membrane porin alteration, and a nonsense mutation in the cirA siderophore gene, resulting in high levels of cefiderocol resistance. Cross-selection can occur between K. pneumoniae and treatments prescribed for other infective agents. K. pneumoniae can stably colonize a patient, and antimicrobial-selective pressure can promote progressive K. pneumoniae resistome evolution, indicating a substantial public health threat.

Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of a novel ST3355 ESBL-producing hypervirulent Klebsiella pneumoniae isolate

Introduction

An extended-spectrum beta-lactamase (ESBL)-hypervirulent Klebsiella pneumoniae (HvKP) strain HKE9 was isolated from the blood in an outpatient.

Methods

The effect of the global regulatory factor RpoS on antimicrobial resistance, pathogenicity, and environmental adaptability was elucidated.

Results

HKE9 is a novel ST3355 (K20/O2a) hypervirulent strain with a positive string test and resistant to cephems except cefotetan. It has a genome size of 5.6M, including two plasmids. CTX-M-15 was found in plasmid 2, and only ompk37 was found in the chromosome. HKE9 could produce bacterial siderophores, and genes of enterobactin, yersiniabactin, aerobactin, and salmochelin have been retrieved in the genome. As a global regulatory factor, knockout of rpoS did not change antimicrobial resistance or hemolytic phenotype while increasing the virulence to Galleria mellonella larvae and showing higher viscosity. Moreover, rpoS knockout can increase bacterial competitiveness and cell adhesion ability. Interestingly, HKE9-M-rpoS decreased resistance to acidic pH, high osmotic pressure, heat shock, and ultraviolet and became sensitive to disinfectants (H2O2, alcohol, and sodium hypochlorite). Although there were 13 Type 6 secretion system (T6SS) core genes divided into two segments with tle1 between segments in the chromosome, transcriptomic analysis showed that rpoS negatively regulated T4SS located on plasmid 2, type 1, and type 3 fimbriae and positively regulate genes responsible for acidic response, hyperosmotic pressure, heat shock, oxidative stress, alcohol and hypochlorous acid metabolism, and quorum sensing.

Discussion

Here, this novel ST3355 ESBL-HvKP strain HKE9 may spread via various clonal types. The important regulation effect of rpoS is the enhanced tolerance and resistance to environmental stress and disinfectants, which may be at the cost of reducing virulence and regulated by T4SS.

Genomic and clinical characterization of Klebsiella pneumoniae carrying the pks island

Background

The pks island and its production of the bacterial secondary metabolite genotoxin, colibactin, have attracted increasing attention. However, genomic articles focusing on pks islands in Klebsiella pneumoniae, as well as comparative genomic studies of mobile genetic elements, such as prophages, plasmids, and insertion sequences, are lacking. In this study, a large-scale analysis was conducted to understand the prevalence and evolution of pks islands, differences in mobile genetic elements between pks-negative and pks-positive K. pneumoniae, and clinical characteristics of infection caused by pks-positive K. pneumoniae.

Methods

The genomes of 2,709 K. pneumoniae were downloaded from public databases, among which, 1,422 were from NCBI and 1,287 were from the China National GeneBank DataBase (CNGBdb). Screening for virulence and resistance genes, phylogenetic tree construction, and pan-genome analysis were performed. Differences in mobile genetic elements between pks-positive and pks-negative strains were compared. The clinical characteristics of 157 pks-positive and 157 pks-negative K. pneumoniae infected patients were investigated.

Results

Of 2,709 K. pneumoniae genomes, 245 pks-positive genomes were screened. The four siderophores, type VI secretion system, and nutritional factor genes were present in at least 77.9% (191/245), 66.9% (164/245), and 63.3% (155/245) of pks-positive strains, respectively. The number and fragment length of prophage were lower in pks-positive strains than in pks-negative strains (p < 0.05). The prevalence of the IS6 family was higher in pks-negative strains than in pks-positive strains, and the prevalence of multiple plasmid replicon types differed between the pks-positive and pks-negative strains (p < 0.05). The detection rate of pks-positive K. pneumoniae in abscess samples was higher than that of pks-negative K. pneumoniae (p < 0.05).

Conclusion

The pks-positive strains had abundant virulence genes. There were differences in the distribution of mobile genetic elements between pks-positive and pks-negative isolates. Further analysis of the evolutionary pattern of pks island and epidemiological surveillance in different populations are needed.

Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in Chile: high-risk ST25 clones and novel mobile elements

Multidrug- and carbapenem-resistant Klebsiella pneumoniae (CR-Kp) are critical threats to global health and key traffickers of resistance genes to other pathogens. Despite the sustained increase in CR-Kp infections in Chile, few strains have been described at the genomic level, lacking details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial susceptibility and performed a comparative genomic analysis of 10 CR-Kp isolates from the Chilean surveillance of carbapenem-resistant Enterobacteriaceae. High resistance was observed among the isolates (five ST25, three ST11, one ST45, and one ST505), which harbored 44 plasmids, most carrying genes for conjugation and resistance to several antibiotics and biocides. Ten plasmids encoding carbapenemases were characterized, including novel plasmids or variants with additional resistance genes, a novel genetic environment for blaKPC-2, and plasmids widely disseminated in South America. ST25 K2 isolates belonging to CG10224, a clone traced back to 2012 in Chile, which recently acquired blaNDM-1, blaNDM-7, or blaKPC-2 plasmids stood out as high-risk clones. Moreover, this corresponds to the first report of ST25 and ST45 Kp producing NDM-7 in South America and ST505 CR-Kp producing both NDM-7 and KPC-2 worldwide. Also, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for a detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of CR-Kp in Chile and South America. IMPORTANCE In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of Klebsiella pneumoniae are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial resistance surveillance, it is still restricted in low- to middle-income countries, including Chile, causing them to be underrepresented in genomic databases and epidemiology surveys. This study provided the first 10 complete genomes of the Chilean surveillance for carbapenem-resistant K. pneumoniae in healthcare settings, unveiling their resistance and virulence determinants and the mobile genetic elements mediating their dissemination, placed in the South American and global K. pneumoniae epidemiological context. We found ST25 with K2 capsule as an emerging high-risk clone, along with other lineages producing two carbapenemases and several other resistance and virulence genes encoded in novel plasmids and genomic islands.

Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK

A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.

Clinical and Bacterial Characteristics Associated with Glove and Gown Contamination by Carbapenem-Resistant Klebsiella pneumoniae in the Health Care Setting

Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a pathogen of significant concern to public health, as it has become increasingly associated with difficult-to-treat community-acquired and hospital-associated infections. Transmission of K. pneumoniae between patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings. However, it is not known whether specific lineages or isolates of K. pneumoniae are associated with increased transmission. Thus, we used whole-genome sequencing to analyze the genetic diversity of 166 carbapenem-resistant K. pneumoniae isolates from five U.S. hospitals in four states as part of a multicenter study examining risk factors for glove and gown contamination by carbapenem-resistant Enterobacterales (CRE). The CRKp isolates exhibited considerable genomic diversity with 58 multilocus sequence types (STs), including four newly designated STs. ST258 was the most prevalent ST, representing 31% (52/166) of the CRKp isolates, but was similarly prevalent among patients who had high, intermediate, and low CRKp transmission. Increased transmission was associated with clinical characteristics including a nasogastric (NG) tube or an endotracheal tube or tracheostomy (ETT/Trach). Overall, our findings provide important insight into the diversity of CRKp associated with transmission from patients to the gloves and gowns of HCP. These findings suggest that certain clinical characteristics and the presence of CRKp in the respiratory tract, rather than specific lineages or genetic content, are more often associated with increased transmission of CRKp from patients to HCP. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a significant public health concern that has contributed to the spread of carbapenem resistance and has been linked to high morbidity and mortality. Transmission of K. pneumoniae among patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings; however, it remains unknown whether particular bacterial characteristics are associated with increased CRKp transmission. Using comparative genomics, we demonstrate that CRKp isolates associated with high or intermediate transmission exhibit considerable genomic diversity, and there were no K. pneumoniae lineages or genes that were universally predictive of increased transmission. Our findings suggest that certain clinical characteristics and the presence of CRKp, rather than specific lineages or genetic content of CRKp, are more often associated with increased transmission of CRKp from patients to HCP.

Multiplicity of blaKPC Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307

In 2021, Klebsiella pneumoniae sequence type 307 (ST307) strains causing pulmonary and bloodstream infections identified in a hospital in Rome, Italy, reached high levels of resistance to ceftazidime-avibactam (CZA). One of these strains reached high levels of resistance to both CZA and carbapenems and carried two copies of blaKPC-3 and one copy of blaKPC-31 located on plasmid pKpQIL. The genomes and plasmids of CZA-resistant ST307 strains were analyzed to identify the molecular mechanisms leading to the evolution of resistance and compared with ST307 genomes at local and global levels. A complex pattern of multiple plasmids in rearranged configurations, coresident within the CZA-carbapenem-resistant K. pneumoniae strain, was observed. Characterization of these plasmids revealed recombination and segregation events explaining why K. pneumoniae isolates from the same patient had different antibiotic resistance profiles. This study illustrates the intense genetic plasticity occurring in ST307, one of the most worldwide-diffused K. pneumoniae high-risk clones.

Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICEKp) among Nonoutbreak OXA-48-Producing Klebsiella pneumoniae Clinical Isolates from Spain and the Netherlands

In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with the spread of OXA-48-producing Klebsiella pneumoniae clinical isolates from The Netherlands (n = 61) and Spain (n = 53). Most isolates shared a chromosomally encoded core of virulence factors, including the enterobactin gene cluster, fimbrial fim and mrk gene clusters, and urea metabolism genes (ureAD). We observed a high diversity of K-Locus and K/O loci combinations, KL17 and KL24 (both 16%), and the O1/O2v1 locus (51%) being the most prevalent in our study. The most prevalent accessory virulence factor was the yersiniabactin gene cluster (66.7%). We found seven yersiniabactin lineages-ybt 9, ybt 10, ybt 13, ybt 14, ybt 16, ybt 17, and ybt 27-which were chromosomally embedded in seven integrative conjugative elements (ICEKp): ICEKp3, ICEKp4, ICEKp2, ICEKp5, ICEKp12, ICEKp10, and ICEKp22, respectively. Multidrug-resistant lineages-ST11, ST101, and ST405-were associated with ybt 10/ICEKp4, ybt 9/ICEKp3, and ybt 27/ICEKp22, respectively. The fimbrial adhesin kpi operon (kpiABCDEFG) was predominant among ST14, ST15, and ST405 isolates, as well as the ferric uptake system kfuABC, which was also predominant among ST101 isolates. No convergence of hypervirulence and resistance was observed in this collection of OXA-48-producing K. pneumoniae clinical isolates. Nevertheless, two isolates, ST133 and ST792, were positive for the genotoxin colibactin gene cluster (ICEKp10). In this study, the integrative conjugative element, ICEKp, was the major vehicle for yersiniabactin and colibactin gene clusters spreading. IMPORTANCE Convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae isolates has been reported mostly related to sporadic cases or small outbreaks. Nevertheless, little is known about the real prevalence of carbapenem-resistant hypervirulent K. pneumoniae since these two phenomena are often separately studied. In this study, we gathered information on the virulent content of nonoutbreak, high-risk clones (i.e., ST11, ST15, and ST405) and other less common STs associated with the spread of OXA-48-producing K. pneumoniae clinical isolates. The study of virulence content in nonoutbreak isolates can help us to expand information on the genomic landscape of virulence factors in K. pneumoniae population by identifying virulence markers and their mechanisms of spread. Surveillance should focus not only on antimicrobial resistance but also on virulence characteristics to avoid the spread of multidrug and (hyper)virulent K. pneumoniae that may cause untreatable and more severe infections.

Hypermucoviscosity Regulator RmpD Interacts with Wzc and Controls Capsular Polysaccharide Chain Length

Klebsiella pneumoniae is a leading cause of nosocomial infections, including pneumonia, bacteremia, and urinary tract infections. Treatment options are increasingly restricted by the high prevalence of resistance to frontline antibiotics, including carbapenems, and the recently identified plasmid-conferred colistin resistance. The classical pathotype (cKp) is responsible for most of the nosocomial infections observed globally, and these isolates are often multidrug resistant. The hypervirulent pathotype (hvKp) is a primary pathogen capable of causing community-acquired infections in immunocompetent hosts. The hypermucoviscosity (HMV) phenotype is strongly associated with the increased virulence of hvKp isolates. Recent studies demonstrated that HMV requires capsule (CPS) synthesis and the small protein RmpD but is not dependent on the increased amount of capsule associated with hvKp. Here, we identified the structure of the capsular and extracellular polysaccharide isolated from hvKp strain KPPR1S (serotype K2) with and without RmpD. We found that the polymer repeat unit structure is the same in both strains and that it is identical to the K2 capsule. However, the chain length of CPS produced by strains expressing rmpD demonstrates more uniform length. This property was reconstituted in CPS from Escherichia coli isolates that possess the same CPS biosynthesis pathway as K. pneumoniae but naturally lack rmpD. Furthermore, we demonstrate that RmpD binds Wzc, a conserved capsule biosynthesis protein required for CPS polymerization and export. Based on these observations, we present a model for how the interaction of RmpD with Wzc could impact CPS chain length and HMV. IMPORTANCE Infections caused by Klebsiella pneumoniae continue to be a global public health threat; the treatment of these infections is complicated by the high frequency of multidrug resistance. K. pneumoniae produces a polysaccharide capsule required for virulence. Hypervirulent isolates also have a hypermucoviscous (HMV) phenotype that increases virulence, and we recently demonstrated that a horizontally acquired gene, rmpD, is required for HMV and hypervirulence but that the identity of the polymeric product(s) in HMV isolates is uncertain. Here, we demonstrate that RmpD regulates capsule chain length and interacts with Wzc, a part of the capsule polymerization and export machinery shared by many pathogens. We further show that RmpD confers HMV and regulates capsule chain length in a heterologous host (E. coli). As Wzc is a conserved protein found in many pathogens, it is possible that RmpD-mediated HMV and increased virulence may not be restricted to K. pneumoniae.

A Nationwide Genomic Study of Clinical Klebsiella pneumoniae Carrying blaOXA-232 and rmtF in China

OXA-232 carbapenemase is becoming a threat in China due to its high prevalence, mortality, and limited treatment options. However, little information is available on the impact of OXA-232-producing Klebsiella pneumoniae in China. This study aims to characterize the clonal relationships, the genetic mechanisms of resistance, and the virulence of OXA-232-producing K. pneumoniae isolates in China. We collected 81 OXA-232-producing K. pneumoniae clinical isolates from 2017 to 2021. Antimicrobial susceptibility testing was performed using the broth microdilution method. Capsular types, multilocus sequence types, virulence genes, antimicrobial resistance (AMR) determinants, plasmid replicon types, and single-nucleotide polymorphism (SNP) phylogeny were inferred from whole-genome sequences. OXA-232-producing K. pneumoniae strains were resistant to most antimicrobial agents. These isolates showed partial differences in susceptibility to carbapenems: all strains were resistant to ertapenem, while the resistance rates to imipenem and meropenem were 67.9% and 97.5%, respectively. Sequencing and capsular diversity analysis of the 81 K. pneumoniae isolates revealed 3 sequence types (ST15, ST231, and one novel ST [ST-V]), 2 K-locus types (KL112 and KL51), and 2 O-locus types (O2V1 and O2V2). The predominant plasmid replicon types associated with the OXA-232 and rmtF genes were ColKP3 (100%) and IncFIB-like (100%). Our study summarized the genetic characteristics of OXA-232-producing K. pneumoniae circulating in China. The results demonstrate the practical applicability of genomic surveillance and its utility in providing methods to prevent transmission. It alerts us to the urgent need for longitudinal surveillance of these transmissible lineages. IMPORTANCE In recent years, the detection rate of carbapenem-resistant K. pneumoniae has increased and represents a major threat to clinical anti-infective therapy. Compared with KPC-type carbapenemases and NDM-type metallo-β-lactamases, OXA-48 family carbapenemases are another important resistance mechanism mediating bacterial resistance to carbapenems. In this study, we investigated the molecular characteristics of OXA-232 carbapenemase-producing K. pneumoniae isolated from several hospitals to clarify the epidemiological dissemination characteristics of such drug-resistant strains in China.

Population dynamics and characteristics of Klebsiella pneumoniae from healthy poultry in Norway

Klebsiella pneumoniae is an important opportunistic pathogen widely studied in relation to human infection and colonization. However, there is a lack of knowledge regarding other niches that K. pneumoniae may inhabit. K. pneumoniae isolated from healthy broiler and turkey flocks in Norway in 2018 have previously been described with regard to population structure, sequence types (STs), and the presence of virulence- and antimicrobial resistance (AMR) genes. In the present study we aimed to evaluate the dynamics of the K. pneumoniae population in poultry over time, with regards to AMR and virulence, and with a special focus on persistence of STs. A total of 391 flocks sampled in 2020 were included in the present study, of which 271 were from broiler flocks and 120 from turkey flocks. Similar to findings from 2018, the occurrence of K. pneumoniae was significantly higher based on culturing in turkey flocks (62.5%) compared to broiler flocks (24.0%). Major STs in 2020 included ST5827 (n = 7), ST37 (n = 7), ST370 (n = 7), ST17 (n = 5), and ST4710 (n = 5). Several STs persisted over time in both host species, including ST35, ST37, ST590, and ST17. This persistence may be due to local re-circulation or reintroduction from parent flocks. Of these five major STs, only ST590 carried AMR genes, indicating that the persistence was not associated with the presence of AMR genes. An ST4710 strain with a hypervirulence-encoding plasmid (p4710; iro5, iuc5) was recovered from turkeys in 2018. The same strain was present in turkeys in 2020, but the plasmid had lost the salmochelin locus. This loss may be attributed to reductive evolution due to the presence of several siderophores within the same isolates. In this study we also characterized a clinical ST4710 isolate from a turkey with airsacculitis. The isolate was closely related to two intestinal ST4710 isolates from healthy turkeys in 2018. These three isolates were sampled within the same location and time frame in 2018, and all carried the full p4710 virulence plasmid. These findings highlight the transmission- and infectious potential of ST4710 in turkeys.

A panel of diverse Klebsiella pneumoniae clinical isolates for research and development

Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.

Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes

Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.

Molecular analysis of clinical Citrobacter spp. isolates: Acquisition of the Yersinia high-pathogenicity island mediated by ICEkp in C. freundii

Background

Studies on Citrobacter spp. are limited, hindering our understanding of its species evolution and medical relevance.

Methods

A total of 164 clinical Citrobacter spp. isolates were collected from 2017 to 2020 and identified by VITEK MALDI-TOF MS or VITEK-2 Gram-Negative Identification Card. All isolates were further analyzed by whole-genome sequencing using a HiSeq sequencer. All sequences were processed using different modules of the PGCGAP integrated package: Prokka and fastANI were used for annotation and average nucleotide identification (ANI), respectively. Antibiotic resistance and virulence genes were identified by searching CARD, ResFinder, and VFDB databases, respectively. Strains were identified using Ribosomal Multi-locus Sequence Typing (rMLST) classification based on 53 ribosome protein subunits (rps). The evolutionary relationship was analyzed using kSNP3 and visualized by iTOL editor v1_1. Genetic environments were compared by BLAST and visualized by Easyfig 2.2.5. The pathogenicity of some Citrobacter freundii isolates was confirmed by Galleria mellonella larvae infection test.

Results

A total of 14 species of Citrobacter spp. were identified from 164 isolates. However, 27 and 11 isolates were incorrectly identified as C. freundii and Citrobacter braakii by MALDI-TOF MS, respectively. In addition, MS also failed to identify Citrobacter portucalensis. The virulence genes mainly encoded proteins related to flagella and iron uptake systems. Citrobacter koseri isolates (n = 28) contained two iron uptake systems, coding yersiniabactin and aerobactin, respectively. C. braakii isolates (n = 32), like Salmonella, carried Vi capsule polysaccharide synthesis genes. The yersiniabactin gene clusters identified in five C. freundii isolates are located on various ICEkp elements and have not been reported previously. Moreover, ICEkp-carrying C. freundii showed diverse pathogenic features.

Conclusion

Conventional methods have significant defects in identifying Citrobacter spp. ICEkp-like elements-mediated acquirement of the Yersinia high-pathogenicity island was identified for the first time in C. freundii.

Modelling the Gastrointestinal Carriage of Klebsiella pneumoniae Infections

Klebsiella pneumoniae is a leading cause of nosocomial and community acquired infections, making K. pneumoniae the pathogen that is associated with the second largest number of deaths attributed to any antibiotic resistant infection. K. pneumoniae colonizes the nasopharynx and the gastrointestinal tract in an asymptomatic manner without dissemination to other tissues. Importantly, gastrointestinal colonization is a requisite for infection. Our understanding of K. pneumoniae colonization is still based on interrogating mouse models in which animals are pretreated with antibiotics to disturb the colonization resistance imposed by the gut microbiome. In these models, infections disseminate to other tissues. Here, we report a murine model to allow for the study of the gastrointestinal colonization of K. pneumoniae without tissue dissemination. Hypervirulent and antibiotic resistant strains stably colonize the gastrointestinal tract of in an inbred mouse population without antibiotic treatment. The small intestine is the primary site of colonization and is followed by a transition to the colon over time, without dissemination to other tissues. Our model recapitulates the disease dynamics of the metastatic K. pneumoniae strains that are able to disseminate from the gastrointestinal tract to other sterile sites. Colonization is associated with mild to moderate histopathology, no significant inflammation, and no effect on the richness of the microbiome. Our model sums up the clinical scenario in which antibiotic treatment disturbs the colonization of K. pneumoniae and results in dissemination to other tissues. Finally, we establish that the capsule polysaccharide is necessary for the colonization of the large intestine, whereas the type VI secretion system contributes to colonization across the gastrointestinal tract. IMPORTANCE Klebsiella pneumoniae is one of the pathogens that is sweeping the world in the antibiotic resistance pandemic. Klebsiella colonizes the nasopharynx and the gut of healthy subjects in an asymptomatic manner, making gut colonization a requisite for infection. This makes it essential to understand the gastrointestinal carriage in preventing Klebsiella infections. Current research models rely on the perturbation of the gut microbiome by antibiotics, resulting in an invasive infection. Here, we report a new model of K. pneumoniae gut colonization that recapitulates key features of the asymptomatic human gastrointestinal tract colonization. In our model, there is no need to disturb the microbiota to achieve stable colonization, and there is no dissemination to other tissues. Our model sums up the clinical scenario in which antibiotic treatment triggers invasive infection. We envision that our model will be an excellent platform upon which to investigate factors enhancing colonization and invasive infections and to test therapeutics to eliminate Klebsiella asymptomatic colonization.