Molecular Epidemiology of Hypervirulent Carbapenemase-Producing Klebsiella pneumoniae

Large-scale comparative analysis reveals phylogenomic preference of blaNDM-1 and blaKPC-2 transmission among Klebsiella pneumoniae

blaNDM-1 and blaKPC-2 are responsible for the global increase in carbapenem-resistant Klebsiella pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on the dissemination of blaNDM-1 and blaKPC-2 is not yet fully understood. This study established a global dataset of 4051 blaNDM-1+ and 10,223 blaKPC-2+ K. pneumoniae genomes, and compared their transmission modes on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher sequence type (ST) richness than blaKPC-2+ genomes, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant differences in ST lineage, antibiotic resistance gene composition, virulence gene composition and genetic environments compared with blaKPC-2+ genomes, suggesting distinct dissemination mechanisms. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast, blaNDM-1+ genomes did not display such a strong preference, confirming that the dissemination of blaNDM-1 mainly depends on horizontal gene transfer. Overall, this study demonstrates different phylogenetic drivers for the dissemination of blaNDM-1 and blaKPC-2, providing new insights into their global transmission dynamics.

Virulence Factors in Klebsiella pneumoniae: A Literature Review

Klebsiella pneumoniae, a member of the autochthonous human gut microbiota, utilizes a variety of virulence factors for survival and pathogenesis. Consequently, it is responsible for several human infections, including urinary tract infections, respiratory tract infections, liver abscess, meningitis, bloodstream infections, and medical device-associated infections. The main studied virulence factors in K. pneumoniae are capsule-associated, fimbriae, siderophores, Klebsiella ferric iron uptake, and the ability to metabolize allantoin. They are crucial for virulence and were associated with specific infections in the mice infection model. Notably, these factors are also prevalent in strains from the same infections in humans. However, the type and quantity of virulence factors may vary between strains, which defines the degree of pathogenicity. In this review, we summarize the main virulence factors investigated in K. pneumoniae from different human infections. We also cover the specific identification genes and their prevalence in K. pneumoniae, especially in hypervirulent strains.

Virulent Klebsiella pneumoniae ST11 clone carrying blaKPC and blaNDM from patients with and without COVID-19 in Brazil

AIMS

Investigated and compared the occurrence of virulence genes fimH, mrkD, irp2, entB, cps, rmpA, and wabG, resistance genes blaKPC and blaNDM, and the genetic variability and clonal relationship of 29 Klebsiella pneumoniae clinical isolates of patients with and without COVID-19, from a hospital in Brazil.

METHODS AND RESULTS

All isolates were resistant to beta-lactams. The genes were investigated by PCR, and for molecular typing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and MLST were used. The detection of blaNDM was greater (n = 23) when compared to that of blaKPC (n = 14). The virulence genes that most occurred were fimH, entB, cps, and wabG, which are responsible for adhesins, siderophore enterobactin, capsule, and lipopolysaccharides, respectively. Among the isolates, 21 distinct genetic profiles were found by ERIC-PCR, with multiclonal dissemination. Four isolates belonged to the ST11 clone.

CONCLUSIONS

The occurrence of the ST11 is worrying as it is a high-risk clone involved in the dissemination of virulent strains throughout the world.

Analysis of virulence profiles in clinical isolates of Klebsiella pneumoniae from renal abscesses: clinical significance of hypervirulent isolates

Introduction

Klebsiella pneumoniae can cause a wide range of infections. Hypervirulent K. pneumoniae (hvKp), particularly associated with the K1 and K2 capsular types, is an increasingly significant microorganism with the potential to cause invasive infections, including renal abscesses. Despite the rising prevalence of hvKp infections, information on renal abscesses caused by K. pneumoniae is limited, and the clinical significance of hvKp associated with specific virulence genes remains elusive.

Methods

This study performed at a 1200-bed tertiary hospital sought to identify the clinical and microbiological characteristics of renal abscesses caused by K. pneumoniae, focusing on various virulence genes, including capsular serotypes and multilocus sequence typing (MLST).

Results

Over an 8-year period, 64 patients with suspected renal abscesses were reviewed. Ten patients diagnosed with K. pneumoniae-related renal abscesses were ultimately enrolled in the study. Among the isolates from the 10 patients, capsular serotype K2 was predominant (40.0%), followed by K1 (30.0%). The most common sequence type by MLST was 23 (40.0%). In particular, six patients (60.0%) harbored specific genes indicative of hvKp: iucA, peg-344, rmpA, and rmpA2.

Conclusions

Our findings highlight the importance of hvKp as a pathogen in renal abscesses. Although the nature of hvKp is relatively unknown, it is widely recognized as a highly virulent pathogen that can infect relatively healthy individuals of various ages and simultaneously cause infections at multiple anatomical sites. Therefore, when treating patients with K. pneumoniae-related renal abscesses, caution is necessary when considering the characteristics of hvKp, such as potential bacteremia, multi-organ abscess formation, and metastatic spread.

Development of a quadruple qRT-PCR assay for simultaneous identification of hypervirulent and carbapenem-resistant Klebsiella pneumoniae

IMPORTANCE

Globally, the increasing number of hypervirulent Klebsiella pneumoniae (hvKp) and carbapenem-resistant Kp (CR-Kp) infections poses a huge public health challenge with high morbidity and mortality. Worrisomely, due to the mobility of elements carrying virulence and drug-resistance genes, the increasing prevalence of CR-hvKp has also been found with an overwhelming mortality rate in recent years. However, the current detection methods for hvKp and CR-Kp have many disadvantages, such as long turnaround time, complex operation, low sensitivity, and specificity. Herein, a more sensitive, rapid, single-reaction, and multiplex quantitative real-time PCR was developed and validated to differentiate the circulating lineages of Kp with excellent performance in sensitivity and specificity, providing a useful tool for the differential diagnosis and the surveillance of the circulating Kp.

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

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

Genetic and Functional Analysis of the pks Gene in Clinical Klebsiella pneumoniae Isolates

The pks gene cluster encodes colibactin, which can cause DNA damage and enhance the virulence in Escherichia coli. However, the role of the pks gene in Klebsiella pneumoniae has not been fully discussed. The aim of this study was to analyze the relationship between the pks gene cluster and virulence factors, as well as to assess antibiotic resistance and biofilm formation capacity in clinical isolates of Klebsiella pneumoniae. Thirty-eight of 95 clinical K. pneumoniae strains were pks positive. pks-positive strains usually infected emergency department patients, and pks-negative strains often infected hospitalized patients. The positive rates of K1 capsular serotype and hypervirulence genes (peg-344, rmpA, rmpA2, iucA, and iroB) were significantly higher in the pks-positive isolates than the pks-negative isolates (P < 0.05). The biofilm formation ability of pks-positive isolates was stronger than that of pks-negative isolates. Antibacterial drug susceptibility test showed the resistance of pks-positive isolates was weaker than that of pks-negative isolates. In conclusion, patients with pks-positive K. pneumoniae infection might have worse treatment outcomes and prognosis. pks-positive K. pneumoniae might have stronger virulence and pathogenicity. Clinical infection with pks-positive K. pneumoniae needs further attention. IMPORTANCE The infection rate with pks-positive K. pneumoniae has been increasing in recent years. Two previous surveys in Taiwan reported 25.6% pks gene islands and 16.7% pks-positive K. pneumoniae strains in bloodstream infections, and Chinese scholars also did a survey of K. pneumoniae bloodstream infections in Changsha, China, and found 26.8% pks-positive K. pneumoniae. In addition, it was found that the pks gene cluster might encode colibactin, which could be related to the virulence of K. pneumoniae. Studies confirmed that the prevalence of colibactin-producing K. pneumoniae was increasing. It is necessary to consider the clear relationship between the pks gene cluster and high pathogenicity in K. pneumoniae.

Functional Characterization of Plasmid-Borne rmpADC Homologues in Klebsiella pneumoniae

Expression of the hypermucoviscosity (HMV) phenotype and capsular polysaccharide (CPS) biosynthesis in Klebsiella pneumoniae were reported to be encoded by genes located in the chromosomal rmp locus. However, the functions of the rmp locus in the virulence plasmid remained unclear, and most of the rmp loci in clinical K. pneumoniae are plasmid carried. In this study, we investigated the functional characteristics of plasmid-borne rmp homologues in clinical hypervirulent K. pneumoniae (hvKP) strains by cloning and introducing such gene homologues into K. pneumoniae strains of different capsule types, followed by the evaluation of phenotypic changes in these strains. Acquisition of the plasmid-borne prmpADC and prmpA2D2 loci were found to result in an increase in mucoviscosity and CPS production in K1 and K2 K. pneumoniae, while only the prmpA2D2 locus contributed to phenotypic changes in the ST11/KL64 strain. Consistently, both rmpD and rmpD2 increased HMV in K1 and K2 K. pneumoniae, while only rmpD2 contributed to HMV in the ST11/KL64 strain; rmpC contributed to CPS overproduction in K1 and K2 strains but not in the ST11/KL64 strain. Furthermore, we proposed a logistic molecular basis of the HMV phenotype of K. pneumoniae on which prmpD2-mediated HMV is attributed to the increase of cell-free CPS production. Our data confirm that the rmp homologues carried by the virulence plasmid play a key role in virulence expression in K. pneumoniae, but the phenotype is highly dependent on the genetic background of the host strain and explained why most of the clinical ST11 strains carry only the prmpA2D2 locus. IMPORTANCE Klebsiella pneumoniae has become the most frequently isolated bacterial pathogen in hospital settings, with a very high mortality rate worldwide. Factors contributing to the virulence of K. pneumoniae are the overproduction of capsular polysaccharide (CPS) as well as the hypermucoviscosity (HMV) phenotype. These two phenotypes were reported to be regulated by rmpA/A2 homologues, which are often carried by virulence plasmids. Here, we determined the functional role of two plasmid-borne rmpA in mediating expression of the HMV phenotype and CPS production in K. pneumoniae. Different capsule types exhibited differences in the expression of HMV and CPS production although they harbored an identical plasmid-borne rmpA or rmpA2 locus, indicating that these virulence-related phenotypes are strongly related to the genetic background of the host strains. Our study provides a novel understanding of the regulation of virulence-related phenotypes and clinical management of K. pneumoniae infections.

Association between Intestinal Colonization and Extraintestinal Infection with Carbapenem-Resistant Klebsiella pneumoniae in Children

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a critical public health threat. However, the association between intestinal colonization and parenteral infection among pediatric patients has not been elucidated. We collected 8 fecal CRKP strains and 10 corresponding CRKP strains responsible for extraintestinal infection from eight patients who did not manifest infection upon admission to the hospital. Paired isolates showed identical resistance to antimicrobials and identical virulence in vitro and in vivo. wzi capsule typing, multilocus sequence typing, and whole-genome sequencing (WGS) indicated high similarity between paired colonizing and infecting isolates. Mutations between colonizing and infecting isolate pairs found by WGS had a distinctive molecular signature of a high proportion of complex structural variants. The mutated genes were involved in pathways associated with infection-related physiological and pathogenic functions, including antibiotic resistance, virulence, and response to the extracellular environment. The latter is important for bacterial infection of environmental niches. Various mutations related to antibiotic resistance, virulence, and colonization that were not associated with any particular mutational hot spot correlated with an increased risk of extraintestinal infection. Notably, novel subclone carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) KL19-ST15 exhibited hypervirulence in experimental assays that reflected the severe clinical symptoms of two patients infected with the clonal strains. Taken together, our findings indicate the association between CRKP intestinal colonization and extraintestinal infection, suggesting that active screening for colonization on admission could decrease infection risk in children. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes an increasing number of nosocomial infections, which can be life-threatening, as carbapenems are last-resort antibiotics. K. pneumoniae is part of the healthy human microbiome, and this provides a potential advantage for infection. This study demonstrated that CRKP intestinal colonization is strongly linked to extraintestinal infection, based on the evidence given by whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence. Apart from these findings, our in-depth analysis of point mutations and chromosome structural variants in patient-specific infecting isolates compared with colonizing isolates may contribute insights into bacterial adaptation underlying CRKP infection. In addition, a novel subclone of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) was observed in the study. This finding highlights the importance of CRKP active surveillance among children, targeting in particular the novel high-risk CR-hvKP clone.

Characterization of KPC-2-producing Klebsiella pneumoniae and affected patients of a pediatric hospital in Brazil

Carbapenemase-producing Klebsiella pneumoniae (CPKp) infections are important threats to pediatric populations. Thus, a retrospective study was conducted in a Brazilian reference pediatric hospital, and 26 CPKp isolates obtained from 23 patients were characterized. The affected population had important underlying diseases, reflecting previous hospitalization and antibiotic use. Most CPKp isolates were resistant to all antibiotic classes, and bla_KPC-2 was the only carbapenemase-encoding gene. bla_CTX-M-15 was common among the isolates, and modification or absence of the mgrB gene was the cause of polymyxin B resistance. Ten different sequence types were identified, and clonal complex 258 was prevalent. Alleles wzi50 and wzi64 were the most recurrent ones regarding K-locus type, with a remarkable contribution of the epidemic ST11/KL64 lineage as a colonizer. Our findings show that lineages associated with the pediatric population are similar to those found in adults, reinforcing the need for epidemiological surveillance to effectively implement prevention and control measures.

Carbapenem-Resistant Klebsiella pneumoniae: Virulence Factors, Molecular Epidemiology and Latest Updates in Treatment Options

Klebsiella pneumoniae is a Gram-negative opportunistic pathogen responsible for a variety of community and hospital infections. Infections caused by carbapenem-resistant K. pneumoniae (CRKP) constitute a major threat for public health and are strongly associated with high rates of mortality, especially in immunocompromised and critically ill patients. Adhesive fimbriae, capsule, lipopolysaccharide (LPS), and siderophores or iron carriers constitute the main virulence factors which contribute to the pathogenicity of K. pneumoniae. Colistin and tigecycline constitute some of the last resorts for the treatment of CRKP infections. Carbapenemase production, especially K. pneumoniae carbapenemase (KPC) and metallo-β-lactamase (MBL), constitutes the basic molecular mechanism of CRKP emergence. Knowledge of the mechanism of CRKP appearance is crucial, as it can determine the selection of the most suitable antimicrobial agent among those most recently launched. Plazomicin, eravacycline, cefiderocol, temocillin, ceftolozane-tazobactam, imipenem-cilastatin/relebactam, meropenem-vaborbactam, ceftazidime-avibactam and aztreonam-avibactam constitute potent alternatives for treating CRKP infections. The aim of the current review is to highlight the virulence factors and molecular pathogenesis of CRKP and provide recent updates on the molecular epidemiology and antimicrobial treatment options.

The making of hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae is a notorious bacterium in clinical practice. Virulence, carbapenem-resistance and their convergence among K. pneumoniae are extensively discussed in this article. Hypervirulent K. pneumoniae (HvKP) has spread from the Asian Pacific Rim to the world, inducing various invasive infections, such as pyogenic liver abscess, endophthalmitis, and meningitis. Furthermore, HvKP has acquired more and more drug resistance. Among multidrug-resistant HvKP, hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP), and carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) are both devastating for their extreme drug resistance and virulence. The hypervirulence of HvKP is primarily attributed to hypercapsule, macromolecular exopolysaccharides, or excessive siderophores, although it has many other factors, for example, lipopolysaccharides, fimbriae, and porins. In contrast with classical determination of HvKP, that is, animal lethality test, molecular determination could be an optional and practical method after improvement. HvKP, including Hv-CRKP and CR-HvKP, has been progressing. R-M and CRISPR-Cas systems may play pivotal roles in such evolutions. Hv-CRKP and CR-HvKP, in particular the former, should be of severe concern due to their being more and more prevalent.

Pyogenic liver abscess-caused Klebsiella pneumoniae in a tertiary hospital in China in 2017: implication of hypervirulent carbapenem-resistant strains

Background

To investigate the epidemiology of Klebsiella pneumoniae (K. pneumoniae) inducing pyogenic liver abscess (PLA) in east China and the role of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP).

Methods

Forty-three K. pneumoniae strains were collected from 43 patients with PLA at Hangzhou, China in 2017. Antimicrobial susceptibility tests, string test, multilocus sequence typing, pulsed-field gel electrophoresis, mobile genetic elements typing, regular PCR and sequencing, and Galleria mellonella (G. mellonella) lethality test were used to elucidate the epidemiology. Clinical data were collected.

Results

K. pneumoniae strains with serotypes K1 and K2 accounted for 69.8%, which shared 46.5% and 23.3% respectively. K. pneumoniae strains with clonal group 23 were predominant with a rate of 34.9%. Such antimicrobials showed susceptible rates over 80.0%: cefuroxime, cefotaxime, gentamycin, ticarcillin/clavulanate, ceftazidime, cefoperazone/tazobactam, cefepime, aztreonam, imipenem, meropenem, amikacin, tobramycin, ciprofloxacin, levofloxacin, doxycycline, minocycline, tigecycline, chloramphenicol, and trimethoprim-sulfamethoxazole. PFGE dendrogram showed 29 clusters for the 43 K. pneumoniae strains. Three Hv-CRKP strains were confirmed by G. mellonella lethality test, showing a constituent ratio of 7.0% (3/43). Totally three deaths were found, presenting a rate of 7.0% (3/43). The three died patients were all infected with Hv-CRKP.

Conclusions

K1 and K2 are the leading serotypes of K. pneumoniae causing PLA, which show highly divergent genetic backgrounds. Aminoglycosides, Generation 2^nd to 4^th cephalosporins, β-lactamase/β-lactamase inhibitors, carbapenems, fluoroquinolones are empirical choices. Hv-CRKP may confer an urgent challenge in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07648-0.

A Case of Meningitis in an Infant Due to Hypervirulent Klebsiella pneumoniae Transmission Within a Family

Hypervirulent Klebsiella pneumoniae (hvKP), an emerging pathotype derived from K. pneumoniae, frequently causes invasive infections of multiple organs and is associated with both high disability and fatality rates. In this study, a case of meningitis in a young infant caused by hvKP is presented. Cytological and biochemical examinations of the cerebrospinal fluid (CSF) revealed purulent meningitis, a diagnosis that was confirmed by a positive CSF culture result. The pathogen was identified as hvKP through analysis of positive virulence-associated genes. Meanwhile, hvKP was also isolated from stool samples of both the infant and her father. Antimicrobial susceptibility, capsular typing, and multilocus sequence typing (MLST) of three isolates from the infant’s CSF and stool and her father’s stool samples were analyzed. The three K. pneumoniae isolates were susceptible to all antibiotics except ampicillin and were identified as capsular serotype K2 and sequence type 86. These genetic relatedness analyses indicated that the strain isolated from the infant’s CSF might have originated from her father’s stool via familial transmission. This case is the first report of meningitis in an infant due to hvKP transmitted within a family.

Prevalence of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae and Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae in China Determined via Mouse Lethality Tests

Objective

To investigate the epidemiology of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-HvKP) and hypervirulent carbapenem-resistant Klebsiella pneumoniae (Hv-CRKP).

Methods

Totally 436 K. pneumoniae strains were collected from 7 hospitals in mainland China between 2017.01 and 2018.02. Sequence types, serotypes, antimicrobial-resistance and virulence genes were analyzed. Additionally, string test, capsule stain, Periodic Acid Schiff stain, fitness analysis, quantitative real-time PCR and mouse lethality test were also performed. Molecular combinations were used to screen putative bla_KPC(+)-HvKP and Hv-bla_KPC(+)-KP, followed by the confirmation of mouse lethality test.

Results

Diverse detection rates were found for the virulence genes, ranging from c-rmpA (0.0%) to entB (100.0%). According to the molecular criteria, 127, 186, 9 and 26 strains were putatively denoted as HvKP, bla_KPC(+)-KP, bla_KPC(+)-HvKP and Hv-bla_KPC(+)-KP. Mouse lethality test confirmed 2 bla_KPC(+)-HvKP strains (JS184 and TZ20) and no Hv-bla_KPC(+)-KP. JS184 showed K2 serotype, thin capsule, positive exopolysaccharid and string test. TZ20 presented K20 serotype, thin capsule, negative exopolysaccharide and string test. Compared with the positive control NTUH-K2044, equal galF expression and growth curves were confirmed for JS184 and TZ20.

Conclusions

Molecular determination of CR-HvKP and Hv-CRKP brings remarkable bias compared with mouse lethality test. The exact prevalence of CR-HvKP is less than 1.0%, which of Hv-CRKP is much lower.

Prostatic Abscess Caused by Klebsiella pneumoniae: A 6-Year Single-Center Study

Hypervirulent Klebsiella pneumoniae (hvKp) is an important strain that can cause multiple organ infections. Although hvKp infection cases are increasing, there is limited information on the prostatic abscesses caused by K. pneumoniae. Furthermore, the clinical significance of hvKp associated with K1 or K2 capsular types or virulence genes in prostatic abscesses remains unclear. Therefore, we aimed to elucidate the clinical and microbiological characteristics of prostatic abscesses caused by K. pneumoniae in relation to various virulence genes. A retrospective study was performed at a 1200-bed tertiary hospital between January 2014 and December 2019. Patients diagnosed with prostatic abscesses with K. pneumoniae isolated from blood, urine, pus, or tissue cultures were enrolled in this study. Our results demonstrate that 30.3% (10/33) of the prostatic abscesses were caused by K. pneumoniae. All strains isolated from patients with prostatic abscesses due to K. pneumoniae were the K1 capsular type, and eight patients (80.0%) carried rmpA and iutA genes that identified hvKp. These findings suggest that hvKp is an important pathogen in prostatic abscesses. Therefore, when treating patients with K. pneumoniae prostatic abscesses, attention should be paid to the characteristics of hvKp, such as bacteremia, multiorgan abscess formation, and metastatic spread.

Changes in molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in the intensive care units of a Greek hospital, 2018-2021

The spread of multi-drug resistant (MDR) Gram-negative bacteria, including Klebsiella pneumoniae, constitutes a global threat. The most frequent mechanism of acquired carbapenem resistance is the production of carbapenemases, especially KPC, NDM, VIM, IMP and OXA-48. We analyzed the epidemiological trend of carbapenem resistance genes of carbapenem-resistant K. pneumoniae (CRKP) strains isolated from critically ill patients in a Greek tertiary hospital. The study included 150 CRKP isolates collected from 116 (77.4%) patients hospitalized in the adult ICU and 17 (11.3%) each in the pediatric and the two neonatal ICUs between March 2018 and March 2021. Identification and antimicrobial susceptibility testing were performed using VITEK-2. A multiplex lateral flow immunoassay was used for the detection of carbapenemases, while the detection of bla VIM, bla KPC, bla NDM, bla IMP and bla OXA-48-like genes was achieved by multiplex PCR. The bla NDM was mainly detected in adults (54/116, 46.9%), while in children the most often detected gene was bla KPC (24/34, 70.6%). The predominant carbapenem resistance gene during 2018-2019 was bla KPC alone or in combination with bla VIM, reaching 44.4% in 2019, while during 2020-2021 the detection of bla NDM prevailed significantly, reaching 45.5 and 60.7% for 2020 and 2021, respectively. A shift in the molecular epidemiology of CRKP was seen during 2018-2021, which is probably associated with the recent excessive empiric use of newer antimicrobials. Surveillance studies and proper and strict implementation of infection control measures are highly needed to decrease the spread of MDR bacteria, including CRKP.

Antimicrobial Susceptibility, Virulence, and Genomic Features of a Hypervirulent Serotype K2, ST65 Klebsiella pneumoniae Causing Meningitis in Italy

The rise of a new hypervirulent variant of Klebsiella pneumoniae (hvKp) was recently reported, mainly linked to the ST23 lineage. The hvKp variants can cause severe infections, including hepatic abscesses, bacteremia, and meningitis, with a particularly disconcerting propensity to cause community-acquired, life-threatening infection among young and otherwise healthy individuals. The present study aimed to report the clinical characteristics of a hypermucoviscous K. pneumoniae strain isolated in Italy and sustaining recurrent meningitis in a patient of Peruvian origin. A further objective was to retrospectively investigate, by means of whole-genome sequencing (WGS) analysis, the genomic features of such an isolate. The hypermucoviscosity phenotype of the strain (sk205y205t) was determined using the string test. Genomic information was obtained by WGS (Illumina) and bioinformatic analysis. Strain sk205y205t was susceptible to most antibiotics, despite the presence of some resistance genes, including bla_SHV-11, bla_SHV-67, fosA, and acrR. The isolate belonged to ST65 and serotype K2, and exhibited several virulence factors related to the hvKp variant. Among these, were the siderophore genes entB, irp2, iroN, iroB, and iucA; the capsule-regulating genes rmpA and rmpA2; and the type 1 and 3 fimbriae fimH27 and mrkD, respectively. A further operon, encoding the genotoxin colibactin (clbA-Q), was also identified. The virulence plasmids pK2044, pRJA166b, and pNDM. MAR were also detected. Phylogenetic investigation showed that this Italian strain is highly similar to a Chinese isolate, suggesting a hidden circulation of this hvKp ST65 K2 lineage.

Innate Host Defense against Klebsiella pneumoniae and the Outlook for Development of Immunotherapies

Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative commensal bacterium and opportunistic pathogen. In healthy individuals, the innate immune system is adept at protecting against K. pneumoniae infection. Notably, the serum complement system and phagocytic leukocytes (e.g., neutrophils) are highly effective at eliminating K. pneumoniae and thereby preventing severe disease. On the other hand, the microbe is a major cause of healthcare-associated infections, especially in individuals with underlying susceptibility factors, such as pre-existing severe illness or immune suppression. The burden of K. pneumoniae infections in hospitals is compounded by antibiotic resistance. Treatment of these infections is often difficult largely because the microbes are usually resistant to multiple antibiotics (multidrug resistant [MDR]). There are a limited number of treatment options for these infections and new therapies, and preventative measures are needed. Here, we review host defense against K. pneumoniae and discuss recent therapeutic measures and vaccine approaches directed to treat and prevent severe disease caused by MDR K. pneumoniae.

Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence

Background

The incidence of hypervirulent (hv) carbapenem-resistant (CR) Klebsiella pneumoniae (Kp) is increasing globally among various clones and is also responsible for nosocomial infections. The CR-hvKp is formed by the uptake of a virulence plasmid by endemic high-risk clones or by the uptake of plasmids carrying antimicrobial resistance genes by the virulent clones. Here, we describe CR-hvKp from India belonging to high-risk clones that have acquired a virulence plasmid and are phenotypically unidentified due to lack of hypermucoviscosity.

Methods

Twenty-seven CRKp isolates were identified to possess rmpA2 by whole-genome sequencing; and resistance and virulence determinants were characterized. By in silico protein modeling (and validation), protein backbone stability analysis, and coarse dynamics study, the fitness of RmpA, RmpA2, and aerobactin-associated proteins-IucA and IutA, were determined to establish a reliable marker for clinical identification of CR-hvKp.

Results

The CR-hvKp belonged to multidrug-resistant (MDR) high-risk clones such as CG11, CG43, ST15, and ST231 and carried OXA-232 as the predominant carbapenemase followed by NDM. The virulence plasmid belonged to IncHI1B replicon type and carried frameshifted and truncated rmpA and rmpA2. This resulted in a lack of hypermucoviscous phenotype. However, functional aerobactin was expressed in all high-risk clones. In silico analysis portrayed that IucA and IutA were more stable than classical RmpA. Furthermore, IucA and IutA had lower conformational fluctuations in the functional domains than the non-functional RmpA2, which increases the fitness cost of the latter for its maintenance and expression among CR-hvKp. Hence, RmpA and RmpA2 are likely to be lost among CR-hvKp owing to the increased fitness cost while coding for essential antimicrobial resistance and virulence factors.

Conclusion

Increasing incidence of convergence of AMR and virulence is observed among K. pneumoniae globally, which warrants the need for reliable markers for identifying CR-hvKp. The presence of non-functional RmpA2 among high-risk clones highlights the significance of molecular identification of CR-hvKp. The negative string test due to non-functional RmpA2 among CR-hvKp isolates challenges phenotypic screening and faster identification of this pathotype. This can potentially be counteracted by projecting aerobactin as a stable, constitutively expressed, and functional marker for rapidly evolving CR-hvKp.