First Case of Liver Abscess in Scandinavia Due to the International Hypervirulent Klebsiella Pneumoniae Clone ST23

The Rapid Emergence of Hypervirulent Klebsiella Species and Burkholderia pseudomallei as Major Health Threats in Southeast Asia: The Urgent Need for Recognition as Neglected Tropical Diseases

The World Health Organization (WHO)'s list of neglected tropical diseases (NTDs) highlights conditions that are responsible for devastating health, social and economic consequences, and yet, they are overlooked and poorly resourced. The NTD list does not include conditions caused by Gram-negative bacilli (GNB). Infections due to GNB cause significant morbidity and mortality and are prevalent worldwide. Southeast Asia is a WHO region of low- and middle-income countries carrying the largest burden of NTDs. Two significant health threats in Southeast Asia are Burkholderia pseudomallei (causing melioidosis) and hypervirulent Klebsiella pneumoniae (HvKp). Both diseases have high mortality and increasing prevalence, yet both suffer from a lack of awareness, significant under-resourcing, incomplete epidemiological data, limited diagnostics, and a lack of evidence-based treatment. Emerging evidence shows that both melioidosis and HvKp are spreading globally, including in high-income countries, highlighting the potential future global threat they pose. In this article, we review both conditions, identifying current trends and challenges in Southeast Asia and areas for future research. We also argue that melioidosis and HvKp merit inclusion as NTDs, and that mandatory global surveillance and reporting systems should be established, and we make an urgent call for research to better understand, detect, and treat these neglected diseases.

One Health Genomic Study of Human and Animal Klebsiella pneumoniae Isolated at Diagnostic Laboratories on a Small Caribbean Island

Klebsiella pneumoniae causes a variety of infections in both humans and animals. In this study, we characterised the genomes of human and animal isolates from two diagnostic laboratories on St. Kitts, a small Caribbean island inhabited by a large population of vervet monkeys. In view of the increased chances of direct or indirect contact with humans and other animal species, we used the One Health approach to assess transmission of K. pneumoniae across host species by sequencing 82 presumptive K. pneumoniae clinical isolates from humans (n = 51), vervets (n = 21), horses (n = 5), dogs (n = 4) and a cat (n = 1). Whole genome sequencing (WGS) was carried out using Illumina technology. De novo assembly was performed in CLC Genomics Workbench v.11.0. Single nucleotide polymorphisms were detected using NASP followed by phylogenetic analysis using IQ-TREE. Virulence and antimicrobial resistance gene contents were analysed using the Kleborate and CGE pipelines. WGS-based analysis showed that 72 isolates were K. pneumoniae sensu stricto and five K. quasipneumoniae and five K. variicola. K. pneumoniae isolates belonged to 35 sequence types (ST), three of which were occasionally shared between humans and animals: ST23, ST37 and ST307. The ST23 strains from vervets formed a separate cluster amongst publicly available sequenced ST23 strains, indicating the presence of a specific vervet sublineage. Animal strains harbored fewer resistance genes and displayed distinct virulence traits that appeared to be host-specific in vervet isolates. Our results show that K. pneumoniae infections on this Caribbean island are usually caused by host-specific lineages.

Detection of extensively drug-resistant and hypervirulent Klebsiella pneumoniae ST15, ST147, ST377 and ST442 in Iran

In this study, we focused on the emergence of extensively drug-resistant (XDR), pandrug-resistant (PDR), and hypervirulent Klebsiella pneumoniae (hvKP) in Iran. During 2018 to 2020 a total of 52 K. pneumoniae isolates were collected from different clinical specimens. The hvKP isolates were identified by PCR amplification of virulence and capsular serotype-specific genes. Hypermucoviscous K. pneumoniae (hmKP) were identified by string test. Carbapenem-resistant hvKP (CR-hvKP), multidrug-resistant hvKP (MDR-hvKP), extensively drug-resistant hvKP (XDR-hvKP), and pandrug-resistant hvKP (PDR-hvKP) were determined by disc diffusion method, Carba-NP test and PCR method. XDR-hvKP isolates were typed by multilocus sequence typing (MLST). Among all K. pneumoniae isolates 14 (26.9%) were identified as hvKP and 78.6% (11/14) of them were hmKP however, none of the classic K. pneumoniae (cKP) isolates were hmKP. The predominant capsular serotype of hvKP was K2 (42.85%) followed by K1 (35.71%). The prevalence of MDR-hvKP, XDR-hvKP and PDR-hvKP isolates were 6 (42.9%), 5 (35.7%) and 1 (7.1%), respectively. ESBL production was found in 85.7% of hvKP isolates and most of them carried bla TEM gene (78.6%) and 6 isolates (42.9%) were CR-hvKP. Among hvKP isolates, 1 (7.1%), 2 (14.3%), 3 (21.4%), 8 (28.6%), and 11 (78.6%) carried bla NDM-6, bla OXA-48, bla CTX-M, bla SHV, and bla TEM genes, respectively. According to MLST analysis, 2, 1, 1, and 1 XDR-hvKP isolates belonged to ST15, ST377, ST442, and ST147, respectively. The occurrence of such isolates is deeply concerning due to the combination of hypervirulence and extensively drug-resistance or pandrug-resistance.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

BACKGROUND

Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.

METHODS

We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool.

RESULTS

K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.

CONCLUSIONS

K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

BACKGROUND

Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.

METHODS

We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool.

RESULTS

K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.

CONCLUSIONS

K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

Identification of a Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae Isolate in the United States

We report on a carbapenemase-producing hypervirulent Klebsiella pneumoniae (CP-hvKP) isolate collected from a U.S. patient at an outpatient clinic. The isolate was identified as K. pneumoniae serotype K1 sequence type 23 and included both a hypervirulence (with rmpA, rmpA2 iroBCDN, peg-344, and iucABCD-iutA genes) and a carbapenemase-encoding (bla _KPC-2) plasmid. The emergence of CP-hvKP underscores the importance of clinical awareness of this pathotype and the need for continued monitoring of CP-hvKP in the United States.

Hypervirulent Klebsiella pneumoniae K1 liver abscess and endogenous endophthalmitis in a Caucasian man

Invasive Liver Abscess Syndrome is the most frequent of a number of infectious syndromes caused by hypervirulent Klebsiella pneumoniae clones. While incidences peak in Southeast Asia, travels to Asia and Asian ethnicity are independent risk factors for infection in the western countries, although non-Asians are infected as well. Although challenging, a prompt diagnosis is of utmost importance to ensure adequate treatment and improve overall survival and visual outcome in cases with ocular involvement.

Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae: Epidemiology, Hypervirulence-Associated Determinants, and Resistance Mechanisms

Klebsiella pneumoniae is one of the most clinically relevant species in immunocompromised individuals responsible for community-acquired and nosocomial infections, including pneumonias, urinary tract infections, bacteremias, and liver abscesses. Since the mid-1980s, hypervirulent K. pneumoniae, generally associated with the hypermucoviscosity phenotype, has emerged as a clinically significant pathogen responsible for serious disseminated infections, such as pyogenic liver abscesses, osteomyelitis, and endophthalmitis, in a generally younger and healthier population. Hypervirulent K. pneumoniae infections were primarily found in East Asia and now are increasingly being reported worldwide. Although most hypervirulent K. pneumoniae isolates are antibiotic-susceptible, some isolates with combined virulence and resistance, such as the carbapenem-resistant hypervirulent K. pneumoniae isolates, are increasingly being detected. The combination of multidrug resistance and enhanced virulence has the potential to cause the next clinical crisis. To better understand the basic biology of hypervirulent K. pneumoniae, this review will provide a summarization and discussion focused on epidemiology, hypervirulence-associated factors, and antibiotic resistance mechanisms of such hypervirulent strains. Epidemiological analysis of recent clinical isolates in China warns the global dissemination of hypervirulent K. pneumoniae strains with extensive antibiotic resistance in the near future. Therefore, an immediate response to recognize the global dissemination of this hypervirulent strain with resistance determinants is an urgent priority.

First case report of non-human primates (Alouatta clamitans) with the hypervirulent Klebsiella pneumoniae serotype K1 strain ST 23: A possible emerging wildlife pathogen

BACKGROUND

Hypervirulent strain of Klebsiella pneumoniae genotype K1 isolates have recently emerged, causing severe pyogenic liver abscess complicated by devastating metastatic infections in humans.

METHODS

We describe a short outbreak of the non-human primate (NHP) research center, associated with a hypervirulent K. pneumoniae. The genetic similarity of the strains was evaluated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) techniques, and virulence encoding genes were detected by polymerase chain reaction (PCR).

RESULTS

The isolates were phenotypically like strains causing community-acquired invasive liver abscess syndrome in humans. All strains exhibited identical PFGE patterns and were found to belong to ST23 and presented a hypermucovisity phenotype and possessed magA and rmpA gene.

CONCLUSION

This is the first case report of NHPs caused by K. pneumoniae displaying a hypermucoviscosity phenotype and belonging to capsular serotypes K1 and ST23.

Two unusual cases of successful treatment of hypermucoviscous Klebsiella pneumoniae invasive syndrome

BACKGROUND

A few Japanese cases of hypermucoviscous Klebsiella pneumoniae (K. pneumoniae) invasive syndrome have recently been reported. Although extrahepatic complications from bacteremic dissemination have been observed, infected aneurysms are rare. Furthermore, the primary source of infection is generally a liver abscess, and is rarely the prostate. Therefore, we report two atypical cases of hypermucoviscous K. pneumoniae invasive syndrome.

CASE PRESENTATION

The first case was an 81-year-old Japanese man with no significant medical history, who was referred to our hospital for vision loss in his right eye. Contrast-enhanced whole-body computed tomography revealed abscesses in the liver and the prostate, and an infected left internal iliac artery aneurysm. Contrast-enhanced head magnetic resonance imaging revealed brain abscesses. Cultures of the liver abscess specimen and aqueous humor revealed K. pneumoniae with the hypermucoviscosity phenotype, which carried the magA gene (mucoviscosity-associated gene A) and the rmpA gene (regulator of mucoid phenotype A). We performed enucleation of the right eyeball, percutaneous transhepatic drainage, coil embolization of the aneurysm, and administered a 6-week course of antibiotic treatment. The second case was a 69-year-old Japanese man with diabetes mellitus, who was referred to our hospital with fever, pollakiuria, and pain on urination. Contrast-enhanced whole-body computed tomography revealed lung and prostate abscesses, but no liver abscesses. Contrast-enhanced head magnetic resonance imaging revealed brain abscesses. The sputum, urine, prostate abscess specimen, and aqueous humor cultures revealed K. pneumoniae with the hypermucoviscosity phenotype, which carried magA and rmpA. We performed enucleation of the left eyeball, percutaneous drainage of the prostate abscess, and administered a 5-week course of antibiotic treatment.

CONCLUSIONS

Hypermucoviscous K. pneumoniae can cause infected aneurysms, and the prostate can be the primary site of infection. We suggest that a diagnosis of hvKP invasive syndrome should be considered in all patients who present with K. pneumoniae infection and multiple organ abscesses.

Hypervirulent Klebsiella pneumoniae clones causing bacteraemia in adults in a teaching hospital in Barcelona, Spain (2007-2013)

Virulent hypermucoviscous Klebsiella pneumoniae strains associated with the magA and rmpA genes have mainly emerged in Asia. We analysed the frequency and the clinical and molecular epidemiology of K. pneumoniae bacteraemia isolates obtained over a 7-year period (2007-2013). Fifty-three of 878 K. pneumoniae invasive isolates (5.4%) showed a hypermucoviscous phenotype (by the string test). Of these, 16 (30.2%) were magA(+)/rmpA(+), 12 (22.6%) were magA(-)/rmpA(+), and the remaining 25 (47.2%) were magA(-)/rmpA(-). After multilocus sequence typing and wzi sequencing, all magA(+)/rmpA(+) isolates were serotype K1 and sequence type (ST)23. Of the 12 magA(-)/rmpA(+) isolates, nine were K2 (ST380, ST86, ST65, ST25 and ST493), and three magA(-)/rmpA(+) isolates had the new wzi allele 122, an unknown serotype, and the new ST1013. The remaining isolates, which were magA(-)/rmpA(-), showed different serotypes and STs. Patients with magA(+)/rmpA(+) or magA(-)/rmpA(+)K. pneumoniae bacteraemia more frequently had pyogenic liver abscesses (PLAs) and pneumonia than patients with magA(-)/rmpA(-)K. pneumoniae bacteraemia (respectively: 21.4% vs. 8%, p 0.26; and 17.9% vs. 0%, p 0.05). In fact, magA(-)/rmpA(-) isolates were similar to the those termed 'classic' K. pneumoniae isolates causing bacteraemia, the urinary and biliary tracts being the main foci of infection. In conclusion, hypervirulent clones (CC23K1, CC86K2, CC65K2, and CC380K2) were infrequent among K. pneumoniae isolates causing bacteraemia in our geographical area. A hypermucoviscous phenotype as determined with the string test is not enough to recognize these clones; additional molecular studies are needed. Patients with magA(+) and/or rmpA(+)K. pneumoniae bacteraemia more frequently had PLAs and pneumonia than patients without hypermucoviscosity genes.

Mapping the Evolution of Hypervirulent Klebsiella pneumoniae

Highly invasive, community-acquired Klebsiella pneumoniae infections have recently emerged, resulting in pyogenic liver abscesses. These infections are caused by hypervirulent K. pneumoniae (hvKP) isolates primarily of capsule serotype K1 or K2. Hypervirulent K1 isolates belong to clonal complex 23 (CC23), indicating that this clonal lineage has a specific genetic background conferring hypervirulence. Here, we apply whole-genome sequencing to a collection of K. pneumoniae isolates to characterize the phylogenetic background of hvKP isolates with an emphasis on CC23. Most of the hvKP isolates belonged to CC23 and grouped into a distinct monophyletic clade, revealing that CC23 is a unique clonal lineage, clearly distinct from nonhypervirulent strains. Separate phylogenetic analyses of the CC23 isolates indicated that the CC23 lineage evolved recently by clonal expansion from a single common ancestor. Limited grouping according to geographical origin was observed, suggesting that CC23 has spread globally through multiple international transmissions. Conversely, hypervirulent K2 strains clustered in genetically unrelated groups. Strikingly, homologues of a large virulence plasmid were detected in all hvKP clonal lineages, indicating a key role in K. pneumoniae hypervirulence. The plasmid encodes two siderophores, aerobactin and salmochelin, and RmpA (regulator of the mucoid phenotype); all these factors were found to be restricted to hvKP isolates. Genomic comparisons revealed additional factors specifically associated with CC23. These included a distinct variant of a genomic island encoding yersiniabactin, colibactin, and microcin E492. Furthermore, additional novel genomic regions unique to CC23 were revealed which may also be involved in the increased virulence of this important clonal lineage.

IMPORTANCE

During the last 3 decades, hypervirulent Klebsiella pneumoniae (hvKP) isolates have emerged, causing severe community-acquired infections primarily in the form of pyogenic liver abscesses. This syndrome has so far primarily been found in Southeast Asia, but increasing numbers of cases are being reported worldwide, indicating that the syndrome is turning into a globally emerging disease. We applied whole-genome sequencing to a collection of K. pneumoniae clinical isolates to reveal the phylogenetic background of hvKP and to identify genetic factors associated with the increased virulence. The hvKP isolates primarily belonged to clonal complex 23 (CC23), and this clonal lineage was revealed to be clearly distinct from nonhypervirulent strains. A specific virulence plasmid was found to be associated with hypervirulence, and novel genetic determinants uniquely associated with CC23 were identified. Our findings extend the understanding of the genetic background of the emergence of hvKP clones.

Clinical and molecular characteristics of multi-clone carbapenem-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae isolates in a tertiary hospital in Beijing, China

OBJECTIVES

To provide the clinical and molecular characteristics of carbapenem-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae (cr-hvKP) in a tertiary hospital in Beijing, China.

METHODS

The clinical characteristics of four patients with cr-hvKP isolates and 29 patients with carbapenem-resistant classic K. pneumoniae (cr-cKP) infections were analyzed retrospectively. The molecular characteristics of cr-hvKP and cr-cKP isolates were compared.

RESULTS

The KPC-2 gene was detected in all cr-hvKPs except for cr-hvKP6. The cr-hvKPs belonged to three sequence types (STs; ST25, ST65, and ST11), with three pulsed-field gel electrophoresis patterns (I, II, and III) and two capsular serotypes (K2 and non-typeable). Although cr-hvKP1-7 did not cause invasive clinical syndromes such as community-acquired liver abscess with or without extrahepatic complications, they were all nosocomially acquired; cr-hvKP1-5 were clones disseminated between patients A and B. Compared with cr-cKPs, pLVPK-related loci, repA, iroN, and K2 capsular serotype were more prevalent in cr-hvKPs, although no significant difference was found in clinical characteristics between patients with cr-hvKP and cr-cKP infection.

CONCLUSIONS

The hypervirulent ST65 and ST25K. pneumoniae, along with carbapenem-resistant clonal populations ST11, appear to have evolved into cr-hvKP strains. The evidence of bi-directional evolution and emergence of hospital-acquired multi-clone cr-hvKP indicates a confluence of virulence and carbapenem resistance, which might pose major problems in the management of K. pneumoniae infection.

Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae

Clinical isolates of Klebsiella pneumoniae are divided into three phylogroups and differ in their virulence factor contents. The aim of this study was to determine an association between phylogroup, virulence factors and mortality following bloodstream infection (BSI) caused by Klebsiella pneumoniae. Isolates from all adult patients with BSI caused by K. pneumoniae admitted to Karolinska University Hospital, Solna between 2007 and 2009 (n = 139) were included in the study. Phylogenetic analysis was performed based on multilocus sequence typing (MLST) data. Testing for mucoid phenotype, multiplex PCR determining serotypes K1, K2, K5, K20, K54 and K57, and testing for virulence factors connected to more severe disease in previous studies, was also performed. Data was retrieved from medical records including age, sex, comorbidity, central and urinary catheters, time to adequate treatment, hospital-acquired infection, and mortality, to identify risk factors. The primary end-point was 30- day mortality. The three K. pneumoniae phylogroups were represented: KpI (n = 96), KpII (corresponding to K. quasipneumoniae, n = 9) and KpIII (corresponding to K. variicola, n = 34). Phylogroups were not significantly different in baseline characteristics. Overall, the 30-day mortality was 24/139 (17.3%). Isolates belonging to KpIII were associated with the highest 30-day mortality (10/34 cases, 29.4%), whereas KpI isolates were associated with mortality in 13/96 cases (13.5%). This difference was significant both in univariate statistical analysis (P = 0.037) and in multivariate analysis adjusting for age and comorbidity (OR 3.03 (95% CI: 1.10–8.36). Only three of the isolates causing mortality within 30 days belonged to any of the virulent serotypes (K54, n = 1), had a mucoid phenotype (n = 1) and/or contained virulence genes (wcaG n = 1 and wcaG/allS n = 1). In conclusion, the results indicate higher mortality among patients infected with isolates belonging to K. variicola. The increased mortality could not be related to any known virulence factors, including virulent capsular types or mucoid phenotype.