Evolution of VIM-1-Producing Klebsiella pneumoniae Isolates from a Hospital Outbreak Reveals the Genetic Bases of the Loss of the Urease-Positive Identification Character

Multidrug-resistant hypervirulent Klebsiella pneumoniae: an evolving superbug

Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) combines high pathogenicity with multidrug resistance to become a new superbug. MDR-hvKP reports continue to emerge, shattering the perception that hypervirulent K. pneumoniae (hvKP) strains are antibiotic sensitive. Patients infected with MDR-hvKP strains have been reported in Asia, particularly China. Although hvKP can acquire drug resistance genes, MDR-hvKP seems to be more easily transformed from classical K. pneumoniae (cKP), which has a strong gene uptake ability. To better understand the biology of MDR-hvKP, this review discusses the virulence factors, resistance mechanisms, formation pathways, and identification of MDR-hvKP. Given their destructive and transmissible potential, continued surveillance of these organisms and enhanced control measures should be prioritized.

Genomically-supported Redefinition of an Outbreak in a Pediatric Unit Caused by blaVIM -harboring Klebsiella michiganensis

BACKGROUND

Klebsiella michiganensis , a member of the Klebsiella oxytoca complex, is an emerging nosocomial pathogen known to frequently carry plasmids with antibiotic-resistance genes, including carbapenemases. Using genomics, this study redefined an outbreak alert of K. michiganensis carrying a blaVIM carbapenemase in a pediatric ward in a Spanish hospital.

METHODS

A total of 31 isolates of Verona integron-encoded metallo-β-lactamase (VIM)-carbapenemase K. oxytoca from suspected outbreak cases and unrelated controls from 2015 to 2022 were analyzed. Whole-genome sequencing (both short and long reads) was applied to determine phylogenetic relationships based on single-nucleotide polymorphisms (SNPs) and identify plasmids and antimicrobial resistance genes.

RESULTS

The sequences from 12 isolates identified in 2021 showed pairwise SNP distances ranging from 0 to 16 SNPs, confirming the outbreak. Examination of isolates before and after the study period revealed 7 additional cases, 2 in 2020 and 5 in 2022. The outbreak comprised 18 isolates from 17 patients in 3 different pediatric wards, together with 1 environmental sample. In all outbreak isolates, the blaVIM-1 gene was located within a gene cassette carried by a class 1 integron on an IncFIB(pQil) plasmid. A genomic network based on SNPs revealed 5 unsampled intermediate nodes, suggesting additional subclones that may have involved healthcare staff, patient relatives or environmental reservoirs. Blood and rectal isolates obtained from the same patient were positioned on separate branches of the network, making a direct evolutionary pathway between them unlikely.

CONCLUSIONS

Our study redefined the full extent of this K. michiganensis -VIM outbreak and highlights the critical importance of genomic analysis in accurately understanding outbreaks in healthcare settings.

NDM-5-producing Klebsiella pneumoniae ST258 in a university hospital in Argentina

BACKGROUND

A drastic increase in carbapenem resistance among Klebsiella pneumoniae isolates occurred during the period 2019-22. Three epidemiological changes could be evidenced: (i) NDM became the predominant carbapenemase; (ii) NDM-5 replaced NDM-1; and (iii) the emergence of NDM-producing K. pneumoniae ST258 (NDM-KpST258).

MATERIALS AND METHODS

Carbapenem-resistant K. pneumoniae isolates from patients on the ICU of a university hospital of Buenos Aires were studied during the period 2019-22. Identification was performed by MS and susceptibility by the Phoenix system (broth microdilution for colistin). Carbapenemase production was detected phenotypically. Molecular studies included PCR with specific primers and WGS (in some isolates).

RESULTS

NDM-producing K. pneumoniae was statistically associated with the use of ceftazidime/avibactam between 2019 and April 2021, whereas in the period from May 2021 to December 2022, it seemed to be related to the presence of NDM-5-KpST258. A gradual increase in the number of urease-negative NDM-Kp-ST258 during 2019-22 was observed. The plasmid origin of NDM-5 was supported by its presence on the IncFII incompatibility group plasmid.

CONCLUSIONS

Our study describes the first outbreak of NDM5-KpST258 at an ICU in Argentina, remarkably associated with considerable changes in the carbapenemase epidemiology. The intrinsic characteristics of ST258 may contribute to increased spread of NDM in hospital settings, resembling KPC-2 dissemination.

Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis

Background

Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae.

Methods

Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed.

Results

Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%.

Conclusion

Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.

Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations

BACKGROUND

Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of novel resistance mechanisms by this species. Longitudinal descriptions of genomic epidemiology of Klebsiella pneumoniae can inform management strategies but data from sub-Saharan Africa are lacking.

METHODS

We present a longitudinal analysis of all invasive K. pneumoniae isolates from a single hospital in Blantyre, Malawi, southern Africa, from 1998 to 2020, combining clinical data with genome sequence analysis of the isolates.

RESULTS

We show that after a dramatic increase in the number of infections from 2016 K. pneumoniae becomes hyperendemic, driven by an increase in neonatal infections. Genomic data show repeated waves of clonal expansion of different, often ward-restricted, lineages, suggestive of hospital-associated transmission. We describe temporal trends in resistance and surface antigens, of relevance for vaccine development.

CONCLUSIONS

Our data highlight a clear need for new interventions to prevent rather than treat K. pneumoniae infections in our setting. Whilst one option may be a vaccine, the majority of cases could be avoided by an increased focus on and investment in infection prevention and control measures, which would reduce all healthcare-associated infections and not just one.

Virulence factors in carbapenem-resistant hypervirulent Klebsiella pneumoniae

Hypervirulence and carbapenem-resistant have emerged as two distinct evolutionary pathotypes of Klebsiella pneumoniae, with both reaching their epidemic success and posing a great threat to public health. However, as the boundaries separating these two pathotypes fade, we assist a worrisome convergence in certain high-risk clones, causing hospital outbreaks and challenging every therapeutic option available. To better understand the basic biology of these pathogens, this review aimed to describe the virulence factors and their distribution worldwide among carbapenem-resistant highly virulent or hypervirulent K. pneumoniae strains, as well as to understand the interplay of these virulence strains with the carbapenemase produced and the sequence type of such strains. As we witness a shift in healthcare settings where carbapenem-resistant highly virulent or hypervirulent K. pneumoniae are beginning to emerge and replace classical K. pneumoniae strains, a better understanding of these strains is urgently needed for immediate and appropriate response.

Genetic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in a Tertiary Hospital in Greece, 2018-2022

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. The study aimed to identify the antimicrobial resistance and accessory genes, the clonal relatedness, and the evolutionary dynamics of selected CRKP isolates recovered in an adult and pediatric intensive care unit of a tertiary hospital in Greece.

METHODS

Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST, and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed using various bioinformatics software.

RESULTS

The isolates belonged to eight sequence types: 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM, and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16, and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323, and ST39 were classified into distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs.

CONCLUSIONS

The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.

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

BACKGROUND

Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage.

METHODS

We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features.

RESULTS

Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype.

CONCLUSIONS

To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.

Colorimetric Detection of Urease-Producing Microbes Using an Ammonia-Responsive Flexible Film Sensor

Urease-producing (ureolytic) microbes have given rise to environmental and public health concerns because they are thought to contribute to emissions of ammonia and to be a virulence factor for infections. Therefore, it is highly important to have the ability to detect such microbes. In this study, a poly(dimethylsiloxane) (PDMS)-based colorimetric film sensor was employed for the detection of urease-producing microbes. The sensor was able to detect the enzyme activity of commercially available urease, as the color and absorbance spectrum of the sensor was observed to change upon being exposed to the reaction catalyzed by urease. The ratio of the absorbance of the sensor at 640 nm to that at 460 nm (A₆₄₀/A₄₆₀) was linearly proportional to the amount of urease present. The performance of the sensor was validated by the results of a sensitivity and selectivity analysis towards thirteen different bacterial strains. Based on the development of blue color of the sensor, the tested bacteria were classified as strongly positive, moderately positive, weakly positive, or negative urease producers. The response of the sensor to ureolytic bacteria was verified using the urease inhibitor phenyl phosphorodiamidate (PPDA). Additionally, the sensor achieved the selective detection of ureolytic bacteria even in the presence of non-ureolytic bacteria. In addition, a used sensor could be reverted to its original state by being subjected to simple aeration, and in this way the same sensor could be used at least five times for the detection of bacterial urease activity.