Genome analysis of Klebsiella oxytoca complex for antimicrobial resistance and virulence genes

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.

Molecular characterization and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill cats and dogs in Portugal

Klebsiella spp. are important pathogens of humans and companion animals such as cats and dogs, capable of causing severe life-threatening diseases. The aim of this study was to characterize the molecular and phenotypic properties of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill companion animals by whole genome sequencing, followed by in vitro assessment of biofilm formation and in vivo pathogenicity using the Galleria mellonella model. Two LPS O-types were identified for all the K. pneumoniae isolates tested (O3B and O1/O2v2) and only one for K. oxytoca isolates (OL104), and the most common STs found were ST11 and ST266. Furthermore, a high diversity of K-locus types was found for K. pneumoniae (KL102; KL105; KL31, and KL13). Within K. pneumoniae, one specific O/K/ST-types combination (i.e., KL105-ST11-O1/O2v2) showed results that were of concern, as it exhibited a high inflammatory response at 12 h post-infection in G. mellonella with 80% of the larvae dead at 72 h post-infection. This virulence potential, on the other hand, did not appear to be directly related to the biofilm-forming capacity. Also, virulence and resistance scores obtained for this set of strains did surpass score 1. The present study demonstrated that Klebsiella spp. isolated from companion animals belonging to STs that can cause human infections and present virulence on an invertebrate model. Thus, this study underscores the role of dogs and cats as reservoirs of resistant Klebsiella spp. that could potentially be transmitted to humans.

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.

Pyogenic liver abscess associated with Klebsiella oxytoca: Mimicking invasive liver abscess syndrome

A pyogenic liver abscess (PLA) is a space-occupying lesion in the liver that is associated with significant morbidity and mortality. We herein present the case of a Japanese 76-year-old man who visited our hospital with fever and back pain lasting 3 weeks after endoscopic treatment for common bile duct stones. He was accompanied by poorly controlled diabetes mellitus (DM) with an HbA1c of 9.7 %. Laboratory tests disclosed elevated C-reactive protein level (22.1 mg/dL) and white cell count (11,910/μL). Abdominal computed tomography (CT) revealed hypodense lesions in the right liver lobe, with abdominal ultrasonography showing an echogenicity-mixed hypoechoic lesion. Percutaneous needle aspiration of a liver lesion was performed under suspicion of a PLA. Subsequent enhanced CT and magnetic resonance imaging confirmed the hepatic lesions in the right lobe as well as a septic pulmonary embolism, right hepatic vein thrombosis, spondylodiscitis, and a retroperitoneal abscess. Gram staining of the abscess drainage revealed gram-negative bacteria. The above findings indicated invasive liver abscess syndrome (ILAS) caused by Klebsiella pneumoniae. However, further examination of blood, urine, and abscess drainage cultures revealed positivity for Klebsiella oxytoca. This case illustrates that K. oxytoca may cause ILAS-like symptoms. Screening for systemic metastatic infection should be considered in patients with PLA due to K. oxytoca in whom therapeutic intervention has been delayed, especially in patients with poorly controlled DM.

Genomic characterization of carbapenem-resistant Klebsiella oxytoca complex in China: a multi-center study

Carbapenem-resistant (CR) Klebsiella oxytoca complex can be associated with high mortality, emerging as a new threat to the public health. K. oxytoca complex is phylogenetically close to K. pneumoniae, one of most common species associated with multidrug resistance in Enterobacterale. The latest research showed that K. oxytoca is a complex of six species. Currently, the epidemiological and genomic characteristics of CR K. oxytoca complex in China are still unclear. Here, we conducted a multi-center study on 25 CR K. oxytoca complex collected from five representative regions in China. These isolates were, respectively, recovered from respiratory tract (12 cases, 48.0%), abdominal cavity (5 cases, 20.0%), blood (4 cases, 16.0%), urine tract (3 cases, 12.0%) and skin or soft tissue (1 cases, 4.0%). Among them, 32.0% (8/25) of patients infected with K. oxytoca complex had a poor prognosis. In this study, three K. oxytoca complex species were detected, namely K. michiganensis, K. oxytoca and K. pasteurii, among which K. michiganensis was the most common. Three carbapenemase genes were identified, including bla_NDM-1 (10, 38.5%), bla_KPC-2 (9, 34.6%) and bla_IMP (6 bla_IMP-4 and 1 bla_IMP-8; 7, 26.9%). Subsequent multilocus sequence typing identified various sequence types (STs), among which ST43, ST92 and ST145 were relatively common. Different from the clonal dissemination of high-risk carbapenem-resistant K. pneumoniae strains, our research revealed a polyclonal dissemination characteristic of CR K. oxytoca complex in China. S1-nuclease PFGE and Southern blot experiment showed that carbapenemase genes were encoded in plasmids of different sizes. Two bla_NDM-harboring plasmids were subsequently sequenced, and were characterized to be IncX3 and IncC incompatibility groups, respectively. This is the first multi-center study of CR K. oxytoca complex in China, which improved our understanding of the prevalence and antimicrobial resistance characteristics of CR K. oxytoca complex in China.

High-resolution microbiome analysis reveals exclusionary Klebsiella species competition in preterm infants at risk for necrotizing enterocolitis

Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~ 2500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiella species colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichia in NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecalis was co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiella strains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.

Bacterial infections epidemiology and factors associated with multidrug resistance in the northern region of Ghana

Bacterial infections caused by multidrug resistant organisms are a major global threat. There is still a knowledge gap on this situation in the Northern Region of Ghana. This study determined the prevalence and resistance profile of bacterial infections. It also identified factors associated with multidrug resistance in the study area. This was a retrospective cross-sectional design and it analyzed data from the samples received at the Tamale Zonal Public Health Reference Laboratory from June 2018 to May 2022. The data were analyzed using the R software version 4.2.0. Univariate and multivariable binary logistic regression analyses were used to determine the factors associated with multidrug resistance. The samples included all specimen types possible. The specimens were collected for the purpose of clinical bacteriology diagnostics. Overall a total of 1222 isolates were obtained. The three (3) main bacteria responsible for infections were: Klebsiella spp. (27%), Moraxella spp. (22%), Escherichia spp. (16%). High resistance levels were found against the tested antibiotics and about 41.60% of the bacterial strains isolated were multidrug resistant. Hospitalization was associated with multidrug resistance in univariate (COR 1.96; 95% CI 1.43-2.71; P-value < 0.001) and multivariable analyses (AOR 1.78; 95% CI 1.28-2.49; P-value < 0.001). There is the need for further research on the molecular epidemiology of antibiotic resistance genes in the study area to effectively control the spread of multidrug resistant pathogens. In addition, efforts to build the capacity of health professionals on infection prevention and control as well as diagnostic and antimicrobial stewardship needs urgent attention.