Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae. The disruption of the mgrB gene by insertion sequences (ISs) is a mechanism mediating colistin resistance. Plasmids encode mobilizable IS elements which integrate into the mgrB gene in K. pneumoniae causing gene inactivation and colistin resistance. The species prevalence of mgrB‐gene disrupting insertion elements ISL3 (ISKpn25), IS5 (ISKpn26), ISKpn14, and IS903B present on plasmids were assessed. IS containing plasmids were also scanned for antimicrobial resistance genes, including carbapenem resistant genes. Plasmids encoding ISs are abundant in K. pneumoniae. IS903B was found in 28 unique Inc groups, while ISKpn25 was largely carried by IncFIB(pQil) plasmids. ISKpn26 and ISKpn14 were most often found associated with IncFII(pHN7A8) plasmids. Of the 34 unique countries which contained any of the IS elements, ISKpn25 was identified from 26. ISKpn26, ISKpn14, and IS903B ISs were identified from 89.3%, 44.9%, and 23.9% plasmid samples from China. Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 IS have a 4.6‐, 6.0‐, and 6.6‐fold higher carbapenemase gene count, respectively, relative to IS903B‐carrying plasmids. IS903B bearing plasmids have a 20‐, 5‐, and 5‐fold higher environmental source isolation count relative to ISKpn25, ISKpn14, and ISKpn26 bearing plasmids. ISKpn25 present on IncFIB(pQil) sourced from clinical settings is established across multiple countries, while ISKpn26, ISKpn14, and IS903B appear most often in China. Carbapenemase presence in tandem with IS elements may help promote an extensively drug resistant profile in K. pneumoniae limiting already narrow treatment options.

Klebsiella pneumoniae (K. pneumoniae) cultures from a hospital-wide outbreak in the UK, which lasted for over 12 months, were sequenced. We sought to sequence and genetically characterise the outbreak strain. Antibiotic Susceptibility Testing (AST) was performed on 65 K. pneumoniae isolates saved from the outbreak. All isolates were sequenced using the Oxford Nanopore Technologies (ONT) MinION flowcell: 10 isolates, including the isolate with the earliest collection date in 2017, were additionally sequenced on the NovaSeq 6000 platform to build high-accuracy nanopore-illumina assemblies. Among the sequenced strains, 60 were typed as ST628. 96.6% (n = 58/60) ST628 strains harboured a large ~247-kb FIB(K) plasmid carrying up to 11 antimicrobial resistance genes, including the extended-spectrum beta-lactamase (ESBL) gene, bla_CTX-M-15. Clonality between the outbreak isolates was confirmed using single nucleotide polymorphism (SNP) typing. The outbreak strains were phylogenetically related to clinical ST628 strains identified in 2012, 6 years prior to the outbreak. A rare ESBL K. pneumoniae K2 ST628 strain harbouring a multi-drug resistant (MDR) plasmid encoding the ESBL gene bla_CTX-M-15 was detected across multiple independent wards during the protracted nosocomial outbreak. Surveillance of this strain is recommended to prevent future nosocomial outbreaks.

Escherichia coli and Klebsiella pneumoniae isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long‐standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long‐read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance‐encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239‐bp FIB(K) pKBM1, from the K. pneumoniae strain, additionally encoded the five AMR genes: sul2, strA, strB, bla_TEM‐1B, and bla_CTX‐M‐15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3‐307_typeA, commonly identified in K. pneumoniae ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.

Infections caused by carbapenem resistant Enterobacteriales (CPE) represent a significant threat in clinical settings. bla _OXA-48 is one of the most frequent carbapenemase genes among Enterobacteriales. The bla _OXA-48 is typically encoded on the prototypical IncL conjugative pOXA-48 plasmid. The pOXA-48 plasmid encodes only the bla _OXA-48 resistance gene. However, aminoglycoside and extended spectrum β-lactamase (ESBL) resistance genes have also been detected on the same pOXA-48 plasmid backbone. These pOXA-48 plasmids encoding additional antimicrobial resistance (AMR) genes have been associated with both poor patient outcome and increased minimal inhibitory concentrations (MICs) to antibiotics including broad-spectrum cephalosporins. The bla _OXA-48 gene was sourced from the pOXA-48 reference plasmid and set as a query using the BLASTn tool. Non-duplicate bla _OXA-48 containing plasmids were downloaded, incompatibility typed and annotated for resistance genes using ResFinder 4.0. Bioinformatic analyses identified three distinct variants of the pOXA-48 plasmid encoding 4, 5, and 6 antimicrobial resistance genes. All plasmids encoded the ESBL bla _CTX-M-14b , bla _OXA-48 and either 2, 3 or 4 aminoglycoside resistance genes, in addition to conjugative transfer machinery. Plasmid variants 1 and 3 encoded aminoglycoside genes bracketed between IS26 and ISEc63 insertion elements, forming a potential transposon. The potential transposon structure had resemblance to the Tn5393 transposon (accession: M96392 ), including both aph(3’’)-Ib, aph(6)-Id genes, and a Tn3 resolvase. The IS element ISEcp1 lies upstream of bla _CTX-M-14b . All three plasmid variants appear related. Notably, all pOXA-48 plasmid variants were identified in multiple countries. In particular, variant 1 including 6 AMR genes was detected in 7 unique countries. Plasmids encoding additional AMR genes were associated with clinical/surveillance samples suggesting antibiotic pressure in clinical settings may promote changes in the resistome of pOXA-48. Acquisition of pOXA-48 resistant plasmids carrying additional AMR genes beyond bla _OXA-48 can change the resistome of susceptible isolates in a single-step, rendering previously susceptible strains refractory to almost all available treatment options.

Antimicrobial resistance in Klebsiella pneumoniae poses a major clinical challenge, driving development in rapid, diagnostic strategies that extend beyond conventional susceptibility testing. Twenty‐three studies demonstrate that using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI–TOF–MS) spectra to create machine learning (ML) models yields rapid and accurate predictions of antibiotic resistance in K. pneumoniae . Across these studies, most models focused on carbapenem resistance and achieved Area Under the Receiver Operating Characteristic Curve (AUROC) values consistently above 0.90, with ensemble algorithms, particularly Random Forest, XGBoost, and Light Gradient Boosting Machine, and deep learning models such as Convolutional Neural Networks attaining accuracies as high as 97% and even AUROCs reaching 0.99 or higher. Sample sizes ranged from 35 to over 15,000 isolates, reinforcing the robustness of these findings across diverse clinical settings. In addition to high discrimination performance, this evaluation reports that ML models developed using MALDI–TOF–MS spectra shorten diagnostic turnaround from days (48–96 h with conventional methods) to minutes or hours, using existing MALDI–TOF–MS equipment for economical implementation. However, ML diagnostic tools remain constrained by limited external validation, spectra preprocessing protocols, and variability between different MALDI–TOF–MS platforms. These limitations may restrict model generalizability and clinical translation, highlighting the need for standardized workflows and larger multicenter evaluations.

Companion animals are increasingly recognised within One Health antimicrobial‐resistance (AMR) surveillance, yet the global genomic structure of dog‐ and cat‐associated Klebsiella pneumoniae remains poorly defined. We assembled a global dataset of 712 domestic dog ( Canis lupus familiaris )– and cat ( Felis catus )–derived K. pneumoniae genomes to define lineage diversity, AMR burden, host‐associated patterns, and overlap with human‐associated populations. Companion‐animal isolates comprised 263 sequence types (STs), but recurrent high‐risk lineages, including ST307, ST11, ST15, and ST147, were prominent. Among 706 isolates from 25 countries, extended‐spectrum β‐lactamase (ESBL) and carbapenemase genes were widely distributed, detected in 303 (42.9%) and 98 (13.9%) isolates, respectively. Cat‐derived isolates showed higher multidrug‐resistance (MDR) prevalence than dog‐derived isolates; 80.0% versus 56.3%, partly reflecting enrichment of epidemic clones, especially ST147. MDR was not confined to infection‐associated samples, indicating that colonisation may represent an important reservoir state. Comparison with 38,106 human‐associated K. pneumoniae isolates revealed extensive ST overlap, with 71.1% of companion‐animal STs and 87.2% of companion‐animal isolates belonging to STs also detected in humans. Focused recombination‐filtered phylogenomics of ST147 identified a closely related MDR cluster containing cat‐, dog‐ and human‐associated genomes, consistent with recent common ancestry and cross‐host cocirculation. Together, these findings reveal domestic dogs and cats harbour globally distributed K. pneumoniae lineages and high‐risk AMR clones also represented in human‐associated populations.