Polymyxin resistance caused by large-scale genomic inversion due to IS26 intramolecular translocation in Klebsiella pneumoniae

IS26 carrying blaKPC-2 mediates carbapenem resistance heterogeneity in extensively drug-resistant Klebsiella pneumoniae isolated from clinical sites

BACKGROUND

Due to the widespread and irrational use of antibiotics, the emergence and prevalence of carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) have become a major challenge in controlling bacterial infections in hospitals. The blaKPC-2 gene located on mobile genetic elements has further complicated the control of resistant bacteria transmission.

RESULTS

In this study, K. pneumoniae strains were isolated from blood cultures of patients. Using the Kirby-Bauer disk diffusion method, we found carbapenem resistance heterogeneity. The resistant subpopulation KPTA-R1 and the sensitive subpopulation KPTA-S1 were purified. Whole-genome sequencing revealed that the blaKPC-2 gene in KPTA-R1 was located on an IncFII plasmid (pKPC-R), within a composite transposon (PCTs) formed by two direct repeats of IS26 elements. The structure was identified as IS26-RecA-ISKpn27-blaKPC-2-ISKpn6-IS26. However, in KPTA-S1, a similar plasmid, pAR-S, lacked this segment. Sequence comparison analysis indicates that the deletion of this blaKPC-2 encoding sequence in this IncFII plasmid is associated with transposition activity mediated by IS26. Multi-sequence comparison of the plasmids showed that the IS26 transposon facilitated the sequence polymorphism of these plasmids.

CONCLUSION

This study reveals the key role of IS26-mediated transposition activity, through homologous recombination, in the emergence of carbapenem resistance heterogeneity in clinical K. pneumoniae strains carrying blaKPC-2. IS26 is able to promote the evolution of resistance in the IncFII plasmid, and through copy-in cointegration or targeted conservative cointegration may result in the acquisition or loss of antibiotic resistance, which may affect clinical care and pose a public health risk.

Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data

Antimicrobial resistance is a global health concern, and methicillin-resistant Staphylococcus aureus (MRSA) is one of the highest-priority organisms exhibiting this phenotype. Here, we performed a national surveillance integrating patient clinical data of S. aureus isolated from bloodstream infections. We performed genome sequencing, standardized antimicrobial susceptibility testing, and collected clinical metadata of 580 S. aureus isolates collected during 2019-2020. We focused on three predominant clonal complexes (CC1, CC5, and CC8) and assesses their microbiological and clinical significance, as well as their distribution across eastern and western Japan. Furthermore, we conducted a genomic comparison of the isolates of 2019-2000 with those of 1994-2000 and investigated the evolutionary trajectory of emerging clones from the three dominant clonal complexes. We revealed that the emerging MRSA ST764-SCCmecII showed the highest mortality rate within 30 days of hospitalization. This high-risk clone diverged from the New York/Japan clone (ST5-SCCmecII), which was inferred to have undergone repeated infections with phages carrying superantigen toxin genes and acquired antimicrobial resistance genes via mobile genetic elements, leading to its emergence around 1994. Overall, we provide a blueprint for a national genomic surveillance study that integrates clinical data and enables the identification and evolutionary characterization of a high-risk clone.

Hypervirulent and carbapenem-resistant Klebsiella pneumoniae: A global public health threat

The evolution of hypervirulent and carbapenem-resistant Klebsiella pneumoniae can be categorized into three main patterns: the evolution of KL1/KL2-hvKp strains into CR-hvKp, the evolution of carbapenem-resistant K. pneumoniae (CRKp) strains into hv-CRKp, and the acquisition of hybrid plasmids carrying carbapenem resistance and virulence genes by classical K. pneumoniae (cKp). These strains are characterized by multi-drug resistance, high virulence, and high infectivity. Currently, there are no effective methods for treating and surveillance this pathogen. In addition, the continuous horizontal transfer and clonal spread of these bacteria under the pressure of hospital antibiotics have led to the emergence of more drug-resistant strains. This review discusses the evolution and distribution characteristics of hypervirulent and carbapenem-resistant K. pneumoniae, the mechanisms of carbapenem resistance and hypervirulence, risk factors for susceptibility, infection syndromes, treatment regimens, real-time surveillance and preventive control measures. It also outlines the resistance mechanisms of antimicrobial drugs used to treat this pathogen, providing insights for developing new drugs, combination therapies, and a "One Health" approach. Narrowing the scope of surveillance but intensifying implementation efforts is a viable solution. Monitoring of strains can be focused primarily on hospitals and urban wastewater treatment plants.

Comprehensive analysis and novel insights into the efficacy of polymyxin B sulfate in the treatment of sepsis caused by carbapenem-resistant gram-negative bacteria

OBJECTIVE

To investigate and analyze the clinical efficacy and safety of polymyxin B sulfate in the treatment of carbapenem-resistant gram-negative bacteria (CR-GNB) in sepsis; in order to provide reference for the clinical diagnosis, treatment and prognosis evaluation of sepsis.

METHODS

The clinical data of 76 patients with CR-GNB sepsis treated with polymyxin B sulfate combined with an anti-infection regimen in the First Affiliated Hospital of Gannan Medical University from January 2020 to February 2024 were retrospectively studied. To analyze and discuss the clinical characteristics, results of the bacterial culture and drug sensitivity, clinical efficacy and prognosis of CR-GNB patients, efficacy comparison of different doses of polymyxin B sulfate treatment regimens, efficacy comparison of different combination regimens based on polymyxin B sulfate, changes in clinical indexes before and after treatment of polymyxin B sulfate, adverse drug reactions and adverse events of polymyxin B sulfate were investigated.

RESULTS

A total of 76 patients with CR-GNB sepsis were included in this study, with 55 males and 21 females, with an average age of 59.86 years old, 44 of which were (57.89%) were > 60 years old. All patients included in this study were treated with polymyxin B based combination therapy, 49 cases (64.47%) received the two-drug combination regimen, 27 cases (35.53%) received the three-drug or more combination regimen, and all the patients had the above treatment followed by systematic symptomatic supportive treatment. Patients in this study received polymyxin B for an average of (8.6±4.3) days, there were 60 (78.95%) patients with effective clinical treatment, and 49 patients (64.47%) achieved pathogen (bacterial) clearance of infection. Twenty-two cases (28.95%) died within 28 days, 31 cases (40.79%) died within 90 days, and the remaining 23 cases (30.26%) survived. There were statistically significant differences in the therapeutic effective rates and bacterial clearance rates among different courses of treatment or different initial doses of polymyxin B (all P < 0.05). Moreover, there were significant differences in APACHE II score, WBC, NE, HGB, platelet count, albumin, NT-proBNP and CRP before and after polymyxin B treatment (all P < 0.001). In this study, 7 cases (9.21%) developed drug-related kidney injury, which recovered or decreased below the pre-medication level after discontinuation or dose adjustment and infection control. Skin darkening (melanin deposition) occurred in 5 cases (6.58%), and the above patients basically returned to normal several months after withdrawal of the drug, but there was still a certain degree of skin pigmentation. Meanwhile, 3 cases (3.95%) had neurotoxic reactions, mainly manifested as numbness at the extremities, and the neurotoxic symptoms were improved after reducing the dosage. Accordingly, there was no statistically significant difference in the prognosis of CR-GNB sepsis patients between different age and gender groups (all P > 0.05), while the treatment course and dosage of polymyxin B had statistically significant effects on the prognosis of CR-GNB sepsis patients (all P < 0.05).

CONCLUSION

A Polymyxin B sulfate based combination regimen is an effective choice for CR-GNB sepsis, which can maximize the survival and prognosis benefits of sepsis patients.

Investigation of the Rapid Emergence of Colistin Resistance in a Newborn Infected with KPC-2-Producing Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae

OBJECTIVES

Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKp) poses a significant threat to public health. This study reports an infection related to hv-CRKp in a premature infant and reveals its colistin resistance and evolutionary mechanisms within the host.

METHODS

Three KPC-producing CRKp strains were isolated from a patient with sepsis and CRKp osteoarthritis who had been receiving colistin antimicrobial therapy. The minimum inhibitory concentrations (MICs) of ceftazidime, ceftazidime-avibactam (CAZ-AVI), meropenem, imipenem, tigecycline, amikacin, minocycline, sulfamethoxazole/trimethoprim, ciprofloxacin, levofloxacin, aztreonam, cefepime, cefoperazone/sulbactam, piperacillin/tazobactam, and colistin were determined using the microbroth dilution method. The whole-genome sequencing analysis was conducted to determine the sequence types (STs), virulence genes, and antibiotic resistance genes of the three CRKp strains.

RESULTS

Whole-genome sequencing revealed that all three CRKp strains belonged to the ST11 clone and carried a plasmid encoding blaKPC-2. The three strains all possessed the iucABCDiutA virulence cluster, peg-344 gene, and rmpA/rmpA2 genes, defining them as hv-CRKp. Further experiments and whole-genome analysis revealed that a strain of K. pneuomniae had developed resistance to colistin. The mechanism found to be responsible for colistin resistance was a deletion mutation of approximately 9000 bp including the mgrB gene.

CONCLUSION

This study characterizes colistin resistance of the ST11 clone hv-CRKp during colistin treatment and its rapid evolution within the host.

Dual-Mechanism Peptide SR25 has Broad Antimicrobial Activity and Potential Application for Healing Bacteria-infected Diabetic Wounds

The rise of antibiotic resistance poses a significant public health crisis, particularly due to limited antimicrobial options for the treatment of infections with Gram-negative pathogens. Here, an antimicrobial peptide (AMP) SR25 is characterized, which effectively kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism without detectable resistance. Meanwhile, an SR25-functionalized hydrogel is developed for the efficient treatment of infected diabetic wounds. SR25 is obtained through genome mining from an uncultured bovine enteric actinomycete named Nonomuraea Jilinensis sp. nov. Investigations reveal that SR25 has two independent cellular targets, disrupting bacterial membrane integrity and restraining the activity of succinate:quinone oxidoreductase (SQR). In a diabetic mice wound infection model, the SR25-incorporated hydrogel exhibits high efficacy against mixed infections of Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA), accelerating wound healing. Overall, these findings demonstrate the therapeutic potential of SR25 and highlight the value of mining drugs with multiple mechanisms from uncultured animal commensals for combating challenging bacterial pathogens.

IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers

SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.