Global Phylogeography and Genomic Epidemiology of Carbapenem-Resistant blaOXA-232-Carrying Klebsiella pneumoniae Sequence Type 15 Lineage

Characteristics of ESBL-positive Klebsiella pneumoniae isolated from paired children with and without diarrhea

BACKGROUND

Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL) colonizing and transmitting in the intestine, especially in children, have significant public health implications. Investigating antibiotic resistance, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and genetic relationships may help us to explore the characteristics and differences of ESBL-positive K. pneumoniae in children with and without diarrhea.

METHODS

After selecting and pairing, 26 pairs of 52 ESBL-positive K. pneumoniae strains were isolated from 323 children with diarrhea and 393 children without diarrhea. Antimicrobial susceptibility test and whole genome sequencing were performed to explore antibiotic resistance, ARGs, and VFGs. The genetic relationship was explored by conducting a maximum likelihood phylogenetic tree and investigating plasmid and sequence type (ST).

RESULTS

All strains showed resistance to cephalosporins, with ESBL-producing genes widely carried (98.1%). Carbapenem-resistant K. pneumoniae (CRKP) were found in both groups. Hypervirulent K. pneumoniae (hvKP) were isolated from children with diarrhea carrying iucA on plasmid. The emergence of ST5670 CRKP and ST2108 hvKP highlighted the necessity for close monitoring of community-acquired K. pneumoniae.

CONCLUSIONS

Severe drug resistance was found among ESBL-positive K. pneumoniae strains isolated from children with and without diarrhea. Attention must be paid to ESBL-positive K. pneumoniae colonized in the intestine of children, and pathogen and ARG monitoring in children should be strengthened, even in healthy people.

Global dissemination of conjugative virulence plasmids co-harboring hypervirulence and multidrug resistance genes in Klebsiella pneumoniae

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) has led to a high mortality rate in the clinical setting and garnered significant attention in the clinical and scientific communities. It is still not clear which major mechanisms mediate the rapid evolution of hvKp in clinical settings since the plasmid-encoding hypervirulence phenotype is considered non-conjugative. In this study, we revealed a conjugative plasmid, p16HN200-Vir, encoding virulence-associated iuc operon (iucABCDiutA) and resulting in a hypervirulent phenotype. In silico analysis of Kp strains from NCBI predicted a total of 94 p16HN200-Vir-like conjugative virulence plasmids. These sequences were identified in 19 sequence types (STs) of the host with significant geographical variations in distribution across countries and continents. Notably, ST11 was predominant in China, while ST147 and ST395 were prominent in the United Kingdom and Russia, respectively. These plasmids could be categorized into seven lineages, some of which formed distinct geographical clusters in China and the UK, while others exhibited a hybrid population. Importantly, most of the plasmids carried different carbapenemases, including blaNDM-1/5 (lineage 6 and 7), and blaOXA-48/232 (lineage 2 and 5). Specifically, plasmids recovered from the United Kingdom and Russia were lineage-specific, with blaNDM-1 present in lineage 6 and blaNDM-5 in lineage 7. Our data suggest that this type of conjugative plasmids has spread around the world and contributed significantly to the current rapid evolution of CR-hvKp in clinical settings. Further surveillance of these types of conjugative plasmids in clinical Kp is warranted.

IMPORTANCE

In this study, we found that the conjugative virulence plasmids containing carbapenem resistance genes could be conjugated to Klebsiella strains, enabling them to express antibiotic resistance and hypervirulence-associated phenotypes simultaneously. More importantly, we observed that the global dissemination of this type of multidrug resistance and hypervirulence conjugative plasmid is lineage specific. The UMAP projection revealed that the regional variations were correlated with ST types and serotypes, which poses a global threat of the CR-hvKp infection worldwide.

Emergence of Tigecycline-Nonsusceptible Carbapenem-Resistant Klebsiella pneumoniae with Metallo-β-Lactamase and Transferable Ceftazidime-Avibactam Resistance in China

In recent years, resistance of Klebsiella pneumoniae to the clinical last-resort drugs carbapenem and tigecycline has intensified, including Metallo-β-Lactamase-producing K. pneumoniae (MBL-KP), which demonstrated resistance to ceftazidime-avibactam (CZA), posing a significant public health threat. This study focused on the carbapenems, CZA, and tigecycline resistance mechanisms of MBL-producing Carbapenem-resistant K. pneumoniae (MBL-CRKP). A retrospective study and genomic epidemiological analysis of Carbapenem-resistant K. pneumoniae (CRKP) strains isolated from Yangzhou City, Jiangsu Province, China, between 2016 and 2023 was conducted. The detection rate of CRKP in Yangzhou City has increased significantly in recent years, with five strains carrying the Metallo-β-Lactamases (MBLs) gene, all of which exhibited resistance to carbapenems and CZA. Two strains even showed reduced susceptibility to tigecycline, with one harboring tmexCD2-toprJ2. Moreover, three CRKP strains carrying both blaKPC-2 and blaNDM-1/blaNDM-29 genes were identified. Plasmids carrying MBL genes can horizontally transfer, leading to the spread of resistance, thus further exacerbating the difficulty of clinical treatment and the spread of resistance. In conclusion, this study not only revealed the resistance of MBL-CRKP strains to clinical last-resort therapeutic drugs but also explored the resistance mechanism and horizontal transfer through genomic analysis. Moreover, this study also suggested that microbial drug resistance surveillance should be conducted from the perspective of "one health" in the future to combat this global health challenge.

Characterization of OXA232-Producing Carbapenem-Resistant Klebsiella pneumoniae: Genomic Analysis and Virulence Assessment

Globally, the infection rate of carbapenem-resistant Klebsiella pneumoniae (CRKP) producing OXA-48-like carbapenemase is increasing, posing a significant public health threat due to its high antibiotic resistance. Between December 2019 and April 2023, ten CRKP strains carrying the OXA-48-like carbapenemase were isolated from inpatients at the First Affiliated Hospital of Kunming Medical University. Wholegenome sequencing (WGS) revealed that all strains carried the OXA-232 gene, a variant of OXA-48-like, located on the non-conjugative ColKP3 plasmid. Sequence typing identified nine strains as ST231 and one as ST11. The ST231 strains carried common virulence genes, including yersiniabactin (ybtA, fyuA, irp2) and aerobactin (iucABCD, iutA), while the ST11 strain carried high-virulence genes (rmpA, rmpA2, peg-344) as well as KPC-2 and OXA-232 carbapenemase genes on separate plasmids, suggesting that CRKP can harbor multiple plasmids with carbapenemase genes. Sequence typing of 264 global ST231 CRKP isolates (n = 264) showed a distinct clonal relationship between our strains and Indian CRKP isolates, indicating potential cross-border transmission. The virulence potential and immune response of the ST231 strains were assessed using a mouse respiratory infection model. The concentrations of inflammatory factors CCL2/MCP-1, IL-6, and TNF-α in the alveolar lavage fluid and blood of the model mice were detected. Combined with the pathological analysis of lung and liver tissues, it reveals variability in virulence and immune response despite carrying identical resistance and virulence genes. This underscores the urgent need for monitoring and tailored public health strategies to combat the global spread of drug-resistant strains.

ESKAPE in China: epidemiology and characteristics of antibiotic resistance

The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.

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.

Genomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying bla NDM-5 and bla KPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China

Background

Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China.

Methods

Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server.

Results

The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla NDM-5, bla KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of bla KPC and bla NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference.

Conclusion

This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.

Clinical and Molecular Characteristics of Patients with Bloodstream Infections Caused by KPC and NDM Co-Producing Carbapenem-Resistant Klebsiella pneumoniae

Purpose

Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM) co-producing carbapenem-resistant Klebsiella pneumoniae (KPC-NDM-CRKP) isolates have been increasingly reported worldwide but have not yet been systematically studied. Thus, we have conducted a study to compare the risk factors, molecular characteristics, and mortality involved in clinical bloodstream infections (BSIs) caused by KPC-NDM-CRKP and KPC-CRKP strains.

Methods

A retrospective study was conducted on 231 patients with BSIs caused by CRKP at Jinling Hospital in China from January 2020 to December 2022. Antimicrobial susceptibility testing, carbapenemase genes detection and whole-genome sequencing were performed subsequently.

Results

Overall, 231 patients were included in this study: 25 patients with KPC-NDM-CRKP BSIs and 206 patients with KPC-CRKP BSIs. Multivariate analysis implicated ICU-acquired BSI, surgery within 30 days, and longer stay of hospitalization prior to CRKP isolation as independent risk factors for KPC-NDM-CRKP BSIs. The 30-day mortality rate of the KPC-NDM-CRKP BSIs group was 56% (14/25) compared with 32.5% (67/206) in the KPC-CRKP BSIs control group (P = 0.02). The ICU-acquired BSIs, APACHE II score at BSI onset, and BSIs caused by KPC-NDM-CRKP were independent predictors for 30-day mortality in patients with CRKP bacteremia. The most prevalent ST in KPC-NDM-CRKP isolates was ST11 (23/25, 92%), followed by ST15 (2/25, 8%).

Conclusion

In patients with CRKP BSIs, KPC-NDM-CRKP was associated with an excess of mortality. The likelihood that KPC-NDM-CRKP will become the next "superbug" highlights the significance of epidemiologic surveillance and clinical awareness of this pathogen.

Genomic characterization and outbreak investigations of methicillin-resistant Staphylococcus aureus in a county-level hospital in China

Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen contributing to healthcare-associated infections, which can result in multiple sites infections. The epidemiological characteristics of MRSA exhibit variability among distinct regions and healthcare facilities. The aim of this study was to investigate the molecular epidemiology and nosocomial outbreak characteristics of MRSA in a county-level hospital in China. A total of 130 non-repetitive MRSA strains were collected from December 2020 to November 2021. Whole-genome sequencing (WGS) was performed to identify antimicrobial resistance and virulence factors. Phylogenetic analysis was conducted to ascertain genetic diversity and phylogenetic relationships. Independent transmission scenarios were determined by the phylogeny derived from single nucleotide polymorphisms (SNPs) within the core genome. All the MRSA isolates were collected from the intensive care unit (30.00%, 39/130), the department of otorhinolaryngology (10.00%, 13/130) and the department of burn unit (9.23%, 12/130). The clinical samples mainly included phlegm (53.85%, 70/130), purulent fluid (24.62%, 32/130), and secretions (8.46%, 11/130). The resistance rates to erythromycin, clindamycin and ciprofloxacin were 75.38, 40.00, and 39.23%, respectively. All the isolates belonged to 11 clonal complexes (CCs), with the major prevalent types were CC5, CC59, and CC398, accounting for 30.00% (39/130), 29.23% (38/130), and 16.92% (22/130), respectively. Twenty sequence types (STs) were identified, and ST59 (25.38%, 33/130) was the dominant lineage, followed by ST5 (23.84%, 31/130) and ST398 (16.92%, 22/130). Three different SCCmec types were investigated, most of isolates were type IV (33.85%, 44/130), followed by type II (27.69%, 36/130) and type III (0.77%, 1/130). The common clonal structures included CC5-ST5-t2460-SCCmec IIa, CC59-ST59-t437-SCCmec IV and CC398-ST398-t034-SCCmec (-), with rates of 16.92% (22/130), 14.62% (19/130), and 13.84% (18/130), respectively. Only 12 panton-valentine leucocidin (PVL) positive strains were identified. Two independent clonal outbreaks were detected, one consisting of 22 PVL-negative strains belongs to CC5-ST5-t2460-SCCmec IIa and the other consisting of 8 PVL-negative strains belongs to CC5-ST5-t311-SCCmec IIa. Overall, our study indicated that the CC5 lineage emerged as the predominant epidemic clone of MRSA, responsible for nosocomial outbreaks and transmission within a county-level hospital in China, highlighting the necessity to strengthen infection control measures for MRSA in such healthcare facilities.

Genomic surveillance indicates clonal replacement of hypervirulent Klebsiella pneumoniae ST881 and ST29 lineage strains in vivo

The emergence of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat, particularly regarding its carriage in the healthy population. However, the genomic epidemiological characteristics and population dynamics of hvKp within a single patient across distinct infection episodes remain largely unknown. This study aimed to investigate the clonal replacement of hvKp K2-ST881 and K54-ST29 lineage strains in a single patient experiencing multiple-site infections during two independent episodes. Two strains, designated EDhvKp-1 and EDhvKp-2, were obtained from blood and cerebrospinal fluid during the first admission, and the strain isolated from blood on the second admission was named EDhvKp-3. Whole-genome sequencing, utilizing both short-read Illumina and long-read Oxford Nanopore platforms, was conducted. In silico multilocus sequence typing (MLST), identification of antimicrobial resistance and virulence genes, and the phylogenetic relationship between our strains and other K. pneumoniae ST881 and ST29 genomes retrieved from the public database were performed. Virulence potentials were assessed through a mouse lethality assay. Our study indicated that the strains were highly susceptible to multiple antimicrobial agents. Plasmid sequence analysis confirmed that both virulence plasmids, pEDhvKp-1 (166,008 bp) and pEDhvKp-3 (210,948 bp), belonged to IncFIB type. Multiple virulence genes, including rmpA, rmpA2, rmpC, rmpD, iroBCDN, iucABCD, and iutA, were identified. EDhvKp-1 and EDhvKp-2 showed the closest relationship to strain 502 (differing by 51 SNPs), while EDhvKp-3 exhibited 69 SNPs differences compared to strain TAKPN-1, which all recovered from Chinese patients in 2020. In the mouse infection experiment, both ST881 EDhvKp-1 and ST29 EDhvKp-3 displayed similar virulence traits, causing 90 and 100% of the mice to die within 72 h after intraperitoneal infection, respectively. Our study expands the spectrum of hvKp lineages and highlights genomic alterations associated with clonal switching between two distinct lineages of hvKP that successively replaced each other in vivo. The development of novel strategies for the surveillance, diagnosis, and treatment of high-risk hvKp is urgently needed.