Dynamic evolution and transmission of a blaNDM-1-bearing fusion plasmid in a clinical Escherichia coli

Antimicrobial peptides: from discovery to developmental applications

Antimicrobial resistance (AMR) has emerged as a significant crisis in global health. Due to their advantageous properties, antimicrobial peptides (AMPs) have garnered considerable attention as a potential alternative therapy to address the AMR crisis. These peptides might disrupt cell membranes or cell walls to exhibit antimicrobial activity, or modulate the immune response to promote recovery from diseases. In recent years, significant progress has been made in the research of AMPs, alongside the emergence of new challenges. This review first systematically summarizes and critically discusses recent advancements in understanding the characteristics and current landscapes of AMPs, as well as their regulatory mechanisms of action and practical applications, particularly those reported or approved within the last 5 years. Additionally, the principles, paths for their identification, and future research trends in AMPs are also analyzed following a discussion of the advantages and disadvantages of AMPs in comparison to conventional antibiotics. Unlike significant prior literature in this field, this report has summarized the latest major discovery methods for AMPs and, more importantly, emphasized their practical applications by supporting various viewpoints using selected examples of AMPs' applications in real-life scenarios. Besides, some emerging hot topics of AMPs, including those derived from gut microbiota and their potential synergistic effects in combating AMR, were profiled. All of these indicate the originality of the report and provide valuable references for future AMP discoveries and applications.

Rapid emergence, transmission, and evolution of KPC and NDM coproducing carbapenem-resistant Klebsiella pneumoniae

Due to the limited treatment options, the widespread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a serious clinical challenge. The emergence of Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM) coproducing CRKP (KPC-NDM-CRKP) further aggravates this issue. In this study, we identified 15 KPC-2-NDM-5-CRKPs as being responsible for an outbreak that involved 10 patients from October 2020 to May 2021. The outbreak was sustained by ST11-KL47-OL101 KPC-2-NDM-5-CRKPs, which exhibited non-susceptible to all antimicrobials available in mainland China. Of these strains, we characterized a conjugative hybrid plasmid co-harboring blaKPC-2 and blaNDM-5 with high stability. Plasmid comparison and phylogenetic analysis were performed to investigate the origin of the hybrid plasmid and its fusion mechanism. It was speculated that the hybrid plasmid might originate from Klebsiella pneumoniae subsp. pneumoniae strain kpn-hnqyy plasmids unnamed1 (encoding NDM-5) and unnamed2 (encoding KPC-2). The fusion of these two plasmids was presumably mediated by IS26. Global genomic surveillance raised an alarm about the increased prevalence of KPC-NDM-CRKPs. Phylogenetic evaluation was carried out with a total of 327 KPC-NDM-CRKP genomes to provide a global perspective on such strains, and potential transmission events in other global regions were also observed during the COVID-19 period. The outbreak of such strains in the real world and the co-transfer of blaKPC and blaNDM would exacerbate the dispersal of KPC-NDM-CRKPs, which poses a severe threat to public health.

Eliminating the tigecycline resistance RND efflux pump gene cluster tmexCD-toprJ in bacteria using CRISPR/Cas9

OBJECTIVES

Tigecycline, a last-resort antibiotic in the tetracycline class, has been effective in treating infections caused by multidrug-resistant bacteria. However, the emergence of the tigecycline resistance gene cluster tmexCD-toprJ, which encodes a resistance-nodulation-division efflux pump, has significantly limited its therapeutic effectiveness. This study aims to explore the potential of CRISPR/Cas9-based plasmids to target and cleave tmexCD-toprJ gene cluster from bacterial plasmids and chromosomal integrative conjugative elements (ICEs), respectively.

METHODS

We developed two CRISPR/Cas9-based plasmids, pCas9Kill and pCas9KillTS. The pCas9Kill plasmid designed to eliminate tmexCD-toprJ from plasmids through electroporation, while the pCas9KillTS plasmid, delivered through conjugation, targeted tmexCD-toprJ within ICEs on the bacterial chromosome. The plasmid modifications were assessed using nanopore long-read sequencing.

RESULTS

Electroporation with the pCas9Kill plasmid resulted in the removal of tmexCD-toprJ from plasmids, restoring bacterial susceptibility to tigecycline. Nanopore sequencing revealed that the plasmids were repaired by insertion sequences after tmexCD-toprJ removal. In contrast, the pCas9KillTS plasmid introduced via conjugation to target tmexCD-toprJ gene cluster on ICEs within the chromosome. This approach led to chromosomal cleavage and subsequent bacterial cell death.

CONCLUSION

Our results demonstrate that both plasmids effectively inactivated tmexCD-toprJ, with pCas9Kill restoring tigecycline susceptibility in plasmid-bearing strains and pCas9KillTS causing targeted cell death in chromosomal ICE-harbouring bacteria. This study highlights the potential of CRISPR/Cas9 systems in addressing antibiotic resistance, providing a promising strategy to combat tigecycline-resistant pathogens.

Dairy farm waste: A potential reservoir of diverse antibiotic resistance and virulence genes in aminoglycoside- and beta-lactam-resistant Escherichia coli in Gansu Province, China

Aminoglycosides (AGs) and beta-lactams are the most commonly used antimicrobials in animal settings, particularly on dairy farms. Dairy farm waste is an important reservoir of antibiotic resistance genes (ARGs) and virulence genes (VGs) in environmental Escherichia coli, which is an important indicator of environmental contamination and foodborne pathogen that potentially threaten human and animal health. In the present study, we aimed to characterize the ARGs and VGs in AG- and beta-lactam-resistant E. coli from dairy farm waste in Gansu Province, China. The dairy farm waste consisted of fecal (n = 265) and sewage (n = 54) samples processed using standard microbiological techniques and the Clinical & Laboratory Standards Institute guidelines. The total DNA of AG- and beta-lactam-resistant E. coli was extracted, and whole-genome sequencing (WGS) was performed using the Illumina NovaSeq platform and analyzed using various bioinformatics tools. In this study, among 84.3% (269/319) of the E. coli strains, 23.8% (64/269) were identified as AG- and beta-lactam-resistant E. coli. WGS analysis revealed a large pool of ARGs belonging to multiple classes such as AGs, beta-lactams, aminocoumarins, fluoroquinolones, macrolides, phenicol, tetracyclines, phosphonic acid, disinfecting and antiseptic agents, elfamycin, rifamycin, and multidrug resistance genes. Furthermore, virulome analysis of 64 E. coli strains revealed clinically important virulence factors associated with adherence, biofilm, invasion, auto-transportation, siderophores, secretion systems, toxins, anti-phagocytosis, quorum sensing, regulation, metabolism, and motility. We identified dairy farm feces and sewage waste as important reservoirs of antimicrobial resistance and virulence determinants in E. coli in Gansu, China, which can threaten human and animal health through ecological exposure and contamination of food and water. We recommend continuous large-scale surveillance in dairy farm settings to formulate protective guidelines for public health safety.

Genomic Characterization of Extended-Spectrum β-Lactamase (ESBL) Producing E. coli Harboring bla OXA-1-catB3-arr-3 Genes Isolated From Dairy Farm Environment in China

Anthropogenic activities in the environment affect the ecosystem and can play an important role in selecting and spreading antibiotic-resistant bacteria (ARB) and genes (ARGs). The dairy farm environment may serve as a hotspot and reservoir for exchanging and spreading ARGs, but studies are scarce. Here, we investigated and characterized the extended-spectrum β-lactamase producing Escherichia coli strains recovered from the dairy farm environment co-harboring bla OXA-1, catB3, and arr-3 genes. The isolates were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS), and multiple bioinformatics tools. Seven E. coli strains co-harboring bla OXA-1, catB3, and arr-3 genes were identified which belonged to distinct sequence types (STs) and carried diverse plasmid replicon types. The conjugation assay revealed a successful transfer of bla OXA-1, catB3, and arr-3 genes into the recipient E. coli J53 with a co-conjugation frequency ranging from (2.25 ± 0.3) × 10-4 to (3.85 ± 0.3) × 10-3. Bioinformatics analysis of WGS revealed the diversity of acquired ARGs, conferring resistance to aminoglycosides, beta-lactams, quinolones, tetracyclines, macrolides, trimethoprim-sulfamethoxazole, phosphonic, phenicol, and rifamycin. The genetic environment analysis showed that aac(6')-Ib-cr-bla OXA-1-catB3-arr-3-qacE1-sul1 was the common genetic backbone among the seven E. coli strains. Among the mobile genetic elements, insertion sequences were the predominant elements as compared to transposons. The phylogenetic analysis demonstrated a close relationship between the E. coli of this study and other strains of human-animal-environment origin retrieved from the NCBI database. This study presented the whole genome-based characterization of E. coli strains carrying the bla OXA-1-catB3-arr-3 genes. It provided evidence that the dairy environment may harbor a variety of ARGs and act as a potential reservoir for their spread in the ecosystem. The results recommend the routine surveillance of ARGs carrying bacteria in dairy environments and the need for additional studies to understand the dissemination mechanism within One Health perspective to prevent their further spread.

Carbapenem Resistance in Acinetobacter calcoaceticus-baumannii Complex Isolates From Kathmandu Model Hospital, Nepal, Is Attributed to the Presence of bla OXA-23-like and bla NDM-1 Genes

The Acinetobacter calcoaceticus-baumannii (ACB) complex, also known as ACB complex, consists of four bacterial species that can cause opportunistic infections in humans, especially in hospital settings. Conventional therapies for susceptible strains of the ACB complex include broad-spectrum cephalosporins, β-lactam/β-lactamase inhibitors, and carbapenems. Unfortunately, the effectiveness of these antibiotics has declined due to increasing rates of resistance. The predominant resistance mechanisms identified in the ACB complex involve carbapenem-resistant (CR) oxacillinases and metallo-β-lactamases (MBLs). This research, conducted at Kathmandu Model Hospital in Nepal, sought to identify genes associated with CR, specifically blaNDM-1, blaOXA-23-like, and blaOXA-24-like genes in carbapenem-resistant Acinetobacter calcoaceticus-baumannii (CR-ACB) complex. Additionally, the study is aimed at identifying the ACB complex through the sequencing of the 16s rRNA gene. Among the 992 samples collected from hospitalized patients, 43 (approximately 4.334%) tested positive for the ACB complex. These positive samples were mainly obtained from different hospital units, including intensive care units (ICUs); cabins; and neonatal, general, and maternity wards. The prevalence of infection was higher among males (58.14%) than females (41.86%), with the 40-50 age group showing the highest infection rate. In susceptibility testing, colistin and polymyxin B exhibited a susceptibility rate of 100%, whereas all samples showed resistance to third-generation cephalosporins. After polymyxins, gentamicin (30.23%) and amikacin (34.88%) demonstrated the highest susceptibility. A substantial majority (81.45%) of ACB complex isolates displayed resistance to carbapenems, with respiratory and pus specimens being the primary sources. Polymerase chain reaction (PCR) revealed that the primary CR gene within the ACB complex at this hospital was bla OXA-23-like, followed by bla NDM-1. To ensure the accuracy of the phenotypic assessment, 12 samples were chosen for 16s rRNA sequencing using Illumina MiSeq™ to confirm that they are Acinetobacter species. QIIME 2.0 analysis confirmed all 12 isolates to be Acinetobacter species. In the hospital setting, a substantial portion of the ACB complex carries CR genes, rendering carbapenem ineffective for treatment.

Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli

Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.