Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates

Clonal Dissemination of NDM-Producing Proteus mirabilis in a Teaching Hospital in Sousse, Tunisia

Proteus mirabilis (P. mirabilis) is an opportunistic pathogen involved in urinary tract infections as well as various nosocomial infections. Emerging resistances to beta-lactams in this species complicates potential treatment since it is intrinsically resistant to colistin. Eleven isolates of carbapenem-non-susceptible P. mirabilis were identified in Sousse Hospital, Tunisia, from January 2018 to December 2022. MICs were determined and isolates were sequenced to determine their resistomes, sequence types, virulence factors, and their clonal relationships. Susceptibility testing showed that all isolates were resistant to carbapenems, aminoglycosides, fluoroquinolones, chloramphenicol, and the trimethoprim/sulfamethoxazole combination. They remained susceptible to the aztreonam/avibactam combination. All isolates produced NDM-1 carbapenemase and ArmA 16S rRNA methylase. In addition, one isolate co-produced the blaVEB-6 gene. All isolates belonged to ST135, and phylogenetic analysis revealed that they were closely related. This study described the first outbreak of NDM-1-producing P. mirabilis in Tunisia.

Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia

The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.

Fitness costs of Tn1546-type transposons harboring the vanA operon by plasmid type and structural diversity in Enterococcus faecium

BACKGROUND

This study analyzed the genetic traits and fitness costs of vancomycin-resistant Enterococcus faecium (VREfm) blood isolates carrying Tn1546-type transposons harboring the vanA operon.

METHODS

All E. faecium blood isolates were collected from eight general hospitals in South Korea during one-year study period. Antimicrobial susceptibility testing and vanA and vanB PCR were performed. Growth rates of E. faecium isolates were determined. The vanA-positive isolates were subjected to whole genome sequencing and conjugation experiments.

RESULTS

Among 308 E. faecium isolates, 132 (42.9%) were positive for vanA. All Tn1546-type transposons harboring the vanA operon located on the plasmids, but on the chromosome in seven isolates. The plasmids harboring the vanA operon were grouped into four types; two types of circular, nonconjugative plasmids (Type A, n = 50; Type B, n = 46), and two types of putative linear, conjugative plasmids (Type C, n = 16; Type D, n = 5). Growth rates of vanA-positive E. faecium isolates were significantly lower than those of vanA-negative isolates (P < 0.001), and reduction in growth rate under vancomycin pressure was significantly larger in isolates harboring putative linear plasmids than in those harboring circular plasmids (P = 0.020).

CONCLUSIONS

The possession of vanA operon was costly to bacterial hosts in antimicrobial-free environment, which provide evidence for the importance of reducing vancomycin pressure for prevention of VREfm dissemination. Fitness burden to bacterial hosts was varied by type and size of the vanA operon-harboring plasmid.

Antibiotic resistance: A key microbial survival mechanism that threatens public health

Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.

Molecular characterization and antibiotic resistance of Staphylococcus aureus strains isolated from patients with diarrhea in Korea between the years 2007 and 2022

To investigate the molecular characteristics and antibiotic resistance of Staphylococcus aureus isolates from patients with diarrhea in Korea, 327 S. aureus strains were collected between 2007 and 2022. The presence of staphylococcal enterotoxin (SE) and toxic shock syndrome toxin-1 (TSST-1) genes in S. aureus isolates was determined by PCR. The highest expression of the TSST-1 gene was found in the GIMNO type (43.1% of GIMNO type). GIMNO type (Type I) refers to each staphylococcal enterotoxin (SE) gene gene (initials of genes): G = seg; I = sei; M = selm; N = seln; O = selo. Moreover, Type I isolates showed a significantly higher resistance to most antibiotics. A total of 195 GIMNO-type S. aureus strains were analyzed using multilocus sequence typing (MLST), and 18 unique sequence types (STs) were identified. The most frequent sequence type was ST72 (36.9%), followed by ST5 (22.1%) and ST30 (16.9%). Interestingly, ST72 strains showed a higher prevalence of MRSA than the other STs. In conclusion, our results were the first reported for S. aureus strains in Korea, which significantly expanded S. aureus genotype information for the surveillance of pathogenic S. aureus and may provide important epidemiological information to resolve several infectious diseases caused by S. aureus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01478-9.

Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis

The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.

Characterization of antibiotic resistance genes and mobile genetic elements in Escherichia coli isolated from captive black bears

The objective of this study was to analyze the antimicrobial resistance (AMR) characteristics produced by antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and gene cassettes in Escherichia coli isolated from the feces of captive black bears. Antimicrobial susceptibility testing was performed by using the disk diffusion method, and both MGEs and integron gene cassettes were detected by polymerase chain reaction. Our results showed that 43.7% (62/142) of the isolates were multidrug resistant strains and 97.9% (139/142) of the isolates were resistant to at least one antibiotic. The highest AMR phenotype was observed for tetracycline (79.6%, 113/142), followed by ampicillin (50.0%, 71/142), trimethoprim-sulfamethoxazole (43.7%, 62/142) and cefotaxime (35.9%, 51/142). However, all isolates were susceptible to tobramycin. tetA had the highest occurrence in 6 ARGs in 142 E. coli isolates (76.8%, 109/142). Ten mobile genetic elements were observed and IS26 was dominant (88.0%, 125/142). ISECP1 was positively associated with five β-lactam antibiotics. ISCR3/14, IS1133 and intI3 were not detected. Seventy-five E. coli isolates (65 intI1-positive isolates, 2 intI2-positive isolates and 8 intI1 + intI2-positive isolates) carried integrons. Five gene cassettes (dfrA1, aadA2, dfrA17-aadA5, aadA2-dfrA12 and dfrA1-aadA1) were identified in the intI1-positive isolates and 2 gene cassettes (dfrA1-catB2-sat2-aadA1 and dfrA1-catB2-sat1-aadA1) were observed in the intI2-positive isolates. Monitoring of ARGs, MGEs and gene cassettes is important to understand the prevalence of AMR, which may help to introduce measures to prevent and control of AMR in E. coli for captive black bears.

Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome

Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which Klebsiella pneumoniae, Enterobacter hormaechei_A, and Escherichia coli_D played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.IMPORTANCEThe transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota. K. pneumoniae, E. hormaechei_A, and E. coli_D were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.

Intracellular Transposition of Mobile Genetic Elements Associated with the Colistin Resistance Gene mcr-1

Mobile colistin resistance (mcr) genes are often located on conjugative plasmids, where their association with insertion sequences enables intercellular and intracellular dissemination throughout bacterial replicons and populations. Multiple mcr genes have been discovered in every habitable continent, in many bacterial species, on both plasmids and integrated into the chromosome. Previously, we showed the intercellular transfer of mcr-1 on an IncI1 plasmid, pMCR-E2899, between strains of Escherichia coli. Characterizing the intracellular dynamics of mcr-1 transposition and recombination would further our understanding of how these important genes move through bacterial populations and whether interventions can be put in place to stop their spread. In this study, we aimed to characterize transfer events from the mcr-1-containing transposon Tn7511 (ISApl1-mcr-1-pap2-ISApl1), located on plasmid pMCR-E2899, using the pBACpAK entrapment vector. Following the transformation of pBACpAK into our DH5α-Azi^r/pMCR-E2899 transconjugant, we captured ISApl1 in pBACpAK multiple times and, for the first time, observed the ISApl1-mediated transfer of the mcr-1 transposon (Tn7511) into the chromosome of E. coli DH5α. Whole-genome sequencing allowed us to determine consensus insertion sites of ISApl1 and Tn7511 in this strain, and comparison of these sites allowed us to explain the transposition events observed. These observations reveal the consequences of ISApl1 transposition within and between multiple replicons of the same cell and show mcr-1 transposition within the cell as part of the novel transposon Tn7511. IMPORTANCE By analyzing the intracellular transfer of clinically relevant transposons, we can understand the dissemination and evolution of drug resistance conferring mobile genetic elements (MGEs) once a plasmid enters a cell following conjugation. This knowledge will help further our understanding of how these important genes move through bacterial populations. Utilizing the pBACpAK entrapment vector has allowed us to determine the mobility of the novel mcr-1-containing transposon Tn7511.