Pseudomonas putida group species as reservoirs of mobilizable Tn402-like class 1 integrons carrying blaVIM-2 metallo-β-lactamase genes

Emergence of aztreonam/avibactam and tigecycline-resistant Pseudomonas putida group Co-producing blaIMP-1, blaAFM-4 and blaOXA-1041 with a novel sequence type ST268 in Southwestern China

OBJECTIVES

The emergence of carbapenem-resistant Pseudomonas putida (CRPP) has raised public awareness. This study investigated two strains from the Pseudomonas putida group that were resistant to carbapenem, tigecycline, and aztreonam-avibactam (ATM-AVI), with a focus on their microbial and genomic characteristics.

METHODS

We assessed the antibiotic resistance profile using broth dilution, disk diffusion, and E-test methods. Efflux pump phenotype testing and real-time quantitative PCR were employed to evaluate efflux pump activity in tigecycline resistance, while polymerase chain reaction was utilized to detect common carbapenem genes. Additionally, whole-genome sequencing was performed to analyze genomic characteristics. The transferability of blaIMP-1 and blaAFM-4 was assessed through a conjugation experiment. Furthermore, growth kinetics and biofilm formation were examined using growth curves and crystal violet staining.

RESULTS

Both strains demonstrated resistance to carbapenem, tigecycline, and ATM-AVI. Notably, NMP can restore sensitivity to tigecycline. Subsequent analysis revealed that they co-produced blaIMP-1, blaAFM-4, tmexCD-toprJ, and blaOXA-1041, belonging to a novel sequence type ST268. Although they were closely related on the phylogenetic tree, they exhibited different levels of virulence. Genetic environment analysis indicated variations compared to prior studies, particularly regarding the blaIMP-1 and blaAFM-4 genes, which showed limited horizontal transferability. Moreover, it was observed that temperature exerted a specific influence on their biological factors.

CONCLUSION

We initially identified two P. putida ST268 strains co-producing blaIMP-1, blaAFM-4, blaOXA-1041, and tmexCD-toprJ. The resistance to tigecycline and ATM-AVI can be attributed to the presence of multiple drug resistance determinants. These findings underscore the significance of P. putida as a reservoir for novel antibiotic resistance genes. Therefore, it is imperative to develop alternative antibiotic therapies and establish effective monitoring of bacterial resistance.

VIM-type metallo-β-lactamase (MBL)-encoding genomic islands in Pseudomonas spp. in Poland: predominance of clc-like integrative and conjugative elements (ICEs)

OBJECTIVES

To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from 2001-2015/16.

METHODS

Twelve P. aeruginosa and 20 P. putida group isolates producing VIM-like MBLs were selected from a large collection of these based on epidemiological and typing data. The organisms represented all major epidemic genotypes of these species spread in Poland with chromosomally located blaVIM gene-carrying integrons. The previously determined short-read sequences were complemented by long-read sequencing in this study. The comparative structural analysis of the GIs used a variety of bioinformatic tools.

RESULTS

Thirty different GIs with blaVIM integrons were identified in the 32 isolates, of which 24 GIs from 26 isolates were integrative and conjugative elements (ICEs) of the clc family. These in turn were dominated by 21 variants of the GI2/ICE6441 subfamily with a total of 19 VIM integrons, each inserted in the same position within the ICE's Tn21-like transposon Tn4380. The three other ICEs formed a novel ICE6705 subfamily, lacking Tn4380 and having different VIM integrons located in another site of the elements. The remaining six non-ICE GIs represented miscellaneous structures. The presence of various integrons in the same ICE sublineage, and of the same integron in different GIs, indicated circulation and recombination of the integron-carrying genetic platforms across Pseudomonas species/genotypes.

CONCLUSIONS

Despite the general diversity of the blaVIM-carrying GIs in Pseudomonas spp. in Poland, a clear predominance of broadly spread and rapidly evolving clc-type ICEs was documented, confirming their significant role in antimicrobial resistance epidemiology.

Novel Resistance Regions Carrying TnaphA6, blaVIM-2, and blaPER-1, Embedded in an ISPa40-Derived Transposon from Two Multi-Resistant Pseudomonas aeruginosa Clinical Isolates

Antibiotic resistance is an alarming problem throughout the world and carbapenem-resistant Pseudomonas aeruginosa has been cataloged as critical in the World Health Organization list of microorganisms in urgent need for the development of new antimicrobials. In this work, we describe two novel resistance regions responsible for conferring a multidrug resistance phenotype to two clinical isolates of P. aeruginosa (Pa873 and Pa6415) obtained from patients hospitalized in the ICU of University Hospital of Uruguay. Bacterial identification and antibiotic susceptibility tests were performed using MALDI-TOF and the Vitek 2 system, respectively. WGS was performed for both isolates using Oxford Nanopore Technologies and Illumina and processed by means of hybrid assembly. Both isolates were resistant to ceftazidime, cefepime, piperacillin-tazobactam, aztreonam, and imipenem. Strain Pa6415 also showed resistance to ciprofloxacin. Both strains displayed MICs below the susceptibility breakpoint for CAZ-AVI plus 4 mg/L of aztreonam as well as cefiderocol. Both resistance regions are flanked by the left and right inverted repeats of ISPa40 in two small regions spanning 39.3 and 35.6 kb, for Pa6415 and Pa873, respectively. The resistance region of Pa6415 includes TnaphA6, and the new Tn7516 consists of IRi, In899, qacEΔ1-sul1-ISCR1, qnrVC6-ISCR1-bla_PER-1-qacEΔ1-sul1, araJ-like, IS481-like tnpA, ISPa17, and IRR. On the other hand, the resistance region of Pa873 includes Tnaph6 and the new Tn7517 (IRi, In899, qacEΔ1-sul1, ISCR1-bla_PER-1-qacEΔ1-sul1, araJ-like, IS481-like tnpA, ISPa17, and IRR). It is necessary to monitor the emergence of genetic structures that threaten to invalidate the available therapeutic resources.

Coexistence of tmexCD3-toprJ1b tigecycline resistance genes with two novel bla VIM-2-carrying and bla OXA-10-carrying transposons in a Pseudomononas asiatica plasmid

Introduction

Tigecycline and carbapenems are considered the last line of defense against microbial infections. The co-occurrence of resistance genes conferring resistance to both tigecycline and carbapenems in Pseudomononas asiatica was not investigated.

Methods

P. asiatica A28 was isolated from hospital sewage. Antibiotic susceptibility testing showed resistance to carbapenem and tigecycline. WGS was performed to analyze the antimicrobial resistance genes and genetic characteristics. Plasmid transfer by conjugation was investigated. Plasmid fitness costs were evaluated in Pseudomonas aeruginosa transconjugants including a Galleria mellonella infection model.

Results

Meropenem and tigecycline resistant P. asiatica A28 carries a 199, 972 bp long plasmid PLA28.4 which harbors seven resistance genes. Sequence analysis showed that the 7113 bp transposon Tn7389 is made up of a class I integron without a 5'CS terminal and a complete tni module flanked by a pair of 25bp insertion repeats. Additionally, the Tn7493 transposon, 20.24 kp long, with a complete 38-bp Tn1403 IR and an incomplete 30-bp Tn1403 IR, is made up of partial skeleton of Tn1403, a class I integron harboring bla _OXA-10, and a Tn5563a transposon. Moreover, one tnfxB3-tmexC3.2-tmexD3b-toprJ1b cluster was found in the plasmid and another one in the the chromosome. Furthermore, plasmid PLA28.4 could be conjugated to P. aeruginosa PAO1, with high fitness cost.

Discussion

A multidrug-resistant plasmid carrying tmexCD3-toprJ1b and two novel transposons carrying bla _VIM-2 and bla _OXA-10 -resistant genes was found in hospital sewage, increasing the risk of transmission of antibiotic-resistant genes. These finding highlight the necessary of controlling the development and spread of medication resistance requires continuous monitoring and management of resistant microorganisms in hospital sewage.

Characterization of a Carbapenem-Resistant BKC-1-Producing Clinical Isolate Belonging to the Pseudomonas putida Group from Brazil

Since its first report, the class A Brazilian Klebsiella carbapenemase (BKC) has been detected only among Enterobacterales isolates from Brazilian hospitals. In this study, we characterized a multidrug-resistant Pseudomonas juntendi clinical isolate and identified a 43.3-kb plasmid carrying bla_BKC-1 and a class 1 integron (In1996) containing the arr-2, qnrVC1, dfrA21, and aac(6')-Ib' gene cassettes. Our results confirm the ability of Pseudomonas putida group isolates to acquire antimicrobial resistance determinants and further act as resistance reservoirs.

A clinical Pseudomonas juntendi strain with blaIMP−1 carried by an integrative and conjugative element in China

Objective

To precisely determine the species of a carbapenem-resistant Pseudomonas strain 1809276 isolated from the urine of a Chinese patient and analyze its integrative and conjugative element (ICE) 1276 formation mechanism.

Methods

Single-molecule real-time (SMRT) sequencing was carried out on strain 18091276 to obtain the complete chromosome and plasmid (pCN1276) sequences, and average nucleotide identity (ANI) was used for precise species identification. The ICEs in GenBank with the same integrase structure as ICE 1276 were aligned. At the same time, the transfer ability of bla_IMP−1 and the antibiotic sensitivity of Pseudomonas juntendi 18091276 were tested.

Results

This bacterium was P. juntendi, and its drug resistance mechanism is the capture of the accA4' gene cassette by the Tn402-like type 1 integron (IntI1-bla_IMP−1) to form In1886 before its capture by the ΔTn4662a-carrying ICE 1276. The acquisition of bla_IMP−1 confers carbapenem resistance to P. juntendi 18091276.

Conclusion

The formation of bla_IMP−1-carrying ICE 1276, its further integration into the chromosomes, and transposition and recombination of other elements promote bacterial gene accumulation and transmission.

Co-production of Classes A and B Carbapenemases BKC-1 and VIM-2 in a Clinical Pseudomonas Putida Group Isolate from Brazil

Emergence of resistance to classical antimicrobial agents is a public health issue, especially in countries with high antimicrobial consumption rates. Carbapenems have been employed as first-choice option for empirical treatment complicated infections. However, in the last decades, frequency of carbapenemase-producing Gram-negative bacteria has rising, demanding the use of alternative antimicrobial agents. By sequencing the entire genomes with short and long reads technologies, we report the isolation and genomic characterization of a carbapenem-resistant Pseudomonas clinical isolate. The identification based on average nucleotide identity indicates a putative new species into the Pseudomonas putida Group, which carries both the bla_BKC-1 and bla_VIM-2 carbapenemase genes. The bla_BKC-1 was found to be on a transferable IncQ plasmid backbone, whereas bla_VIM-2 was found in a new integron, In2126 (intl1∆-bla_VIM-2-aacA7-bla_VIM-2∆-aacA27-3'CS), described in this study. Our findings indicate that co-occurrence of classes A and B carbapenemase enzymes underscores the evolving emergence of more complex antimicrobial resistance in opportunistic pathogens.

Genomic Epidemiology of MBL-Producing Pseudomonas putida Group Isolates in Poland

Introduction

Pseudomonas putida group are described as low-incidence opportunistic pathogens, but also as a significant reservoir of antimicrobial resistance (AMR) genes, including those of metallo-β-lactamases (MBLs). Our objective was the molecular and genomic characterization of MBL-producing P. putida (MPPP) group isolates from Poland, focusing on population structures, successful genotypes and MBL-encoding integrons.

Methods

During a country-wide MBL surveillance in Pseudomonas spp., 59 non-duplicate MPPP isolates were collected from 36 hospitals in 23 towns from 2003 to 2016. All of the isolates were subjected to whole-genome sequencing (WGS), followed by species identification, multi-locus sequence typing (MLST), single-nucleotide polymorphism (SNP)-based phylogenetic/clonality analysis, resistome determination, and susceptibility testing.

Results

The study collection comprised 12 species, of which P. alloputida (n = 19), P. monteilii (n = 15), and P. asiatica (n = 11) prevailed, while the others were P. kurunegalensis, P. putida, P. soli, P. mosselii, P. juntendi, and four potentially new species. MLST classified the isolates into 23 sequence types (STs) of which 21 were new, with three main clones, namely P. alloputida ST69, P.monteilii ST95 and P. asiatica ST15. The isolates produced VIM-like MBLs only, largely VIM-2 (n = 40), encoded by 24 different class 1 integrons (ten new), a number of which occurred also in P. aeruginosa and/or Enterobacterales in Poland. The plasmid pool was dominated by IncP-9, IncP-2, and pMOS94-like types. Multiple isolates were extensively drug-resistant.

Conclusions

This study, being one of the most comprehensive analyses of MPPP so far, has shown high diversity of the isolates in general, with three apparently international lineages, each internally diversified by MBL-encoding structures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-022-00659-z.

Evaluation of Pseudomonas fulva PS9.1 and Bacillus velezensis NWUMFkBS10.5 as Candidate Plant Growth Promoters during Maize-Fusarium Interaction

Based on in vitro assessments, molecular and chemical analysis, Pseudomonas fulva PS9.1 and Bacillus velezensis NWUMFkBS10.5 are candidate biocontrol agents for plant disease management including maize fusariosis, a disease caused by members of the Fusarium species. This in vivo study evaluated the bio-protective potential of the aforementioned rhizobacteria strains on maize against the proliferation of the pathogenic fungus Fusarium graminearum (Fg). The study results show that the bacterized plants were not susceptible to Fg aggression and the antagonists displayed the capability to proliferate in the presence of other likely competing microflora. The screen-house data also suggest that the presence of resident soil microbiota impacted the activity of antagonists (PS9.1 and NWUMFkBS10.5). This variation was recorded in the soil treatments (sterilized and unsterilized soil). In all the experimental periods, bacterized maize plants with or without Fg inoculation significantly (p = 0.05) grew better in unsterilized soil. Besides, during the experimental periods, all the consortia treatments with or without Fg infection regardless of the soil used demonstrated appreciable performance. The result of this study suggests that the microbial agents can actively colonize the surface of their maize plant host, improve plant growth, and suppress the growth of phytopathogens. Considering their overall performance in this screen-house evaluation, P. fulva PS9.1 and B. velezensis NWUMFkBS10.5 have potential for field applications. All safety issues regarding their use under field conditions and risks associated with their extended-release into the environmental will, however, be assessed prior to further bioformulation, field investigation, and scale-up.