Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals

Background

VIM metallo-β-lactamases are enzymes characterized by the ability to hydrolyze all β-lactams. Usually, bla _VIM-like genes are carried by class 1 integrons. In the Czech Republic, only sporadic cases of VIM-producing Enterobacterales have been reported in which those isolates carried the VIM-1 carbapenemase-encoding integron In110. However, during 2019-2020, an increased number was reported. Therefore, the aim of the current study was to characterize the genetic elements involved in the increased spread of bla _VIM genes.

Materials and methods

32 VIM-producing Enterobacterales collected between 2019 and 2020 were subjected to: antimicrobial susceptibility testing, integron analysis, and short reads sequencing. Based on the results, 19 isolates were selected as representative and sequenced using Sequel I platform.

Results

The 32 VIM-producing isolates exhibited variations in the MICs of carbapenems. Based on short-read data, 26 of the 32 sequenced isolates harbored the bla _VIM-1 allele while six isolates carried the bla _VIM-4 gene. The most prevalent was the In110 integron (n = 24) and two isolates carried the In4873 class 1 integron. The bla _VIM-4 allele was identified in class 1 integrons In1174 (n = 3), In416 (n = 1), In2143 (n = 1) and In2150. Long reads sequencing revealed that the bla _VIM was carried by: pKPC-CAV1193-like (n = 6), HI1 (pNDM-CIT; n = 4), HI2 (n = 3), FIB (pECLA; n = 2) and N (n = 1) incompatibility groups. Two bla _VIM-carrying plasmids could not be typed by the database, while another one was integrated into the chromosome.

Conclusion

We observed the spread of VIM-encoding integrons, mainly of In110, among Enterobacterales isolated from Czech hospitals, but also an increased number of novel elements underlining the ongoing evolution.

Impact of Peptidoglycan Recycling Blockade and Expression of Horizontally Acquired β-Lactamases on Pseudomonas aeruginosa Virulence

In the current scenario of antibiotic resistance magnification, new weapons against top nosocomial pathogens like Pseudomonas aeruginosa are urgently needed. The interplay between β-lactam resistance and virulence is considered a promising source of targets to be attacked by antivirulence therapies, and in this regard, we previously showed that a peptidoglycan recycling blockade dramatically attenuated the pathogenic power of P. aeruginosa strains hyperproducing the chromosomal β-lactamase AmpC. Here, we sought to ascertain whether this observation could be applicable to other β-lactamases. To do so, P. aeruginosa wild-type or peptidoglycan recycling-defective strains (ΔampG and ΔnagZ) harboring different cloned β-lactamases (transferable GES, VIM, and OXA types) were used to assess their virulence in Galleria mellonella larvae by determining 50% lethal doses (LD50s). A mild yet significant LD50 increase was observed after peptidoglycan recycling disruption per se, whereas the expression of class A and B enzymes did not impact virulence. While the production of the narrow-spectrum class D OXA-2 entailed a slight attenuation, its extended-spectrum derivatives OXA-226 (W159R [bearing a change of W to R at position 159]), OXA-161 (N148D), and principally, OXA-539 (D149 duplication) were associated with outstanding virulence impairments, especially in recycling-defective backgrounds (with some LD50s being >1,000-fold that of the wild type). Although their exact molecular bases remain to be deciphered, these results suggest that mutations affecting the catalytic center and, therefore, the hydrolytic spectrum of OXA-2-derived enzymes also drastically impact the pathogenic power of P. aeruginosa. This work provides new and relevant knowledge to the complex topic of the interplay between the production of β-lactamases and virulence that could be useful to build future therapeutic strategies against P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is one of the leading nosocomial pathogens whose growing resistance makes the development of therapeutic options extremely urgent. The resistance-virulence interplay has classically aroused researchers' interest as a source of therapeutic targets. In this regard, we describe a wide array of virulence attenuations associated with different transferable β-lactamases, among which the production of OXA-2-derived extended-spectrum β-lactamases stood out as a dramatic handicap for pathogenesis, likely as a side effect of mutations causing the expansion of their hydrolytic spectrums. Moreover, our results confirm the validity of disturbing peptidoglycan recycling as a weapon to attenuate P. aeruginosa virulence in class C and D β-lactamase production backgrounds. In the current scenario of dissemination of horizontally acquired β-lactamases, this work brings out new data on the complex interplay between the production of specific enzymes and virulence attenuation that, if complemented with the characterization of the underlying mechanisms, will likely be exploitable to develop future virulence-targeting antipseudomonal strategies.

Occurrence of NDM-1, VIM-1, and OXA-10 Co-Producing Providencia rettgeri Clinical Isolate in China

Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections related to hospital-acquired Infections. In recent years, P. rettgeri clinical strains producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamase which reduce the efficiency of antimicrobial therapy have been reported. However, there are few reports of P. rettgeri co-producing two metallo-β-lactamases in one isolate. Here, we first reported a P. rettgeri strain (P138) co-harboring bla_NDM-1, bla_VIM-1, and bla_OXA-10. The specie were identified using MALDI-TOF MS. The results of antimicrobial susceptibility testing by broth microdilution method indicated that P. rettgeri P138 was resistant to meropenem (MIC = 64μg/ml), imipenem (MIC = 64μg/ml), and aztreonam (MIC = 32μg/ml). Conjugation experiments revealed that the bla_NDM-1-carrying plasmid was transferrable. The carbapenemase genes were detected using PCR and confirmed by PCR-based sequencing. The complete genomic sequence of the P. rettgeri was identified using Illumina (Illumina, San Diego, CA, USA) short-read sequencing (150bp paired-end reads), and many common resistance genes had been identified, including bla_NDM-1, bla_VIM-1, bla_OXA-10, aac(6’)-Il, aadA5, ant(2’’)-Ia, aadA1, aac(6’)-Ib3, aadA1, aph(3’)-Ia, aac(6’)-Ib-cr, qnrD1, qnrA1, and catA2. The bla_NDM-1 gene was characterized by the following structure: IS110–TnpA–IntI1–aadB–IS91–GroEL–GroES–DsbD–PAI–ble–bla_NDM-1–IS91–QnrS1–IS110. Blast comparison revealed that the bla_NDM-1 gene structure shared >99% similarity with plasmid p5_SCLZS62 (99% nucleotide identity and query coverage). In summary, we isolated a P. rettgeri strain coproducing bla_NDM-1, bla_VIM-1, and blaOXA-10. To the best of our acknowledge, this was first reported in the world. The occurrence of the strain needs to be closely monitored.

Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy

Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the bla_VIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the bla_VIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and bla_VIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.

Identification of a blaVIM-1-Carrying IncA/C2 Multiresistance Plasmid in an Escherichia coli Isolate Recovered from the German Food Chain

Within the German national monitoring of zoonotic agents, antimicrobial resistance determination also targets carbapenemase-producing (CP) Escherichia coli by selective isolation from food and livestock. In this monitoring in 2019, the CP E. coli 19-AB01133 was recovered from pork shoulder. The isolate was assigned to the phylogenetic group B1 and exhibited the multi-locus sequence-type ST5869. Molecular investigations, including whole genome sequencing, of 19-AB01133 revealed that the isolate carried the resistance genes bla_VIM-1, bla_SHV-5 and bla_CMY-13 on a self-transmissible IncA/C₂ plasmid. The plasmid was closely related to the previously described VIM-1-encoding plasmid S15FP06257_p from E. coli of pork origin in Belgium. Our results indicate an occasional spread of the bla_VIM-1 gene in Enterobacteriaceae of the European pig population. Moreover, the bla_VIM-1 located on an IncA/C₂ plasmid supports the presumption of a new, probably human source of carbapenemase-producing Enterobacteriaceae (CPE) entering the livestock and food chain sector.

Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy

Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the bla_VIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using “Microbial Assembly”. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6′)-Ib4, ant(3″)-Ia, aph(3″)-Ib, aph(3′)-XV, aph(6)-Id), beta-lactam resistance (bla_SHV-12, bla_VIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the bla_VIM-1 gene in Italy.

Evaluation of Metallo-β-Lactamase-Production and Carriage of bla-VIM Genes in Pseudomonas aeruginosa Isolated from Burn Wound Infections in Isfahan

Background

Metallo-β-lactamase-production among Gram-negative bacteria, including Pseudomonas aeruginosa, has become a challenge for treatment of infections due to these resistant bacteria.

Objectives

The aim of the current study was to evaluate the metallo-β-lactamase-production and carriage of bla-_VIM genes among carbapenem-resistant P. aeruginosa isolated from burn wound infections.

Patients and Methods

A cross-sectional study was conducted from September 2014 to July 2015. One hundred and fifty P. aeruginosa isolates were recovered from 600 patients with burn wound infections treated at Imam-Musa-Kazem Hospital in Isfahan city, Iran. Carbapenem-resistant P. aeruginosa isolates were screened by disk diffusion using CLSI guidelines. Metallo-β-lactamase-producing P. aeruginosa isolates were identified using an imipenem-EDTA double disk synergy test (EDTA-IMP DDST). For detection of MBL genes including bla-_VIM-1 and bla-_VIM-2, polymerase chain reaction (PCR) methods and sequencing were used.

Results

Among the 150 P. aeruginosa isolates, 144 (96%) were resistant to imipenem by the disk diffusion method, all of which were identified as metallo-β-lactamase-producing P. aeruginosa isolates by EDTA-IMP DDST. Twenty-seven (18%) and 8 (5.5%) MBL-producing P. aeruginosa isolates harbored bla-_VIM-1 and bla-_VIM-2 genes, respectively.

Conclusions

Our findings showed a high occurrence of metallo-β-lactamase production among P. aeruginosa isolates in burn patient infections in our region. Also, there are P. aeruginosa isolates carrying the bla-_VIM-1 and bla-_VIM-2 genes in Isfahan province.

High prevalence of blaVIM-1 gene in bacteria from Brazilian soil

This study investigated bacteria from soil samples to (i) determine the main bacterial genera and species having resistance to carbapenem and other β-lactams and (ii) establish if the mechanism of resistance was due to the production of metallo-β-lactamases. The isolates were characterized by PCR for metallo-β-lactamases and integrons, by antimicrobial susceptibility testing, and by sequencing. The antimicrobial profile of 40 imipenem-resistant Gram-positive soil isolates from all Brazilian regions demonstrated that 31 (77.5%) of them were multidrug resistant. Among the 40 isolates, 19 presented the bla_VIM gene and class 1 integrons by PCR. Six of the 19 isolates were identified as Paenibacillus sp., 12 as Bacillus sp., and just 1 was classified as Staphylococcus sp., by sequencing of the 16S rRNA gene. These results suggest that bacteria from soil can act as a source of bla_VIM-1 genes, representing a threat to public health.

Molecular detection of metallo-β-lactamase gene blaVIM-1 in imipenem-resistant Pseudomonas aeruginosa strains isolated from hospitalized patients in the hospitals of Isfahan

BACKGROUND

Pseudomonas aeruginosa is an opportunistic human pathogen that causes serious problems, especially in people, who have immunodeficiency. In recent times, metallo-β-lactamase (MBLs) resistance in this bacterium has led to some difficulties in treating bacterial infections. The metallo-beta-lactamase family of genes, including blaVIM-1, is being reported with increasing frequency worldwide. The aim of this study is the detection of the metallo-β-lactamase gene blaVIM-1 in imipenem-resistant P. aeruginosa (IRPA) strains isolated from hospitalized patients.

MATERIALS AND METHODS

In this study, 106 P. aeruginosa samples were isolated from various nosocomial infections. The isolates were identified, tested for susceptibility to various antimicrobial agents by the Kirby-Bauer disk diffusion method, and all the imipenem-resistant isolates were screened for the presence of MBLs by using the combined disk (IMP-EDTA). The minimal inhibitory concentration (MIC) of imipenem was determined by E-test on the Mueller-Hinton agar. To detect the blaVIM-1 gene, the isolates were subjected to a polymerase chain reaction (PCR).

RESULTS

Of all the P. aeruginosa isolates, 62 (58.5%) were found to be imipenem-resistant P. aeruginosa (MIC ≥32 μg/ml). Twenty-six (42%) of the imipenem-resistant isolates were MBL positive. None of these isolates carried the blaVIM-1 gene using the PCR assay.

CONCLUSION

The results demonstrated the serious therapeutic threat of the MBL-producing P. aeruginosa populations. The rate of imipenem resistance due to MBL was increased dramatically. Early detection and infection-control practices are the best antimicrobial strategies for this organism. None of MBL-producing isolates in this study carry the blaVIM-1 gene; therefore, another gene in the MBL family should be investigated.