Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases

Piza-Buitrago, Adriana; Rincón, Verónica; Donato, John C; Saavedra, Sandra Yamile; Duarte, Carolina; Morero, Jaime; Falquet, Laurent; Reguero, María Teresa

doi:10.1186/s12866-020-02030-z

Cited by 15 publications

(18 citation statements)

References 68 publications

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“…Since then, NDM-1producing P. rettgeri has been reported in various parts of the world (Pillai et al, 2011;Barrios et al, 2013;Carvalho-Assef et al, 2013;Mataseje et al, 2014;Pasteran et al, 2014;An et al, 2016). Reports in Nepal (Tada et al, 2014) as well as reports in Colombia (Marquez-Ortiz et al, 2017;Piza-Buitrago et al, 2020), and Korea (Shin et al, 2018), commonly associate P. rettgeri with high resistance rates to carbapenems. This resistance characteristic in P. rettgeri is commonly associated with the production of bla NDM-1 .…”

Section: Discussionmentioning

confidence: 99%

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

Shen

Huang

Shi

et al. 2022

Front. Cell. Infect. Microbiol.

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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 blaNDM-1, blaVIM-1, and blaOXA-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 blaNDM-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 blaNDM-1, blaVIM-1, blaOXA-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 blaNDM-1 gene was characterized by the following structure: IS110–TnpA–IntI1–aadB–IS91–GroEL–GroES–DsbD–PAI–ble–blaNDM-1–IS91–QnrS1–IS110. Blast comparison revealed that the blaNDM-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 blaNDM-1, blaVIM-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.

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Section: Discussionmentioning

confidence: 99%

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

Shen

Huang

Shi

et al. 2022

Front. Cell. Infect. Microbiol.

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“…With respect to the nature and organization of identified antibiotic resistance determinants, P. vermicola DSM_17385 appears generally similar to non-clinical strains from other Providencia species including P. rettgeri and P. stuartii . Striking features are both the complete absence of multi drug resistance plasmids and integrons and the related absence of the range of beta-lactamases found in clinical P. rettgeri and P. stuartii strains that are the main sources of the MDR phenotype occurring in Providencia [ 41 ]. These findings are fully in line with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of MDR carrying genetic elements operating between human pathogens.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, P. vermicola has been reported to be a fish pathogen [ 32 – 34 ]. Several Providencia species, including P. vermicola, [ 35 , 36 ] have been described as remarkably resistant to high concentrations of metals [ 37 – 40 ] and to several types of antibiotics [ 35 , 36 , 41 ]. During the past decade, a multi drug resistance (MDR) phenomenon linked to the spread of integrons carrying antibiotic resistance genes including the New Delhi metallo-lactamase gene ( ndm1) has gained clinical importance globally.…”

Section: Introductionmentioning

confidence: 99%

“…During the past decade, a multi drug resistance (MDR) phenomenon linked to the spread of integrons carrying antibiotic resistance genes including the New Delhi metallo-lactamase gene ( ndm1) has gained clinical importance globally. The ndm1 encoded carbapenemase enables pathogenic enterobacteria, including P. rettgeri and P. stuartii , to hydrolyze a wide spectrum of ß-lactam antibiotics [ 41 , 42 ].…”

Section: Introductionmentioning

confidence: 99%

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Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

et al. 2021

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Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

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“…OXA-72 carbapemenase was detected in P. rettgeri. [1], [15], [16], [17] Resistance to these antibiotics may also be due to non-carbapenemase mechanisms consisting of changes in penicillin-binding proteins or in outer membrane proteins or activation of effluxpumps [1], [13], [18].…”

Section: Introductionmentioning

confidence: 99%

Providencia Species – Involvement in Pathology and Multidrug Resistance in a Romanian County Hospital

Idomir

2021

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The aim of the study was to evaluate the distribution on hospital wards, the spectrum of infections and the pattern of antimicrobial resistance of Providencia strains identified between 01.01.2018-31.12.2020 in the samples of the patients hospitalized in the Clinical County Emergency Hospital of Brasov. 380 strains of Providencia species were identified in the medical and surgical wards, especially in ICU (76.84%), Internal medicine ward (5.79%) and General surgery (3.95%). More frequently, Providencia spp. were isolated from tracheobronchial secretions (35.79%), pus (22.89%) and urine (19.74%). The levels of antimicrobial resistance of Providencia strains were very high for all the tested antimicrobials.

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Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases

Cited by 15 publications

References 68 publications

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

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

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Providencia Species – Involvement in Pathology and Multidrug Resistance in a Romanian County Hospital

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