# Genome-based insights into the resistome and associated-mobilome of extended-spectrum cephalosporins resistant Morganellaceae spp

Lucie Laval, Karine Praud, Sébastien Leclercq, Axel Cloeckaert, Marie-Cécile Ploy, Olivier Barraud, Benoît Doublet

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## ► To cite this version:

Lucie Laval, Karine Praud, Sébastien Leclercq, Axel Cloeckaert, Marie-Cécile Ploy, et al.. Genome-based insights into the resistome and associated-mobilome of extended-spectrum cephalosporins resistant Morganellaceae spp. 38. Réunion Interdisciplinaire de Chimiothérapie Anti-Infectieuse (RICAI), Dec 2018, Paris, France. , P10. hal-03356666

HAL Id: hal-03356666

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Submitted on 28 Sep 2021

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## Introduction

The *Morganellaceae* family contains bacteria present in water, soil or in the intestinal tract of humans and animals. *Proteus mirabilis* and *Morganella morganii* are opportunistic pathogens responsible for various infections ranging from minor to life-threatening issues (urinary tract infections to septicemia). The apparent emergence of multidrug-resistant (MDR) *Morganellaceae* strains harbouring mobile genetic elements with extended-spectrum-β-lactamase (ESBL), AmpC cephalosporinase and/or metallo-β-lactamase (MBL) resistance genes is a serious threat to public health. Since the last decade, several MDR Integrative Conjugative or Mobilizable Elements (ICE or IME) belonging to the SXT or SGI1 families have been described to spread extended-spectrum cephalosporins (ESC) resistance in clinical *Morganellaceae* strains of diverse origins.

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Here, we characterized the resistome and mobilome of ESC-resistant *Morganellaceae* strains from various sources through phenotypic and genomic approaches.

## Material and methods

* **83 Morganellaceae strains** based on the criteria of **ESC resistance** were isolated from humans and animals in France, Bulgaria and Taiwan between 1996 and 2017.

* **After PCR screening of major ESBL/AmpC resistance genes** and MDR mobile genetic elements, **66 Morganellaceae strains** were whole-genome sequenced on IonProton™ platform at the Limoges Genomic Research Facility.

* **WGS analysis** was performed to determine the phylogenetic diversity using bowtie2/PhyML/iTOL tree (microbial core genome alignment & SNP detection). The ResFinder and PlasmidFinder tools available at the Center for Genomic Epidemiology were used for identification of acquired resistance genes and plasmid replicon typing, respectively.

## Results

### ✓ Phenotypic antimicrobial resistance

* **Nearly all ESBL/AmpC/MBL-producing *Morganellaceae* strains** showed multidrug resistance phenotype (47/52 strains resistant to > 3 antibiotic classes).

* **3 human clinical *P. mirabilis* strains** isolated in Bulgaria were extensively-drug resistant showing only susceptibility to aztreonam.

<table><caption>**Table 1.** ESBL/AmpC/MBL resistance genes in *Morganellaceae* spp.</caption><thead><tr><th></th><th>ESBL</th><th>AmpC</th><th>MBL</th></tr></thead><tbody><tr><td rowspan="4"><i>P. mirabilis</i></td><td>CTX-M (21)</td><td rowspan="4">CMY (13)</td><td rowspan="4">VIM (3)</td></tr><tr><td>VEB (9)</td></tr><tr><td>TEM (3)</td></tr><tr><td>SHV (3)</td></tr><tr><td><i>M. morganii</i></td><td>CTX-M (6)</td><td>/</td><td>/</td></tr><tr><td><i>P. rettgeri</i></td><td>CTX-M (2)</td><td>/</td><td>/</td></tr><tr><td><i>P. penneri</i></td><td>/</td><td>CMY (1)</td><td>/</td></tr></tbody></table>

### ✓ ESBL/AmpC/MBL resistance genes (Table 1)

* **The CTX-M ESBLs** were predominant with a large diversity of variants:

* bla<sub>CTX-M-15</sub>, bla<sub>CTX-M-3</sub>, bla<sub>CTX-M-14</sub>, bla<sub>CTX-M-2</sub>, bla<sub>CTX-M-24</sub>, bla<sub>CTX-M-1</sub>, bla<sub>CTX-M-11</sub>

* Six *P. mirabilis* strains harboured simultaneously up to 3 ESBL/AmpC/MBL resistance genes.

### ✓ Phylogeny, MDR mobile genetic elements and horizontal gene transfer

* **The phylogenetic analysis** revealed a great diversity among *P. mirabilis* strains except few clusters (Fig. 1).

* **Surprisingly**, only 20 out of 66 *Morganellaceae* strains harboured conjugative elements carrying ESBL/AmpC/MBL resistance genes, mainly conjugative IncA/C plasmids or SXT-related elements.

* Moreover, 31 *Morganellaceae* strains contained a MDR SXT or SGI1 integrative elements; few strains carrying elements of both families.

<figure><img src="image_4.png" /><figcaption>**Fig. 2.** Schematic view of SGI1-V.</figcaption></figure>

* **All ESBL resistance genes** bla<sub>VEB-6</sub> were carried by the MDR integrative mobilizable element SGI1-V in epidemiologically-unrelated but clusterized *P. mirabilis* strains of animal and human origins (Fig. 1 & 2).

<figure><img src="image_5.png" /><figcaption>**Fig. 3.** Schematic view of SXT ICEs (SXT, R391, ICEPmiJpn1, and ICEPmiChn1).</figcaption></figure>

* **The cephalosporinase AmpC gene** bla<sub>CMY-2</sub> was carried by conjugative IncA/C plasmids or ICEs related to ICEPmiJpn1 (Fig. 1 & 3).

## Conclusions

* ✓ In contrast to *Enterobacteriaceae* spp., ESBL/AmpC/MBL resistance genes were not mainly located on conjugative plasmids in *Morganellaceae* spp.

* ✓ **Conjugative IncA/C plasmids** and the IncA/C-related ICEs belonging to the **SXT and SGI1** families play an important role in the spread of ESBL and AmpC resistance genes in the *Morganellaceae* family.

* ✓ Further WGS analyses are ongoing to confirm the localization of ESBL/AmpC/MBL resistance genes and to fully characterize the different MDR mobile genetic elements implicated in the spread of ESC resistance.

## Acknowledgments

We thank Denys Brand and Nathalie Winter from the Féri (Fédération de Recherche en Infectiologie Région Centre Val-de-Loire) to have supported Lucie Laval by a Master fellowship.