Comparative genomics of carbapenemase-producingMorganella spp

Abstract

ABSTRACTBackgroundMorganellaare opportunistic pathogens involved in various infections. InMorganella, intrinsic resistance to multiple antibiotics including colistin combined with the emergence of carbapenemase-producers (CP) strongly limits the antimicrobial armamentarium.MethodsFrom 2013 to 2021, 172 highly drug-resistant (XDR)Morganellaisolates from 8 European countries and Canada, two reference strains from the Pasteur Institute collection and two susceptible isolates were characterized by WGS, antimicrobial susceptibility testing and biochemical tests. Complete genomes from Genbank (n=103) were included for genomic analysis. Intrinsic resistance mechanism to polymyxins was deciphered by combining genetic analysis with mass spectrometry on the lipid A.FindingsMorganellacould be separated into 4 species namedM. psychrotolerans, M. sibonii, M. morganiiand a new species represented by a unique strain.Morganella morganiiincluded two subspecies:M. morganiisubsp.morganii(the most prevalent) andM. morganiisubsp.intermedius. Intrinsic resistance to tetracycline and conservation of metabolic pathways correlated this refined taxonomy. CP were mostly identified among five ‘high-risk’ clones ofM. morganiisubsp.morganii. A single nucleotide polymorphism (SNP) cut-off of 100 was used to decipher outbreaks involving this species. Cefepime-zidebactam and ceftazidime-avibactam were the most potent antimicrobials towards the 172 XDRMorganellaspp. isolates of our collection (including 145 CP) except for metallo-β-lactamase-producers. The intrinsic resistance to polymyxins corresponds to the addition of L-Ara4N on the lipid A.InterpretationThis global characterization of the widest collection of XDRMorganellaspp. highlighted the need to clarify the taxonomy, deciphered intrinsic resistance mechanisms and paved the way for further genomic comparisons.FundingNoneRESEARCH IN CONTEXTEvidence before this studyOn January 28th2022, we have searched for the terms “Morganella” and “carbapenemase” in all published reports available in PubMed with no language restriction. We identified a total of 43 articles and most of them (41/43) corresponded to a report of a single isolate of carbapenemase-producingMorganella morganii. Only one article aimed to decipher the antimicrobial susceptibility on a collection ofProteus, ProvidenciaandMorganellaisolated from global hospitalized patients with intra-abdominal and urinary tract infections. However, this collection only included 7M. morganiiisolates. On March 2021, when we finished the inclusions in our collection, only 104 genomes ofMorganellaspp. were available in the NCBI database.Since September 2021, very few reports were published on carbapenemase-producing Morganella with the exception of a study from Xiang Get al. reported 40 multi-drug resistantM. morganiiisolates recovered from three hospitals in China from 2014 to 2020. Unfortunately, this collection included only two carbapenemase-producingM. morganiiisolates (one OXA-48 and one IMP-1). A report of KPC-producingM. morganiiin Japan and a longitudinal study of carbapemase-producing Enterobactrales in Taiwan that did not focused on Morganella.We also searched in PubMed for the terms ‘Morganella sibonii” or “Morganella psychrotolerans” in all published reports with no language restrictions. Our search identified a total of 20 articles. None of them was related to antimicrobial resistance and no study deciphered theMorganellaspp. epidemiology on clinical isolates.Added values of this studyThis global characterization involved the widest collection ofMorganellaspp. isolates ever reported (barely doubling the number ofMorganellaspp. genomes in Genbank). In addition, 145 isolates of this worldwide collection made of 172 multidrug resistantMorganellaspp. were carbapenemase producers for which therapeutic alternatives are scarce due to intrinsic resistance to last resort molecules, such as polymyxin.First, we found that cefepime-zidebactam and ceftazidime-avibactam were the most potent antimicrobials towards XDRMorganellaspp. isolates except for metallo-β-lactamase-producers.Then, we observed that carbapenemase-encoding genes were present in differentMorganellaspecies highlighting necessary changes in the taxonomy.Morganellagenus could be divided into 4 species namedM. psychrotolerans, M. sibonii, M. morganiiand a new species represented by a unique strain.Morganella morganiiincludes two subspecies:M. morganiisubsp.morganii(the most prevalent) andM. morganiisubsp.intermedius. We demonstrated that this refined taxonomy correlated with the intrinsic resistance to tetracycline, which was found only inM. sibonii, as well as several metabolic pathways (e.g. trehalose assimilation, type III (T3SS) and type IV secretion system (T6SS), etc.…).In addition, we highlighted five “high-risk” clones of carbapenemase-producingM. morganiisubsp.morganiithat have already disseminated worldwide. Combining whole genome sequencing (WGS) data with epidemiological investigations, we demonstrated that a cut-off of 100 single nucleotide polymorphisms (SNPs) could be used to discriminate clonally-related from sporadic independent isolates. This information is of the utmost importance since WGS is now considered as the reference method to identify and follow outbreaks.The intrinsic resistance ofMorganellaspp. to polymyxins was well-known but the underlying mechanism was unclear. Here, we demonstrated that the addition of L-Ara4N on the lipid A ofMorganellais involved.Implications of all the available evidenceThe identification of “high-risk” clones among highly-drug resistantMorganellaspp. paves the way of future investigations to better understand and hopefully limit the spread of these bugs. Additionally, our results identified new components and virulence factors of someMorganellaspecies (e.g. T6SS and T3SS inM. sibonii) that deserve further investigation since they might be implicated in the bacterial lifestyle of this genus.