ABSTRACT
We characterized a collection of IMI-like-producing Enterobacter spp. isolates (n = 112) in France. The main clone corresponded to IMI-1-producing sequence type 820 E. cloacae subspecies cloacae that was involved in an outbreak. Clinicians should be aware of potential antimicrobial resistance among these bacteria.
Subject(s)
Anti-Bacterial Agents , Bacterial Proteins , Enterobacter cloacae , Enterobacteriaceae Infections , Microbial Sensitivity Tests , beta-Lactamases , beta-Lactamases/genetics , beta-Lactamases/metabolism , France/epidemiology , Enterobacter cloacae/genetics , Enterobacter cloacae/enzymology , Enterobacter cloacae/isolation & purification , Enterobacter cloacae/drug effects , Enterobacteriaceae Infections/epidemiology , Enterobacteriaceae Infections/microbiology , Humans , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Anti-Bacterial Agents/pharmacology , History, 21st Century , Disease OutbreaksABSTRACT
BACKGROUND: Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp. METHODS: This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A. FINDINGS: Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate. We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-ß-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A. INTERPRETATION: This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons. FUNDING: None.
Subject(s)
Anti-Bacterial Agents , Bacterial Proteins , Enterobacteriaceae Infections , Genome, Bacterial , Microbial Sensitivity Tests , Morganella , Phylogeny , beta-Lactamases , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , beta-Lactamases/genetics , beta-Lactamases/metabolism , Anti-Bacterial Agents/pharmacology , Genome, Bacterial/genetics , Humans , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/epidemiology , Morganella/genetics , Genomics , Whole Genome Sequencing , Europe/epidemiology , Carbapenems/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Colistin/pharmacologyABSTRACT
Campylobacter sp. is widely considered a leading causative agent of bacterial food-borne gastrointestinal illness. Discitis and endocarditis caused by Campylobacter spp. are extremely rare. We describe the case of a 94-year-old man who was admitted for recent lumbar pain, diarrhea, and fever. C. fetus and C. coli were identified by MALDI-TOF from blood and stool samples respectively. MRI of the spine showed L5-S1 discitis. Patient was treated with 6 weeks of amoxicillin with clinical and microbiological response until cardiac implantable electronic device (CIED) related endocarditis occurred four weeks after the end of the antibiotic treatment. He was treated with another 6 weeks amoxicillin regimen, with a favorable outcome after a 6-month follow-up. Enteric infection with Campylobacter spp. in a debilitated patient should raise the possibility of a co-infection with another more invasive species such as C. fetus, leading to systemic invasion. In case of Campylobacter fetus bacteremia, a search for endocarditis and spondylodiscitis is recommended even in the absence of specific clinical signs.
ABSTRACT
BackgroundSince 2021, an emergence of New Delhi metallo-ß-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54â¯kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2â¯mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
Subject(s)
Klebsiella Infections , Klebsiella pneumoniae , Humans , Klebsiella pneumoniae/genetics , Anti-Bacterial Agents/pharmacology , Klebsiella Infections/drug therapy , Klebsiella Infections/epidemiology , Bayes Theorem , Multilocus Sequence Typing , Drug Resistance, Multiple, Bacterial/genetics , beta-Lactamases/genetics , Plasmids/genetics , Microbial Sensitivity TestsABSTRACT
IMPORTANCE: The emergence of carbapenemase producers in Enterobacterales mostly involves Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae complex species. However, in France, we observed the emergence and the rapid dissemination of carbapenemase in Citrobacter spp. In this study, we demonstrated that a wide variety of carbapenemases is produced by many different species of Citrobacter spp. However, we clearly identify three high-risk clones of Citrobacter freundii, ST8, ST22, and ST91 that drive the spread of carbapenemase in France. This epidemiological study paves the way of further analysis that would aim to identify the virulence factors involved in this pellicular ability of these three clones to disseminate at the hospital.
Subject(s)
Enterobacteriaceae Infections , Humans , Molecular Epidemiology , Enterobacteriaceae Infections/epidemiology , Bacterial Proteins/genetics , Citrobacter/genetics , Escherichia coliABSTRACT
Cefiderocol resistance is increasingly reported in New Delhi metallo-ß-lactamase-producing Enterobacterales. Genomic and phenotypic analysis of Escherichia coli sequence type 361, a primary clone causing carbapenemase spread in France, revealed mutations leading to cefiderocol resistance. Continued genomic surveillance of carbapenem-resistant Enterobacterales could clarify prevalence of cefiderocol-resistant E. coli in Europe.
Subject(s)
Escherichia coli , Gammaproteobacteria , Escherichia coli/genetics , France/epidemiology , Europe , Cephalosporins/pharmacology , CefiderocolABSTRACT
OBJECTIVES: Neonatal sepsis caused by multidrug-resistant (MDR) bacteria has a high morbidity and mortality, especially in low- and middle-income countries. Here, the molecular mechanisms of multidrug resistance in bacteria responsible for neonatal sepsis were determined. METHODS: From July to December 2019, documented bacteraemia from 524 neonates hospitalised in a neonatal intensive care unit in Morocco were collected. Whole-genome sequencing was used to characterise the resistome; multi-locus sequence typing was used to investigate phylogeny. RESULTS: Among the 199 cases of documented bacteraemia, 40 (20%) and 20 (10%) were caused by MDR Klebsiella pneumoniae and Enterobacter hormaechei, respectively. Of these, 23 (38.5%) were early neonatal infections (≤3 days of life). Twelve different sequence types (STs) were observed among K. pneumoniae isolates, the most prevalent being ST1805 (n = 10) and ST307 (n = 8). Twenty-one K. pneumoniae isolates (53%) possessed the blaCTX-M-15 gene, six of which co-produced OXA-48; two, NDM-7; and two, OXA-48 and NDM-7. The blaOXA-48 gene was present in 11 K. pneumoniae isolates (27.5%); blaNDM-1, in 13 (32.5%); and blaNDM-7, in 4 (10.0%). Eighteen E. hormaechei isolates (90.0%) produced an extended-spectrum ß-lactamase (ESBL). Three were SHV-12 producers that co-produced CMY-4 and NDM-1, and 15 were CTXM-15 producers, of which 6 co-produced OXA-48. Twelve different STs belonging to three different E. hormaechei subspecies were observed, with one to four isolates. K. pneumoniae and E. hormaechei isolates belonging to the same ST had less than 20 single nucleotide polymorphism differences and were found throughout the study period, highlighting their endemic presence in the neonatal intensive care unit. CONCLUSION: Thirty percent of neonatal sepsis cases (23 early and 37 late) were caused by highly drug-resistant carbapenemase- and/or ESBL-producing Enterobacterales.
Subject(s)
Bacteremia , Klebsiella Infections , Neonatal Sepsis , Sepsis , Infant, Newborn , Humans , Intensive Care Units, Neonatal , Klebsiella Infections/microbiology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Multilocus Sequence Typing , Neonatal Sepsis/epidemiology , Neonatal Sepsis/drug therapy , Morocco/epidemiology , beta-Lactamases/genetics , Klebsiella pneumoniae/genetics , Sepsis/drug therapy , Bacteremia/epidemiology , Bacteremia/drug therapySubject(s)
Escherichia coli , Siderophores , Escherichia coli/genetics , Escherichia coli/metabolism , Amino Acid Substitution , Cephalosporins/pharmacology , Anti-Bacterial Agents/pharmacology , Microbial Sensitivity Tests , beta-Lactamases/metabolism , Drug Resistance, Multiple, Bacterial/genetics , CefiderocolABSTRACT
Background: Avibactam, relebactam and vaborbactam are ß-lactamase inhibitors that proved their efficiency against KPC-producing Enterobacterales. Regarding their inhibitor activity towards Ambler's class A extended spectrum ß-lactamases (ESBL) and Ambler's class C cephalosporinase (AmpC), they should be active on most of the carbapenem-resistant non-carbapenemase-producing Enterobacterales (CR non-CPE). Objectives: Determine the in vitro activity of ceftazidime-avibactam, imipenem-relebactam and meropenem-vaborbactam and comparators against CR non-CPE. Methods: MICs to ceftazidime/avibactam, imipenem/relebactam, meropenem/vaborbactam, but also temocillin, ceftolozane/tazobactam, ertapenem, colistin, eravacycline and tigecycline were determined by broth microdilution (ThermoFisher) on a collection of 284 CR non-CPE (inhibition zone diameter < 22 mm to meropenem). Whole genome sequencing was performed on 90 isolates to assess the genetic diversity as well as resistome. Results: According to EUCAST breakpoints, susceptibility rates of ceftazidime, imipenem, meropenem and ertapenem used at standard dose were 0.7%, 45.1%, 14.8% and 2.5%, respectively. Increased exposure of ceftazidime, imipenem and meropenem led to reach 3.5%, 68.3% and 67.7% susceptibility, respectively. Using the EUCAST clinical breakpoints, susceptibility rates of ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam were 88.4%, 81.0% and 80.6%, respectively. Susceptibility rates of temocillin, ceftolozane/tazobactam, tigecycline, eravacycline, and colistin were 0%, 4.6%, 27.8%, 54.9% and 90.1%. MICs distributions with and without the presence of the inhibitor demonstrated a better ability of avibactam and relebactam compared to vaborbactam to restore susceptibility to the associated ß-lactam. Conclusions: This study demonstrated the in vitro efficacy of ceftazidime/avibactam, imipenem/relebactam and to a lesser extent meropenem/vaborbactam against CR non-CPE. Moreover, to test all ß-lactams/ß-lactamases inhibitors combinations without a priori for CRE, non-CPE is crucial since resistance to one of the ß-lactam/ß-lactamase inhibitor combinations does not predict resistance to another molecule, depending on the resistance mechanisms involved.
ABSTRACT
OBJECTIVES: Ceftolozane-tazobactam (C/T) proved its efficacy for the treatment of infections caused by non-carbapenemase producing Pseudomonas aeruginosa and Enterobacterales. Here, we aimed to provide susceptibility data on a large series of Enterobacterales since the revision of EUCAST categorization breakpoints in 2020. METHODS: First, C/T susceptibility was determined on characterized Enterobacterales resistant to third generation cephalosporins (3GCs) (extended spectrum ß-lactamase [ESBL] production or different levels of AmpC overexpression) (n = 213) and carbapenem-resistant Enterobacterales (CRE) (n = 259), including 170 carbapenemase producers (CPE). Then, 1632 consecutive clinical Enterobacterales responsible for infection were prospectively collected in 23 French hospitals. C/T susceptibility was determined by E-test® (biomérieux) and broth microdilution (BMD) (Sensititre™, Thermo Scientific) to perform method comparison. RESULTS: Within the collection isolates, 88% of 3GC resistant strains were susceptible to C/T, with important variation depending on the resistance mechanism: 93% vs. 13% susceptibility for CTX-M and SHV-ESBL producers, respectively. Only 20% of the CRE were susceptible to C/T. Among CPE, 80% of OXA-48-like producers were susceptible to C/T, whereas all metallo-ß-lactamase producers were resistant. The prospective study revealed that 95.6% of clinical isolates were susceptible to C/T. Method comparison performed on these 1632 clinical isolates demonstrated 99% of categorization agreement between MIC to C/T determined by E-test® in comparison with the BMD (reference) and only 74% of essential agreement. CONCLUSION: Overall, C/T showed good activity against wild-type Enterobacterales, AmpC producers, and ESBL-producing Escherichia coli but is less active against ESBL-producing Klebsiella pneumoniae, and CRE. E-test® led to an underestimation of the MICs in comparison to the BMD reference.
Subject(s)
Anti-Bacterial Agents , Pseudomonas Infections , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Prospective Studies , Enterobacteriaceae/genetics , Pseudomonas aeruginosa , Pseudomonas Infections/drug therapy , Cephalosporins/pharmacology , Cephalosporins/therapeutic use , Tazobactam/pharmacology , Tazobactam/therapeutic use , Escherichia coli , beta-Lactamases/geneticsABSTRACT
During 2013-2021, increased prevalence of oxacillinase 232-producing Enterobacterales was observed in France, mostly driven by its emergence in Klebsiella pneumoniae. Whole-genome sequencing identified that oxacillinase 232-producing K. pneumoniae belonged to 14 sequence types (STs), among which 2 polyclonal high-risk clones, ST-231 and ST-2096, were overrepresented.
Subject(s)
Carbapenem-Resistant Enterobacteriaceae , Klebsiella Infections , Humans , Klebsiella pneumoniae/genetics , Klebsiella Infections/epidemiology , Klebsiella Infections/drug therapy , beta-Lactamases/genetics , Bacterial Proteins/genetics , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Microbial Sensitivity TestsABSTRACT
Relebactam and vaborbactam are among the newest ß-lactamase inhibitors marketed. They were originally designed to inhibit the Ambler class A carbapenemase KPC. In this study, susceptibility to imipenem/relebactam and meropenem/vaborbactam was determined against a collection of OXA-48-like-producing Enterobacterales (n = 407). The clonality and resistomes of the isolates were determined by whole-genome sequencing. Comparison was performed with other relevant antibiotics such as carbapenems alone, ceftazidime/avibactam and ceftolozane/tazobactam. Addition of relebactam and vaborbactam did not significantly modify the MIC50 and MIC90 values obtained for imipenem and meropenem alone. In contrast, addition of avibactam strongly restored ceftazidime susceptibility. According to European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, MIC50/MIC90 values were at 2/4, 2/4, 2/8, 2/8, 32/>32 and 0.5/2 mg/L for imipenem, imipenem/relebactam, meropenem, meropenem/vaborbactam, ceftazidime and ceftazidime/avibactam, respectively. No differences were observed depending on the species. This study highlights the lack of benefit in vitro for carbapenem/inhibitor combination compared with carbapenem alone against OXA-48-producing isolates as well as the difficulties in comparing molecules since carbapenem/inhibitor combinations were not developed with the same dosage of carbapenem.
Subject(s)
Ceftazidime , beta-Lactamase Inhibitors , Anti-Bacterial Agents/pharmacology , Azabicyclo Compounds/pharmacology , Boronic Acids , Carbapenems/pharmacology , Ceftazidime/pharmacology , Drug Combinations , Imipenem/pharmacology , Meropenem/pharmacology , Microbial Sensitivity Tests , Tazobactam , beta-Lactamase Inhibitors/pharmacology , beta-Lactamases/geneticsABSTRACT
BACKGROUND: Despite the fact that carbapenem-resistant Enterobacterales (CRE) mostly cause urinary tract infections (UTIs), only few studies have focused on the efficacity of mecillinam against these CRE. OBJECTIVES: To evaluate the mecillinam susceptibility of a huge collection of CRE, including carbapenemase-producing Enterobacterales (CPE) and non-CPE (ESBL and AmpC producers with decreased permeability of the outer membrane). METHODS: A total of 8310 non-duplicate clinical CRE, including 4042 OXA-48-like producers, 1094 NDM producers, 411 VIM producers, 174 KPC producers, 42 IMI producers, 153 multiple-carbapenemase producers and 45 isolates producing other types of carbapenemases (such as IMP-like enzymes or GES-5), were included in the study. WGS was performed on all CPE using Illumina technology. Categorization of susceptibility to mecillinam was performed using disc diffusion (mecillinam discs at 10â µg; I2A, France) according to EUCAST recommendations. The results were interpreted according to EUCAST guidelines (S ≥15â mm). RESULTS: Significantly higher susceptibility rates were observed for carbapenem-resistant Proteus spp. (85%) and carbapenem-resistant Escherichia coli (84%), which are the two most common species responsible for UTIs, than for Klebsiella pneumoniae (67%), Enterobacter cloacae complex (75%), Citrobacter spp. (65%), Serratia spp. (34%) and Morganella morganii (12%). Susceptibility rates were 84%, 71% and 91% for OXA-48-like, NDM and IMI producers and 70% for non-CPE CRE. Mecillinam was less active against VIM and KPC producers (14% and 0%, respectively). CONCLUSIONS: Mecillinam might be an alternative for the treatment of infections due to CRE, particularly UTIs, except for VIM and KPC producers and for M. morganii and Serratia spp species.
Subject(s)
Enterobacteriaceae Infections , Urinary Tract Infections , Humans , Amdinocillin/therapeutic use , Bacterial Proteins , beta-Lactamases , Carbapenems/pharmacology , Carbapenems/therapeutic use , Enterobacteriaceae Infections/drug therapy , Escherichia coli , Microbial Sensitivity Tests , Urinary Tract Infections/drug therapyABSTRACT
OBJECTIVES: Cefiderocol is a catechol-substituted cephalosporin dedicated to the treatment of infections caused by multidrug resistant gram-negative rods. Cefiderocol susceptibility testing might be complex. We compared cefiderocol susceptibility testing methods on a relevant collection of carbapenem-resistant Enterobacterales. METHODS: CE-IVD (European CE marking required for all in vitro diagnostic (IVD)) broth microdilution (BMD) plate (ThermoFisher, Waltham, MA, USA) using regular Mueller-Hinton broth, MIC test strip (Liofilchem, Teramo, Italy), and disk diffusion (Liofilchem) were compared to a frozen BMD plate prepared with iron depleted Mueller-Hinton broth. First, a collection of 100 entirely sequenced carbapenem-resistant Enterobacterales was used to compare these methods. Then, a prospective comparison of disk diffusion and CE-IVD BMD was performed on 827 consecutive carbapenem non-susceptible Enterobacterales including 634 carbapenemase-producers. RESULTS: Compared to reference method, CE-IVD BMD plate gave 95.0% (95% CI, 88.8-97.9) categorisation agreement (CA), 2.8% (95% CI, 0.4-14.2) very major errors (VME), and 1.6% (95% CI, 0.3-8.7) major errors (ME) with high reproducibility. MIC strip gave only 63% (95% CI, 53.2-71.8) of CA and 94.9% (95% CI, 83.1-98.6) of VME due to critical underestimation of the MICs. Disk diffusion gave 77% (95% CI, 67.9-84.2) CA with additional 8% of the isolates within the area of technical uncertainty of 18-22 mm. Prospectively, disk diffusion gave 81.7% (95% CI, 79.0-84.2) CA, 23.3% (95% CI, 15.1-34.2%)VME, and 4.9% (95% CI, 3.6-6.7) ME. Additionally, 21.3% (95% CI, 18.6-24.2) of CRE were within the area of technical uncertainty. DISCUSSION: Commercial CE-IVD BMD (ThermoFisher) is accurate for cefiderocol MIC determination in difficult-to-treat Enterobacterales whereas MIC test strip (Liofilchem), that was formulated for Pseudomonas aeruginosa only, should be avoided. Disk diffusion might be useful for screening, but many of these CRE have to be re-tested using BMD to assess definitive categorization.
Subject(s)
Anti-Bacterial Agents , Carbapenems , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , Cephalosporins , Humans , Microbial Sensitivity Tests , Reproducibility of Results , CefiderocolABSTRACT
Infections caused by extended-spectrum ß-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are constantly rising worldwide and are often reported as causative agent of outbreaks in intensive care units (ICUs). During the first wave of the COVID-19 pandemic, bacterial cross-transmission was thought unlikely to occur due to the reinforcement of hygiene measures and prevention control. However, we report here an ESBL-producing K. pneumoniae (ST394) isolate responsible for a nosocomial outbreak in an ICU dedicated to COVID-19 patients.
ABSTRACT
Resistance to the ceftazidime (CAZ)-avibactam (AVI) combination is increasingly being reported. Here, we report a CAZ-AVI-resistant Klebsiella pneumoniae strain belonging to the high-risk sequence type 307 (ST307) clone and producing Klebsiella pneumoniae carbapenemase 39 (KPC-39), a single-amino-acid variant of KPC-3 (A172T). Cloning experiments, steady-state kinetic parameters, and molecular dynamics simulations revealed a loss of carbapenemase activity and increased affinity for CAZ. KPC-39 was identified in a patient without prior exposure to CAZ-AVI, suggesting silent dissemination in European health care settings.
Subject(s)
Ceftazidime , Klebsiella Infections , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Azabicyclo Compounds/pharmacology , Bacterial Proteins/genetics , Ceftazidime/pharmacology , Drug Combinations , Humans , Klebsiella Infections/drug therapy , Klebsiella pneumoniae/genetics , Microbial Sensitivity Tests , beta-Lactamases/geneticsABSTRACT
Since 2016, OXA-244-producing Escherichia coli has been increasingly isolated in France. We sequenced 97 OXA-244-producing E. coli isolates and found a wide diversity of sequence types and a high prevalence of sequence type 38. Long-read sequencing demonstrated the chromosomal location of blaOXA-244 inside the entire or truncated Tn51098.
Subject(s)
Escherichia coli Infections , Escherichia coli , Anti-Bacterial Agents , Bacterial Proteins/genetics , Escherichia coli/genetics , France , Humans , Microbial Sensitivity Tests , Multilocus Sequence Typing , Plasmids , beta-Lactamases/geneticsABSTRACT
Carbapenemase-producing Enterobacterales (CPE) is a major public-health concern. Here we describe the occurrence of blaVIM-2 in three isolates of Enterobacter hormaechei subsp. steigerwaltii. The blaVIM-2 gene was part of a class II transposon Tn1332 and was embedded in a remnant of a class 1 integron. Tn1332 was carried by a large, conjugative, non-typeable plasmid. The three isolates belonged to sequence type 90 (ST90). Two isolates (90H2 and 90H3) were highly related [<10 single nucleotide polymorphisms (SNPs)], whereas isolate 104D2 exhibited more than 50 SNPs and Tn1332 was inserted in a different place in the plasmid. Another IncHI-type plasmid carrying the extended-spectrum ß-lactamase (ESBL) gene blaCTX-M-15 was identified in 90H2 and 90H3. Among the three isolates, isolate 104D2 was negative for detection of carbapenemase activity using the biochemical Carba NP test, despite the presence of Tn1332 on the same plasmid. Mutants of 104D2 with higher minimum inhibitory concentrations (MICs) for carbapenems were obtained and one mutant (m104D2) was analysed. In contrast to 104D2, mutant m104D2 gave a positive Carba NP test. The mutant possessed two copies of Tn1332 per cell and a nonsense mutation in WecA, an enzyme involved in enterobacterial common antigen and peptidoglycan intermediate biosynthesis. This study describes the first occurrence of Tn1332 in Enterobacterales and the phenotypic diversity of VIM-2-producing E. hormaechei.
Subject(s)
Anti-Bacterial Agents/pharmacology , DNA Transposable Elements , Enterobacter/drug effects , Enterobacter/genetics , Enterobacteriaceae Infections/microbiology , beta-Lactamases/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Carbapenems/pharmacology , DNA, Bacterial/genetics , Drug Resistance, Bacterial , Enterobacteriaceae Infections/epidemiology , France/epidemiology , Humans , Integrons , Microbial Sensitivity Tests , Mutation , Phenotype , Phylogeny , Plasmids/genetics , Polymorphism, Single NucleotideABSTRACT
In Enterobacterales, the most common carbapenemases are Ambler's class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.
Subject(s)
Bacterial Proteins/biosynthesis , Proteus mirabilis/enzymology , Proteus mirabilis/genetics , beta-Lactamases/biosynthesis , Animals , Bacterial Proteins/classification , Bacterial Proteins/genetics , Belgium , Chromosomes, Bacterial/genetics , DNA Transposable Elements/genetics , DNA, Bacterial/genetics , France , Genes, Bacterial/genetics , Humans , Plasmids/genetics , Proteus mirabilis/isolation & purification , beta-Lactamases/classification , beta-Lactamases/geneticsABSTRACT
BACKGROUND: OXA-244, a single amino acid variant of OXA-48, demonstrates weaker hydrolytic activity towards carbapenems and temocillin compared with OXA-48. Of note, these antimicrobials are present in high concentrations in several carbapenemase-producing Enterobacterales (CPE) screening media. As a result, some screening media fail to grow OXA-244-producing isolates, while the prevalence of OXA-244 producers is constantly increasing in France. METHODS: Here, we evaluate the performance of three commercially available CPE screening media [ChromID® CARBA SMART (bioMérieux), Brilliance™ CRE (Thermo Fisher) and mSuperCARBA™ (MAST Diagnostic)] for their ability to detect OXA-244 producers (n = 101). As OXA-244 producers may also express an ESBL, two additional ESBL screening media were tested (Brilliance™ ESBL and ChromID® BLSE). MICs of temocillin and imipenem were determined by broth microdilution. The clonality of OXA-244-producing Escherichia coli isolates (n = 97) was assessed by MLST. RESULTS: Overall, the sensitivity of the ChromID® CARBA SMART, Brilliance™ CRE and mSuperCARBA™ media were 14% (95% CI = 8.1%-22.5%), 54% (95% CI = 43.3%-63.4%) and 99% (95% CI = 93.8%-100%), respectively, for the detection of OXA-244 producers. Among the 101 OXA-244-producing isolates, 96% were E. coli and 77%-78% grew on ESBL screening media. MLST analysis identified five main STs among OXA-244-producing E. coli isolates: ST38 (n = 37), ST361 (n = 17), ST69 (n = 12), ST167 (n = 11) and ST10 (n = 8). CONCLUSIONS: Our results demonstrated that the mSuperCARBA™ medium is very efficient in the detection of OXA-244 producers, unlike the ChromID® CARBA SMART medium. The high prevalence of ESBLs among OXA-244 producers allowed detection of 77%-78% of them using ESBL-specific screening media.