Resistance to ceftazidime-avibactam (CAZ-AVI) is a growing problem. This study describes the selection of CMY-219, a CMY-42 variant (G156D), conferring resistance to CAZ-AVI in an OXA-484-producing Escherichia coli ST410 after treatment. It raises concern about the risk of selection of CMY variants under CAZ-AVI exposure in ST410 and related clones, which commonly carry CMY-42, are prone to carbapenemase acquisition, and harbor modified PBP3.

BACKGROUND:Carbapenemase-producing Enterobacterales (CPE) have been designated by the World Health Organization as critical global priority pathogens. Their widespread dissemination and nosocomial outbreaks pose a major public health threat. This study examined the transmission patterns and genetic characteristics of CPE isolated in New Caledonia between 2013 and 2022. METHODS:A total of 214 CPE isolates were collected, comprising 199 non-duplicate clinical isolates from 164 patients and 15 environmental isolates from hospital surfaces. Isolates were characterized using phenotypic methods and whole-genome sequencing. RESULTS:Among clinical isolates, the most prevalent genera was Enterobacter (n = 68; 34%) and Klebsiella (n = 50; 25%), with 194 isolates (98%) harbouring IMP-type carbapenemases. WGS of 89 selected CPE revealed the predominance of the blaIMP-4 gene (n = 82; 92%). This gene was primarily associated with IncM2-type plasmids carrying a class 1 integron, identified in 65 sequenced isolates. Long-read sequencing resolved these plasmids into seven distinct variants, differentiated by integron structures and a 9305-bp insertion. Genomic, phenotypic, and epidemiological triangulation have identified 12 hospital spread events, with 10 linked to IMP-4 IncM2 plasmids, whose transferability is confirmed by conjugation assays. CONCLUSION:These results highlighted the pivotal role of plasmid-mediated dissemination in CPE spread and emphasize the urgency of enhanced surveillance to curb silent transmission. The study provided critical insights for targeted infection control strategies in New Caledonia healthcare system, with broader implications for regional antimicrobial resistance containment.

Since 2022, the diversity of OXA-48 variants has increased in France. We analyzed the dissemination of five recent variants (OXA-1181, OXA-1201, OXA-1205, OXA-1207, and OXA-1226) mostly identified on plasmids in high-risk Escherichia coli clones. Three of them (OXA-1181, OXA-1205, and OXA-1207) displayed the same Ser244Trp substitution with no significant impact on the β-lactams hydrolytic profile.IMPORTANCEThis study described the recent emergence of five variants (OXA-1181, OXA-1201, OXA-1205, OXA-1207, and OXA-1226) in France. These variants were mostly identified in Escherichia coli high-risk clones. In addition, most of these new OXA-48 variants (OXA-1181, OXA-1205, and OXA-1207) were derived, interestingly, from OXA-181, OXA-232, and OXA-484 variants due to the apparition of the same S244W substitution, a residue that delimits the active site cavity. Together, these results threaten the dissemination of these OXA-48 variants in the community, highlighting the need for continuous monitoring to better understand their epidemiology and dissemination.

Phage-plasmids (P-Ps) are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges and to the formation of hybrid or defective elements, which limits accurate detection of P-Ps. To address this challenge, we developed tyPPing, an easy-to-use method that efficiently detects and types P-Ps with high accuracy. It searches for distinct frequencies and sets of conserved proteins to separate P-Ps from plasmids and phages. tyPPing's strength comes from both its precise predictions and its ability to systematically type P-Ps, including the assignment of confidence levels. We tested tyPPing on several databases and a collection of incomplete (draft) genomes. While predictions rely on the quality of assemblies, we detected high-quality P-Ps and experimentally proved them to be functional. Compared to other classification methods, tyPPing is designed to detect distinct P-P types and surpasses other tools in terms of sensitivity and scalability. P-Ps are highly diverse, making the systematic identification of new types a difficult task. By combining tyPPing with other tools, however, we show a valuable foundation for addressing this challenge. How to use tyPPing and other approaches is documented in our GitHub repository: github.com/EpfeiferNutri/Phage-plasmids/.IMPORTANCEMobile genetic elements, such as phages and plasmids, are diverse and drive bacterial evolution through horizontal gene transfer. Phage-plasmids, of which many carry antibiotic resistance genes or virulence factors, are both phages and plasmids and have life cycles of temperate phages and plasmids. This makes accurate classification difficult as current computational tools typically classify them as one or the other. We addressed this problem by developing tyPPing, a new and highly precise method, to systematically identify, separate, and catalog phage-plasmids. We demonstrated that tyPPing is highly accurate and broadly compatible. It provides a reliable foundation for all future studies involving phages and plasmids, ranging from agriculture environments to pathogenic strains of clinical settings.

Objectives:Carbapenemase-producing Klebsiella pneumoniae (CPKp) represents a major public health threat due to limited treatment options, especially in low- and middle-income countries where colistin often remains the last active antibiotic. Here we investigated clinical carbapenem and colistin-resistant Kp isolates (CCoRKp) from Tunisia between January and June 2023. Materials and methods:Kp isolates were identified by MALDI-TOF, broth microdilution susceptibility testing, NG-Test CARBA5 lateral flow immunoassay, Carba NP test, plasmid analysis and by whole-genome sequencing (WGS) for MLST, genetic relatedness and resistome characterization. Results:Among the 263 Kp isolates collected, 101 (38.4%) were carbapenem resistant and 34 (12.9%) were carbapenem and colistin resistant. Twelve isolates exhibited an extremely drug-resistant phenotype, with in vitro activity retained only for eravacycline and aztreonam/avibactam, two agents that are currently unavailable for clinical use in Tunisia. Nine out of 10 patients who were treated with broad-spectrum antibiotics, including colistin and imipenem, died. WGS revealed OXA-48 and NDM-5 (12/12), CTX-M-15 (9/12) and the 16SRNA methylase ArmA (11/12) and identified ST 101 (n = 5), ST147 (n = 3) and ST 383 (n = 4), suggesting multi-clonal outbreak. While OXA-48 producing ST101 and ST147 were already present in a 2013 collection, ST383 has never been reported in the hospital nor in Tunisia. Conclusion:Here we report double carbapenemase producing and colistin-resistant Kps with limited therapeutic options. Major efforts are needed in infection control and availability of novel molecules in Tunisia to restore safe conditions in hospitals.

Carbapenemase-producing Enterobacterales (CPEs) have globally emerged and spread beyond human compartments. However, data in wild animals, especially from low- and middle-income countries, such as Algeria, are still very scarce. Here, we investigated CPEs recovered from feces samples collected between October 2021 and June 2023 from wild terrestrial and aquatic mammals, wild migratory/nesters/sedentary birds, and zoo animals, including their environment (water, food, and fecal samples of animal care workers) distributed over six Algerian provinces. Carbapenem-resistant Enterobacterales were characterized using MALDI-TOF-MS, Carba NP, immunochromatographic assay NG-Test CARBA 5, antimicrobial susceptibility testing, and whole-genome sequencing. Thirty CPEs were identified out of the 1,899 samples collected (1.6%). The carriage rate was higher in captive animals (3.2%) than in wild animals (1.2%). Twenty-six produced OXA-48, three OXA-244, and one OXA-181, along with CTX-M-15 ESBL. Clonal expansion of Enterobacter hormaechei hoffmannii ST145 and Klebsiella pneumoniae ST13 was evidenced. Plasmid analysis confirmed that 24/30 isolates harbored a transferable 62 kb IncL pOXA-48 plasmid. Five/six E. coli isolates belonged to high-risk clones with chromosome-mediated blaOXA-244 gene in three isolates, blaOXA-48 in two isolates, and blaOXA-181 gene encoded on an IncFII-ColKP3 hybrid plasmid in one isolate. This study showed widespread dissemination of OXA-48-like producing Enterobacterales in free and captive wild animals, largely driven by epidemic plasmids and clones. It underscores the role of wild animals as a reservoir of CPEs, particularly species living close to humans, such as gulls and pigeons, and occasionally food-producing animals, increasing the risk of bidirectional dissemination between animal, environmental, and human sectors.IMPORTANCEThe global rise of carbapenemase-producing Enterobacterales (CPEs) harboring blaOXA-48-like has been increasingly documented in clinical settings. However, their emergence and transmission in wild and captive animals are less documented. This study provides a high-resolution genomic characterization of CPEs isolated from the feces of wild animals, especially migratory birds, and from captive wild animals, to evaluate the potential risk of dissemination through these animals. Whole-genome sequencing data, genetic investigations, and antimicrobial susceptibility results highlighted the spread of multidrug-resistant CPEs in both animals and humans. The widespread detection of blaOXA-48 across multiple niches suggests sustained circulation beyond hospital settings in Algeria. Human-associated lineages, such as E. coli ST131, ST38, and ST540, were identified with a clear link with humans. This study demonstrates carriage of CPEs in multiple bird species living in areas commonly inhabited by humans and provides further evidence for an effective dissemination of resistance in wildlife, facilitated by feeding habits.

Carbapenemase-producing Enterobacterales (CPE) present limited therapeutic options. Optimal treatment requires identifying the carbapenemase type, often requiring confirmatory testing beyond routine susceptibility results. We develop MALCA, a machine-learning classifier that uses routine disc diffusion antibiogram results to directly detect CPE and identify the carbapenemase type. From 11,992 clinical isolates, we build a stepwise random-forest pipeline and derive two classifiers based on panels of 22 or 8 antibiotics (MALCA-22 and MALCA-8). In an external validation study involving 8514 isolates, both MALCA classifiers achieved sensitivity and specificity >96% for CPE detection, outperforming European and French algorithms developed for CPE screening. For the most prevalent carbapenemases, MALCA achieve sensitivities exceeding 97% and specificities above 98%, particularly for OXA-48-like, NDM, and KPC producers. MALCA is a rapid, and inexpensive diagnostic tool that uses solid antibiogram data to detect and type CPE, enabling earlier targeted therapy and diagnostic guidance without additional reagents or human resources.

Carbapenemase-producing Serratia spp. are increasingly implicated in healthcare-associated infections. This study aimed to characterize the genetic diversity, resistance mechanisms, and susceptibility to last resort antimicrobials of carbapenem-resistant Serratia spp. in France. From 2016 to 2024, 193 carbapenemase-producing Serratia spp. from France were investigated. WGS enabled species identification, MLST typing, resistome characterization and phylogenetic analysis. Antimicrobial susceptibility was assessed by broth microdilution, focusing on last resort antimicrobials. Intrinsic resistance to polymyxins was explored by genomic analysis and lipid A mass spectrometry. S. sarumanii (54%) and S. nevei (41%) dominated the epidemiology while no S. marcescens was identified. The most prevalent carbapenemases were OXA-48-like (56%), NDM (25%), IMP (8%), and VIM (7%). MLST identified 67 sequence types (ST) with 42% of the isolates belonging to four high-risk clones: ST-601, ST-298, ST-477, ST-600 and ST-474. β-lactamse susceptibility was low, but aztreonam-avibactam remained highly active (98%). Intrinsic resistance to polymyxin did not result from lipid A modifications as reported for Proteae. In France, carbapenemase-producing Serratia spp. were dominated by S. sarumanii and S. nevei. The absence of S. marcescens, the genus leader, highlighted the need to update the MALDI-TOF database. This study highlights Serratia as an underestimated reservoir of multidrug resistance.

INTRODUCTION:Eravacycline is a novel glycylcycline with broad activity against Gram-negative bacteria, including carbapenem-resistant Enterobacterales. This study aimed to evaluate the performance of gradient diffusion strips and disc diffusion methods for eravacycline susceptibility testing in comparison with a reference broth microdilution method. MATERIALS AND METHODS:A total of 303 carbapenem-non-susceptible Enterobacterales clinical isolates collected at the French National Reference Center were included. Eravacycline susceptibility was determined using broth microdilution (reference method), two gradient diffusion strips (BioMérieux Etest® and Liofilchem) and two different discs (MAST and i2a). Performances were assessed according to ISO 20776-2 guidelines using essential agreement (EA), bias, categorical agreement (CA) and error rates. RESULTS:Eravacycline exhibited lower MICs than tigecycline across all species, with higher susceptibility observed in E. coli. Neither gradient strips nor disc diffusion methods met ISO performance criteria when considering the full collection. However, when only E. coli isolates were considered, Liofilchem gradient strips and both disc diffusion methods achieved acceptable performance, whereas BioMérieux Etest® showed acceptable EA despite high bias. CONCLUSION:While eravacycline shows strong in vitro activity against carbapenem-resistant Enterobacterales, current gradient strip and disc diffusion methods demonstrate limited reliability on Enterobacterales, although good performances were achieved for E. coli. These findings highlight the need for cautious interpretation and further optimization of routine susceptibility testing methods.

OBJECTIVES:To characterize the intrinsic carbapenemase of Sphingobacterium spp. MATERIALS AND METHODS:Sphingobacterium spp. clinical isolates (n = 63) were collected in several French laboratories from 2012 to 2022. Antibiotic susceptibility was assessed by disc diffusion. MICs of last resort antimicrobials (including carbapenems, ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol) were determined by broth microdilution. WGS was performed on all isolates using the Illumina method. Cloning of the Sphingobacterium spiritivorum β-lactamase encoding gene, blaSPI-1, allowed expression of a novel metallo-β-lactamase (MBL), SPI-1, in Escherichia coli. Enzymatic kinetic parameters were determined with β-lactams as substrates. RESULTS:Among the 64 Sphingobacterium isolates collected we identified six species, of which S. spiritivorum (n = 24) was the most prevalent followed by S. multivorum (n = 20), S. siyangense (n = 16), S. lactis (n = 2), S. thalpophilum (n = 1) and S. faecium (n = 1). Sphingobacterium isolates displayed a phenotype of multidrug resistance including resistance to last resort β-lactams and β-lactam-β-lactamase inhibitors (with MIC50 at 4, 4 and 2 mg/L for ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol, respectively). The most effective drugs were fluoroquinolones, tigecycline and eravacycline. All S. spiritivorum displayed a carbapenemase activity that correlated with the identification of SPI-1 encoding genes. SPI-like variants (n = 10) shared 93.7% amino-acid identity, but only 50.6% identity with the closest CGB-1 MBL intrinsic of Chryseobacterium gleum. Characterization of SPI-1 showed a strong hydrolytic activity towards most β-lactams including carbapenems. CONCLUSION:S. spiritivorum was the most prevalent species of Sphingobacterium identified in clinical samples. All S. spiritivorum-like species produced a chromosomally encoded SPI-like MBL that might be challenging for the treatment of infections caused by this bacterial species.

OBJECTIVES:This study analysed a large French collection of carbapenemase-producing Klebsiella oxytoca complex (KoC) isolates (2017-2023) to map species and carbapenemase distributions and identify emerging lineages. We further investigated virulence traits to understand the epidemiological success of the dominant ST-2 lineage. METHODS:We conducted a retrospective study of all KoC isolates received at the French National Reference Center for Antimicrobial Resistance from 2017 to 2023. Whole-genome sequencing was performed to assess species assignment, phylogeny, and sequence types. Virulence analyses included biofilm formation assays (on abiotic surfaces and eukaryotic cells) and Galleria mellonella infection models. RESULTS:K. oxytoca sensu stricto remained the most prevalent species among the KoC. OXA-48-like enzymes were the most common carbapenemases, and two major lineages predominated: ST-141 and, far ahead, ST-2. The success of ST-2 appears linked to its low virulence combined with a strong capacity for long-term persistence. CONCLUSION:Our findings confirm that K. oxytoca comprises a complex of distinct species whose taxonomy warrants continued revision. ST-2 circulates widely in France and, despite its limited virulence, shows remarkable persistence, making it an epidemiological important lineage.

OBJECTIVES:The global spread of Klebsiella pneumoniae carbapenemase (KPC)-type carbapenemases has historically been driven by clonal group CG258, but increasing clonal diversification has recently been reported. We aimed to provide a comprehensive phenotypic and genomic characterization of KPC-producing Enterobacterales referred to French National Center (NRC) for Antimicrobial Resistance between 2019 and 2023. MATERIALS AND METHODS:A total of 419 KPC-producing Enterobacterales were referred to the French NRC for Antimicrobial Resistance. Antimicrobial susceptibility testing was performed by broth microdilution. Whole-genome sequencing was conducted for 404 isolates. AMR gene detection, MLST and SNP-based phylogeny were used to analyse resistance mechanisms, clonal structure and outbreak dynamics. RESULTS:KPC-producing Enterobacterales accounted for ∼2% of all carbapenemase-producing Enterobacterales. The K. pneumoniae species complex represented 86% (363/419) of isolates. KPC-3 predominated (328/419, 78%), followed by KPC-2 (87/419, 21%). Additional carbapenemases were detected in 11 isolates. Ceftazidime-avibactam, imipenem-relebactam and meropenem-vaborbactam showed high in vitro activity (97.8%, 95.8% and 97.9% susceptibility, respectively). MLST of 353 K. pneumoniae genomes identified 45 sequence types (STs); ST307 predominated (39.4%) and was associated with a major outbreak in northern France. ST147 (8.8%) and ST512 (7.6%) were also prevalent. Fifteen isolates from ST11, ST39, ST101, and ST395 had high virulence score of 4 (iuc-positive). CONCLUSIONS:KPC-producing K. pneumoniae referred to the French NRC show marked clonal diversification. The emergence of resistant isolates and convergent resistance-virulence profiles underscore the need for sustained genomic surveillance.

Morganella spp., part of the Morganellaceae family, are opportunistic pathogens commonly found in the human gut microbiota. They are highly adaptable, cause various types of infections, and are difficult to treat due to virulence factors and resistance genes. In 2017, Morganella became part of the WHO Bacterial Pathogen Priority List (BPPL). In 2024, a genomic study revealed significant differences between clinically relevant species, particularly between M. sibonii and M. morganii, with M. sibonii possessing a unique type VI secretion system (T6SS) operon. This study aimed to explore the distribution and diversity of T6SS in Morganella species. A retrospective analysis of 293 Morganella genomes from 1966 to 2023 was conducted. The T6SS clusters and subtypes were annotated using the SecReT6 platform and RAST, with phylogenetic analysis performed on tssB genes. Putative effectors and immunity proteins were identified through in silico analysis using BlastP and Alphafold. We identified that M. sibonii isolates possess four T6SS clusters of subtypes i1, i3 v.1, i3 v.2, and i5. In contrast, most M. morganii isolates lacked T6SS, with only one-third containing a subtype i1 T6SS. Notably, M. morganii frequently (95%, 117/123 effectors) harbored a T6SS-predicted TseV effector, while M. sibonii exhibited a greater diversity of effectors. This study highlights species-specific T6SS patterns among Morganella genus and suggests that T6SS might play a crucial role in bacterial lifestyle competition and host-pathogen interactions. It paves the way for future research on Morganella pathogenicity.

OBJECTIVES:Carbapenem resistance in Acinetobacter baumannii is usually mediated by acquired carbapenemases. Here we investigated an alternative mechanism involving variants of the intrinsic Acinetobacter-derived cephalosporinase (ADC). METHODS:Eighteen clonally related clinical isolates collected between 2019 and 2024 in a French long-term care facility were analysed together with four epidemiologically related isolates from additional hospitals. Antimicrobial susceptibility testing, whole-genome sequencing, cloning experiments, site-directed mutagenesis and enzyme kinetic analyses were performed to assess the contribution of ADC variants to carbapenem susceptibility. RESULTS:All isolates were resistant to broad-spectrum cephalosporins, and 72% and 83% were resistant to imipenem and meropenem, respectively. Whole-genome sequencing identified a novel ADC variant, designated ADC-200, differing from ADC-30 by a single amino-acid substitution (S318T) and located downstream of ISAba1. Cloning experiments demonstrated that ADC-200 production increased meropenem MICs compared with reference ADC enzymes. Introduction of the S318T substitution into ADC-50 reproduced this phenotype, indicating that this residue plays a key role in modulating meropenem susceptibility. Kinetic analyses showed increased catalytic efficiency for meropenem hydrolysis in ADC variants harbouring the S318T substitution. Single nucleotide polymorphism-based phylogenetic analysis revealed clonal dissemination of ADC-200-producing isolates belonging to international clone 2 across several institutions. CONCLUSIONS:Our findings demonstrate that naturally occurring ADC variants can contribute to reduced susceptibility to meropenem in epidemic A. baumannii lineages. Although this mechanism alone confers only moderate increases in carbapenem MICs, its occurrence in widespread clones highlights the importance of genomic surveillance to detect emerging resistance determinants beyond classical carbapenemases.

OXA-48-producing Enterobacterales (OXA-48-PE) represent a growing global health threat. Most of OXA-48-PE remain categorized susceptible to carbapenems, which might encourage their use despite uncertain clinical efficacy. This study evaluated clinical outcomes of infections caused by OXA-48-PE treated with carbapenem compared with alternative active therapies. The analyses were performed at three levels: a descriptive analysis of the French cohort, a comparative descriptive analysis of all published studies, and a meta-analysis restricted to studies providing direct comparisons between carbapenem-based and alternative active regimens. Between September 2021 and March 2023, 59 patients with monomicrobial OXA-48-PE infections were included in a French multicenter retrospective cohort. In parallel, a systematic review was conducted to identify clinical studies published through 31 December 2024, reporting outcomes of OXA-48-PE infections. In the French cohort, the overall 30-day mortality was 49.1%. Clinical failure occurred in 57.1% of patients receiving meropenem monotherapy, including patients infected with isolates exhibiting meropenem MICs within the susceptible range. Across 12 clinical studies (817 patients), carbapenem therapy was associated with high and variable crude mortality (52%), whereas newer agents active against OXA-48-PE, particularly ceftazidime-avibactam, were associated with lower and more consistent crude mortality (30.7%). In the primary meta-analysis of 6 human comparative studies, carbapenem therapy was associated with an increased risk of clinical failure compared with alternative active regimens (OR = 2.02; 95% CI = 1.05-3.88). Despite apparent in vitro susceptibility, carbapenem therapy was consistently associated with unfavourable clinical outcomes in OXA-48-PE infections, supporting the prioritization of alternative active agents whenever available.

BACKGROUND AND OBJECTIVES:Carbapenemase-producing Enterobacterales (CPE) are a public health concern. Developing novel antibiotics, particularly combinations of β-lactam/β-lactamase inhibitors active against carbapenemases, is critical. Three recent combinations, cefepime-enmetazobactam, cefepime-taniborbactam and cefepime-zidebactam, are among the most promising. To assess the in vitro activity of these three combinations against a collection of recent CPE clinical isolates and to analyse resistance patterns. METHODS:MICs were determined for 1600 CPE isolates collected over 6-month period in 2024 at the French National Reference Centre for Antimicrobial Resistance. All isolates were fully characterized by whole-genome sequencing. RESULTS:Among KPC producers, cefepime-enmetazobactam susceptibility was 54%, with higher MICs in Klebsiella pneumoniae ST-307, ST-101 and ST-258. It was active against 90% of OXA-48-like producers and resistance was primarily observed in Citrobacter freundii ST-22 and K. pneumoniae ST-2096.Cefepime-taniborbactam showed excellent activity against KPC- (100%), OXA-48-like (95%), and VIM producers (98%), but lower efficacy (76%) against NDM producers. Resistance was mainly found in NDM-5 producers, especially E. coli ST-140, ST-167, and K. pneumoniae ST-147. All resistant E. coli displayed a 4-amino-acid insertion in PBP3.Cefepime-zidebactam exhibited strong activity towards all CPE types; regarding MBLs, its low MIC values were comparable to aztreonam-avibactam and lower than cefiderocol. Resistant isolates were mostly clonal NDM-14-producing K. pneumoniae ST-147. No cross-resistance, including with aztreonam-avibactam, was observed. CONCLUSIONS:This study support the use of cefepime-enmetazobactam against ESBL/OXA-48-like co-producers. Cefepime-taniborbactam may be use against KPC and VIM producers and could represent a second-line option for NDM. Cefepime-zidebactam shows the most promising activity against MBLs, although already emerging resistance calls for caution.

SUMMARYMetallo-beta-lactamases are an ever-growing problem. Since the discovery of the beta-lactamase of Bacillus cereus in the late 1960s, many class B beta-lactamases have been reported, with three main families being NDM-, IMP-, and VIM-like. IMP- and VIM-like carbapenemases have been identified in a wide variety of Gram-negative bacteria. VIM-type carbapenemases are widely distributed, primarily represented by two main clusters, VIM-1 and VIM-2, and have been found in both Enterobacterales and non-fermenters. IMP-type carbapenemases are characterized by a significant genetic diversity and low identity between subgroups. This carbapenemase is more prevalent in Asia but has been identified globally, in both Enterobacterales and non-fermenters, as observed for VIM-type carbapenemases. The genetic diversity of IMP- and some VIM-type carbapenemases limits their detection. This review aims to discuss the genetic diversity, epidemiology, and biochemical characteristics of VIM- and IMP-type carbapenemases. It also evaluates the efficacy of commercially available detection tests and the in vitro activity of recently developed inhibitors.

Objectives Morganella are opportunistic pathogens increasingly reported in clinical settings. While their phylogeny has been recently updated, no multilocus sequence typing (MLST) scheme is currently available. Developing a MLST scheme can be challenging due to the absence of a strict definition for housekeeping gene selection. Methods A quantitative statistical estimator the multilocus correlation score (MCS) was defined to measure the discriminatory power of MLST schemes. The MCS is calculated as the sum of the variation ratio between selected loci compared to the whole genome. The average MCS for 25 existing MLST schemes on >3500 strains was calculated. The MLST scheme for Morganella was designed and tested on a collection of n = 328 clinical isolates. This MLST scheme was also validated by using conventional PCR and Sanger sequencing. Results MCS calculated on n = 25 tested MLST scheme allows the selection of an optimal set of genes for Morganella spp. We developed a standardized MLST scheme that can be used for all M. morganii and M. sibonii. This scheme is freely available via the Pasteur database: https://bigsdb.pasteur.fr/. In our collection of 328 clinical isolates, a total of n = 110 sequence types (STs) were identified, including n = 63 for Morganella morganii subsp. morganii, n = 18 for Morganella morganii subsp. intermedius and n = 29 for Morganella sibonii. Comparison with phylogenetic analysis indicated a good correlation of clones obtained by phylogeny and ST. Conclusions This study provides a MLST scheme for Morganella spp. offering a tool for tracking clonal complexes circulating worldwide.

OBJECTIVES:The rise of carbapenemase-producing Enterobacterales (CPE) represents a major public health threat, as highlighted in numerous reports from international health organizations. However, a significant data gap remains for certain regions, particularly Sub-Saharan Africa (SSA). The aim of this study is to characterize CPE isolates from patients returning from SSA at both phenotypic and genomic levels. METHODS:This retrospective study analysed 408 CPE received at the French National Reference Center between 2015 and 2022 and collected from patients returning from SSA. Antibiotic susceptibility testing and WGS were performed to assess phenotypic and genomic diversity. RESULTS:Among 408 isolates collected from 29 countries, 55.1% produced oxacillinase-48 (OXA-48)-like carbapenemases, predominantly OXA-181, while 46.3% produced NDM (New Delhi metallo-β-lactamase), with NDM-5 being the major variant despite regional disparities. Temporal analysis revealed a trend shifting from OXA-48-like producers to NDM producers.Ceftazidime-avibactam was effective against 100% of non-metallo-β-lactamase producers. Cefiderocol, amikacin and colistin were effective on 73%, 86.7% and 98.4% of all CPEs respectively. Genomic analysis revealed a polyclonal dissemination among K. pneumoniae strains, whereas three E. coli clonal complexes were dominant (CC410, CC167, CC448). CONCLUSION:This study provides a comprehensive characterization of CPE isolated from patients returning from SSA. WGS allowed the identification of major circulating clones, their associated resistance genes, and their susceptibility to last-resort antibiotics.

BACKGROUND:Carbapenemase-producing Enterobacterales (CPE) are an urgent global health threat, especially in resource-limited countries. Here we determined the prevalence and the molecular characteristics of CPE isolated from infections in Dakar, Senegal. METHOD:From January 2019 to December 2020, Enterobacterales with reduced susceptibility to ertapenem (diameter < 25 mm) from infections were collected at the Pasteur Institute of Dakar. Carbapenemases were detected using biochemical and immunochromatographical assays. WGS was used to determine resistome, MLST, plasmids, virulence genes and genetic relatedness. RESULTS:Of the 1045 Enterobacterales collected during the study period, 86 had a diameter around ertapenem of <25 mm (8%) and 19 were confirmed as CPE (2%). These included Escherichia coli (n = 6) [ST410 (n = 3), ST405 (n = 2) and ST2083], Enterobacter spp. (n = 6) [ST231 (n = 3), ST245, ST760 and ST960] and Klebsiella spp. (n = 5) (ST22, ST25, ST231, ST1535, ST4843), Citrobacter freundii ST22 (n = 1) and Citrobacter koseri with unknown ST (n = 1). blaOXA-48 (n = 7; 35%), blaOXA-181 (n = 7; 35%) and blaNDM-5 (n = 6; 30%) genes were identified. C. freundii ST22 harboured blaNDM-5, blaOXA-48 and blaCTX-M-15 genes. Some E. coli isolates belonging to the high-risk clone ST410 were closely related (<20 SNPs) to isolates recovered in France from patients returning from Senegal, suggesting transnational spread. In addition, 5/6 carbapenemase-producing E. coli isolates possessed a four amino acid insertion in PBP3, conferring reduced susceptibility to aztreonam/avibactam and cefiderocol. CONCLUSIONS:This study highlights the spread of NDM-5 and OXA-181 in Senegal, and reports the first co-occurrence of NDM-5 and OXA-48 in sub-Saharan Africa. The spread of CPE, especially in high-risk clones, underscores the urgent need for continued surveillance and targeted interventions.