Molecular analysis of OXA-48-producing Escherichia coli in Switzerland from 2019 to 2020.

OXA-48-type ß-lactamases are the most prevalent carbapenemase-type in Enterobacterales in Switzerland, predominantly found in Escherichia coli and Klebsiella pneumoniae. Bacteria-producing OXA-48-type enzymes are endemic in some parts of the world, including Europe and North Africa, and are a frequent cause of nosocomial infections. Despite the emergence of numerous OXA-48-type variants, the original variant, OXA-48, remains the most prevalent in E. coli. This study describes the epidemiology of OXA-48-producing E. coli isolates submitted to the Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) between January 2019 and December 2020

Ongoing dissemination of OXA-244 carbapenemase-producing Escherichia coli in Switzerland and their detection.

OXA-244 is a derivative of OXA-48 showing weaker carbapenemase activity, compromising the detection of corresponding producers in clinical laboratories. Since 2017, the Swiss National Reference Center for Emerging Antibiotic Resistance noticed an increased identification of OXA-244-producing Escherichia coli (n=15) within the country. Different methods (biochemical and immunoassay tests, screening culture media) were tested for the detection of OXA-244 producers. Whole genome sequencing was used to investigate the genetic relatedness between the isolates and the genetic structures at the origin of the acquisition of the bla <sub>OXA-244</sub> gene. The mSuperCARBA® medium and the NG-Test CARBA5 assay were found to be suitable tools for detecting all OXA-244-producing isolates. Other selective media did not perform optimally. Among the fifteen strains, five sequence types were identified, with ST38 being predominant. The bla <sub>OXA-244</sub> gene was located on the chromosome for all isolates. Overall, detection of OXA-244 producers is challenging and specific guidelines must be followed

Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?

We performed a comprehensive phylogenomic analysis of 925 extraintestinal pathogenic Escherichia coli (ExPEC) ST38 genomes from 38 countries and diverse hosts and sources. The phylogeny resolved two broad clades: A (593 strains; 91% human) and B (332 isolates; 42% human), each with distinct ST38 clusters linked to the carriage of specific bla CTX-M alleles, often in association with other antibiotic resistance genes, class 1 integrons and specific plasmid replicon types. Co-carriage of fyuA and irp2 virulence genes, a reliable proxy for carriage of the Yersinia high-pathogenicity island, featured in 580 (62.7%) genomes. ST38 lineages carrying combinations of ExPEC and intestinal pathogenic Escherichia coli virulence factors were also identified. The F plasmid replicon was identified in 536 (58%) genomes, and 112 of these (21%) carry cjrABC-senB, a virulence operon frequently identified in pandemic ExPEC sequence types. Most (108; 96.4%) cjrABC-senB+ ST38 isolates were from human and other sources, except food animals, and were associated with F5:A-:B10 (41 isolates), F1:A2:B20 (20 isolates), and F24:A-:B1 (15 isolates) F replicon types. ST38 genomes that were inferred to carry a ColV-F virulence plasmid (69; 7.4%) were mostly from human (12; 17.4%), avian (26; 37.7%), or poultry (10; 6.9%) sources. We identified multiple examples of putative inter-host and host-environment transmission events, where genomes differed by <35 SNPs. This work emphasizes the importance of adopting a One Health approach for phylogenomic studies that seek to improve understanding of antimicrobial resistance and pathogen evolution

OXA-48-like carbapenemases in the UK: an analysis of isolates and cases from 2007 to 2014

Objectives: OXA-48-like carbapenemases have spread worldwide since 2001. We analysed patient and microbiological data for UK isolates with these enzymes as confirmed by the national reference laboratory from November 2007 - December 2014.  Methods: MICs were determined using BSAC agar dilution. Isolates with reduced susceptibility or resistance to at least one carbapenem and high-level resistance to both piperacillin/tazobactam (MIC ≥ 64 mg/L) and temocillin (MICs ≥ 128 mg/L) were screened by PCR for blaOXA-48-like genes. The genomes of around half of the isolates were sequenced, with MLST types, resistance genes and plasmid replicon types inferred. Patient data provided by sending laboratories were reviewed.  Results: Isolates (n=741) with OXA-48-like carbapenemases were submitted from 111 UK laboratories, representing 536 patients. Almost all (99%; 736/741) were Enterobacteriaceae, predominantly Klebsiella pneumoniae (55%; 408), and most (80%; 595) were from inpatients. WGS of 351 non-duplicate isolates identified blaOXA-48 as the most common variant, found in two-thirds (235/351) of isolates, followed by blaOXA-181 (68), blaOXA-232 (32), blaOXA-244 (10), blaOXA-484 (5) and blaOXA-245 (1). Among K. pneumoniae (163/351), E.coli (114/351), and E. cloacae (42/351), 119 STs were identified. Mapping analyses revealed that 63% (222/351) of isolates harboured plasmids that shared >99% identity to one of four known plasmids; pOXA-48a (44%; 154/351), pOXA-232 (10%; 34/351), pOXA181 (9%; 30/351), and pKP3-A (1%; 4/351); the remaining 37% of isolates harboured blaOXA-48-like in unknown environments.  Conclusions: OXA-48-like carbapenemases are an increasing problem in the UK. This study highlights both the role of successful plasmids and polyclonal nature of their dissemination

Whole genome sequencing,molecular typing and in vivovirulence of OXA-48-producingEscherichia coli isolates includingST131 H30-Rx, H22 and H41subclones

Carbapenem-resistant Enterobacteriaceae, including the increasingly reported OXA-48 Escherichia coli producers, are an emerging public health threat worldwide. Due to their alarming detection in our healthcare setting and their possible presence in the community, seven OXA-48-producing, extraintestinal pathogenic E. coli were analysed by whole genome sequencing as well as conventional tools, and tested for in vivo virulence. As a result, five E. coli OXA-48-producing subclones were detected (O25:H4-ST131/PST43-fimH30-virotype E; O25:H4-ST131/PST9-fimH22-virotype D5, O16:H5-ST131/ PST506-fimH41; O25:H5-ST83/PST207 and O9:H25-ST58/PST24). Four ST131 and one ST83 isolates satisfied the ExPEC status, and all except the O16:H5 ST131 isolate were UPEC. All isolates exhibited local inflammatory response with extensive subcutaneous necrosis but low lethality when tested in a mouse sepsis model. The blaOXA-48 gene was located in MOBP131/IncL plasmids (four isolates) or within the chromosome (three ST131 H30-Rx isolates), carried by Tn1999-like elements. All, except the ST83 isolate, were multidrug-resistant, with additional plasmids acting as vehicles for the spread of various resistance genes. This is the first study to analyse the whole genome sequences of blaOXA-48-positive ST131, ST58 and ST83 E. coli isolates in conjunction with experimental data, and to evaluate the in vivo virulence of blaOXA-48 isolates, which pose an important challenge to patient management

Treatment of infections with OXA-48 producing Enterobacteriaceae

Carbapenemase-producing (CPE) contribute significantly to the global public health threat of antimicrobial resistance. OXA-48, and its variants, are unique carbapenemases with low level hydrolytic activity toward carbapenems, but no intrinsic activity against expanded spectrum cephalosporins. is usually located on a plasmid, but may also be integrated chromosomally, and these genes have progressively disseminated throughout Europe and the Middle East. Despite the inability of OXA-48-like carbapenemases to hydrolyse expanded spectrum cephalosporins, pooled isolates demonstrate high variable resistance to ceftazidime and cefepime, respectively, likely to represent high rates of extended-spectrum beta-lactamase (ESBL) co-production. data from pooled studies suggests that avibactam is the most potent beta-lactamase inhibitor when combined with ceftazidime, cefepime, aztreonam, meropenem or imipenem. Resistance to novel avibactam combinations such as imipenem/avibactam or aztreonam/avibactam has not yet been reported in OXA-48 producers, although only few clinical isolates have been tested. Although combination therapy is thought to improve chances of clinical cure and survival in CPE infection, successful outcomes were seen in ∼70% of patients with infections caused by OXA-48-producing treated with ceftazidime/avibactam monotherapy. A carbapenem in combination with either amikacin or colistin has achieved treatment success in a few case reports. Uncertainty remains over the best treatment options and strategies used to manage these infections. Newly available antibiotics such as ceftazidime/avibactam show promise, however recent reports of resistance are concerning. Newer choices of antimicrobial agents will likely be required to combat this problem

Molekulárně-epidemiologická analýza izolátů z čeledi enterobakteriaceae a rodu pseudomonas rezistentní ke karbapenenům

Currently, the development of bacterial resistance is one of the major healthcare problems. Especially, the significant continuous increase of carbapenem-resistant Gram-negative bacteria, which most often affected seriously ill hospitalized patients, is a cause for great concern. Worldwide dissemination of carbapenemase-encoding genes is largely associated with mobile genetic elements and the clonal spread of high-risk clones. The dissertation thesis is focused on a molecular-epidemiological mapping of carbapenemase-positive Gram-negative isolates detected in hospital settings throughout the Czech Republic. Since 2015, a significant increase of carbapenemase-producing Enterobacteriaceæ (CPE) was detected in our country, mainly attributed to the dissemination of OXA-48 and NDM enzymes. Studies focusing on the first big outbreaks as well as sporadic cases of OXA-48 and NDM carbapenemases were performed. Results showed that blaOXA-48-carrying plasmids, which are derivatives of the archetypal IncL plasmid pOXA-48 originally described in Turkey, play a major role in the dissemination of OXA-48 enzymes in Czech hospitals. This finding is in agreement with the data from previous studies reported worldwide. The study of NDM-positive isolates revealed that IncX3 plasmids are the main factor contributing to the...Rozvoj a šíření antibiotické rezistence představuje jeden z nejzávažnějších medicínských problémů současnosti. Pokračující vzestup incidence karbapenem-rezistentních gramnegativních izolátů, které často postihují vážně stonající pacienty, je reálným důvodem k obavám. Celosvětová diseminace karbapenemáz je významně spojena s přenosem genů rezistence prostřednictvím mobilních genetických elementů a klonálním šíření epidemiologicky úspěšných kmenů. Zaměřením této disertační práce je molekulárně-epidemiologická analýza gramnegativních karbapene- máza-pozitivních kmenů zachycených v nemocnicích na území České republiky. Od roku 2015 byl v České republice zaznamenán signifikantní nárůst incidence karbapenemáza-pozi- tivních Enterobacteriaceæ (CPE), převážně způsobený rozšířením enzymů OXA-48 a NDM. Podařilo se nám zmapovat první velké epidemické epizody a sporadické izoláty detekované v ČR. Výsledky studie zaměřená na enzymy OXA-48-like prokázaly, že plasmidy nesoucí gen blaOXA-48, které byly identifikovány jako deriváty archetypálního IncL plazmidu původně detekovaného v Turecku, hrají hlavní roli v šíření enzymu OXA-48 v českých nemocnicích. Toto zjištění je ve shodě s výsledky publikací z ostatních zemí světa. Studie zabývající se NDM-pozitivními izoláty prokázala, že IncX3 enzymy představují hlavní...Ústav mikrobiologieLékařská fakulta v PlzniFaculty of Medicine in Pilse

The current burden of carbapenemases: Review of significant properties and dissemination among gram-negative bacteria

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups