Draft genome sequence of Proteus mirabilis NO-051/ 03, representative of a multidrug-resistant clone spreading in Europe and expressing the CMY-16 AmpC-type β-lactamase

Proteus mirabilis NO-051/03, representative of a multidrug-resistant clone expressing the CMY-16 AmpC-type β-lactamase and circulating in Europe since 2003, was sequenced by a MiSeq platform using a paired-end approach. The genome was assembled in 100 scaffolds with a total length of 4,197,318 bp. Analysis of the draft genome sequence revealed the presence of several acquired resistance determinants to β-lactams, aminoglycosides, phenicols, tetracyclines, trimethoprim, and sulfonamides, of one plasmid replicon, and of a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) adaptive immune system

Characterization of two new CTX-M-25-group extended-spectrum β-lactamase variants identified in Escherichia coli isolates from Israel.

OBJECTIVES: We characterized two new CTX-M-type extended-spectrum β-lactamase (ESBL) variants in Escherichia coli isolates from stool samples of two elderly patients admitted at the Tel Aviv Sourasky Medical Center, Israel. Both patients underwent treatment with cephalosporins prior to isolation of the E. coli strains. METHODS: ESBLs were detected by the double-disk synergy test and PCR-sequencing of β-lactamase genes. The bla(CTX-M) genes were cloned into the pCR-BluntII-TOPO vector in E. coli TOP10. The role of amino-acid substitutions V77A and D240G was analyzed by site-directed mutagenesis of the bla(CTX-M-94) and bla(CTX-M-100) genes and comparative characterization of the resulting E. coli recombinants. MICs of β-lactams were determined by Etest. Plasmid profiling, mating experiments, replicon typing and sequencing of bla(CTX-M) flanking regions were performed to identify the genetic background of the new CTX-M variants. RESULTS: The novel CTX-M β-lactamases, CTX-M-94 and -100, belonged to the CTX-M-25-group. Both variants differed from CTX-M-25 by the substitution V77A, and from CTX-M-39 by D240G. CTX-M-94 differed from all CTX-M-25-group enzymes by the substitution F119L. Glycine-240 was associated with reduced susceptibility to ceftazidime and leucine-119 with increased resistance to ceftriaxone. bla(CTX-M-94) and bla(CTX-M-100) were located within ISEcp1 transposition units inserted into ∼93 kb non-conjugative IncFI and ∼130 kb conjugative IncA/C plasmids, respectively. The plasmids carried also different class 1 integrons. CONCLUSIONS: This is the first report on CTX-M-94 and -100 ESBLs, novel members of the CTX-M-25-group

Dissemination of extensively drug-resistant NDM-producing Providencia stuartii in Europe linked to patients transferred from Ukraine, March 2022 to March 2023

BackgroundThe war in Ukraine led to migration of Ukrainian people. Early 2022, several European national surveillance systems detected multidrug-resistant (MDR) bacteria related to Ukrainian patients.AimTo investigate the genomic epidemiology of New Delhi metallo-β-lactamase (NDM)-producing Providencia stuartii from Ukrainian patients among European countries.MethodsWhole-genome sequencing of 66 isolates sampled in 2022-2023 in 10 European countries enabled whole-genome multilocus sequence typing (wgMLST), identification of resistance genes, replicons, and plasmid reconstructions. Five blaNDM-1-carrying-P. stuartii isolates underwent antimicrobial susceptibility testing (AST). Transferability to Escherichia coli of a blaNDM-1-carrying plasmid from a patient strain was assessed. Epidemiological characteristics of patients with NDM-producing P. stuartii were gathered by questionnaire.ResultswgMLST of the 66 isolates revealed two genetic clusters unrelated to Ukraine and three linked to Ukrainian patients. Of these three, two comprised blaNDM-1-carrying-P. stuartii and the third blaNDM-5-carrying-P. stuartii. The blaNDM-1 clusters (PstCluster-001, n = 22 isolates; PstCluster-002, n = 8 isolates) comprised strains from seven and four countries, respectively. The blaNDM-5 cluster (PstCluster-003) included 13 isolates from six countries. PstCluster-001 and PstCluster-002 isolates carried an MDR plasmid harbouring blaNDM-1,blaOXA-10, blaCMY-16, rmtC and armA, which was transferrable in vitro and, for some Ukrainian patients, shared by other Enterobacterales. AST revealed PstCluster-001 isolates to be extensively drug-resistant (XDR), but susceptible to cefiderocol and aztreonam-avibactam. Patients with data on age (n = 41) were 19-74 years old; of 49 with information on sex, 38 were male.ConclusionXDR P. stuartii were introduced into European countries, requiring increased awareness and precautions when treating patients from conflict-affected areas.</p

Dissemination of extensively drug-resistant NDM-producing Providencia stuartii in Europe linked to patients transferred from Ukraine, March 2022 to March 2023

BackgroundThe war in Ukraine led to migration of Ukrainian people. Early 2022, several European national surveillance systems detected multidrug-resistant (MDR) bacteria related to Ukrainian patients.AimTo investigate the genomic epidemiology of New Delhi metallo-β-lactamase (NDM)-producing Providencia stuartii from Ukrainian patients among European countries.MethodsWhole-genome sequencing of 66 isolates sampled in 2022-2023 in 10 European countries enabled whole-genome multilocus sequence typing (wgMLST), identification of resistance genes, replicons, and plasmid reconstructions. Five blaNDM-1-carrying-P. stuartii isolates underwent antimicrobial susceptibility testing (AST). Transferability to Escherichia coli of a blaNDM-1-carrying plasmid from a patient strain was assessed. Epidemiological characteristics of patients with NDM-producing P. stuartii were gathered by questionnaire.ResultswgMLST of the 66 isolates revealed two genetic clusters unrelated to Ukraine and three linked to Ukrainian patients. Of these three, two comprised blaNDM-1-carrying-P. stuartii and the third blaNDM-5-carrying-P. stuartii. The blaNDM-1 clusters (PstCluster-001, n = 22 isolates; PstCluster-002, n = 8 isolates) comprised strains from seven and four countries, respectively. The blaNDM-5 cluster (PstCluster-003) included 13 isolates from six countries. PstCluster-001 and PstCluster-002 isolates carried an MDR plasmid harbouring blaNDM-1,blaOXA-10, blaCMY-16, rmtC and armA, which was transferrable in vitro and, for some Ukrainian patients, shared by other Enterobacterales. AST revealed PstCluster-001 isolates to be extensively drug-resistant (XDR), but susceptible to cefiderocol and aztreonam-avibactam. Patients with data on age (n = 41) were 19-74 years old; of 49 with information on sex, 38 were male.ConclusionXDR P. stuartii were introduced into European countries, requiring increased awareness and precautions when treating patients from conflict-affected areas.</p

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study

Background: Gaps in the diagnostic capacity and heterogeneity of national surveillance and reporting standards in Europe make it difficult to contain carbapenemase-producing Enterobacteriaceae. We report the development of a consistent sampling framework and the results of the first structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals. Methods: National expert laboratories recruited hospitals with diagnostic capacities, who collected the first ten carbapenem non-susceptible clinical isolates of K pneumoniae or E coli and ten susceptible same-species comparator isolates and pertinent patient and hospital information. Isolates and data were relayed back to national expert laboratories, which made laboratory-substantiated information available for central analysis. Findings: Between Nov 1, 2013, and April 30, 2014, 455 sentinel hospitals in 36 countries submitted 2703 clinical isolates (2301 [85%] K pneumoniae and 402 (15%) E coli). 850 (37%) of 2301 K pneumoniae samples and 77 (19%) of 402 E coli samples were carbapenemase (KPC, NDM, OXA-48-like, or VIM) producers. The ratio of K pneumoniae to E coli was 11:1. 1·3 patients per 10 000 hospital admissions had positive clinical specimens. Prevalence differed greatly, with the highest rates in Mediterranean and Balkan countries. Carbapenemase-producing K pneumoniae isolates showed high resistance to last-line antibiotics. Interpretation: This initiative shows an encouraging commitment by all participants, and suggests that challenges in the establishment of a continent-wide enhanced sentinel surveillance for carbapenemase-producing Enterobacteriaeceae can be overcome. Strengthening infection control efforts in hospitals is crucial for controlling spread through local and national health care networks

Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors

Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-beta-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential beta-lactamase stable beta-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.Peer reviewe

"Heavily armed" pseudomonoas aeruginosa: mechanisms and genetic background of drug resistance.

Występujące powszechnie i narastające zjawisko oporności na antybiotyki wśród bakterii chorobotwórczych jest jednym z największych wyzwań dzisiejszej medycyny zakażeń. Szczególne zagrożenie stanowią zakażenia szpitalne wywoływane przez wielooporne szczepy określonych gatunków, np. Pseudomonas aeruginosa. Jest to patogen oportunistyczny, odznaczający się opornością naturalną na kilka klas stosowanych antybiotyków. Dzięki wysokiej plastyczności genomu, obejmującej różnorodne mutacje funkcjonalne (strukturalne i regulacyjne) oraz pozyskiwanie obcego DNA, jest w stanie szybko adaptować się do niesprzyjających warunków środowiska. Szczególnie niepokoi zdolność nabywania przez P. aeruginosa dodatkowych cech oporności, co w połączeniu z naturalnymi mechanizmami czyni ten patogen wybitnie trudnym do zwalczania. Bakteria ta jest w stanie wywoływać m. in. ostre zapalenie płuc, zakażenia łożyska krwi, skóry i tkanek miękkich (w tym ran operacyjnych i oparzeniowych). Jest również czynnikiem etiologicznym zakażeń przewlekłych, towarzyszących np. mukowiscydozie. Antybiotykami stosowanymi obecnie przeciwko zakażeniom P. aeruginosa są najczęściej cefalosporyny III i IV generacji, karbapenemy, fluorochinolony i aminoglikozydy. W związku z malejącą liczbą dostępnych, skutecznych opcji terapeutycznych pracuje się nad nowymi terapeutykami lub nowatorskim wykorzystywaniem dotąd już poznanych.The rapid spread of antibiotic resistance (AMR) in pathogenic bacteria is one of the greatest challenges of modern infectiology. In particular, the most threatening are nosocomial infections caused by multi-drug-resistant strains of several major species, such as Pseudomonas aeruginosa. This opportunistic pathogen exibits a broad-spectrum of natural resistance. Due to its high genome plasticity, comprising functional mutations and acquisition of foreign DNA, P. aeruginosa can easily adapt and persist in harsh environmental niches. The critical issue is its outstanding ability to acquire diverse AMR mechanisms, including those encoded by mobile genetic determinants. In addition to the intrinsic resistance, P. aeruginosa can be highly resistant to all of the currently available antipseudomonadal antimicrobials. P. aeruginosa is the etiological agent of a variety of infections, including acute pneumonia, bloodstream infections or skin and soft tissue infections (e. g. postoperative or burn wounds). It is responsible also for chronic infections, like those in cystic fibrosis (CF) patients. The major antimicrobials used in P. aeruginosa infections are newer-generation cephalosporins, carbapenems, fluoroquinolones or aminoglycosides. Owing to limitations of the effective therapeutic options against P. aeruginosa, new antimicrobials and novel indications and thus applications for older drugs are being developed

Outbreak of Vancomycin-Resistant Enterococci in a Hospital in Gdańsk, Poland, due to Horizontal Transfer of Different Tn1546-Like Transposon Variants and Clonal Spread of Several Strains

Twenty-two vancomycin-resistant enterococcal (VRE) isolates of the VanA phenotype (21 Enterococcus faecium isolates and 1 E. faecalis isolate), representative of a large outbreak that occurred in a hospital in Gdańsk, Poland, were studied. All of the isolates demonstrated resistance to a wide variety of other antimicrobial agents in addition to glycopeptides. Several lines of evidence suggested that the outbreak most probably consisted of two epidemics that followed the independent introduction of VanA determinants into two separate hematological wards of the hospital. This hypothesis is supported by the fact that isolates recovered in these wards possessed two different polymorphs of the highly conserved DNA region encompassing the vanRSHAX genes and two distinct polymorph types of Tn1546-like transposons, which contain these genes. According to pulsed-field gel electrophoresis data, the outbreak in the adult hematology ward (HW) was highly polyclonal, which suggested a major role for the horizontal transmission of Tn1546-like elements among nonrelated strains of E. faecium and E. faecalis in this environment. On the other hand, the outbreak in the pediatric hematology ward (PHW) was most probably due to the clonal spread of two epidemic E. faecium strains, which had exchanged a plasmid carrying the Tn1546-like transposon. Restriction fragment length polymorphism studies of transposons and their insertion loci in plasmid DNA have suggested that numerous isolates from both HW and PHW contained two or more copies of Tn1546-like elements that underwent diversification due to various genetic modifications. The reported data demonstrated a very complex epidemiology of the first, and up to now the only, VanA VRE outbreak characterized in Poland