Clonal transmission of NDM-5-producing Escherichia coli belonging to high-risk sequence type ST405

Characterization of ESBL/AmpC-producing extraintestinal Escherichia coli (ExPEC) in dogs treated at a veterinary hospital in Brazil

The clinical aspects and lineages involved in Extraintestinal pathogenic Escherichia coli (ExPEC) infections in dogs remain largely unknown. In this study, we investigated the antimicrobial resistance and molecular structures of ExPECs isolated from infected dogs in Brazil. Samples were obtained from dogs (n = 42) with suspected extraintestinal bacterial infections. Phylogroup B2 was predominant (65.1%). No association was observed between the site of infection, phylogroups, or virulence factors. Almost half of the isolates (44.2%) were MDR, and 20.9% were extended-spectrum β-lactamase (ESBL)-positive. E. coli isolates that were resistant to fluoroquinolones (27.9%) were more likely to be MDR. The CTX-M-15 enzyme was predominant among the ESBL-producing strains, and seven sequence types were identified, including the high-risk clones ST44 and ST131. Single SNPs analysis confirmed the presence of two clonal transmissions. The present study showed a high frequency of ExPECs from phylogroup B2 infecting various sites and a high frequency of ESBL-producing strains that included STs frequently associated with human infection. This study also confirmed the nosocomial transmission of ESBL-producing E. coli, highlighting the need for further studies on the prevention and diagnosis of nosocomial infections in veterinary settings.

Rapid cross-border emergence of NDM-5-producing Escherichia coli in the European Union/European Economic Area, 2012 to June 2022

Whole genome sequencing data of 874 Escherichia coli isolates carrying bla NDM-5 from 13 European Union/European Economic Area countries between 2012 and June 2022 showed the predominance of sequence types ST167, ST405, ST410, ST361 and ST648, and an increasing frequency of detection. Nearly a third (30.6%) of these isolates were associated with infections and more than half (58.2%) were predicted to be multidrug-resistant. Further spread of E. coli carrying bla NDM-5 would leave limited treatment options for serious E. coli infections.

Molecular surveillance reveals the emergence and dissemination of NDM-5-producing Escherichia coli high-risk clones in Germany, 2013 to 2019

BackgroundCarbapenemase-producing Enterobacterales (CPE) are rapidly increasing worldwide, also in Europe. Although prevalence of CPE in Germany is comparatively low, the National Reference Centre for Multidrug-resistant Gram-negative Bacteria noted annually increasing numbers of NDM-5-producing Escherichia coli isolates.AimAs part of our ongoing surveillance programme, we characterised NDM-5-producing E. coli isolates received between 2013 and 2019 using whole genome sequencing (WGS).MethodsFrom 329 identified NDM-5-producing E. coli, 224 isolates from known geographical locations were subjected to Illumina WGS. Analyses of 222 sequenced isolates included multilocus sequence typing (MLST), core genome (cg)MLST and single-nucleotide polymorphism (SNP)-based analyses.ResultsResults of cgMLST revealed genetically distinct clusters for many of the 43 detected sequence types (ST), of which ST167, ST410, ST405 and ST361 predominated. The SNP-based phylogenetic analyses combined with geographical information identified sporadic cases of nosocomial transmission on a small spatial scale. However, we identified large clusters corresponding to clonal dissemination of ST167, ST410, ST405 and ST361 strains in consecutive years in different regions in Germany.ConclusionOccurrence of NDM-5-producing E. coli rose in Germany, which was to a large extent due to the increased prevalence of isolates belonging to the international high-risk clones ST167, ST410, ST405 and ST361. Of particular concern is the supra-regional dissemination of these epidemic clones. Available information suggest community spread of NDM-5-producing E. coli in Germany, highlighting the importance of epidemiological investigation and an integrated surveillance system in the One Health framework.

A Nationwide Plasmidome Surveillance in Thailand Reveals a Limited Variety of New Delhi Metallo-β-Lactamase-Producing Carbapenem-Resistant Enterobacteriaceae Clones and Spreading Plasmids

Despite frequent identification of plasmids carrying carbapenemase genes, the transfer of plasmids carrying carbapenemase genes is not well recognized in clinical settings because of technical limitations. To investigate the detailed mechanisms of the spread of carbapenem-resistant Enterobacteriaceae (CRE), we performed multifaceted genomic surveillance of CRE isolates in Thailand and analyzed their plasmidome. We analyzed 371 Enterobacteriaceae isolates carrying bla_NDM-1 and 114 Enterobacteriaceae isolates carrying bla_NDM-5 obtained from clinical samples of 473 patients in 11 representative hospitals located in six provinces in Thailand between 2012 and 2017. The complete structures of plasmids carrying bla_NDM and chromosomal phylogeny were determined by combining Southern blotting hybridization analysis and our previously performed whole-genome short-read sequencing data. Dissemination of the bla_NDM-5 gene among the Enterobacteriaceae isolates in Thailand was mainly owing to the nationwide clonal spread of Escherichia coli ST410 and regional clonal spreads of Escherichia coli ST361 and ST405. Analysis of bla_NDM-1-carrying isolates revealed nationwide dissemination of two specific plasmids and nationwide clonal dissemination of Klebsiella pneumoniae ST16 accompanied with regional disseminations of three distinctive K. pneumoniae clones (ST231, ST14, and ST147) with different plasmids. Dissemination of CRE carrying bla_NDM in Thailand is mainly based on nationwide clonal expansions of E. coli ST410 carrying bla_NDM-5 and K. pneumoniae ST16 carrying bla_NDM-1, nationwide dissemination of two distinctive plasmids carrying bla_NDM-1, and accumulation of clonal expansions in regional areas. Although the overuse of antibiotics can promote CRE dissemination, the limited variety of transmitters highlights the importance of preventing horizontal dissemination among patients.

Extraintestinal Pathogenic Escherichia coli ST405 Isolate Coharboring blaNDM-5 and blaCTXM-15: A New Threat in Mozambique

The development of carbapenem resistance in extraintestinal pathogenic Escherichia coli (ExPEC) has significant clinical implications, particularly in countries where second-line antimicrobials are not readily available, rendering treatments ineffective, and ExPEC infections untreatable. Thus, early detection of high-risk ExPEC lineages and raising awareness of the specific mechanisms underlying carbapenem resistance are mandatory for the selection of appropriate treatment options and the prevention of E. coli spread. This study aims to investigate the phenotypic and genotypic features of the first NDM-5 carbapenemase-producing ExPEC strain isolated from the blood of a patient admitted to the Maputo Central Hospital (MCH), in Mozambique. E. coli SSM100 isolate was identified by MALDI-TOF, it displayed high-level resistance to third generation cephalosporins, carbapenems, fluoroquinolones, and aminoglycosides, performing antimicrobial susceptibilities testing by VITEK 2 system. E. coli SSM100 isolate was classified through whole-genome sequencing as ST405-D-O102: H6, a globally distributed lineage associated with antimicrobial resistance, carrying the blaNDM-5 gene located on an F1:A1:B49 plasmid, coharboring blaCTX-M-15, blaTEM-1, aadA2, sul1, and dfrA12 genes. In addition, mutations in gyrA (S83L and D87N), parC (S80I and E84V), and parE (I529L) conferring fluoroquinolone resistance were also found. Moreover, SSM100 isolate carried 88 virulence genes, of which 28 are reported to be associated with UPEC. The emergence of NDM-5 carbapenemase in a pandemic ST405-D-O102:H6 clone in Mozambique is of great concern. Locations of extended-spectrum β-lactamase determinants and NDM-5 carbapenemase gene on IncF-plasmid can increase their spread reinforcing the need for antimicrobial surveillance and the urgent introduction of carbapenemase detection tests in diagnostic laboratories of the country.

Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS

OBJECTIVES

NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes.

METHODS

High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain.

RESULTS

Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125.

CONCLUSIONS

In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.

Characterization of the IncFII-IncFIB(pB171) Plasmid Carrying bla NDM-5 in Escherichia coli ST405 Clinical Isolate in Japan

Purpose

New Delhi metallo-β-lactamase 5 (NDM-5) shows stronger resistance to carbapenems and broad-spectrum cephalosporins than NDM-1 because NDM-5 differs from NDM-1 by two amino acid substitutions. In this study, our aim was to characterize a NDM-5-producing Escherichia coli isolate KY1497 from a patient with urinary tract infection in Japan, who had no recent history of overseas travel.

Patients and Methods

NDM-5-producing E. coli isolate KY1497 was detected in the urine sample of a patient hospitalized in a tertiary hospital in Japan. The complete genome sequence of isolate KY1497 was determined by short- and long-read sequencing with hybrid assembly, followed by multilocus sequence typing (MLST), core-genome phylogeny analysis, plasmid analysis, and transconjugation experiments.

Results

KY1497 was classified as ST405 by MLST, and core-genome phylogeny exhibited the closest lineage to the clinical isolates in Nepal (IOMTU605) and Canada (FDAARGOS_448). KY1497 harbors bla_NDM-5 in the IncFII-IncFIB(pB171) replicon plasmid (pKY1497_1, 123,767 base pairs). Plasmid analysis suggested that the cognate plasmids of pKY1497_1 have a minor plasmid background, rather than the globally disseminated IncX3 plasmid carrying bla_NDM-5. Transconjugation analysis revealed that pKY1497_1 is transmissible to the recipient E. coli J53 strain.

Conclusion

We characterized a novel Inc replicon plasmid (IncFII-IncFIB[pB171]) carrying bla_NDM-5 and its host E. coli strain. NDMs are associated with a high risk of infection worldwide because of their antibiotic resistance and untreatable and hard-to-treat infections. Other patients in the hospital showed negative results for carbapenem-resistant Enterobacteriaceae. As NDM-producing strains are only sporadically detected in Japan, attention should be provided to the community prevalence of NDM-producing E. coli strains to prevent nosocomial infections.

Intestinal co-colonization with different carbapenemase-producing Enterobacterales isolates is not a rare event in an OXA-48 endemic area

BACKGROUND

The current spread of carbapenemase-producing Enterobacterales (CPE) is a great concern.

METHODS

We recovered 198 CPE from 162 patients admitted in our Hospital (March 2014-March 2016) during the R-GNOSIS European Project. Microbiological features and plasmid characteristics of CPE recovered from patients co-colonized with multiple CPE were studied.

FINDINGS

Thirty patients (18.5%; CI 95%= 12.5%-24.5%) presented co-colonization with multiple CPE producing the same (CPE-SC) (15.4%) or a different carbapenemase (CPE-DC) (4.3%). OXA-48 (83.3%) was the most frequent carbapenemase, followed by VIM-1 (26.7%), NDM-1 (10%) and KPC-3 (3.3%). CPE-DC-patients had longer admissions [63 days (20-107)] than the other patients. Moreover, hospital stay until CPE detection was lower [9 days (5-14)] (p = 0.0052) in CPE-SC-patients than in those with a single colonization; 56% showed co-colonization in the first positive sample, although most of them had previous admissions and had received multiple antibiotic treatments. CPE were more frequently recovered in clinical samples from co-colonized [CPE-DC (28.6%), CPE-SC (24%)] patients than from patients with a single CPE (15.2%). Among CPE-SC-OXA-48 [80% (p = 0.11)], K. pneumoniae [88% (p = 0.006)] and E. coli [84% (p < 0.001)] were the most frequent species. In 60% of patients, K. pneumoniae and E. coli species were simultaneously recovered, frequently after a single OXA-48-K. pneumoniae colonization. High-risk clones (ST11, ST15, ST307) were detected in OXA-48-K. pneumoniae but a higher clonal diversity was found among E. coli. A frequent in-vivo cross-species plasmid transmission was shown, due to a dominant plasmid (IncL-pOXA-48), but also involving related or unrelated bla _VIM-1-, bla _NDM-1- and bla _KPC-3-encoding plasmids.

INTERPRETATION

CPE co-colonization status should be monitored during epidemiological surveillance cultures, as these patients might be at a higher risk for infection.

FUNDING

European Commission Framework Programme 7 and Instituto de Salud Carlos III, Spain.

Outbreak of NDM-1+CTX-M-15+DHA-1-producing Klebsiella pneumoniae high-risk clone in Spain owing to an undetectable colonised patient from Pakistan

Here we describe an outbreak due to NDM-1+CTX-M-15+DHA-1-producing Klebsiella pneumoniae (NDM-1-Kp) in Spain related to a patient previously admitted to a healthcare centre in an endemic area (Pakistan). Nine colonised patients were detected in the Neurosurgery ward between September 2015 and February 2016 during the R-GNOSIS European Project. NDM-1-Kp isolates from clinical samples were also recovered in three of these patients. Surveillance culture at admission was negative in the index case, but NDM-1-Kp colonisation was detected 27 days later after receiving antibiotic treatment. Co-colonisation with a second NDM-1-Kp isolate was identified in this patient 61 days post-admission. Overall length of stay (LOS = 75 days) (P < 0.01) and LOS until carbapenemase detection (LOS-1 = 36 days) was longer in NDM-1-Kp carriers than in patients with other carbapenemase-producing Enterobacterales. Intervention strategies were implemented after the outbreak declaration and NDM-1-Kp transmission was contained. Among the NDM-1-Kp isolates, two clones [ST437 (index case and Patient 2) and ST101 (index case and Patients 3-9)] with different IncFIB NDM-1-containing plasmids were identified. Whole-genome sequencing revealed a high content of antimicrobial resistance genes in both isolates in addition to a large number of virulence factors. Colonisation with other epidemic (OXA-48-ST11-K. pneumoniae and VIM-1-ST54-K. pneumoniae) and non-epidemic (VIM-1-ST908-K. pneumoniae and VIM-ST431-Escherichia coli) clones was also detected in two NDM-1 carriers. Implementation of adequate infection control measures and uninterrupted active surveillance programmes for detecting patients with a low colonisation status are crucial to prevent the introduction and dissemination of NDM-type enzymes in our region.

Genotypic and Phenotypic Characterization of Clinical Escherichia coli Sequence Type 405 Carrying IncN2 Plasmid Harboring bla NDM-1

We report a bla NDM-carrying ST405 Escherichia coli recovered from the abdominal fluid of a patient in Shandong, China. This strain belonged to the high-risk phylogenetic group D and carried the virulence genes, papG II, papG III, papC, and iroN. In addition to bla NDM-1, this isolate carried the quinolone resistance gene acc(6')-Ib and extended-spectrum β-lactamase (ESBL) genes bla CTX-M-15 and bla CTX-M-14. bla NDM-1 was located on a 41 Kb IncN2 self-transmissible plasmid. The IncN2 plasmid named as pJN24NDM1 was fully sequenced and analyzed. Genome comparative analysis showed that IncN2 plasmids harboring carbapenem-resistance genes possessed conserved backbones and variable accessory regions. Phylogenetic analysis of 87 IncN plasmids based on orthologous genes indicated that 9 IncN2 plasmids fell into one phylogenetic clade, while 4 IncN3 plasmids were in two phylogenetic clades of the 74 IncN1 plasmids. The presence of IncN2 plasmids harboring bla NDM in the high-risk clone ST405 E. coli raises serious concerns for its potential of dissemination.