Occurrence and characterization of NDM-5-producing Escherichia coli from retail eggs

Shelter dogs as reservoirs of international clones of Escherichia coli carrying mcr-1.1 and blaCTX-M resistance genes in Lima, Peru

Antimicrobial resistance (AMR) poses a critical public health threat worldwide, particularly at the human-animal interface where cross-transmission of critical priority Enterobacterales, such as Escherichia coli, have become increasingly reported. Worryingly, E. coli encoding extended-spectrum β-lactamases (ESBLs) has been documented in companion animals worldwide. Conversely, the presence of mcr genes, which confer resistance to polymyxins, in bacteria from pets remains more infrequent. In this study, we sequenced and reported on the first genomic data of E. coli strains carrying mcr-1 and/or blaCTX-M genes isolated from rectal swabs of stray dogs in a shelter in the city of Lima, Peru. Antimicrobial susceptibility revealed that E. coli strains exhibited a multidrug resistance profile. In addition to mcr-1 and blaCTX-M genes, other clinically relevant resistance determinants were identified, with notably presence of blaTEM-176 and the novel blaSCO-2 variant. The association of mcr-1.1 and IncI2 plasmid was confirmed. Several virulence genes were detected, classifying strains as putative extraintestinal pathogenic E. coli. Multilocus sequence typing prediction recognized diverse sequence types (ST), including ST155, ST189, ST657, ST746, ST1140, ST3014, and ST7188. This study represents the first report of mcr-positive E. coli in dogs from Peru, emphasizing the need for continuous surveillance and genomic characterization to better understand the transmission dynamics of these critical resistance genes at the human-animal interface. Furthermore, our results provide evidence that stray, and shelter dogs could be a reservoir for the spread of WHO priority pathogens, and/or polymyxin and β-lactam resistance genes, which is a public health and One Health concern that requires appropriate management strategies.

Characterisation of blaNDM-5-bearing IncHI2 plasmid from Escherichia fergusonii in China

OBJECTIVE

Carbapenems are considered to be the last resort for serious infections caused by multidrug-resistant Gram-negative bacteria, and the emergence of carbapenem-resistant Enterobacteriaceae has posed a serious threat to human health. However, carbapenem resistance is rarely reported in Escherichia fergusonii. In this study, a New Delhi metallo-β-lactamase (NDM)-5-producing E. fergusonii strain, EFSXRJ10, was isolated from a chicken in China.

METHODS

Minimal inhibitory concentrations were determined using broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence of the NDM-positive isolate was obtained using the Illumina NovaSeq and Oxford Nanopore GridION sequencing platforms, followed by hybrid assembly with Unicycler. In the plasmid conjugation assay, a sodium azide-resistant Escherichia coli strain, J53, was employed as the recipient.

RESULTS

Strain EFSXRJ10 was resistant to ampicillin, amoxycillin-clavulanic acid, gentamicin, spectinomycin, tetracycline, florfenicol, sulfafurazole, cefotaxime, ceftazidime, apramycin and meropenem. The blaNDM-5 gene was located on the IncHI2 plasmid, which can be transferred by conjugation at a frequency of (4.78 ± 0.67) × 10-5. The blaNDM-5-carrying plasmid, which harbours 14 antibiotic resistance genes belonging to the IncHI2/ST3 type and exhibiting high similarity to other blaNDM-5-carrying IncHI2 plasmids, was deposited in GenBank. The genetic structure containing blaNDM-5 was organised as 'IS3000-ΔISAba125-IS5-ΔISAba125-blaNDM-5-bleMBL-trpF-dsbD-IS26-∆umuD-∆ISKox3-∆IS3000'.

CONCLUSIONS

This is the first report characterising the blaNDM-5-bearing IncHI2 plasmid in E. fergusonii. Surveillance and control measures should be implemented to halt transmission of blaNDM-5 in food animals.

Emergence of a bla NDM-5 Carrying IncHI2/IncHI2A Plasmid in a Multidrug Resistant Clinical ST1431 Escherichia coli Strain

Carbapenems are the last-resort antibiotics used to treat infections caused by bacterial pathogens. Many bacterial pathogens have evolved to produce NDM carbapenemases to hydrolyze carbapenems, posing a great challenge to public health. In this study, we report a multidrug resistant clinical E. coli strain 673. Strain 673 belongs to sequence type (ST) 1431 and carries several plasmids, p673-blaTEM-1B, p673-blaCTX-M-55, p673-blaNDM-5, p673-13272, and p673-6468. p673-blaNDM-5 is an IncHI2/IncHI2A-type plasmid harboring several antibiotic resistance genes, including bla NDM-5, strA, strB, and dfrA. The bla NDM-5 gene was surrounded by two IS26 elements in p673-blaNDM-5, indicating that IS26 could mediate the integration of bla NDM-5 into p673-blaNDM-5. p673-blaCTX-M-55 is an IncFII-type plasmid harboring fosA, aadA1, and bla CTX-M-55. p673-blaTEM-1B is an IncFIB-type plasmid harboring bla TEM-1B and dfrA5. p673-13272 is a ColRNAI-type plasmid that does not carry any drug resistance genes. This is the first report that a bla NDM-5-bearing IncHI2/IncHI2A-type plasmid has emerged in a clinical E. coli strain in China. Our findings suggest that IS26 mediates the integration of bla NDM-5 into p673-blaNDM-5. The spread of bla NDM-5-bearing plasmids is a clinical challenge and endangers public health.

Mobile genetic elements contributing to horizontal gene transfer of blaNDM among Escherichia coli in the community setting

OBJECTIVE

To investigate the distribution of carbapenem-resistant Enterobacterales (CRE) in the community and to describe the genomic characteristics.

METHODS

CRE screened from fecal samples in healthy people at the health examination center of a tertiary hospital in China underwent Whole genome sequencing (WGS) to analyze genotypic characteristics of CRE. The flanking DNA sequence of blaNDM-5 and mcr1.1 genes were analyzed by Gcluster software.

RESULTS

A total of 7187 fecal samples were screened, and CRE carriage was detected in 0.4 % of the sampled population. In total, 30 Escherichia coli, one Citrobacter freundii and one Klebsiella aerogene were screened. The 30 carbapenem-resistant Escherichia coli (CREC) isolates displayed slight resistance to amikacin (13.3 %) and aztreonam (20.0 %). All the CRE isolates contained blaNDM, and blaNDM-5 (84.4 %) was the most common one. B1 (n = 11) and A (n = 7) were predominant phylogroups. Furthermore, 34 distinct plasmid replicons, 67 different VFs, 22 distinct STs, 17 different FimH types, 26 O:H serotypes as well as 74 MGEs including 61 insertion sequences and 13 transposons were identified. The flanking DNA sequence analysis of blaNDM-5 and mcr1.1 genes indicates the key role of horizontal transfer of blaNDM-5 in the CRE development evidenced by diverse STs and phylogenetic tree.

CONCLUSION

E. coli was the most predominant CRE isolates in community setting, and blaNDM (blaNDM-5) was the main CHβL encoding genes. The high prevalence of ARGs was associated with high resistance to commonly used antimicrobials. Besides, the genetic diversity of these isolates suggested the key role of blaNDM horizontal transfer in the CRE development. Thus, active screening of blaNDM in communities is particularly important for the prevention and control of CRE.

Emergence of tet(X4)-positive Enterobacterales in retail eggs and the widespread of IncFIA(HI1)-HI1A-HI1B(R27) plasmids carrying tet(X4)

The proliferation of antimicrobial-resistant microbes and resistance genes in various foods poses a serious hazard to public health. The plasmid-mediated tigecycline resistance gene tet(X4) has been detected in Enterobacterales from various niches but has not yet been reported in eggs. This study aimed to investigate the occurrence and characteristics of tigecycline-resistant strains from retail eggs. A total of 144 eggs were purchased from farmers' markets in Guangdong province, China, and eggshell (n = 144) and egg content (n = 96) samples were used to screen for tigecycline-resistant strains. Eight Escherichia coli strains (two ST195, one ST48, ST8165, ST752, ST93, ST189, and ST224) and one Klebsiella pneumoniae strain (ST252) recovered from eight (5.56 %, 8/144) egg samples (eggshells, n = 6; egg content, n = 2) were positive for tet(X4). Notably, the two E. coli ST195 strains were closely (15-54 SNPs) related to all the tet(X4)-positive E. coli ST195 from various origins (food animals, foods, migratory birds, human, and environment) deposited in GenBank. The E. coli ST224 showed a close phylogenetic relationship (9-12 SNPs) with two tet(X4)-positive E. coli strains from chicken feces and retail chicken in Guangdong province. The hybrid plasmid IncFIA(HI1)-HI1A-HI1B(R27) constitutes the predominant tet(X4) vector both herein (7/9, 77.78 %) and in the GenBank database (32/160, 20 %). The tet(X4)-positive IncFIA(HI1)-HI1A-HI1B(R27) plasmids, sharing highly similar structures, have been widely disseminated across China. However, the IncFIA(HI1)-HI1A-HI1B(R27) plasmids exhibit poor stability and low conjugation frequency. The contamination of tet(X4)-positive bacteria internally and externally in retail eggs poses a prospective food safety threat. More attention should be paid to the spread of the tet(X4) gene via epidemic clone E. coli ST195 and the plasmid IncFIA(HI1)-HI1A-HI1B(R27).