Emergence of Escherichia coli isolates producing NDM-1 carbapenemase from waterfowls in Hainan island, China

High prevalence and transmission of blaNDM-positive Escherichia coli between farmed ducks and slaughtered meats: An increasing threat to food safety

The emergence of carbapenem-resistant bacteria especially carbapenem-resistant Escherichia coli (CREC) in food animals poses a serious threat to food safety and public health. Reports about the dissemination of carbapenem-resistant bacteria along the food animal production chain are scattered and mainly focus on swine and chicken. Abuse of antibiotics in duck farms is common especially in China which has the largest duck production industry, however, the CREC transmission between farmed ducks and slaughtered meats remains unclear and the role of slaughterhouse in disseminating CREC among duck meats remains largely unknown. Herein, we collected 251 fecal samples from five typical duck farms along with 125 slaughtered meat samples (25 from each farm) in the corresponding slaughterhouse in Anhui Province, China, in December 2018. All samples were screened for CREC isolates which were analyzed for the presence of carbapenemase genes and colistin resistance gene mcr. The resistance profiles, transferability, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing and phylogenetic analysis of the CREC isolates from both ducks and meats were further characterized. This is the first report presenting the high prevalence of blaNDM-positive CREC isolates in ducks from duck farms (57.8 %) and slaughtered meats (33.6 %) in the corresponding slaughterhouse. Among the 203 blaNDM-positive CREC isolates obtained in this study, 19.2 % harbored mcr-1 and all CREC isolates showed resistance to nearly all currently available antibiotics (except tigecycline). Of note, mcr-1 was found in 17.8 % of the meat-derived CREC carrying blaNDM. Based on the PFGE analysis, clonal spread of blaNDM-positive CREC including some also carrying mcr-1 was found between farmed ducks and slaughtered duck meats even from different farms. Special attention should be paid to the clonal dissemination of meat-derived CREC within the slaughterhouse, which contributed to the high prevalence of blaNDM in slaughtered meats. Additionally, horizontal transmission mainly mediated by transferable blaNDM-5-bearing IncX3 plasmids, untypable blaNDM-1-bearing plasmids and mcr-1-bearing IncHI2 plasmids further facilitated the rapid spread of such multidrug-resistant strains. Notably, the blaNDM-bearing plasmids and mcr-1-bearing plasmids in CREC from meats were highly similar to those from animals and humans. More worryingly, the phylogenomic analysis showed that CREC isolates from both ducks and corresponding meats clustered with previously reported human CREC isolates carrying mcr-1 in different geographical areas including China. These findings further prove that the CREC and resistance plasmids in farmed ducks could transmit to meats even from different farms via the slaughterhouse and then trigger infections in humans. The high prevalence and clonal transmission of CREC isolates including those also carrying mcr-1 between ducks and meats are alarming, and urgent control measures are required to reduce the dissemination of such organisms.

Prevalence of Antibiotic Resistance and Virulence Genes in Escherichia coli Carried by Migratory Birds on the Inner Mongolia Plateau of Northern China from 2018 to 2023

(1) Background: Antibiotic resistance in bacteria is an urgent global threat to public health. Migratory birds can acquire antibiotic-resistant and pathogenic bacteria from the environment or through contact with each other and spread them over long distances. The objectives of this study were to explore the relationship between migratory birds and the transmission of drug-resistant pathogenic Escherichia coli. (2) Methods: Faeces and swab samples from migratory birds were collected for isolating E. coli on the Inner Mongolia Plateau of northern China from 2018 to 2023. The resistant phenotypes and spectra of isolates were determined using a BD Phoenix 100 System. Conjugation assays were performed on extended-spectrum β-lactamase (ESBL)-producing strains, and the genomes of multidrug-resistant (MDR) and ESBL-producing isolates were sequenced and analysed. (3) Results: Overall, 179 isolates were antibiotic-resistant, with 49.7% MDR and 14.0% ESBL. Plasmids were successfully transferred from 32% of ESBL-producing strains. Genome sequencing analysis of 91 MDR E. coli strains identified 57 acquired resistance genes of 13 classes, and extraintestinal pathogenic E. coli and avian pathogenic E. coli accounted for 26.4% and 9.9%, respectively. There were 52 serotypes and 54 sequence types (STs), including ST48 (4.4%), ST69 (4.4%), ST131 (2.2%) and ST10 (2.2%). The international high-risk clonal strains ST131 and ST10 primarily carried blaCTX-M-27 and blaTEM-176. (4) Conclusions: There is a high prevalence of multidrug-resistant virulent E. coli in migratory birds on the Inner Mongolian Plateau. This indicates a risk of intercontinental transmission from migratory birds to livestock and humans.

Antimicrobial resistance, serogroups, virulence gene profiles and MLST of Escherichia coli from giant panda

Escherichia coli is a major bacterial pathogen which causes diarrhea in the giant panda. This study investigated the biological characteristics of 100 E. coli strains isolated from fecal samples collected from 100 captive giant pandas of different age groups and sexes. A standard Kirby-Bauer disk diffusion antimicrobial susceptibility test was performed with the isolates and we then further evaluated the antibiotic resistance genes (ARGs) by high-throughput quantitative PCR. Additionally, we then analyzed O serogroups through a slide agglutination test, virulence genes and the multi-locus sequence typing (MLST) by PCR. Antimicrobial susceptibility testing demonstrated that the 100 E. coli strains were mainly resistant to ENR (68%), AM (56%), IPM (55%), AMX (54%) and CA (52%), but were susceptible to MEM and FOX. The resistance to TZP, AK, FEP, CAZ, AMS, AZM, AT and IPM was significantly related to age (p < 0.05); the resistance rate of E. coli isolated from female giant pandas to N was significantly higher than in males (p < 0.05). Forty-five different types of ARGs were found, which included a total of 2,258 ARGs, in the 100 E. coli isolates. The top 10 of detection rate of ARGs were: acrA-04, acrA-05, aacC, blaCTX-M-04, ampC-04, blaSHV-01, blaTEM, sul2, blaOXY, tetA-02. ARGs aac (6')I1, blaCTX-M-03, tetD-02, blaSHV-02 and blaOXY were significantly related to age (p < 0.05), blaSHV-02, blaNDM and ampC-04 were related to sex (p < 0.05). Twelve different O serogroups from 32 E. coli isolates were distinguished, including O4, O8, O9, O15, O18, O20, O55, O88, O112, O157, O158, and O167. The most prevalent O serotype was O20, but O28, O45, O101, O149, and O152 were not detected. Fourteen different types of virulence genes were detected in the 100 E. coli isolates, of which papA (99%) were highly detected, while hlyA, elt and estA were not detected. MLST showed that 41 STs, which had one CCs and six groups with SLVs, in the 100 E. coli strains were identified, the main type was ST37. Our results advocate the need of strict biosecurity and surveillance programs in order to prevent the spread of pathogenic bacteria in the captive giant panda population.

Dissemination and prevalence of plasmid-mediated high-level tigecycline resistance gene tet (X4)

With the large-scale use of antibiotics, antibiotic resistant bacteria (ARB) continue to rise, and antibiotic resistance genes (ARGs) are regarded as emerging environmental pollutants. The new tetracycline-class antibiotic, tigecycline is the last resort for treating multidrug-resistant (MDR) bacteria. Plasmid-mediated horizontal transfer enables the sharing of genetic information among different bacteria. The tigecycline resistance gene tet(X) threatens the efficacy of tigecycline, and the adjacent ISCR2 or IS26 are often detected upstream and downstream of the tet(X) gene, which may play a crucial driving role in the transmission of the tet(X) gene. Since the first discovery of the plasmid-mediated high-level tigecycline resistance gene tet(X4) in China in 2019, the tet(X) genes, especially tet(X4), have been reported within various reservoirs worldwide, such as ducks, geese, migratory birds, chickens, pigs, cattle, aquatic animals, agricultural field, meat, and humans. Further, our current researches also mentioned viruses as novel environmental reservoirs of antibiotic resistance, which will probably become a focus of studying the transmission of ARGs. Overall, this article mainly aims to discuss the current status of plasmid-mediated transmission of different tet(X) genes, in particular tet(X4), as environmental pollutants, which will risk to public health for the "One Health" concept.

Vertical and horizontal distributions of clinical antibiotic resistance genes and bacterial communities in Danjiangkou Reservoir, China

The Danjiangkou Reservoir is an important water source for the middle route of the South-to-North Water Diversion Project in China. The current anthropogenic pollution of this reservoir is a great public health concern. Therefore, the horizontal and vertical distributions of seven clinical antibiotic resistance genes (ARGs) and bacterial communities in the Danjiangkou Reservoir were investigated using qPCR and next-generation sequencing, respectively. The average relative abundance of ARGs was 3.01 × 10^-4 to 1.90 × 10^-3 and 4.66 × 10^-4 to 1.85 × 10^-3 in horizontal and vertical profiles, respectively. There was a significant difference in the vertical composition of ARGs, which was caused by different media (i.e. water column vs. sediment). No significant differences in the composition of ARGs were found in the horizontal profile. Proteobacteria was the most abundant phylum, followed by Actinobacteria in the Danjiangkou Reservoir. The beta diversity pattern of the microbial communities in the vertical profile was consistent with that of the ARGs. Moreover, a significant difference in the horizontal composition of the bacterial communities among these water columns was found. All of these factors have resulted in noticeably different co-occurrence patterns of ARGs and bacterial communities between water columns and surface sediment samples. ARGs were closely associated with Proteobacteria and Chloroflexi in the sediment samples, indicating potential anthropogenic pollution in the Danjiangkou Reservoir. Although there was no significant correlation between the occurrence of ARGs and 11 opportunistic pathogens, our results point to potential risks for the development of multi-resistant pathogens due to the simultaneous presence of ARGs and pathogens in the study area. These results provide a good basis for thorough ecological evaluation and remediation of the Danjiangkou Reservoir.