Prevalence and genetic analysis of chromosomal mcr-3/7 in Aeromonas from U.S. animal-derived samples

Authors: WANG, YAN - Chinese Center For Disease Control; HOU, NAXIN - Volunteer; Rasooly, Reuven; Gu, Yong; He, Xiaohua

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2021
Publication Date: 4/30/2021
Citation: Wang, Y., Hou, N., Rasooly, R., Gu, Y.Q., He, X. 2021. Prevalence and genetic analysis of chromosomal mcr-3/7 in Aeromonas from U.S. animal-derived samples. Frontiers in Microbiology. 12. Article 667406. https://doi.org/10.3389/fmicb.2021.667406.
DOI: https://doi.org/10.3389/fmicb.2021.667406

Interpretive Summary: Colistin is the last line of antibiotics against multidrug resistant bacteria. However, its clinical efficacy has been jeopardized since the emergence of mobile colistin-resistance mcr genes. Compared with plasmid-borne mcr, data on the prevalence of chromosomally encoded mcr genes in bacteria was limited. The presence of chromosome-borne mcr genes indicates the existence of stabilized heritage of the mcr genes, which is a potential threat because they can have a direct impact on human health. In this study, we screened 5,169 animal-origin samples, including chicken, beef, pork, poultry and fish collected by FSIS and identified 14 Aeromonas isolates that carried mcr-3/7 genes from catfish and poultry samples. This is the first systemic and large-scale investigation on the prevalence of chromosomal mcr in U.S. raw meat. The potential risk of chromosome-borne mcr on dissemination of colistin-resistance is analyzed using genetic information obtained from the whole genome sequences of 14 mcr-positive bacterial isolates.

Technical Abstract: The prevalence of mcr-positive bacteria in 5,169 domestic animal-derived samples collected by USDA Food Safety and Inspection Service between October 2018 and May 2019 was investigated. A procedure including enriched broth culture and real-time PCR targeting mcr-1 to mcr-8 were used for the screening. Fifteen positive isolates were identified, including one plasmid-born mcr-1-positive Escherichia coli strain, EC2492 (reported elsewhere) and 14 mcr-3/7-positive strains from poultry, catfish and chicken rinse samples. Analysis of 16S rRNA and whole genome sequences revealed that all strains belonged to Aeromonas. Data from phylogenetic analysis of seven housekeeping genes, including gyrB, rpoD, gyrA, recA, dnaJ, dnaX and atpD, indicated that nine strains belonged to Aeromonas hydrophila and five strains belonged to A. jandaei. Antimicrobial tests showed that almost all mcr-positive strains exhibited high resistance to colistin with MICs = 128mg/L, except one A. jandaei strain, which showed a borderline resistance with a MIC of 2mg/L. A segment containing two adjacent mcr-3 and mcr-3-like genes was found in two A. hydrophila and one A. jandaei strains and a variety of IS-like elements were found in the flanking regions of this segment. A mcr-3-related lipid A phosphoethanolamine transferase gene was present in all 14 Aeromonas strains, while an additional mcr-7-related lipid A phosphoethanolamine transferase gene was found in 5 A. jandaei strains only. In addition to mcr genes, other antimicrobial resistance genes, including blaOXA-12/OXA-724, aqu-2, tru-1, cepS, cphA, imiH, ceph-A3, ant(3'')-IIa, aac(3)-VIa and sul1 were observed in chromosomes of some Aeromonas strains. The relative high prevalence of chromosome-borne mcr-3/7 genes and the close proximity of various IS elements to these genes highlights the need for continued vigilance to reduce the mobility of these colistin-resistance genes among food animals.