Antimicrobial Resistance and Comparative Genomic Analysis of Elizabethkingia anophelis subsp. endophytica Isolated from Raw Milk

Abstract

Elizabethkingia anophelis is an emerging multidrug-resistant pathogen that causes severe nosocomial and community-acquired infections worldwide. We report the first case of E. anophelis isolation in Russia and the first isolation from raw cow’s milk. The ML-44 demonstrated resistance to 28 antimicrobials of 33 tested in the disk-diffusion test. Whole genome-based phylogeny showed ML-44 strain clustered together with the F3201 strain isolated from a human patient in Kuwait in 1982. Both strains were a part of the “endophytica” clade. Another clade was formed by subsp. anophelis strains. Each of the E. anophelis compared genomes carried 18 to 21 antibiotic resistance determinants. The ML-44 chromosome harbored nine efflux system genes and three beta-lactamase genes, along with six other antimicrobial resistance genes. In total, 72 virulence genes were revealed. The set of virulence factors was quite similar between different E. anophelis strains and included LPS and capsule encoded genes, type IV pili, oxidative stress response genes, and genes encoding TIVSS and TVISS effectors. The particular interest caused the mip and zmp1 gene homologs, which can be essential for intracellular survival. In sum, our findings suggest that raw milk might be a source of E. anophelis harboring a set of virulence factors and a broad resistance to generally used antimicrobials.

Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption

“…The widely distributed multidrug-resistance efflux pump system and target-modification genes acR-tolC and soxR were detectable in all samples, similarly to the permeability-reducing soxS gene. The adeF gene, responsible for developing resistance to fluoroquinolones and tetracyclines through efflux pumps, was detected in all samples, which was also identified by Andriyanov et al in raw milk samples [42]. The abaQ gene, determining resistance to fluoroquinolones via efflux pumps, was only identified in raw milk samples, similar to the findings of Tóth et al [17].…”

The First Reported Case of Elizabethkingia anophelis From Nepal

“…One thing to be noted while studying drug sensitivity is the disk diffusion method and Etest are not appropriate for antibiotic sensitivity testing (AST) assays for E. anophelis due to the high rate of errors. Studies done in South Korea and the USA using disk diffusion test or agar dilution test compared to sensitivity test done using broth microdilution test in Taiwan and Singapore showed large discrepancies [ 5 , 13 ]. Thus, although disk diffusion is an easier and faster method of testing, the broth microdilution test represents the gold standard for antimicrobial sensitivity testing, as was done in our case [ 13 ].…”

“…Since the first reported human infection was identified in the Central African Republic in a neonate in 2011 [ 3 ], multiple community outbreaks as well as hospital outbreaks have been reported. Elizabethkingia anophelis , notorious for antibiotic resistance, has been one of the deadliest micro-organisms with high case fatality rates [ 4 , 5 ]. In this case report, we present the case of a middle-aged male who succumbed fatally to the infection, which, to the best of our understanding, remains the first reported case of Elizabethkingia anophelis from Nepal.…”

Whole-genome sequence and resistance determinants of four Elizabethkingia anophelis clinical isolates collected in Hanoi, Vietnam

“…All members of the Elizabethkingia genus are mainly considered to be environmental bacteria because they are ubiquitous in various natural reservoirs such as soil, freshwater bodies and insect or amphibian guts 5 – 7 . E. anophelis is commonly found in the midgut of different mosquito species, including the malaria vectors Anopheles gambiae and Anopheles stephensi 8 – 13 , and has already been detected from animal food products such as raw bovine milk 14 . Infections caused by E. anophelis tend to be rare but problematic, usually displaying lethality rates of 23.5–33.3% 15 – 17 and up to 70% 18 .…”