Global evolutionary epidemiology, phylogeography and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones: A One Health analyses

Abstract

Background. The global epidemiology and resistomes dynamics of multidrug-resistant Citrobacter spp., Enterobacter hormaechei, Klebsiella variicola, morganella morganii, Proteus mirabilis and Providencia spp. have not been described, despite their importance as emerging opportunistic clinical pathogens. Methods. The genomes of the above-mentioned organisms were curated from PATRIC and NCBI and used for evolutionary epidemiology, phylogeography and resistome analyses. The phylogeny trees were drawn using RAXmL and edited with Figtree. The resistomes were curated from GenBank and the phylogeography was manually mapped. Results and conclusion. Mcr-9 and other mcr variants were highly prevalent in E. hormaechei subsp. and substantial in C. freundii whilst KPC, OXA-48, NDM, IMP, VIM, TEM, OXA and SHV were abundant in global E. hormaechei subsp., Citrobacter freundii, P. mirabilis, P. stuartii and P. rettgeri clones/clades. Species-specific ampCs were highly conserved in respective species whilst fluoroquinolones, aminoglycosides, macrolides, fosfomycin, chloramphenicol, tetracycline, sulphamethoxazole and trimethoprim resistance mechanisms were abundantly enriched in almost all clades of most of the species, making them extensively and pandrug resistant; K. variicola, C. amalonaticus and C, koseri had relatively few resistance genes. Vertical and horizontal resistome transmissions as well as local and international dissemination of strains evolving from common ancestors were observed, suggesting the anthroponotic, zoonotic, and food-/water-borne infectiousness of these pathogens. There is a global risk of pandrug resistant strains escalating local and international outbreaks of antibiotic-insensitive infections, initiating the dawn of a post-antibiotic era.

Risk factors for, and molecular epidemiology and clinical outcomes of, carbapenem‐ and polymyxin‐resistant Gram‐negative bacterial infections in pregnant women, infants, and toddlers: a systematic review and meta‐analyses

“…( n = 49), and Proteus mirabilis/vulgaris ( n = 99), were also implicated in carbapenem resistance in infants/neonates. Hence, clinicians must be on a lookout for all these species as potential bearers of carbapenemases, particularly those that are intrinsically resistant to polymyxins: the Proteeae and Serratia spp 49–51 …”

“…Hence, clinicians must be on a lookout for all these species as potential bearers of carbapenemases, particularly those that are intrinsically resistant to polymyxins: the Proteeae and Serratia spp. [49][50][51] Notably, CR A. baumannii, E. coli, and K. pneumoniae harboring mobile plasmid-borne carbapenemases cause outbreaks in neonates with sepsis, pneumonia, and other infections in NICUs in several countries worldwide, resulting in very high mortalities (Fig. 3; and Table S1, online only).…”

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses

“…GNB are continuously evolving as new genetic elements emerges and outspreads [3][4][5] , increasing the incidence and dissemination of MDR infections that pose a huge threat to public health globally 6 . High demands for and over prescription of antibiotics in humans and animals have resulted in an increasing burden of AR globally 7,8 . Increasing rates of AR in GNB have influenced and driven the need for novel antibiotics and newer treatment therapies 9,10 .…”

“…Therefore, plasmid borne ARGs such as mcr and carbapenemases are widespread due to their faster dissemination rate among bacteria species 40 . Owing to the close connection between humans, animals, and the environment (water, soil, air, and communities/built environment), ARGS and virulence mechanisms can be disseminated between these three domains through bacterial hosts and plasmids 7,8,46 . Thus, antibiotics administration in livestock/food-producing animals may select and spread antibiotic-resistant GNB to humans and the environment through the food chain 7,8,46 and their faeces/farm effluents, respectively.…”

“…Owing to the close connection between humans, animals, and the environment (water, soil, air, and communities/built environment), ARGS and virulence mechanisms can be disseminated between these three domains through bacterial hosts and plasmids 7,8,46 . Thus, antibiotics administration in livestock/food-producing animals may select and spread antibiotic-resistant GNB to humans and the environment through the food chain 7,8,46 and their faeces/farm effluents, respectively. Therefore, applying the One Health concept, which describes the interaction between humans, animals, and the environment, may be effective in reducing the spread of ARGs between these domains 47 .…”