Elizabethkingia anophelis is a non-fermenting gram-negative rod bacterium that was first isolated from the midgut of mosquitoes in 2011 [1]. The first case of human infection was reported in Central Africa in 2013 [2], and more than 60 cases of multi-state outbreaks were reported in the United States during 2015–16 [3]. The number of reported cases in Asian countries (i.e. Hong Kong, Taiwan, and Singapore) has been increasing; however, there has not been a report of life-threatening infection by E. anophelis published in Japan so far.

For species identification of bacteria, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is used in clinical microbiology laboratories; however, this method sometimes cannot distinguish the genus Elizabethkingia at a species level due to the lack of adequate coverage by commercial reference databases [4,5]. Whole-genome sequencing is also a powerful tool for identifying species, determining the relatedness of different species and strains, and characterizing genomic features. As of March 2022, 184 whole genome sequences that belong to the genus Elizabethkingia are available in the NCBI Refseq database. In recent reports about genomic features of E. anophelis, a number of antimicrobial resistance genes were identified, such as those coding for β-lactamases, including the metallo-β-lactamase genes blaBlaB and blaGOB, and for efflux pumps, which may contribute to conferring resistance to many antibiotics [[6], [7], [8], [9], [10]]. In addition, pathogen-associated virulence factor homologs were also identified such as capsular polysaccharide synthesis (CPS) gene clusters and genes for several secretion systems [[6], [7], [8], [9]].

In this study, we described two patients with pneumonia or meningitis accompanied with sepsis caused by E. anophelis, the first cases reported in Japan. Additionally, to determine the phylogenetic origin and genomic features of the two E. anophelis strains, we compared their genomes with strains from other sources and regions worldwide.