Genomic epidemiology and global diversity of the emerging bacterial pathogenElizabethkingia anophelis

Abstract

Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/ elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.

The antibiotic resistance and pathogenicity of a multidrug‐resistant Elizabethkingia anophelis isolate

“…Routine phenotypic and biochemical tests often fail to distinguish them from other bacteria; moreover, E. anophelis has been frequently misdiagnosed as E. meningoseptica (previously known as Chryseobacterium meningosepticum ) with automated microbial identification systems (Kampfer et al, ; Lau et al, ; Nicholson et al, ; Teo et al, ). Often, molecular methods (i.e., the 16SrRNA sequencing, MALDI‐TOF MS) fail to resolve different Elizabethkingia species (Breurec et al, ; Han et al, ). Empirical treatments are difficult because of multiple drug resistance and lack of drug susceptibility testing standards for these bacteria.…”

Risk Factors, Antimicrobial Susceptibility Patterns and Carbapenem Resistance Mechanisms of Elizabethkingia anophelis Clinical Isolates From a University Tertiary Hospital in Southwest China

“…reveals that besides β-lactamases, there are also numerous putative e ux pump proteins including: CzcABC family e ux RND transporter, E ux ABC transporter (ATP-binding protein), MATE family of MDR e ux pump, small multidrug resistance family (SMR) protein and MFS-type transporter. Interestingly however, none of these transporters have been phenotypically characterized [5,18,19,20]. It was therefore critical to investigate the function of these putative e ux pumps.…”

“…PCR experiments were used to detect the presence of 37 blaGOB, 37 blaBlaB and 36 blaCME β-lactamase genes in 39 E. anophelis isolates (Table 4). Sequence alignments showed that E. anophelis strains harbored 2 types of the blaCME gene, blaCME-1 (n = 34) and blaCME-2 (n = 2), 8 types of the blaBlaB gene, including blaBlaB-29 (17), blaBlaB-2 (7), blaBlaB-1 (5), blaBlaB-17 (3), blaBlaB-3 (1), blaBlaB-9 (1), blaBlaB-33 (1) and blaBlaB-34 (1), and 8 types of the blaGOB gene, including blaGOB-38 (19), blaGOB-20 (8), blaGOB-32 (3), blaGOB-50 (3), blaGOB-39 (1), blaGOB-4 (1), blaGOB-40 (1) and blaGOB-45 (1). The most commonly detected combination of β-lactamases was CME-1 + BlaB-29 + GOB-38 (n = 17).…”

“…So far however, the susceptibility patterns of E. anophelis isolates have not been reported in China, especial with data collated using the more robust broth dilution method. Genome-wide analysis reveals that this multidrug-resistant pathogen carries a class A serine-β-lactamase, CME, 2 metallo-β-lactamases, GOB and BlaB, in addition to numerous putative e ux pump genes [5,18,19,20]. However, no studies have focused on the functions of these βlactamases and putative e ux pumps in E. anophelis isolates.…”

Peer Review #2 of "Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species (v0.2)"

“…Because of their ability to accumulate different resistance mechanisms and a growing number of more vulnerable hosts, the prevalence of multidrug-resistant Elizabethkingia species has increased in the past decades, limiting the options for treatment (Janda & Lopez 2017;Jean et al 2014b). For instance, resistance to carbapenems is mediated by metallo-β-lactamases (Breurec et al 2016;Chen et al 2017;Colapietro et al 2016). A previous report indicated that fluoroquinolones are PeerJ reviewing PDF | (2018:05:28531:1:1:NEW 11 Aug 2018)…”