Comparative resistomics analysis of multidrug-resistant Chryseobacteria

Abstract

Chryseobacteria consists of important human pathogens that can cause a myriad of nosocomial infections. We isolated four multidrug-resistant Chryseobacterium bacteria from activated sludge collected at domestic wastewater treatment facilities in the New York Metropolitan area. Their genomes were sequenced with Nanopore technology and used for a comprehensive resistomics comparison with 211 Chryseobacterium genomes available in the public databases. A majority of Chryseobacteria harbor 3 or more antibiotic resistance genes (ARGs) with the potential to confer resistance to at least two types of commonly prescribed antimicrobials. The most abundant ARGs, including β-lactam class A (blaCGA-1 and blaCIA) and class B (blaCGB-1 and blaIND) and aminoglycoside (ranA and ranB), are considered potentially intrinsic in Chryseobacteria. Notably, we reported a new resistance cluster consisting of a chloramphenicol acetyltransferase gene catB11, a tetracycline resistance gene tetX, and two mobile genetic elements (MGEs), IS91 family transposase and XerD recombinase. Both catB11 and tetX are statistically enriched in clinical isolates as compared to those with environmental origins. In addition, two other ARGs encoding aminoglycoside adenylyltransferase (aadS) and the small multidrug resistance pump (abeS), respectively, are found co-located with MGEs encoding recombinases (e.g., RecA and XerD) or transposases, suggesting their high transmissibility among Chryseobacteria and across the Bacteroidota phylum, particularly those with high pathogenicity. High resistance to different classes of β-lactam, as well as other commonly used antimicrobials (i.e., kanamycin, gentamicin, and chloramphenicol), was confirmed and assessed using our isolates to determine their minimum inhibitory concentrations. Collectively, though the majority of ARGs in Chryseobacteria are intrinsic, the discovery of a new resistance cluster and the co-existence of several ARGs and MGEs corroborate interspecies and intergenera transfer, which may accelerate their dissemination in clinical environments and complicate efforts to combat bacterial infections.

FIGURE 1

A phylogenetic tree of 215 Chryseobacterium genomes based on the resistomes. The left column depicts the three sources of Chryseobacterium isolates (i.e., animal, clinical and environment), and the right heat map shows the abundance of antibiotic resistance genes (ARGs) found in the genomes of these isolates.

FIGURE 2

Significant differences in key ARGs between different sources. The heatmap shows the level of enrichment based on Fisher's exact test with adjusted p < 0.001.

FIGURE 3

(A) Comparative analysis between the catB‐tetX‐flanking regions in Chryseobacterium genomes and those from the genomes of other species in the Bacteroidota phylum. Shades show conserved regions of higher than 94% similarity in nucleotide sequences. (B) Two models of tetX‐catB11 resistance clusters.

FIGURE 4

Comparative analysis between the aadS‐flanking regions in Chryseobacterium genomes and those from the genomes of other species in the Bacteroidota phylum. Shades show conserved regions of higher than 98% similarity in nucleotide sequences.

FIGURE 5

Potential genome rearrangements in the flanking regions of abeS based on the comparative analysis between the environmental and clinical Chryseobacterium isolates.