Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

Identification and characterisation of colistin-resistant Acinetobacter colistiniresistens co-producing IMP-1 and OXA-58 carbapenemases

Background

Carbapenem-resistant Acinetobacter is of increasing global concern because infections are challenging to treat with standard antibiotics. Here, we identified a previously uncharacterised Acinetobacter sp. clinical isolate as Acinetobacter colistiniresistens co-producing IMP-1 and OXA-58. We also examined expression of genes related to antibiotic susceptibility and drug resistance, including bla IMP.

Methods

The isolate was deposited at the National Institute of Technology and Evaluation (NITE) as Acinetobacter sp. NBRC 110496. Susceptibility was defined according to the Clinical and Laboratory Standards Institute (CLSI) breakpoints. Genomic and clonal analyses were performed to identify species and resistance genes.

Results

The isolate was resistant to β-lactams, including broad-spectrum cephalosporins and carbapenems, polymyxins, and trimethoprim/sulfamethoxazole. Genomic analysis identified the isolate as A. colistiniresistens harbouring bla IMP-1, bla OXA-58, bla OXA-670, aac(6')-Ib, aac(6')-Ij, ant(3")-I I, aph(3')-VI, msrE, mphE, and sul1. Colistin resistance was associated with the eptA-like gene, which encodes a lipid A-modifying enzyme. SNP-based phylogenetic analysis revealed that the strain clustered with other strains isolated in Japan. The IMP-1/OXA-58-producing strain described in this study has a novel integron structure surrounding bla IMP-1, aacA and sul1.

Conclusions

Colistin-resistant IMP-1/OXA-58-co-producing A. colistiniresistens was identified in a patient. This isolate could serve as a reservoir for carbapenemase-producing organisms. This study suggests that screening for colistin-resistant isolates is crucial to preserve colistin as a therapeutic agent for multidrug-resistant bacteria. Identification of this MDR isolate in Asia, and the danger of it spreading worldwide, should raise serious concerns.

Characterization of a colistin resistant, hypervirulent hospital isolate of Acinetobacter courvalinii from Canada

Non-baumannii Acinetobacter spp. are becoming more prevalent in clinical settings including those that present resistance to last-resort antibiotics such as colistin. AB222-IK40 is an Acinetobacter courvalinii strain isolated from the Ottawa Hospital Research Institute located in Ottawa, Canada. To our knowledge, it is the first report of clinical A. courvalinii in Canada. Based on the susceptibility profile, AB222-IK40 is resistant to colistin and non-susceptible to ertapenem. Whole-genome sequencing allowed for genomic investigation into colistin resistance mechanisms. No previously identified mechanism(s) were observed, but a mobile colistin resistance (mcr)-like gene and a UDP-glucose dehydrogenase gene were identified. Based on phylogenomic analyses, the mcr-like gene is an intrinsic phosphoethanolamine transferase. This gene family is implicated in one of the many mechanisms responsible for colistin resistance in Acinetobacter baumannii as well as Acinetobacter modestus. UDP-glucose dehydrogenase is involved in colistin resistance in Enterobacterales and has been shown to be involved in capsule formation in A. baumannii. Global lipidomics revealed greater abundance of phosphatidyl-myo-inositol and lyso-phosphatidyl ethanolamine moieties in the membrane of A. courvalinii than in A. baumannii. Lipidomic profiles showed differences that were probably responsible for the colistin resistance phenotype in AB222-IK40. This isolate was also hypervirulent based on survival assays in Galleria mellonella. As this is the first report of A. courvalinii from a hospital in Canada, this species may be an emerging clinical pathogen, and therefore, it is important to understand this mechanism of its colistin resistance and hypervirulence.

Targeted amplicon sequencing facilitated a novel risk assessment framework for assessing the prevalence of broad spectrum bacterial and coronavirus diseases

How to effectively leverage wastewater data to estimate the risk of various infectious diseases remains a great challenge. To address this issue, we conducted continuous wastewater surveillance in Dalian city during the summer-autumn seasons of 2022, targeting coronavirus and bacterial diseases. The surveillance included daily sampling at a wastewater treatment plant (WWTP) and weekly sampling in three sewersheds. Targeting the bacteria's 16S rRNA gene and the coronavirus's RNA-dependent RNA polymerase (RdRp) gene, we first employed RT-PCR and amplicon sequencing techniques to analyze the presence and phylogenetic relationship of detected coronavirus and bacterial pathogens. Next, qPCR was used to quantify the abundances of detected coronavirus and bacterial species. Based on the daily shedding dynamics of SARS-CoV-2, a novel model was developed to predict daily new cases. Based on the medium shedding density of 12 pathogens, two thresholds of sewage pathogen load (indicating 0.1 % and 1 % infection rates) were proposed. Our PanCoV RT-PCR detected coronavirus on 12th August and from 26th August to 12th September 2022. Targeted amplicon sequencing further identified human coronavirus OC43 (hCoV-OC43) on 12th August and the SARS-CoV-2 Omicron variant since 26th August in samples from WWTPs and sewersheds. Phylogenetic analysis revealed that hCoV-OC43 from this study belonged to genotype K and suggested a close relationship between the amplified coronavirus sequences from wastewater and clinical samples in a local COVID-19 outbreak on 26th August. Amplicon sequencing targeting the bacterial 16S rRNA gene also revealed the presence of several bacterial pathogens. Finally, we assessed the microbial risk of specific pathogens in sewersheds and identified a number of pathogens that reached high (>1 % prevalence) and medium risk levels (>0.1 % prevalence) at sewershed B. Our findings underline wastewater surveillance as a valuable early warning system for coronavirus and other waterborne bacterial diseases, complementing public health response measures.