Emergence of uncommon KL38-OCL6-ST220 carbapenem-resistant Acinetobacter pittii strain, co-producing chromosomal NDM-1 and OXA-820 carbapenemases

Identification and characterization of the capsule depolymerase Dpo27 from phage IME-Ap7 specific to Acinetobacter pittii

Among the Acinetobacter genus, Acinetobacter pittii stands out as an important opportunistic infection causative agent commonly found in hospital settings, which poses a serious threat to human health. Recently, the high prevalence of carbapenem-resistant A. pittii isolates has created significant therapeutic challenges for clinicians. Bacteriophages and their derived enzymes are promising therapeutic alternatives or adjuncts to antibiotics effective against multidrug-resistant bacterial infections. However, studies investigating the depolymerases specific to A. pittii strains are scarce. In this study, we identified and characterized a capsule depolymerase, Dpo27, encoded by the bacteriophage IME-Ap7, which targets A. pittii. A total of 23 clinical isolates of Acinetobacter spp. were identified as A. pittii (21.91%, 23/105), and seven A. pittii strains with various K locus (KL) types (KL14, KL32, KL38, KL111, KL163, KL207, and KL220) were used as host bacteria for phage screening. The lytic phage IME-Ap7 was isolated using A. pittii 7 (KL220) as an indicator bacterium and was observed for depolymerase activity. A putative tail fiber gene encoding a polysaccharide-degrading enzyme (Dpo27) was identified and expressed. The results of the modified single-spot assay showed that both A. pittii 7 and 1492 were sensitive to Dpo27, which was assigned the KL220 type. After incubation with Dpo27, A. pittii strain was susceptible to killing by human serum; moreover, the protein displayed no hemolytic activity against erythrocytes. Furthermore, the protein exhibited sustained activity across a wide pH range (5.0-10.0) and at temperatures between 20 and 50°C. In summary, the identified capsule depolymerase Dpo27 holds promise as an alternative treatment for combating KL220-type A. pittii infections.

Exploring Nocardia's ecological spectrum and novel therapeutic frontiers through whole-genome sequencing: unraveling drug resistance and virulence factors

Nocardia farcinica is the leading pathogen responsible for nocardiosis, a life-threatening infection primarily affecting immunocompromised patients. In this study, the genomic sequence of a clinically isolated N. farcinica sample was sequenced. Subsequently, the assembled genome was annotated to identify antimicrobial resistance and virulence genes, as well as plasmid and prophages. The analysis of the entire genome size was 6,021,225 bp, with a GC content of 70.78% and consists of 103 contigs and N50 values of 292,531 bp. The genome analysis revealed the presence of several antimicrobial resistance genes, including RbpA, mtrA, FAR-1, blaFAR-1, blaFAR-1_1, and rox. In addition, virulence genes such as relA, icl, and mbtH were also detected. The present study signifies that N. farcinica genome is pivotal for the understanding of antimicrobial resistance and virulence genes is crucial for comprehending resistance mechanism, and developing effective strategies to combat bacterial infections effectively, especially adhesins and toxins. This study aids in identifying crucial drug targets for combating multidrug-resistant N. farcinica in the future.

Genome sequence of a tigecycline-resistant Acinetobacter seifertii recovered in human bloodstream infection in China

OBJECTIVES

The phylogenetic characteristics of Acinetobacter seifertii clinical strain are not well-studied. Here, we reported one tigecycline-resistant ST1612Pasteur A. seifertii isolated from bloodstream infections (BSI) in China.

METHODS

Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing (WGS) was performed and annotation was conducted using rapid annotations subsystems technology (RAST) server. Multilocus sequence typing (MLST), capsular polysaccharide (KL), and lipoolygosaccharide (OCL) were analysed using PubMLST and Kaptive. Resistance genes, virulence factors, and comparative genomics analysis were performed. Cloning, mutations of efflux pump-related genes, and expression level were further investigated.

RESULTS

The draft genome sequence of A. seifertii ASTCM strain is made up of 109 contigs with a total length of 4,074,640 bp. Based on the RAST results, 3923 genes that belonged to 310 subsystems were annotated. Acinetobacter seifertii ASTCM was ST1612Pasteur with KL26 and OCL4, respectively. It was resistant to gentamicin and tigecycline. ASTCM harboured tet(39), sul2, and msr(E)-mph(E), and one amino acid mutation in Tet(39) (T175A) was further identified. Nevertheless, the signal mutation failed to contribute to susceptibility change of tigecycline. Of note, several amino acid substitutions were identified in AdeRS, AdeN, AdeL, and Trm, which could lead to overexpression of adeB, adeG, and adeJ efflux pump genes and further possibly lead to tigecycline resistance. Phylogenetic analysis showed that a huge diversity was observed among A. seifertii strains based on 27-52,193 SNPs difference.

CONCLUSION

In summary, we reported a tigecycline-resistant ST1612Pasteur A. seifertii in China. Early detection is recommended to prevent their further spread in clinical settings.

Complete genetic characterization of carbapenem-resistant Acinetobacter johnsonii, co-producing NDM-1, OXA-58, and PER-1 in a patient source

The emergence of carbapenemase-producing Acinetobacter spp. has been widely reported and become a global threat. However, carbapenem-resistant A. johnsonii strains are relatively rare and without comprehensive genetic structure analysis, especially for isolates collected from human specimen. Here, one A. johnsonii AYTCM strain, co-producing NDM-1, OXA-58, and PER-1 enzymes, was isolated from sputum in China in 2018. Antimicrobial susceptibility testing showed that it was resistant to meropenem, imipenem, ceftazidime, ciprofloxacin, and cefoperazone/sulbactam. Whole-genome sequencing and bioinformatic analysis revealed that it possessed 11 plasmids. bla OXA-58 and bla PER-1 genes were located in the pAYTCM-1 plasmid. Especially, a complex class 1 integron consisted of a 5' conserved segment (5' CS) and 3' CS, which was found to carry sul1, arr-3, qnrVC6, and bla PER-1 cassettes. Moreover, the bla NDM-1 gene was located in 41,087 conjugative plasmids and was quite stable even after 70 passages under antibiotics-free conditions. In addition, six prophage regions were identified. Tracking of closely related plasmids in the public database showed that pAYTCM-1 was similar to pXBB1-9, pOXA23_010062, pOXA58_010030, and pAcsw19-2 plasmids, which were collected from the strains of sewage in China. Concerning the pAYTCM-3 plasmids, results showed that strains were collected from different sources and their hosts were isolated from various countries, such as China, USA, Japan, Brazil, and Mexico, suggesting that a wide spread occurred all over the world. In conclusion, early surveillance is warranted to avoid the extensive spread of this high-risk clone in the healthcare setting.