Genomic Characterization of Clinical Extensively Drug-Resistant Acinetobacter pittii Isolates

Chopjitt, Peechanika; Putthanachote, Nuntiput; Ungcharoen, Ratchadaporn; Hatrongjit, Rujirat; Boueroy, Parichart; Akeda, Yukihiro; Tomono, Kazunori; Hamada, Shigeyuki; Kerdsin, Anusak

doi:10.3390/microorganisms9020242

Cited by 13 publications

(15 citation statements)

References 57 publications

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“…Interest in Acinetobacter spp. genomes is rising, while comparative analysis including other species than A. baumannii is scarce, involving the lack of information on the pathogenic A. pittii [2,[23][24][25]. When we performed this analysis on our clinical strains through the panOCT software, we obtained a pan-genome of 4154 genes, distributed between the core-genome of 3014 genes, and accessory single genomes from 25 (HUMV4336) to 396 (HUMV6483) genes (Figure 1A).…”

Section: Discussionmentioning

confidence: 99%

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

2022

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Antimicrobial-resistant pathogenic bacteria are an increasing problem in public health, especially in the healthcare environment, where nosocomial infection microorganisms find their niche. Among these bacteria, the genus Acinetobacter which belongs to the ESKAPE pathogenic group harbors different multi-drug resistant (MDR) species that cause human nosocomial infections. Although A. baumannii has always attracted more interest, the close-related species A. pittii is the object of more study due to the increase in its isolation and MDR strains. In this work, we present the genomic analysis of five clinically isolated A. pittii strains from a Spanish hospital, with special attention to their genetic resistance determinants and plasmid structures. All the strains harbored different genes related to β-lactam resistance, as well as different MDR efflux pumps. We also found and described, for the first time in this species, point mutations that seem linked with colistin resistance, which highlights the relevance of this comparative analysis among the pathogenic species isolates.

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Section: Discussionmentioning

confidence: 99%

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

2022

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“…The terms multidrug resistance (MDR), extensive drug resistance (XDR) and pandrug resistance (PDR) were used worldwide to define the non-susceptibility level of isolates, which are resistant to at least one agent in three or more antimicrobial categories, to at least one agent in all but two or fewer categories and to all agents in all categories, respectively ( Magiorakos et al., 2012 ). MDR A. pittii including those resistant to antibiotics quinolones, carbapenems, etc., was reported across continents, yet PDR A. pittii was rarely reported ( Gu et al., 2015 ; Brasiliense et al., 2019 ; Chen et al., 2019a ; Cosgaya et al., 2019 ; Chopjitt et al., 2021 ). Here, we report the case of a patient with acute exacerbations of chronic obstructive pulmonary disease (AECOPD) three years after double lung transplantation (DLT) and developed severe pneumonia associated with PDR A. pittii infection.…”

Section: Introductionmentioning

confidence: 99%

Emergence of ST63 Pandrug-Resistant Acinetobacter pittii Isolated From an AECOPD Patient in China

Yang

Dong

Chen

et al. 2021

Front. Cell. Infect. Microbiol.

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Acinetobacter sp. is among the ESKAPE organisms which represent the major nosocomial pathogens that exhibited a high resistance rate. A. pittii, frequently associated with antimicrobial resistance particularly to carbapenems, is one of the most common Acinetobacter species causing invasive infection. Pandrug resistant A. pittii has rarely been reported. Here, we report the case of a patient with acute exacerbations of chronic obstructive pulmonary disease three years after double lung transplantation and developed severe pneumonia associated with pandrug resistant A. pittii infection. Phenotypic and genomic characteristics of this pandrug resistant isolate (17-84) was identified, and the mechanisms underlying its resistance phenotypes were analyzed. Isolate 17-84 belonged to ST63, carried a non-typable and non-transferable plasmid encoding multiple acquired resistance genes including carbapenemase gene blaOXA-58. Point mutations and acquired resistance genes were identified which were associated with different drug resistance phenotypes. To our knowledge, this is the first detailed phenotypic and genomic characterization of PDR A. pittii causing severe infections in clinical settings. Findings from us and others indicate that A. pittii could serve as a reservoir for carbapenem determinants. The emergence of such a superbug could pose a serious threat to public health. Further surveillance of PDR A. pittii strains and implementation of stricter control measures are needed to prevent this emerging pathogen from further disseminating in hospital settings and the community.

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“…Regarding the carbapenem-resistant A. pittii isolates, an outbreak of ST63 clone that carried a 45-kb bla NDM-1 -bearing plasmid was reported in an ICU in China (Yang et al, 2012). In addition, Chopjitt et al (2021) reported the ST63, ST396, and ST220 carbapenem-resistant A. pittii strains from the perspective of clinical characteristics and genome-based single nucleotide polymorphism (SNP). However, no studies completely clarify the chromosome and plasmid structures of bla NDM-1 -positive carbapenem-resistant A. pittii strain.…”

Section: Discussionmentioning

confidence: 99%

“…The species belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (ACB complex) including A. calcoaceticus, A. baumannii, A. dijkshoorniae, A. lactucae, A. nosocomialis, A. pittii, and A. seifertii are of great importance (Sarshar et al, 2021). Among these species, A. pittii is an important opportunistic pathogen that mainly causes healthcareassociated infections, including bloodstream infections (BSIs), pneumonia, and urinary tract infections (UTIs) (Pailhories et al, 2018;Chopjitt et al, 2021). One important contributing factor to these nosocomial infections is their ability to survive in stressful environments and, consequently, how difficult they are to eradicate (Chapartegui-Gonzalez et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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

Tian

Xing

et al. 2022

Front. Cell. Infect. Microbiol.

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ObjectiveTo characterize one KL38-OCL6-ST220 carbapenem-resistant Acinetobacter pittii strain, co-producing chromosomal NDM-1 and OXA-820 carbapenemases.MethodsA. pittii TCM strain was isolated from a bloodstream infection (BSI). Antimicrobial susceptibility tests were conducted via disc diffusion and broth microdilution. Stability experiments of blaNDM-1 and blaOXA-820 carbapenemase genes were further performed. Whole-genome sequencing (WGS) was performed on the Illumina and Oxford Nanopore platforms. Multilocus sequence typing (MLST) was analyzed based on the Pasteur and Oxford schemes. Resistance genes, virulence factors, and insertion sequences (ISs) were identified with ABRicate based on ResFinder 4.0, virulence factor database (VFDB), and ISfinder. Capsular polysaccharide (KL), lipooligosaccharide outer core (OCL), and plasmid reconstruction were tested using Kaptive and PLACNETw. PHASTER was used to predict prophage regions. A comparative genomics analysis of all ST220 A. pittii strains from the public database was carried out. Point mutations, average nucleotide identity (ANI), DNA–DNA hybridization (DDH) distances, and pan-genome analysis were performed.ResultsA. pittii TCM was ST220Pas and ST1818Oxf with KL38 and OCL6, respectively. It was resistant to imipenem, meropenem, and ciprofloxacin but still susceptible to amikacin, colistin, and tigecycline. WGS revealed that A. pittii TCM contained one circular chromosome and four plasmids. The Tn125 composite transposon, including blaNDM-1, was located in the chromosome with 3-bp target site duplications (TSDs). Many virulence factors and the blaOXA-820 carbapenemase gene were also identified. The stability assays revealed that blaNDM-1 and blaOXA-820 were stabilized by passage in an antibiotic-free medium. Moreover, 12 prophage regions were identified in the chromosome. Phylogenetic analysis showed that there are 11 ST220 A. pittii strains, and one collected from Anhui, China was closely related. All ST220 A. pittii strains presented high ANI and DDH values; they ranged from 99.85% to 100% for ANI and from 97.4% to 99.9% for DDH. Pan-genome analysis revealed 3,200 core genes, 0 soft core genes, 1,571 shell genes, and 933 cloud genes among the 11 ST220 A. pittii strains.ConclusionsThe coexistence of chromosomal NDM-1 and OXA-820 carbapenemases in A. pittii presents a huge challenge in healthcare settings. Increased surveillance of this species in hospital and community settings is urgently needed.

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Genomic Characterization of Clinical Extensively Drug-Resistant Acinetobacter pittii Isolates

Cited by 13 publications

References 57 publications

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

Emergence of ST63 Pandrug-Resistant Acinetobacter pittii Isolated From an AECOPD Patient in China

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

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