Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure

Molecular characterization of putative antibiotic resistance determinant and virulence factors genes of Acinetobacter baumannii strains isolated from intensive care unit patients in Riyadh, Saudi Arabia

BACKGROUND

Multidrug resistance in Acinetobacter baumannii (A. baumannii) is a major global health threat. The resistance in A. baumannii is attributed to numerous factors, including antimicrobial resistance and virulence-determinant genes. Hence, the present study aimed to screen antibiotic resistance and virulence factors genes in 67 A. baumannii strains isolated from patients admitted to several hospitals in Riyadh City, Saudi Arabia.

METHOD

The A. baumannii isolates were confirmed by the VITEK-2 automated system and 16S rRNA phylogenetic relatedness. The phenotypic and genotypic resistance patterns of these isolates were also analyzed using conventional and molecular methods.

RESULTS

Our finding showed that 94 % of isolated strains were MDR, and more than 94 % were resistant to the β-lactams group, particularly carbapenems, and the ciprofloxacin group. An intermediate resistance pattern was obtained with trimethoprim-sulfamethoxazole (71.6 %) and gentamicin (59.7 %). The lowest resistant patterns showed with colistin (5 %). The distribution of of resistance genes oxa-23, imp-like, oxa-24-like, tem, oxa-40, carb, oxa-58, floR, dfrA1 and qnrS were 100 %, 76.1 %, 64.1 %, 25.3 %, 23.8 %, 16.4 %, 14.9 %, 44.7 %, 5.9 % and 2.9 %, respectively. The distribution of virulence genes baP, pld, paaE, and surA1 was 98.5 %, followed by basD, traT, Omp33-36, and bauA were 97 %, 77.6 %, 74.4 %, and 64.1 %, respectively.

CONCLUSION

The study showed a strong relationship between virulence factors, especially biofilm formation, and antibiotic resistance.

Diverse Acinetobacter species and Plasmid-Driven spread of carbapenem resistance in pharmaceutical settings in China

Acinetobacter species have emerged as a significant public health concern due to their remarkable capacity to acquire antimicrobial resistance. Environmental reservoirs play a crucial role in spreading antimicrobial resistance genes and potentially pathogenic bacteria to clinical settings. However, most studies on nonhuman isolates have focused on a limited sample size. Comprehensive population sampling on One Health principles is essential to monitor the antibiotic resistome and virulome in Acinetobacter spp. Here, we identified three carbapenems-resistant Acinetobacter spp. isolates harboring blaNDM-1 and discovered two novel Acinetobacter species in pharmaceutical production environments. A total of 94 Acinetobacter spp. strains were isolated from pharmaceutical production environments across 17 cities in China, forming 17 distinct Acinetobacter clusters comprising two novel species and 15 previously known species. Phylogenetic analysis indicated that Acinetobacter spp. isolated from pharmaceutical settings are predominantly confined to these settings. Genomic analysis revealed 10 specific families of blaCHDL genes in 51 isolates and blaNDM-1 in three isolates. The overall rates of phenotypic resistance to antimicrobials were low among Acinetobacter spp. isolates, with less than 10 % resistance observed for all tested drugs, and only three isolates carrying blaNDM-1 were resistant to carbapenems. The blaNDM-1 gene was located in approximately 49 kb PTU-Pse8 conjugative plasmids with conserved backbones, although plasmid pXH1688-NDM displayed enhanced growth and stability. Two novel Acinetobacter species, A. yuyunsongii sp. nov. and A. chenhuanii sp. nov., were characterized using phenotypic and genomic analyses. Particularly, A. yuyunsongii sp. nov. XH1639 harbors a blaOXA-58-carrying conjugative plasmid and exhibits multidrug-resistant phenotype. Our study advances Acinetobacter taxonomy and underscores the urgency of monitoring the dynamics of Acinetobacter species in environmental sources to implement effective measures to mitigate transmission risks to healthcare facilities.

Phenotypic and genotypic characterization of clinical carbapenem-resistant Acinetobacter species harboring the metallo-beta-lactamases IMP-8 or NDM-1 in China

Carbapenem-resistant Acinetobacter spp. pose a significant challenge in clinical settings due to limited treatment options for nosocomial infections. Carbapenem-hydrolyzing class D beta-lactamases are the primary cause for carbapenem resistance, while metallo-beta-lactamases (MBLs) New Delhi metallo beta-lactamase (NDM) and imipenemase (IMP) also contribute. This study investigated five MBL-producing Acinetobacter spp. strains isolated from a clinic in China in 2010. The blaIMP-8-carrying A1014 was the first identified CRAB among all known STPas150 isolates worldwide. Through whole-genome sequencing and the southern blot analysis, we determined that blaIMP-8 was located on a pR4WN-type plasmid and blaNDM-1 was located on four distinct pSU1904NDM-type plasmids. The blaIMP-8 gene was identified within a class 1 integron organized as a 5'-conserved segment (intI), variable region (blaIMP-8-aac(6')-Ib), and 3'-conserved segment (qacEΔ1/sul1). All available sequences of blaIMP variants in A. baumannii from the NCBI were investigated and classified into five types of class 1 integrons. All blaNDM-1 plasmids were transferable, and the blaNDM-1 genes were in a conservative region. Additionally, multiple resistance genes, including those conferring resistance to aminoglycosides, tetracyclines, and macrolides, were detected on plasmids from these strains. All strains were resistant to meropenem and imipenem, while they were all susceptible to tigecycline and intermediate to polymyxin. A207 and A1014 were susceptible to cefiderocol, and only blaIMP-8-carrying A1014 had low MIC value (4/2 µg/mL) toward cefoperazone/sulbactam. In conclusion, we characterized the phenotypic and genotypic features of one IMP-8-producing and four NDM-1-producing plasmids recovered from Acinetobacter spp. strains isolated in 2010, contributing to the understanding of the dissemination and evolution of these enzymes.

IMPORTANCE

Given the low prevalence of IMP among A. baumannii and the limited sequencing technology in earlier years, research on blaIMP in A. baumannii is scarce, and genetic information on blaNDM-1-producing Acinetobacter spp. strains isolated in earlier years is limited. This study revisited five MBL-carrying Acinetobacter spp. strains isolated in 2010, characterizing their phenotypic and genotypic features. This retrospective analysis serves as a form of "bacterial archaeology," providing evidence of the evolutionary changes in genetic elements conferring antibiotic resistance.

Discovery of novel BfmR inhibitors restoring carbapenem susceptibility against carbapenem-resistant Acinetobacter baumannii by structure-based virtual screening and biological evaluation

The emergence and spread of Acinetobacter baumannii pose a severe threat to public health, highlighting the urgent need for the next generation of therapeutics due to its increasing resistance to existing antibiotics. BfmR, a response regulator modulating virulence and antimicrobial resistance, shows a promising potential as a novel antimicrobial target. Developing BfmR inhibitors may propel a new therapeutic direction for intractable infection of resistant strains. In this study, we conducted a structure-based hierarchical virtual screening pipeline combining molecular docking, molecular dynamic simulation, and MM/GBSA calculation to sift the Specs chemical library and finally discover three novel potential BfmR inhibitors. The three hits can reduce the MIC of meropenem for the carbapenem-resistant Acinetobacter baumannii (CRAB) strain ZJ06. Similar to the BfmR knockout strain, Cmp-98 was demonstrated to downregulate the expression of K locus genes, indicating it as a BfmR inhibitor. Bacteria underwent harmful morphological changes after treatment with these inhibitors. Molecular dynamic simulations found that all the hits tend to dynamically bind to different positions of the phosphorylation site of BfmR. Wherein we identified a potential inhibitory-binding cleft, beside a possible activated binding cleft at the edge of the phosphorylation site. Restraining the ligand binding poses may help exert inhibitory effects. This study reports a group of new scaffold BfmR inhibitors, offering new insights for novel antibiotic therapeutics against CRAB.

Characteristics of Oral Acinetobacter spp. and Evolution of Plasmid-Mediated Carbapenem Resistance in Bacteremia Patients with Hematological Malignancies

Background

Patients with hematological malignancies are more susceptible to infections, leading to a poor prognosis. Acinetobacter colonization is a risk factor for secondary bacteremia.

Methods

Antibiotic susceptibility phenotypes and genomic characteristics of 48 oral Acinetobacter spp. and one bloodstream Acinetobacter baumannii from patients with hematological malignancies were analyzed by antimicrobial susceptibility tests and whole-genome sequencing. We conducted comparative genomic analysis of oral and blood isolates from the same patient.

Results

A. baumannii was the most common (72.92%, 35/48) Acinetobacter species in oral Acinetobacter spp. isolates. Seventeen different A. baumannii sequence types were identified using the Pasteur MLST scheme; however, the dominant global clones GC1 and GC2 were not present. Among the isolates, 46 (95.8%) were carbapenem-susceptible Acinetobacter spp. One patient treated with meropenem for 15 days developed A. baumannii bacteremia 46 days after the isolation of oral A. baumannii AOR07. Oral and bloodstream isolates from the same patient were closely related to only four non-synonymous mutations on the chromosome. The bla OXA-58 gene was transferred between plasmids through XerCD-mediated recombination, leading to an elevated copy number, causing carbapenem resistance in bloodstream isolates.

Conclusion

Oral Acinetobacter spp. may cause secondary bacteremia. The amplification and transfer of bla OXA-58 in the plasmids explained the increased carbapenem resistance in the bloodstream isolate.

Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital

The interruption of bacteriological surveillance due to the COVID-19 pandemic brought serious consequences, such as the collapse of health systems and the possible increase in antimicrobial resistance. Therefore, it is necessary to know the rate of resistance and its associated mechanisms in bacteria causing hospital infections during the pandemic. The aim of this work was to show the phenotypic and molecular characteristics of antimicrobial resistance in ESKAPE bacteria in a Mexican tertiary care hospital in the second and third years of the pandemic. For this purpose, during 2021 and 2022, two hundred unduplicated strains of the ESKAPE group (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) were collected from various clinical sources and categorized by resistance according to the CLSI. An analysis of variance (ANOVA) complemented by the Tukey test was performed to search for changes in antimicrobial susceptibility profiles during the study period. Finally, the mechanisms of resistance involved in carbapenem resistance were analyzed, and the search for efflux pumps and high-risk sequence types in A. baumannii was performed by multilocus analysis (MLST). The results showed no changes in K. pneumoniae resistance during the period analyzed. Decreases in quinolone resistance were identified in E. coli (p = 0.039) and P. aeruginosa (p = 0.03). Interestingly, A. baumannii showed increases in resistance to penicillins (p = 0.004), aminoglycosides (p < 0.001, p = 0.027), carbapenems (p = 0.027), and folate inhibitors (p = 0.001). Several genes involved in carbapenem resistance were identified (blaNDM, blaVIM, blaOXA, blaKPC, blaOXA-40, and blaOXA-48) with a predominance of blaOXA-40 and the adeABCRS efflux pump in A. baumannii. Finally, MLST analysis revealed the presence of globally distributed sequence types (ST369 and ST758) related to hospital outbreaks in other parts of the world. The results presented demonstrate that the ESKAPE group has played an important role during the COVID-19 pandemic as nosocomial antibiotic-resistant pathogens and in particular A. baumannii MDR as a potential reservoir of resistance genes. The implications of the increases in antimicrobial resistance in pathogens of the ESKAPE group and mainly in A. baumannii during the COVID-19 pandemic are analyzed and discussed.

A mathematician's guide to plasmids: an introduction to plasmid biology for modellers

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.

High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020

Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.

Nomogram for predicting 90-day mortality in patients with Acinetobacter baumannii-caused hospital-acquired and ventilator-associated pneumonia in the respiratory intensive care unit

OBJECTIVE

We built a prediction model of mortality risk in patients the with Acinetobacter baumannii (AB)-caused hospital-acquired (HAP) and ventilator-associated pneumonia (VAP).

METHODS

In this retrospective study, 164 patients with AB lower respiratory tract infection were admitted to the respiratory intensive care unit (RICU) from January 2019 to August 2021 (29 with HAP, 135 with VAP) and grouped randomly into a training cohort (n = 115) and a validation cohort (n = 49). Least absolute shrinkage and selection operator regression and multivariate Cox regression were used to identify risk factors of 90-day mortality. We built a nomogram prediction model and evaluated model discrimination and calibration using the area under the receiver operating characteristic curve (AUC) and calibration curves, respectively.

RESULTS

Four predictors (days in intensive care unit, infection with carbapenem-resistant AB, days of carbapenem use within 90 days of isolating AB, and septic shock) were used to build the nomogram. The AUC of the two groups was 0.922 and 0.823, respectively. The predictive model was well-calibrated; decision curve analysis showed the proposed nomogram would obtain a net benefit with threshold probability between 1% and 100%.

CONCLUSIONS

The nomogram model showed good performance, making it useful in managing patients with AB-caused HAP and VAP.