Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii

Genomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome

Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.

Secondary bacterial infections of Carbapenem-Resistant Acinetobacter baumannii in patients with COVID-19 admitted to Chinese ICUs

BACKGROUND

A significant proportion of patients who are hospitalized with coronavirus disease 2019 (COVID-19), particularly those being admitted to ICUs, exhibit the development of secondary bacterial infections (SBIs). However, there is a lack of detailed epidemiological investigations and genetic information of Carbapenem-Resistant Acinetobacter baumannii (CRAB) based on whole genome sequencing (WGS), which is one of the frequently detected bacteria among COVID-19 patients, to confirm alterations in the clonal structure and infection mechanism.

RESULTS

A total of 37 unique CRAB strains, sourced from patients, along with an additional 2 CRAB strains form the environment, were isolated. Among the cohort of 37 patients, 22 individuals succumbed to CRAB infection, resulting in a mortality rate of 54.46%. The median duration of illness for these patients was 7.95 days, highlighting the severity and rapid progression of CRAB infections in this patient population. A total of 22 CRAB strains, isolated from deceased individuals, in addition to two strains isolated from the environment, were subjected to further investigation. All 24 CRAB isolates exhibited a high ability to form biofilm and displayed a similar spectrum of resistance. Except for two isolates from patients with COVID-19, all the remaining CRAB isolates were categorized as ST195 and demonstrated highly close genetic background based on analysis of WGS. The ST195 strain of CRAB harbored three copies of the blaOXA-23 gene located on the chromosome, each of which was carried by Tn2006. Notably, one Tn2006 element was integrated within Tn6022, leading to the formation of AbaR4-like resistance islands Tn6166-I.

CONCLUSIONS

Our findings underscore the significance of SBIs in the COVID-19 pandemic, particularly those caused by CRAB and specifically those belonging to MLST types that were previously prevalent in ICUs.

Aminoglycoside resistance dynamics and its predictive value for carbapenem resistance in multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae

OBJECTIVES

The rise of multidrug-resistant (MDR) bacterial pathogens, including carbapenem-resistant Acinetobacter baumannii (CRAB) and Klebsiella pneumoniae (CRKP), poses a global healthcare challenge. Aminoglycosides remain among the few effective therapeutic options, but increasing resistance threatens their efficacy. This study investigates aminoglycoside consumption and resistance dynamics, focusing on the predictive value of aminoglycoside resistance for future carbapenem resistance.

METHODS

Data on aminoglycoside use (amikacin, gentamicin, tobramycin) and resistance were retrospectively collected (2010-2024). Resistance patterns were assessed using the Antibiotic Resistance Index and Resistance Instability Index. Correlation analyses examined associations between aminoglycoside consumption and resistance, including delayed effects, and between aminoglycoside and meropenem resistance.

RESULTS

We analyzed 4582 A. baumannii and 36,049 K. pneumoniae isolates. Among them, 2462 CRAB and 309 CRKP isolates were identified. Amikacin was the most used aminoglycoside, with stable resistance in CRAB and higher variability in CRKP. Gentamicin showed the most unstable resistance. In CRAB, aminoglycoside resistance - especially amikacin (r = 0.73) - was strongly correlated with meropenem resistance, suggesting predictive potential. In CRKP, predictive correlations were weaker; gentamicin showed the highest (r = 0.62).

CONCLUSIONS

Aminoglycoside resistance trends, particularly for amikacin in CRAB, may serve as early indicators of emerging carbapenem resistance. Integrating such data into surveillance and stewardship frameworks could improve early detection and response to MDR threats.

Biofilm formation capacity and Carbapenem-resistance in Acinetobacter-calcoaceticus-baumannii isolated from inpatients in a tertiary care hospital in Nepal

OBJECTIVE

Acinetobacter calcoaceticus-baumannii complex (ACBC), as an emerging global burden to various clinical infections, has a huge problem in empirical therapy due to the increasing resistance to the majority of antibiotics. The ability of biofilm formation added to its antimicrobial resistance and helped its persistence and survival in the environment. To associate biofilm formation with carbapenem resistance, a hospital-based cross-sectional study was carried out from February 2020 to August 2020 at Kathmandu Model Hospital, Kathmandu, Nepal. ACBC was identified from the clinical samples following standard Microbiological procedures. A modified Kirby-Bauer disk diffusion method was performed to assay the antibiotic susceptibility testing of ACBC isolates to various antibiotic classes. A quantitative adherence assay was used to determine the biofilm assay. A conventional Polymerase Chain Reaction (PCR) method was used to find the targeted biofilm-related genes, Bap, csuE, and blaPER1 using specific primers.

RESULTS

Out of 665 different clinical samples, bacterial growth was observed in 281 (42.3%) clinical samples. Of these, 32 (11.4%) isolates were identified as ACBC. Out of 32 ACBC isolates, 29 (90.6%) of which were carbapenem-resistant. All carbapenem-resistant ACBC isolates were found to be sensitive to Polymixin B and Colistin. Out of 29 CR-ACBC, 17.2% of isolates were resistant to Tigecycline. The majority of ACBC isolates (93.8%) were multidrug-resistant (MDR) while 13 (40.6%) of isolates were extensively drug-resistant (XDR). A total of 31 ACBC isolates were biofilm producers, out of which 2 were strong biofilm producers followed by 8 moderate, and 21 were weak biofilm producers. The occurrence of biofilm-forming genes; Bap, csuE, and blaPER1 genes were found to be 65.6%, 65.6%, and 56.3% respectively among ACBC clinical isolates. A significant association was observed between carbapenem resistance, biofilm formation, and biofilm-related genes.

CONCLUSION

The higher rate of MDR and XDR ACBC isolates associated with biofilm formation in the study alarms the ACBC-related infection in clinical settings among inpatients. The hospital environment and clinical equipment are potential sources of biofilm-forming isolates. Hence, the effective sterilization of clinical equipment and hospital environment are utmost and a strong policy should be made to prescribe the proper antibiotic based on antibiogram profile to fight against an emerging threat of ACBC infections.

Genomic characteristics of the multiresistant Acinetobacter baumannii global clone 1 reference strain A297/RUH875

OBJECTIVES

Acinetobacter baumannii ST1, also known as global clone 1 (GC1), is a globally distributed lineage associated with antimicrobial resistance (AMR). The multiresistant isolate A297/RUH8751, recovered from a urinary tract infection in the Netherlands in 1984, has served as a reference strain for ST1. We aimed to generate and analyse the complete genome sequence of A297/RUH8751 to provide insights into its genomic features, antibiotic resistance determinants and phylogenetic placement.

METHODS

WGS was performed using Oxford Nanopore GridION and Illumina HiSeq platforms. Assembly was conducted with Autocycler v0.2.1. Genomic features, including antibiotic resistance genes, insertion sequences and restriction-modification systems, were characterized using ResFinder, ISFinder and REBASE. Comparative analyses were conducted with the draft genome of NIPH 527, which also represents RUH875, to assess sequence variations. Phylogenetic analysis was performed to determine the evolutionary placement of A297/RUH875 within GC1.

RESULTS

The complete genome of RUH875 (A297) consists of a 3 965 450 bp chromosome and three plasmids: pA297-1 (pRAY*; 6078 bp), pA297-2 (8731 bp) and pA297-3 (a 200 kb conjugative plasmid). The chromosome harbours the AbaR21 genomic resistance island, carrying seven antibiotic resistance genes and six prophage regions. Notably, bap1 and bap2, biofilm-associated genes, were fully resolved, with bap1 identical to that of A. baumannii A1-the earliest GC1 isolate. Comparative analysis with A1 revealed 122 SNPs, with clustered variations suggesting potential recombination events. Phylogenetic analysis confirmed A297/RUH875 as a distinct lineage within GC1. The completed genome sequence provides a reference, in addition to strain A1, for studying AMR evolution in GC1 and enhances comparative genomic analyses.

Phage-antibiotic synergy to combat multidrug resistant strains of Gram-negative ESKAPE pathogens

Bacteriophage-antibiotic-synergy (PAS) was investigated to target Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii and Enterobacter cloacae. Whole genome sequencing indicated that bacteriophage KPW17 targeting K. pneumoniae, clustered with genus Webervirus, ECSR5 targeting E. cloacae clustered with Eclunavirus, PAW33 targeting P. aeruginosa clustered with Bruynoghevirus, while ABTW1 targeting A. baumannii clustered with Vieuvirus. PAS analysis showed that the combination of ciprofloxacin (CIP) and levofloxacin (LEV) with PAW33 resulted in the synergistic eradication of all tested P. aeruginosa strains. Similarly, the combined use of doripenem (DOR) and LEV with KPW17 resulted in the synergistic eradication of the environmental and clinical K. pneumoniae strains, while the combined use of DOR and gentamicin (CN) with ECSR5 was synergistic against the clinical E. cloacae NCTC 13406. Gentamicin with ECSR5, however, only exhibited an additive effect for E. cloacae 4L, while ABTW1 with piperacillin-tazobactam (TZP) and imipenem (IPM) resulted in an indifferent interaction between the bacteriophage and tested antibiotics against the clinical A. baumannii AB3, i.e., the activity of the combination is equal to the activity of most active agent. Thus, while the observed PAS may offer an opportunity for the re-introduction or more efficient application of certain antibiotics to combat antibiotic resistance, extensive research is required to determine the optimal phage-antibiotic combinations, dosages and treatment regiments.

Genomic insights of predominant international high-risk clone ST2 Acinetobacter baumannii isolates in Saudi Arabia

OBJECTIVES

Carbapenem-resistant Acinetobacter baumannii (CRAB), particularly the globally prevalent ST2 clone, poses significant threats in the Gulf Cooperation Council region through extensive drug resistance, high virulence, and efficient gene transfer. This study investigates the epidemiological and genomic characteristics of CRAB in the Jazan region, using whole genome sequencing to understand its transmission and genetic determinants.

METHODS

Sixty-five clinical A. baumannii isolates exhibiting phenotypic resistance to carbapenems (meropenem, imipenem, and ertapenem) were collected from various tertiary hospitals in the Jazan region. The presence of prevalent carbapenemase genes among these isolates was examined using two sets of multiplex polymerase chain reaction (PCR). Forty-eight isolates confirmed as carbapenemase producers were selected for WGS analysis.

RESULTS

Among the 65 clinical CRAB isolates, the adult ICU exhibited the highest prevalence of CRAB (76.9%). Multiplex PCR identified 48 (73.8%) isolates as carbapenemase producers, all harboring blaOXA-51-like genes. Specifically, blaOXA-23 was detected in 39 isolates (60%), blaNDM in 8 (12.3%), and blaOXA-24 in one isolate. These 48 carbapenemase-producing isolates also carried virulence-associated genes related to adherence, biofilm formation, immune evasion, iron acquisition and regulation, and serum resistance. Whole-genome sequencing (WGS) revealed that 39 (81.2%) of the carbapenemase-positive isolates belonged to ST2, followed by ST85 and ST107, with the KL152 locus as the most common capsule type.

CONCLUSIONS

The study indicates a significant rise in the ST2 clone in the Arabian Gulf, particularly in Saudi Arabia, and underscores the need for ongoing surveillance of less common clones such as ST85 and ST107 to manage public health risks effectively.

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China

In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology has hindered understanding of its population dynamics. Here, we analyzed 1506 non-repetitive BSI-causing A. baumannii isolates from 76 Chinese hospitals over a decade (2011-2021). We identified 149 sequence types (STs) and 101 K-locus types (KLs), revealing increased population diversity. International clone (IC) 2 accounted for 81.74% of isolates, with a notable shift in prevalent STs: ST208 increased while ST191 and ST195 declined, aligning with global trends. ST208 exhibited higher virulence, greater antibiotic resistance, enhanced desiccation tolerance, and more complex transmission patterns compared to ST191 and ST195. Its genomic plasticity drives its adaptation and spread. Using the high-resolution Oxford MLST scheme, this study uncovered greater diversity and genetic factors behind ST208's rise. A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one, highlighting the urgent need to address its growing threat. These findings have critical implications for infection control and public health policies.

The fitness connection of antibiotic resistance

More than three decades ago multidrug-resistant (MDR) clones of the pathogens: Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Clostridioides difficile, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii have started to disseminate across wide geographical areas. A characteristic feature of all these MDR lineages is the carriage of some mutations in the quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV which besides conferring resistance to fluoroquinolones are associated with a fitness benefit. Several lines of evidence strongly suggest that extra fitness conferred by these mutations facilitated the dissemination of the international MDR lineages. MDR pathogens require extra energy to cover the fitness cost conferred by the excess antibiotic resistance gene cargo. However, extra energy generated by upgraded metabolic activity was demonstrated to increase the uptake of antibiotics enhancing susceptibility. Accordingly, MDR bacteria need additional positive fitness schemes which, similarly to the QRDR advantage, will not compromise resistance. Some of these, not clone-specific effects are large genomes, the carriage of low-cost plasmids, the transfer of plasmid genes to the chromosome, the application of weak promoters in integrons and various techniques for the economic control of the activity of the integrase enzyme including a highly sophisticated system in A. baumannii. These impacts - among others - will confer a fitness advantage promoting the spread of MDR pathogens. However, even the potential of extra fitness generated by the combined effect of various schemes is not without limit and virulence-related genes or less relevant antibiotic resistance gene cargoes will often be sacrificed to permit the acquisition of high-priority resistance determinants. Accordingly major MDR clone strains are usually less virulent than susceptible isolates. In summary, a fitness approach to the research of antibiotic resistance is very useful since the fitness status of MDR bacteria seem to profoundly impact the capacity to disseminate in the healthcare setting.

Comprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria

BACKGROUND

Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed.

RESULTS

Most isolates (57.67%) originated from South-west Nigeria. Isolates of human origin accounted for 33.86%, while environmental sources comprised 6.87%, and 59.27% lacked information on the source of isolation. The cgMLST analysis revealed a multitude of genomic lineages circulating in Nigeria. The MLST Oxford scheme identified 44 sequence types (STs) in 62.96% of strains, with ST1089 being the most prevalent. The MLST Pasteur could assign 95.77% of strains to 49 STs, with ST2(IC2) and ST85(IC9) being the most dominant. Antimicrobial resistance analysis detected 168 genes encoding resistance to 12 antibiotic classes, with cephalosporin, carbapenem, and aminoglycoside resistance genes being the most prevalent. Notably, blaADC-79 (23.81%), blaOXA-23 (30.69%), and aph(3″)-Ib (30%) were frequent variants encountered. Seventeen multi-efflux system genes conferring resistance to multiple antibiotic classes were identified. Virulence gene analysis revealed 137 genes encoding six mechanisms, with genes for nutritional factors, effector delivery systems, and biofilm production being the most prevalent.

CONCLUSION

This study highlights the diversity in AMR and virulence genes of A. baumannii in Nigeria, emphasizing the need for ongoing genomic surveillance to inform infection control and develop antibiotic resistance management strategies.

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii

The proliferation of multi-drug resistant (MDR) bacteria is driven by the global spread of epidemic lineages that accumulate antimicrobial resistance genes (ARGs). Acinetobacter baumannii, a leading cause of nosocomial infections, displays resistance to most frontline antimicrobials and represents a significant challenge to public health. In this study, we conduct a comprehensive genomic analysis of over 15,000 A. baumannii genomes to identify a predominant epidemic super-lineage (ESL) accounting for approximately 70% of global isolates. Through hierarchical classification of the ESL into distinct lineages, clusters, and clades, we identified a stepwise evolutionary trajectory responsible for the worldwide expansion and transmission of A. baumannii over the last eight decades. We observed the rise and global spread of a previously unrecognized Clade 2.5.6, which emerged in East Asia in 2006. The epidemic of the clade is linked to the ongoing acquisition of ARGs and virulence factors facilitated by genetic recombination. Our results highlight the necessity for One Health-oriented research and interventions to address the spread of this MDR pathogen.

Newly isolated terpenoids (covering 2019-2024) from Aspergillus species and their potential for the discovery of novel antimicrobials

The rapid emergence of drug-resistant microbial pathogens has posed challenges to global health in the twenty-first century. This development has significantly made most antibiotics ineffective in the treatment of infections they cause, resulting in increasing treatment costs and annual death rates. To address the challenge posed by these pathogens, we explore the potential of secondary metabolites from Aspergillus species as a source of new and effective therapeutic agents to treat drug-resistant infections. Terpenoids, a distinct group of natural products, are extensively distributed in plants and fungi, and have been attributed with significant antibacterial, anticancer, and antiviral activities. In this review, we present an overview of Aspergillus species, and review the novel terpenoids isolated from them from 2019 to April 2024, highlighting anti-infective activity against members of the ESKAPE pathogens. We further focus on the strategies through which the structural framework of these new terpenoids could be modified and/or optimized to feed a pipeline of new lead compounds targeting microbial pathogens. Overall, this review provides insight into the therapeutic applications of terpenoids sourced from Aspergillus species and the potential for the discovery of new compounds from these fungi to combat antimicrobial resistance.

Companions in antimicrobial resistance: examining transmission of common antimicrobial-resistant organisms between people and their dogs, cats, and horses

SUMMARYNumerous questions persist regarding the role of companion animals as potential reservoirs of antimicrobial-resistant organisms that can infect humans. While relative antimicrobial usage in companion animals is lower than that in humans, certain antimicrobial-resistant pathogens have comparable colonization rates in companion animals and their human counterparts, which inevitably raises questions regarding potential antimicrobial resistance (AMR) transmission. Furthermore, the close contact between pets and their owners, as well as pets, veterinary professionals, and the veterinary clinic environment, provides ample opportunity for zoonotic transmission of antimicrobial-resistant pathogens. Here we summarize what is known about the transmission of AMR and select antimicrobial-resistant organisms between companion animals (primarily dogs, cats, and horses) and humans. We also describe the global distribution of selected antimicrobial-resistant organisms in companion animals. The impact of interspecies AMR transmission within households and veterinary care settings is critically reviewed and discussed in the context of methicillin-resistant staphylococci, extended-spectrum β-lactamase and carbapenemase-producing bacteria. Key research areas are emphasized within established global action plans on AMR, offering valuable insights for shaping future research and surveillance initiatives.

Genomic analysis of early ST32 Acinetobacter baumannii strains recovered in US military treatment facilities reveals distinct lineages and links to the origins of the Tn6168 ampC transposon

OBJECTIVES

To study the population structure and genomic characteristics, including antimicrobial resistance genes, plasmid types and surface polysaccharide type, of the globally distributed Acinetobacter baumannii belonging to ST32 (Institut Pasteur scheme).

METHODS

Antibiotic resistance phenotype for 19 antibiotics was determined using Vitek 2. Whole-genome sequencing was performed using the Illumina MiSeq platform. Genomes were assembled using Newbler. Phylogenetic analysis was done by determining the core-genome alignments using Panaroo v1.3, analysed in IQ-Tree2 v2.2.0.3 to construct Maximum Likelihood trees using the RaxML software. Resistance genes and IS were identified using the Abricate programme, and ISFinder databases.

RESULTS

One hundred and thirty-three (n = 133) ST32 A. baumannii isolates were analysed in this study. These genomes originated mainly from US military treatment facilities (n = 113), but also included additional publicly available genomes in GenBank (n = 20) recovered from a broad geographic distribution extending to Asia and South America. Phylogenetic analysis of all 133 genomes revealed at least four clades, with over 80 genomes forming a tightly clustered branch, suggesting they are likely to represent outbreak strains. Analysis of the ampC region showed that ST32 strains played a significant role in the formation of the widely distributed ampC transposon, Tn6168, and supplying DNA segments containing an ISAba1-ampC from ST32s via homologous recombination.

CONCLUSIONS

ST32 strains played a significant role in the evolution of antibiotic resistance in several widely distributed sequence types including ST1 (global clone 1) and ST3.

Genomic insights into drug resistance and virulence determinants in rare pyomelanin-producing clinical isolates of Acinetobacter baumannii

PURPOSE

Clinical isolates of multi-drug resistant Acinetobacter baumannii are a major cause of nosocomial infections, often attributed to the highly adaptable genome that helps it to thrive under environmental selection pressure. Here, we aim to provide genotypic-based surveys and comparative whole genome sequencing (WGS) analysis to explore the genomics of the rare pyomelanin-forming clinical isolates of A. baumannii from India.

METHODS

A total of 54 clinical isolates of A. baumannii obtained from two tertiary care hospitals were genotyped using repetitive sequence-based PCR (REP-PCR) for elucidating their molecular epidemiology, followed by their resistance profiling through the determination of minimum inhibitory concentration using the micro broth dilution method. The isolates' virulence and antibiotic-resistant determinants were detected by PCR screening, followed by biofilm quantification. Pyomelanin pigment produced by A. baumannii isolates was isolated and chemically characterized. Finally, WGS of three pigment-producing and one non-producing A. baumannii strains was performed to explore the factors contributing to their variability.

RESULTS

REP-PCR genotyping identified around 8 clusters, with all isolates being multidrug-resistant (MDR). Pyomelanin-producing isolates were strong biofilm formers, characterized by the concurrent presence of 'pgaB, BfmR, BfmS, ompA, and cusE' biofilm-related genes. These pigmented strains belonged to ST2Pas and co-harbored blaOXA-23, blaADC-25, aph (3')-VIa, armA, aph (6)-Id, tet(B) and msr(E) genes. Thirteen common IS elements and biosynthetic gene clusters of arylpolyene, NI-siderophore, and NRP-metallophore were identified. Notably, genomic islands containing aminoglycoside 3'-phosphotransferase, oxidative stress, two-component response regulators, efflux pump-related, toxin-antitoxin protein, and virulence-related genes were also mapped by WGS.

CONCLUSION

The pyomelanin-forming isolates were MDR and virulent. The elucidation of WGS analysis provided critical insights for understanding the epidemiology, virulome, and mobilome of rare pigment-producing A. baumannii strains.

Exploring the clinical outcomes and molecular characteristics of Acinetobacter baumannii bloodstream infections: a study of sequence types, capsular types, and drug resistance in China

Background

Bloodstream infections (BSIs) caused by Acinetobacter baumannii have been associated with high mortality. To improve the outcomes of patients, this study explored the clinical characteristics and outcomes of patients with BSIs, as well as the phenotypic and genomic characteristics of these isolates.

Methods

A retrospective cohort study was conducted involving A. baumannii BSIs cases from 2020 to 2023 in a tertiary hospital. The clinical characteristics of all A. baumannii isolates were evaluated. Virulence phenotypes of all isolates were evaluated using the growth curve, biofilm-forming assay, antiserum complement killing, and G.mellonella killing assay. Furthermore, whole-genome sequencing (WGS) was utilized to analyze genomic characteristics.

Results

The 30-day mortality rate of 67 patients with BSIs was 55.22%. Patients in the death group had significantly lower platelet counts and higher CRP levels than those in the survival group. Additionally, higher rates of antibiotic use (≥2 classes) and greater carbapenem exposure were observed. Among the isolates, CRAb accounted for 80.6%, ST2 accounted for 76.12%, and KL2/3/7/77/160 accounted for 65.67%. The predominant KL type was KL3, found in 19.4% of the isolates. All ST2 and KL2/3/7/77/160 isolates were CRAb. Among the isolates, 90.7% of the CRAb isolates coharbored blaOXA-23 and blaOXA-66 , while one coharbored blaNDM-1 and blaOXA-23 . Compared with non-ST2 and non KL2/3/7/77/160 infections, ST2 and KL2/3/7/77/160 infections had higher mortality rates (66.0% vs. 23.5%, P=0.002; 65.90% vs. 34.78%, P=0.015). Patients with ST2 and KL2/3/7/77/160 infections underwent more invasive procedures, received two or more antibiotics and carbapenem therapy before isolation, and had lower serum albumin levels. These isolates exhibited significantly higher resistance to antimicrobial agents. No significant differences in virulence phenotypes were observed between the two groups, except for biofilm formation between the ST2 and non-ST2 groups (P=0.002). However, these isolates harbored more virulence genes related to iron uptake and biofilm formation.

Conclusion

The mortality rate associated with BSIs caused by A. baumannii is high. It is of great significance for clinicians to pay attention to the risk factors of the clinical characteristics of patients and to identify the ST and KL types of the strains causing the infection at an early stage.

Rani F, Alattraqchi AG, Ismail S, A. Rahman NI, Cleary DW, Clarke SC, Yeo CC. Whole-genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020), revealed the predominance of the Global Clone 2 lineage

Carbapenem-resistant Acinetobacter baumannii is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 A. baumannii isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011-2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (n=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu A. baumannii clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2Pasteur of the Global Clone 2 lineage identified as the dominant ST (n=76/126; 60.3%). The ST2Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195Oxford (n=35) and ST208Oxford (n=17). Various antimicrobial resistance genes were identified with the bla OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (n=90/126; 71.4%). Plasmid-encoded rep genes were identified in nearly all (n=122/126; 96.8%) of the isolates with the majority being Rep_3 family (n=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2Pasteur isolates harbouring them. This study provided a genomic snapshot of the A. baumannii isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2Pasteur lineage, indicating the entrenchment of this clone in the hospital.

Analysis of the genome data of Acinetobacter baumannii UOL-KIMZ-24, exhibiting multiple drug resistance through efflux pumps

Acinetobacter baumannii is a well-known opportunistic pathogen, responsible for various nosocomial infections. A. baumannii UOL-KIMZ-24 was previously isolated from a clinical specimen, collected from Lahore General Hospital, Lahore (LGH), Pakistan, dated 3rd March, 2022. During the initial screening for antimicrobial susceptibility, the UOL-KIMZ-24 was found a multiple drug resistant (MDR) strain. However, the detailed genomic insights for genes e.g. responsible for exhibiting antibiotic resistance via efflux pumps, have not yet been reported from A. baumannii strains, recovered from LGH. The current research to fills this gap by isolating, whole genome sequencing and subsequent post-sequencing analysis for addressing and identifying the efflux pumps associated genes, responsible for multiple drug resistant in A. baumannii. In a hybrid approach, short reads were processed through Illumina platform, while long reads were sequenced by MinION MK1B sequencing technique. The assembled and annotated genome of the UOL-KIMZ-24 revealed that it has 4048631 bp genome size with 179 contigs, 38.9 % GC content, 3628 protein coding sequences, 80 tRNA and 7 rRNA. The analysis of antibiotic-resistance genes (AMR) depicted 27 genes. where the genes encoding efflux pumps such as adeABC, adeRS, adeJK, and adeMN were the more prominent. In addition, sequence typing (ST) study showed that UOL-KIMZ-24 strain lies in ST2, six prophage sequences and 73 virulence factors were also identified in the studied UOL-KIMZ-24. Such an all-inclusive study uncovered the genetic flexibility of UOL-KIMZ-24 genome for acquiring MDR against in-practice antibiotics.

Whole genome sequencing characterization and comparative genome analysis of Acinetobacter baumannii JJAB01: A comprehensive insights on antimicrobial resistance and virulence genotype

The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individuals. Whole-Genome Sequencing studies are efficient in providing accurate genetic information, aiding in detecting outbreaks, surveillance of resistance, and controlling infection transmission. In this study, we investigated the whole genome of a clinical isolate A. baumannii JJAB01 which sourced from a urine sample of an Intensive Care Unit (ICU) patient. This strain showed resistance to 24 available antibiotics, signifying Extremely Drug Resistant (XDR) and high potential for pathogenicity. Whole Genome Sequencing was performed using Illumina, and the raw reads were evaluated using the FastQC tool. Genome assembly and annotation were performed with Unicycler and the RAST server. The JJAB01 genome is 4.07 Mb with a GC content of 38.9 %. A total of 51 and 31 virulence factors and antimicrobial-resistant (AMR) genes were predicted using the VFDB and CARD databases. Comparative genome studies were carried out on virulence factors, resistance genes, prophages, and Multi-Locus Sequence Typing (MLST) across twelve closely related A. baumannii genomes, including JJAB01, X4-584, X4-705, 2023CK-00423, 2023CK-00890, 2023CK-00127, 2022CK-00066, B20AB01, B20AB10, F20AB03, G20AB08, and X4-65. These computational investigations in this study emphasis the multidimensional nature of the ICU strain JJAB01 and its genetic similarity to other strains, thereby enhancing our understanding of drug resistance and the pathogenicity associated with A. baumannii infections.

Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains

Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.

Ex vivo assessment of sulbactam-durlobactam clearance during continuous renal replacement therapy to guide dosing recommendations

Sulbactam-durlobactam is approved for the treatment of hospital-acquired and ventilator-associated bacterial pneumonia caused by susceptible isolates of Acinetobacter baumannii-calcoaceticus complex. Patients with serious Acinetobacter infections may require support with continuous renal replacement therapy (CRRT), which presents challenges for optimal dosing of antibiotics. Sulbactam-durlobactam dosing regimens were derived for this population using an ex vivo CRRT model and Monte Carlo simulation (MCS). Transmembrane clearance (CLTM) was determined in hemofiltration (CVVH) and hemodialysis (CVVHD) modes using the Prismaflex M100 and HF1400 hemofilter sets and with effluent rates of 1, 2, and 3 L/h. Pre-filter, post-filter blood, and effluent samples were collected over 60 min to calculate sieving (SC) and saturation (SA) coefficients for CVVH and CVVHD, respectively. An established population pharmacokinetic model was integrated with the CLTM; then, a 1,000 patient MCS was conducted to determine exposures of potential dosing regimens. Adsorption and degradation in the ex vivo CRRT model were negligible. The overall mean ± standard deviation SC/SA was 1.14 ± 0.12 and 0.93 ± 0.08 for sulbactam and durlobactam, respectively. In multivariable regression analyses, effluent rate was the primary driver of CLTM for both drugs. For effluent rates <3 L/h, sulbactam-durlobactam 1 g-1g q8h as 3 h infusion achieved a high probability of pharmacodynamic target attainment while retaining area under the curve exposures consistent with the standard dose in non-CRRT patients. For effluent rates ≥3 to 5 L/h, the optimal regimen was 1 g-1g q6h 3 h infusion. Sulbactam-durlobactam regimens that provide optimum drug exposures for efficacy and safety were identified for CRRT based on the prescribed effluent rate.

Characterization and genomic analysis of the highly virulent Acinetobacter baumannii ST1791 strain dominating in Anhui, China

The multidrug-resistant Acinetobacter baumannii clonal complex 92 is spreading worldwide due to its high-frequency gene mutation and recombination, posing a significant threat to global medical and health safety. Between November 2021 and April 2022, a total of 132 clinical A. baumannii isolates were collected from a tertiary hospital in China. Their growth ability and virulence of these isolates were assessed using growth curve analyses and the Galleria mellonella infection model. The genetic characteristics of the isolates were further examined through whole-genome sequencing. ST1791O/ST2P isolates represented the largest proportion of isolates in our collection and exhibited the highest growth rate and strongest virulence among all sequence types (STs) analyzed. Whole-genome sequences from 14,159 clinical isolates were collected from the National Center for Biotechnology Information database, and only nine ST1791O/ST2P isolates were detected. Comparative genomic analysis revealed that ST1791O/ST2P carried 11 unique genes, 5 of which were located within the capsular polysaccharide synthesis (cps) gene cluster. Single nucleotide polymorphisms (SNPs) between ST1791O/ST2P and other isolates were primarily found in the cps gene cluster. Among the other isolates, ST195O/ST2P and ST208O/ST2P exhibited the smallest SNP differences from ST1791O/ST2P, while ST195O/ST2P and ST1486O/ST2P had high homology. The ST1791O/ST2P strain in Anhui, China, displayed significant homology with ST195O/ST2P, ST208O/ST2P, and ST1486O/ST2P isolates. Compared to other isolates in this study, ST1791O/ST2P exhibited strong growth ability and virulence. Therefore, preventing the further spread of ST1791O/ST2P should be a top public health priority.

Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with blaOXA-23 gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread.

METHODS

We conducted a retrospective study of CRAB patients at three teaching hospitals from 2019 to 2022. We identified bacterial isolates, collected clinical data, and performed antimicrobial susceptibility testing. Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around blaOXA-23. Phylogenetic tree was constructed to analyze the genetic relationship of isolates.

RESULTS

A total of 92 non-repetitive CRAB isolates were collected, with sputum samples accounting for the majority (94.57%, n = 87) of samples. These were distributed into ST2, with ST2 identified to have the highest prevalence of infection, accounting for 99.99% (n = 91) of all isolates. The major resistance genes identified were blaOXA-23, blaOXA-66, blaOXA-51, and blaADC. Also, 92 CRAB strains showed high levels of resistance to common clinical antibiotics, but not minocycline. Meanwhile, most of the isolates carried virulence genes such as various ompA, csuA, csuB, csuC, csuD, abaI, abaR, lpxC, lpxA, and bmfRS. Single nucleotide polymorphism (SNP) analyses further indicated that the bacterial genome was progressively polymorphic with time. We analyzed the environment of the blaOXA-23 gene and found that CRAB accumulated in the context of prominent environmental antibiotic exposure and had longer survival times in the antibiotic environment, resulting in the tendency of bacteria to develop greater antibiotic resistance.

CONCLUSIONS

We find that CRAB is prevalent within the ICU and is progressively resistant to antibiotics over time. Enhanced clinical understanding and timely management of CRAB infections will be crucial to minimize or even eliminate the spread of CRAB within the ICU setting.

An integrative review on the risk factors, prevention, and control strategies for carbapenem-resistant Acinetobacter baumannii colonization in critically ill patients

The presence of carbapenem-resistant Acinetobacter baumannii (CRAb) has become one of the leading causes of life-threatening, hospital-acquired infections globally, especially with a notable prevalence in intensive care units (ICUs). The cross-transmission of microorganisms between patients and the hospital setting is crucial in the development of CRAb colonization and subsequent infections. Recent studies indicate that colonization typically precedes infection, suggesting the effectiveness and necessity of preventing CRAb colonization as a primary method to lower infection risks. As CRAb infections tend to draw more attention due to their severe symptoms and poor outcomes, understanding the link between colonization and infection is equally vital. To establish a foundation for prevention and control strategies against CRAb colonization in ICUs, we present a comprehensive review of research pertaining to CRAb in ICUs. This encompasses an analysis of the resistance mechanisms and epidemiological characteristics of CRAb, a discussion on associated risk factors, adverse outcomes, and an evaluation of detection methods and preventive strategies.

Colistin Resistance in Acinetobacter baumannii: Basic and Clinical Insights

The emergence of drug-resistant bacteria has posed a significant problem in medical institutions worldwide. Colistin, which targets lipopolysaccharide (LPS), serves as a last-resort antimicrobial agent against multidrug-resistant Gram-negative bacteria. Nevertheless, Acinetobacter baumannii, a pathogen with a worldwide prevalence of antimicrobial resistance, has been reported to develop resistance to colistin frequently. In this review, we discuss how A. baumannii acquires resistance to colistin, focusing on modification as well as loss of LPS present in its outer membrane, which is the primary mechanism of A. baumannii's resistance to colistin. Basic and clinical insights regarding colistin resistance in A. baumannii have been discussed in isolation. Therefore, we discuss the relationship between these 2 colistin resistance mechanisms in terms of the frequency and fitness of genetic mutations based on the insights from basic studies and clinical settings. We concluded that understanding the detailed mechanisms of colistin drug resistance requires a comprehensive understanding of both the frequency of mutations and the effects of selection pressure. Finally, we highlight the importance of promoting research from both basic science and clinical perspectives.

Treatment Approaches for Carbapenem-Resistant Acinetobacter baumannii Infections

Carbapenem-resistant Acinetobacter baumannii has been associated with over three hundred thousand annual deaths globally. It is resistant to most available antibiotics and associated with high morbidity and mortality. No global consensus currently exists for treatment strategies that balance safety and efficacy because of heterogeneity of treatment regimens in current clinical practice and scarcity of large-scale controlled studies arising from difficulties in establishing robust clinical outcomes. This review outlines the epidemiology and resistance mechanisms of carbapenem-resistant A. baumannii, then summarizes available clinical data on each approved agent with activity against this pathogen. Emerging treatment options such as cefiderocol and sulbactam-durlobactam show promise, but their success hinges on comprehensive clinical validation and access in regions most impacted by this pathogen. New therapeutic modalities that are in various stages of clinical development are also discussed.

Molecular Epidemiology and Genetic Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolates from the ICU of a Tertiary Hospital in East China

Purpose

To evaluate the clinical characteristics, antimicrobial resistance (AMR) phenotypes and genotypes, and homology features of carbapenem-resistant Acinetobacter baumannii (CRAB) in intensive care unit (ICU) and to provide basis for effectively prevention, control and treatment of nosocomial infections caused by CRAB.

Methods

A total of 39 CRAB strains isolated from hospitalized patients in the ICU and neurosurgical ICU (NICU) between 2020 and 2023 were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). Virulence factor genes (VFGs), antimicrobial resistance genes (ARGs), multilocus sequencing typing (MLST), complete genome multilocus sequencing typing (cgMLST), average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analyses were performed using WGS.

Results

All CRAB strains were 100% resistant to ciprofloxacin, ceftazidime, piperacillin/tazobactam, and ticarcillin/clavulanic acid. A total of 48 antimicrobial resistance genes (ARGs) were found in the 39 CRAB strains, including blaOXA-66, blaOXA-23, blaADC-30, blaADC-73, gyrA, ant(3″)-IIa, aph(3″)-Ib, aph(6)-Id, tetB, tetR, sul1, sul2, LpxC and LpxA which confered resistance to carbapenems, cephalosporins, fluoroquinolones, aminoglycosides, tetracycline and sulfonamides. There were 128 VFGs, including genes encoding the AdeFGH efflux pump, lipopolysaccharide (LpsBLC), outer membrane protein A (OmpA), penicillin-binding protein (PbpG), biofilm-associated proteins (bap, pgaBCD, CsuABCDE), type VI secretion system protein (Tss), quorum sensing protein (AbaI/AbaR). Six clonal lineages were identified by Oxford MLST method, whereas one sequence type (ST2) was identified using the Pasteur MLST method. ANI analysis, heat map of SNP analysis, and phylogenetic tree based on core SNP revealed six clusters, and the strain classification results were consistent with these different methods. Ten clonal lineages were identified by cgMLST.

Conclusion

The CRAB strains were ST2 clones accompanied by severe resistance to commonly used antibiotics and abundant ARGs and VFGs in genotype. Strict measures should be implemented to prevent and control transmissions and infections. CgMLST and SNPs analyses showed excellent discriminatory power in homology analysis.

Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistant Acinetobacter baumannii from whole genome sequencing and gene expression

Whole genome sequencing (WGS) potentially represents a rapid approach for antimicrobial resistance genotype-to-phenotype prediction. However, the challenge still exists to predict fully minimum inhibitory concentrations (MICs) and antimicrobial susceptibility phenotypes based on WGS data. This study aimed to establish an artificial intelligence-based computational approach in predicting antimicrobial susceptibilities of multidrug-resistant Acinetobacter baumannii from WGS and gene expression data. Antimicrobial susceptibility testing (AST) was performed using the broth microdilution method for 10 antimicrobial agents. In silico multilocus sequence typing (MLST), antimicrobial resistance genes, and phylogeny based on cgSNP and cgMLST strategies were analyzed. High-throughput qPCR was performed to measure the expression level of antimicrobial resistance (AMR) genes. Most isolates exhibited a high level of resistance to most of the tested antimicrobial agents, with the majority belonging to the IC2/CC92 lineage. Phylogenetic analysis revealed undetected transmission events or local outbreaks. The percentage agreements between AMR phenotype and genotype ranged from 70.08% to 89.96%, with the coefficient of agreement (κ) extending from 0.025 and 0.881. The prediction of AST employed by deep neural network models achieved an accuracy of up to 98.64% on the testing data set. Additionally, several linear regression models demonstrated high prediction accuracy, reaching up to 86.15% within an error range of one gradient, indicating a linear relationship between certain gene expressions and the corresponding antimicrobial MICs. In conclusion, neural network-based predictions could be used as a tool for the surveillance of antimicrobial resistance in multidrug-resistant A. baumannii.

Genomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2

Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636. Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined.

Overall status of carbapenem resistance among clinical isolates of Acinetobacter baumannii: a systematic review and meta-analysis

BACKGROUND

Resistance to carbapenems, the first-line treatment for infections caused by Acinetobacter baumannii, is increasing throughout the world. The aim of the present study was to determine the global status of resistance to carbapenems in clinical isolates of this pathogen, worldwide.

METHODS

Electronic databases were searched using the appropriate keywords, including: 'Acinetobacter' 'baumannii', 'Acinetobacter baumannii' and 'A. baumannii', 'resistance', 'antibiotic resistance', 'antibiotic susceptibility', 'antimicrobial resistance', 'antimicrobial susceptibility', 'carbapenem', 'carbapenems', 'imipenem', 'meropenem' and 'doripenem'. Finally, following some exclusions, 177 studies from various countries were included in this study. The data were then subjected to a meta-analysis.

RESULTS

The average resistance rate of A. baumannii to imipenem, meropenem and doripenem was 44.7%, 59.4% and 72.7%, respectively. A high level of heterogeneity (I2 > 50%, P value < 0.05) was detected in the studies representing resistance to imipenem, meropenem and doripenem in A. baumannii isolates. Begg's and Egger's tests did not indicate publication bias (P value > 0.05).

CONCLUSIONS

The findings of the current study indicate that the overall resistance to carbapenems in clinical isolates of A. baumannii is relatively high and prevalent throughout the world. Moreover, time trend analysis showed that the resistance has increased from the year 2000 to 2023. This emphasizes the importance of conducting routine antimicrobial susceptibility testing before selecting a course of treatment, as well as monitoring and controlling antibiotic resistance patterns in A. baumannii strains, and seeking novel treatment options to lessen the emergence and spread of resistant strains and to reduce the treatment failure.

ESKAPE in China: epidemiology and characteristics of antibiotic resistance

The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.

Pathogenicity and virulence of Acinetobacter baumannii: Factors contributing to the fitness in healthcare settings and the infected host

Acinetobacter baumannii is a common cause of healthcare-associated infections and hospital outbreaks, particularly in intensive care units. Much of the success of A. baumannii relies on its genomic plasticity, which allows rapid adaptation to adversity and stress. The capacity to acquire novel antibiotic resistance determinants and the tolerance to stresses encountered in the hospital environment promote A. baumannii spread among patients and long-term contamination of the healthcare setting. This review explores virulence factors and physiological traits contributing to A. baumannii infection and adaptation to the hospital environment. Several cell-associated and secreted virulence factors involved in A. baumannii biofilm formation, cell adhesion, invasion, and persistence in the host, as well as resistance to xeric stress imposed by the healthcare settings, are illustrated to give reasons for the success of A. baumannii as a hospital pathogen.

Isolation of a blaNDM-1-positive strain in Israel predating the earliest observations from India

blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, is thought to have emerged in India, as its initial detection in 2008 was linked to this country, and subsequent retrospective surveys had so far established the earliest blaNDM-positive strains to be isolated in India in 2005. Molecular dating and analyses suggest blaNDM emerged within Acinetobacter species decades prior to 2005 on a Tn125 transposon. Despite early reports of elevated rates of carbapenem-resistant Acinetobacter species in Israel starting in the 1990s, limited molecular data are available from this location. We searched for blaNDM among Acinetobacter species isolated in Israel between 2001 and 2006. One A. junii strain, Ajun-H1-3, isolated in January 2004, carried blaNDM-1 within a Tn125-like transposon on a 49-kb plasmid, pNDM-Ajun-H1-3, making Ajun-H1-3 the earliest NDM-positive isolate observed to date. The pNDM-Ajun-H1-3 plasmid matched numerous BJ01-like NDM-positive plasmids identified from 2005 onward in Acinetobacter species as well as Enterobacterales. These results indicate the need for further retrospective work on global strain archives to shed light on the conditions favoring the emergence as well as subsequent evolution and spread of blaNDM.

IMPORTANCE

This study presents the earliest observation of blaNDM-1, isolated in a geographical region distant from where it is believed to have originated. In doing so, this study provides novel insights into the emergence and spread of blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, and its associated mobile genetic elements. It also sheds light on the conditions that foster the evolution of antimicrobial resistance, one of the greatest public health challenges we face.

Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health, particularly in intensive care units (ICUs). Here we report a three-month longitudinal genomic surveillance study conducted in a Hangzhou ICU in 2021. This followed a three-month study conducted in the same ICU in 2019, and infection prevention and control (IPC) interventions targeting patients, staff and the ICU environment. Most A. baumannii isolated in this ICU in 2021 were CRAB (80.9%; 419/518) with higher-level resistance to carbapenems. This was accompanied by the proportion of global clone 2 (GC2) isolates falling from 99.5% in 2019 to 50.8% (213/419) in 2021. The phylogenetic diversity of GC2 increased, apparently driven by regular introductions of distinct clusters in association with patients. The remaining CRAB (40.2%; 206/419) were a highly clonal population of ST164. Isolates of ST164 carried blaNDM-1 and blaOXA-23 carbapenemase genes, and exhibited higher carbapenem MIC50/MIC90 values than GC2. Comparative analysis of publicly available genomes from 26 countries (five continents) revealed that ST164 has evolved towards carbapenem resistance on multiple independent occasions. Its success in this ICU and global capacity for acquiring resistance determinants indicate that ST164 CRAB is an emerging high-risk lineage of global concern.

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.

Characterization of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure

The carbapenem-resistant Acinetobacter baumannii isolate BAL062 is a clinical reference isolate used in several recent experimental studies. It is from a ventilator-associated pneumonia (VAP) patient in an intensive care unit at the Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam in 2009. Here, BAL062 was found to belong to the B sub-lineage of global clone 2 (GC2) isolates in the previously reported outbreak (2008 and 2012) of carbapenem-resistant VAP A. baumannii at the HTD. While related sub-lineage B outbreak isolates were extensively antibiotic-resistant and carry GC2-associated genomic resistance islands, AbGRI1, AbGRI2, and AbGRI3, BAL062 has lost AbGRI3 and three aminoglycoside resistance genes, armA, aacA4, and aphA1, leading to amikacin, tobramycin and kanamycin susceptibility. The location of Tn2008VAR found in the chromosome of this sub-lineage was also corrected. Like many of the outbreak isolates, BAL062 carries the KL58 gene cluster at the capsular polysaccharide (CPS) synthesis locus and an annotation key is provided. As information about K type is important for the development of novel CPS-targeting therapies, the BAL062 K58-type CPS structure was established using NMR spectroscopy. It is most closely related to K2 and K93, sharing similar configurations and linkages between K units, and contains the rare higher monosaccharide, 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac), the 8-epimer of Pse5Ac7Ac (5,7-di-N-acetylpseudaminic acid). Inspection of publicly available A. baumannii genomes revealed a wide distribution of the KL58 locus in geographically diverse isolates belonging to several sequence types that were recovered over two decades from clinical, animal, and environmental sources.IMPORTANCEMany published experimental studies aimed at developing a clearer understanding of the pathogenicity of carbapenem-resistant Acinetobacter baumannii strains currently causing treatment failure due to extensive antibiotic resistance are undertaken using historic, laboratory-adapted isolates. However, it is ideal if not imperative that recent clinical isolates are used in such studies. The clinical reference isolate characterized here belongs to the dominant A. baumannii GC2 clone causing extensively resistant infections and has been used in various recent studies. The correlation of resistance profiles and resistance gene data is key to identifying genes available for gene knockout and complementation analyses, and we have mapped the antibiotic resistance genes to find candidates. Novel therapies, such as bacteriophage or monoclonal antibody therapies, currently under investigation as alternatives or adjuncts to antibiotic treatment to combat difficult-to-treat CRAb infections often exhibit specificity for specific structural epitopes of the capsular polysaccharide (CPS), the outer-most polysaccharide layer. Here, we have solved the structure of the CPS type found in BAL062 and other extensively resistant isolates. As consistent gene naming and annotation are important for locus identification and interpretation of experimental studies, we also have correlated automatic annotations to the standard gene names.

Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.

Handwashing sinks as reservoirs of carbapenem-resistant Acinetobacter baumannii in the intensive care unit: a prospective multicenter study

Introduction

The extent to which sinks are contaminated by carbapenem-resistant Acinetobacter baumannii (CRAB) in intensive care units (ICUs) and the association between these contaminated sinks and hospital-acquired CRAB infections during the non-cluster period remains largely unknown. Here, we performed a prospective multicenter study in 16 ICUs at 11 tertiary hospitals in Chengdu, China.

Methods

We sampled sinks, collected CRAB clinical isolates, and conducted whole-genome sequencing and analysis.

Results

A total of 789 swabs were collected from 158 sinks, and 16 CRAB isolates were recovered from 16 sinks, resulting in a contamination rate of 10.16%. Twenty-seven clinical isolates were collected during the study period. The majority (97.67%, 42/43) of the CRAB isolates belonged to ST2, and 36 (83.72%) of them had both bla OXA-23 and bla OXA-66. The 43 strains belonged to 12 clones. One certain clone caused multiple contaminations of seven sinks in one GICU. Two clones of ST2 bla OXA-23 and bla OXA-66-carrying sink strains were likely the sources of the two clusters in the two GICUs, respectively. Five ST2 bla OXA-23-carrying isolates were found to be common clones but were recovered from two hospitals.

Conclusion

The contamination rate of CRAB in handwashing sinks is high in some local ICUs, and the contaminated sinks can serve as environmental reservoirs for CRAB clusters.

Analysis of risk factors and different treatments for infections caused by carbapenem-resistant Acinetobacter baumannii in Shaanxi, China

BACKGROUND

The global threat of Carbapenem-resistant Acinetobacter baumannii (CRAB) has intensified as resistance to carbapenems continues to rise in recent decades. We aimed to explore risk factors, molecular epidemiology, and antimicrobial therapy of CRAB infection.

METHODS

The clinical data of 110 patients infected with A. baumannii from December 2021 to December 2022 were retrospectively analyzed. Patients were divided into a carbapenem-resistance group (55 patients) and carbapenem-sensitive group (CSAB; 55 patients) based on resistance to carbapenem, and the risk factors of patients infected with CRAB were analyzed. Fifty-five patients with CRAB infection who received antimicrobial therapy were divided into a combination therapy group (45 patients) and a monotherapy group (10 patients), and differences between the two groups were compared. Whole-genome sequencing analysis was performed to assess resistance genes. Phylogenetic analysis was performed to explore the characteristics of CRAB isolates.

RESULTS

Among the total 110 patients, the rate of poor prognosis in the CRAB group was 43.6% (24/55). Mechanical ventilation (odds ratio [OR] = 5.364, 95% confidence interval [CI] 1.462-19.679, P = 0.011) and puncture (OR = 19.935, 95% CI 1.261-315.031, P = 0.012) were independent risk factors for CRAB infection. Of 55 patients in the antimicrobial regimen study, 45 received combination therapy (including dual, triple, or quadruple antibiotic therapy) and 10 received monotherapy. Univariate analysis revealed significant differences between the combination group and monotherapy group for admission to the intensive care unit and wound infection (P < 0.05). The CRAB strains of 26 patients taking carbapenem-based combination therapy were mainly ST208, ST1968, and ST195, among which patients with ST1968 strains had higher 28-day mortality. Furthermore, the blaOXA-23 gene was harbored in ST1968, ST195, and ST208.

CONCLUSIONS

Mortality was significantly higher in patients infected with CRAB than with CSAB. Mechanical ventilation and puncture were independent risk factors in predicting CRAB infections. The distribution of CRAB was dominated by ST208, ST1968, and ST195, among which patients with ST1968 had higher 28-day mortality. The blaOXA-23 gene appears to be widely disseminated.

The context of blaOXA-23 gene in Iraqi carbapenem-resistant Acinetobacter baumannii isolates belonging to global clone 1 and global clone 2

BACKGROUND AND OBJECTIVES

Of the genes conferring resistance to carbapenems in Acinetobacter baumannii, the blaOXA-23 gene is the most widely found across the world. The gene carrying blaOXA-23 transposons in A. baumannii isolates of global clones GC1 and GC2 is found worldwide. Here, we examined whether transposons play a role in the dissemination of the blaOXA-23 in globally distributed clones, GC1 and GC2 A. baumannii isolates from Iraq.

MATERIALS AND METHODS

The 119 non-repetitive A. baumannii isolates including 94 recovered from clinical specimens and 25 isolates from hospital environment between September 2021 and April 2022 from different medical centers located at various regions in Baghdad, Iraq. The global clones (GC) and the genes encoding carbapenem resistance, including blaOXA-23, blaOXA-24, and blaOXA-58 were identified using multiplex PCR assays. Antibiotic susceptibility testing was performed by the Kirby-Bauer disk diffusion susceptibility method. The transposons carrying blaOXA-23 were examined using PCR mapping. In cases when carbapenem susceptible A. baumannii isolates were found, they were subjected to E test, full length sequencing of blaOXA-Ab (blaOXA-51-like) and Institut Pasteur multi-locus sequence typing scheme.

RESULTS

All but two isolates (92 clinical and 25 environmental) were identified carbapenem-resistant A. baumannii (CRAB). Of 117 CRAB isolates, 20 belong to GC1, 19 contained blaOXA-23; of them, 17 isolates harbored the blaOXA-23 located on Tn2006. Among the 46 CRAB belonging to GC2, 39 contained blaOXA-23; of them, 34 carried the blaOXA-23 located on Tn2006. The remaining GC1 and GC2 isolates, one GC1 as well as one GC2 isolate, were susceptible to imipenem, doripenem, and meropenem and considered carbapenem-susceptible A. baumannii (CSAB). Full-length sequencing of the blaOXA-Ab and MLST for the two CSAB isolates belonging to GC1 and GC2 confirmed that the GC1 isolate belongs to ST 623 and contained an allele that encodes an blaOXA-69 variant of the blaOXA-Ab while the GC2 belong to ST2 and carried an blaOXA-66 variant.

CONCLUSION

This study provides evidence for the dissemination of blaOXA-23 on the Tn2006 in CRAB isolates in Baghdad, Iraq. It appears that this transposon is widespread in GC1 and 2 isolates as in the other parts of the world. Interestingly, one GC1 and one GC2 isolate from Iraq were found to be susceptible to carbapenem while the isolates belonging to GC1 and GC2 have so far rarely been found to be susceptible to carbapenem globally.

Colorimetric Loop-Mediated Isothermal Amplification Assays Accurately Detect blaOXA-23-like and ISAba1 Genes from Acinetobacter baumannii in Pure Cultures and Spiked Human Sera

Carbapenem resistance in Acinetobacter baumannii is a critical global health threat attributed to transferrable carbapenemase genes. Carbapenemase genotyping using polymerase chain reaction (PCR) presents a challenge in resource-limited settings because of its technical requirements. This study designed new loop-mediated isothermal amplification (LAMP) primers using multiple sequence alignment-based workflows, validated the primer performance against multiple target variants in silico, and developed novel LAMP assays (LAntRN-OXA23 and LAntRN-ISAba1) to detect the transferable blaOXA-23-like carbapenemase genes and ISAba1 elements in pure cultures and A. baumannii-spiked serum samples. The designed LAMP primers bind to the conserved regions of their highly polymorphic targets, with their in silico performance comparable with other published primers. The in vitro LAMP assays (using 30 PCR-profiled A. baumannii and 10 standard multidrug-resistant gram-negative isolates) have 100% concordance with the PCR-positive clinical samples, limits of detection as low as 1 pg/µL (200 copies/µL), and specificities of 57.89-100%. Both assays produced positive results when testing DNA samples (extracted using a commercial kit) from blaOXA-23-like and ISAba1-blaOXA-51-like PCR-positive A. baumannii-spiked normal human sera (five set-ups per target). In summary, the LAMP assays accurately detected the target genes and have applications in infection management, control, and point-of-care testing in resource-limited healthcare settings.

ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics

The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.

More than just the gene: investigating expression using a non-native plasmid and host and its impact on resistance conferred by β-lactamase OXA-58 isolated from a hospital wastewater microbiome

With the escalation of hospital-acquired infections by multidrug resistant bacteria, understanding antibiotic resistance is of paramount importance. This study focuses on the β-lactamase gene, blaOXA-58, an important resistance determinant identified in a patient-facing hospital wastewater system. This study aimed to characterize the behaviour of the OXA-58 enzyme when expressed using a non-native plasmid and expression host. blaOXA-58 was cloned using a pET28a(+)/Escherichia coli BL21(DE3) expression system. Nitrocefin hydrolysis and antimicrobial susceptibility of OXA-58-producing cells were assessed against penicillin G, ampicillin, meropenem, and amoxicillin. blaOXA-58 conferred resistance to amoxicillin, penicillin G, and ampicillin, but not to meropenem. This was unexpected given OXA-58's annotation as a carbapenemase. The presence of meropenem also reduced nitrocefin hydrolysis, suggesting it acts as a competitive inhibitor of the OXA-58 enzyme. This study elucidates the phenotypic resistance conferred by an antimicrobial resistance gene (ARG) obtained from a clinically relevant setting and reveals that successful functional expression of ARGs is multifaceted. This study challenges the reliability of predicting antimicrobial resistance based solely on gene sequence alone, and serves as a reminder of the intricate interplay between genetics and structural factors in understanding resistance profiles across different host environments.

Polyvinylpyrrolidone capped silver nanoparticles enhance the autophagic clearance of Acinetobacter baumannii from human pulmonary cells

Acinetobacter baumannii, an opportunistic pathogen has shown an upsurge in its multi-drug resistant isolates. OmpA of A. baumannii induces incomplete autophagy and apoptosis in host cells. Various therapeutic alternatives are under investigation against A. baumannii. Here, the major emphasis has been laid on comparing the efficacy of AgNP with different capping agents. OmpA targeted lead, Ivermectin capped AgNP (IVM-AgNP) has been compared with the antibacterial polyvinylpyrrolidone capped AgNP (PVP-AgNP) for their role in the modulations of host autophagy. Upregulation of p62 and LC3B confirmed by real-time PCR analysis indicated an increased autophagic flux upon the treatment with AgNPs. The elongation and closure of autophagic vacuoles was also supported by upregulated Atg genes (Atg4, Atg3, Atg5) in A. baumannii infected cells after treatment with AgNP. Autophagic flux increased on treatment with PVP-AgNP as suggested by the rise in mcherryLC3B fluorescence in A549 cells treated with PVP-AgNP as compared to the GFP-LC3B of IVM-AgNP. This suggests that PVP-AgNP treatment more effectively promotes the elongation and maturation stages of autophagy by increasing autophagic flux. These results indicate that capped AgNPs have the efficiency to revert the incomplete autophagy induced by A. baumannii back to normal autophagic levels.

Whole-genome sequencing of two multidrug-resistant acinetobacter baumannii strains isolated from a neonatal intensive care unit in Egypt: a prospective cross-sectional study

BACKGROUND

Acinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium.

OBJECTIVES

This study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt.

METHODS

Following the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed.

RESULTS

Two isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them.

CONCLUSIONS

A low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.

Screening of the Pandemic Response Box library identified promising compound candidate drug combinations against extensively drug-resistant Acinetobacter baumannii

Infections caused by antimicrobial-resistant Acinetobacter baumannii pose a significant threat to human health, particularly in the context of hospital-acquired infections. As existing antibiotics lose efficacy against Acinetobacter isolates, there is an urgent need for the development of novel antimicrobial agents. In this study, we assessed 400 structurally diverse compounds from the Medicines for Malaria Pandemic Response Box for their activity against two clinical isolates of A. baumannii: A. baumannii 5075, known for its extensive drug resistance, and A. baumannii QS17-1084, obtained from an infected wound in a Thai patient. Among the compounds tested, seven from the Pathogen box exhibited inhibitory effects on the in vitro growth of A. baumannii isolates, with IC50s ≤ 48 µM for A. baumannii QS17-1084 and IC50s ≤ 17 µM for A. baumannii 5075. Notably, two of these compounds, MUT056399 and MMV1580854, shared chemical scaffolds resembling triclosan. Further investigations involving drug combinations identified five synergistic drug combinations, suggesting potential avenues for therapeutic development. The combination of MUT056399 and brilacidin against A. baumannii QS17-1084 and that of MUT056399 and eravacycline against A. baumannii 5075 showed bactericidal activity. These combinations significantly inhibited biofilm formation produced by both A. baumannii strains. Our findings highlight the drug combinations as promising candidates for further evaluation in murine wound infection models against multidrug-resistant A. baumannii. These compounds hold potential for addressing the critical need for effective antibiotics in the face of rising antimicrobial resistance.

Molecular epidemiology, microbiological features and infection control strategies for carbapenem-resistant Acinetobacter baumannii in a German burn and plastic surgery center (2020-2022)

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAB) frequently causes both healthcare-associated infections and nosocomial outbreaks in burn medicine/plastic surgery and beyond. Owing to the high antibiotic resistance, infections are difficult to treat, and patient outcomes are often compromised. The environmental persistence capability of CRAB favors its transmission in hospitals. A comprehensive analysis and understanding of CRAB epidemiology and microbiology are essential for guiding management.

METHODS

A three-year retrospective cohort study (2020-2022) was conducted in a German tertiary burn and plastic surgery center. In addition to epidemiological analyses, microbiological and molecular techniques, including whole-genome sequencing, were applied for the comprehensive examination of isolates from CRAB-positive patients.

RESULTS

During the study period, eight CRAB cases were found, corresponding to an overall incidence of 0.2 CRAB cases per 100 cases and an incidence density of 0.35 CRAB cases per 1000 patient-days. Six cases (75%) were treated in the burn intensive care unit, and four cases (50%) acquired CRAB in the hospital. Molecular analyses comprising 74 isolates supported the epidemiologic assumption that hospital acquisitions occurred within two separate clusters. In one of these clusters, environmental CRAB contamination of anesthesia equipment may have enabled transmission. Furthermore, molecular diversity of CRAB isolates within patients was observed.

CONCLUSIONS

CRAB can pose a challenge in terms of infection prevention and control, especially if cases are clustered in time and space on a ward. Our study demonstrates that high-resolution phylogenetic analysis of several bacterial isolates from single patients can greatly aid in understanding transmission chains and helps to take precision control measures.

Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne blaOXA-23

Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant threat to hospitalized patients as effective therapeutic options are scarce. Based on the genomic characteristics of the CRAB strain AB2877 harboring chromosome-borne blaOXA-23, which was isolated from the bronchoalveolar lavage fluid (BALF) of a patient in a respiratory intensive care unit (RICU), we systematically analyzed antibiotic resistance genes (ARGs) and the genetic context associated with ARGs carried by CRAB strains harboring chromosome-borne blaOXA-23 worldwide. Besides blaOXA-23, other ARGs were detected on the chromosome of the CRAB strain AB2877 belonging to ST208/1806 (Oxford MLST scheme). Several key genetic contexts associated with the ARGs were identified on the chromosome of the CRAB strain AB2877, including (1) the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph(6)-Id (2); the resistance island AbGRI3 harboring armA and mph(E)-msr(E) (3); the Tn3-like composite transposon containing blaTEM-1D and aph(3')-Ia; and (4) the structure "ISAba1-blaADC-25." The first two genetic contexts were most common in ST195/1816, followed by ST208/1806. The last two genetic contexts were found most frequently in ST208/1806, followed by ST195/1816.IMPORTANCEThe blaOXA-23 gene can be carried by plasmid or chromosome, facilitating horizontal genetic transfer and increasing carbapenem resistance in healthcare settings. In this study, we focused on the genomic characteristics of CRAB strains harboring the chromosome-borne blaOXA-23 gene, and the important genetic contexts associated with blaOXA-23 and other ARGs were identified, and their prevalent clones worldwide were determined. Notably, although the predominant clonal CRAB lineages worldwide containing the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph (6)-Id was ST195/1816, followed by ST208/1806, the CRAB strain AB2877 in our study belonged to ST208/1806. Our findings contribute to the knowledge regarding the dissemination of CRAB strains and the control of nosocomial infection.

Antibiotic resistance: a global crisis, problems and solutions

Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.

Clinical and microbiological features of a cohort of patients with Acinetobacter baumannii bloodstream infections

PURPOSE

Acinetobacter baumannii is emerging as a pathogen that is a focus of global concern due to the frequent occurrence of the strains those are extensively resistant to antibiotics. This study was aimed to analyze the clinical and microbiological characteristics of a cohort of patients with A. baumannii bloodstream infections (BSIs) in western China.

METHODS

A retrospective study of the patients at West China Hospital of Sichuan University with A. baumannii BSIs between Jan, 2018 and May, 2023 was conducted. Antimicrobial susceptibility of A. baumannii isolates was tested by microdilution broth method. Whole-genome sequencing and genetic analysis were also performed for these isolates.

RESULTS

Among the 117 patients included, longer intensive care unit stay, higher mortality, and more frequent invasive procedures and use of more than 3 classes of antibiotics were observed among the carbapenem-resistant A. baumannii (CRAB)-infected group (n = 76), compared to the carbapenem-susceptible A. baumannii (CSAB)-infected group (n = 41, all P ≤ 0.001). Twenty-four sequence types (STs) were determined for the 117 isolates, and 98.7% (75/76) of CRAB were identified as ST2. Compared to non-ST2 isolates, ST2 isolates exhibited higher antibiotic resistance, and carried more resistance and virulence genes (P < 0.05). In addition, 80 (68.4%) isolates were CRISPR-positive, showed higher antibiotic susceptibility, and harbored less resistance and virulence genes, in comparison to CRISPR-negative ones (P < 0.05). Phylogenetic clustering based on coregenome SNPs indicated a sporadic occurrence of clonal transmission.

CONCLUSION

Our findings demonstrate a high frequency of ST2 among A. baumannii causing BSIs, and high antibiotic susceptibility of non-ST2 and CRISPR-positive isolates. It is necessary to strengthen the surveillance of this pathogen.