Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database

Regional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia)

OBJECTIVES

This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenem-resistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the blaOXA-51 variant, capsule polysaccharide locus (KL) and lipooligosaccharide outer core locus (OCL) types.

METHODS

Of 336 isolates submitted to the Andalusian reference laboratory (PIRASOA; December 2017-2020), 73 were subjected to WGS (MiSeq). The following analyses were performed: bacterial identification (ribosomal MLST), carbapenemase gene detection (Resfinder 4.0), PS delineation (MLST by MLSTfinder 2.0 and cgMLST by Ridom SeqSphere+), and KL types and OCL types (Kaptive tool).

RESULTS

The carbapenemases detected were blaOXA-23 (n = 41), blaOXA-58 (n = 26), blaOXA-24 (n = 5), blaOXA-72 (n = 1) and blaNDM-1 (n = 2). The PS revealed one major ST2 clone (n = 54) and seven minor ST clones by MLST, and 41 lineages by cgMLST. Thirty-five lineages were detected only in a single hospital whereas five lineages were observed in several hospitals and provinces. blaOXA-66 was the most frequent blaOXA-51 variant and was mainly associated with the ST2 clone. Eleven KL types and 3 OCL types were assigned, with KL2 (n = 27), KL7 (n = 16) and OCL1 being the most frequent.

CONCLUSIONS

The PS of CR A. baumannii in Andalusia is characterized by a dominant ST2/blaOXA-23 clone and several lineages, showing local spread of lineages in most hospitals, and intercenter or interregional spread of a few lineages. Single-locus blaOXA-51-like typing and KL typing may be useful as complementary preliminary typing tool.

Risk and Prognostic Factors for Bloodstream Infections Due to Clonally Transmitted Acinetobacter baumannii ST2 with armA, blaOXA-23, and blaOXA-66: A Retrospective Study

Background

Multidrug-resistant Acinetobacter baumannii (MDR-AB) is a major cause of bacterial bloodstream infections (BSIs), associated with high morbidity and mortality. The risk and prognostic factors for BSIs caused by clonally transmitted A. baumannii ST2, carrying armA, blaOXA-23 and blaOXA-66, remain unclear.

Methods

We retrospectively analyzed 97 hospitalized patients with A. baumannii BSI (January 2019-May 2022). Whole-genome sequencing and bioinformatic analysis characterized the strains. Clinical data were reviewed to identify risk factors for secondary BSIs, A. baumannii BSIs with mixed infections involving extra-bloodstream pathogens, and mortality predictors.

Results

High-risk clone sequence type (ST) 2 was identified in 87 isolates (89.7%), with 86 exhibiting clonal dissemination. Carbapenems and aminoglycosides resistance occurred in 78.4% of strains, linked to armA, blaOXA-23, and blaOXA-66. Patients' median age was 56.6 years (range: 11-93), with males comprising 62.9%. Elderly patients (>65 years) accounted for 40.2%, 85.6% had hospital stays >10 days, and 84.5% had ICU admissions. Adverse outcomes were observed in 55.7% of cases. ICU admission (OR = 5.144, 95% CI: 1.290-20.511, P = 0.020) and open injury (OR = 5.998, 95% CI: 1.164-30.892, P = 0.032) were specific risk factors significantly associated with BSIs, while the presence of three or more underlying diseases (OR = 6.419, 95% CI: 2.074-19.866, P = 0.001) was significantly associated with increased mortality risk.

Conclusion

The majority of A. baumannii strains causing BSIs in this study belonged to multidrug-resistant ST2 lineage, harboring armA, blaOXA-23 and blaOXA-66. Risk factors for secondary and mixed infections included prolonged ICU stays, mechanical ventilation (≥7 days), and open injuries, while poor prognosis was linked to severe comorbidities and extended invasive ventilation. Targeted infection control strategies are critical to reducing mechanical ventilation duration and managing open injuries in high-risk patients.

Comprehensive Genome Analysis of Colistin-Only-Sensitive KPC-2 and NDM1-1-Coproducing Klebsiella pneumoniae ST11 and Acinetobacter baumannii ST2 From a Critically Ill Patient With COVID-19 in Saudi Arabia: Whole Genome Sequencing (WGS) of K. pneumoniae ST11 and A. baumannii ST2

The COVID-19 pandemic has intensified the issue of multidrug-resistant (MDR) infections, particularly in intensive care units (ICUs). This study documents the first known case of coinfection with two extensively drug-resistant (XDR) bacterial isolates in a critically ill patient with COVID-19 in Saudi Arabia. Both XDR isolates were recovered from blood and were resistant to all tested antimicrobial agents except colistin. Whole genome sequencing (WGS) revealed that the K. pneumoniae isolate KP-JZ107 had sequence type 11 (ST11) and core genome MLST (cgMLST 304742), while the A. baumannii isolate AB-JZ67 had ST2 and cgMLST 785. KP-JZ107 was found to possess the virulence plasmid KpVP-type-1, carbapenemase genes bla NDM and bla KPC , and numerous antimicrobial-resistant genes (ARGs). The AB-JZ67 isolate had several biofilm-related genes, including biofilm-associated protein (BAP), csuE, and pgaB, and multiple ARGs, including bla ADC-25, bla OXA-23, and bla OXA-66. Our findings suggest that the coexistence of KP-JZ107 and AB-JZ67 isolates may indicate their widespread presence in ICUs, requiring comprehensive surveillance studies across all hospitals.

Whole genome sequencing and genomic characteristics analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates in two hospitals in China

Nosocomial outbreaks caused by carbapenem-resistant Acinetobacter baumannii (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The A. baumannii isolates were mainly collected from the ICU and isolated from the sputum (71.43%, 15/21), followed by urine (14.29%, 3/21). Twenty-one A. baumannii strains possessed a multidrug-resistant (MDR) profile, and whole-genome sequencing showed that they all carried blaOXA-23. Based on the Pasteur multilocus sequence typing (MLST) scheme, all strains were typed into a sequence type 2 (ST2). Based on the Oxford MLST scheme, six strains belonged to ST540, three of which were ST208, and four strains were assigned to ST784. Kaptive showed most of the strains (38.10%, 8/21) contained KL93. As for the lipoolygosaccharide (OC locus) type, OCL1c and OCL1d were identified, accounting for 33.33% (7/21) and 66.67% (14/21), respectively. Based on the BacWGSTdb server, we found that the strains belonging to ST540 and ST784 were all collected from China. However, the ST938 strains were isolated from Malaysia and Thailand. Comparative genomics analysis showed that the AB10 strain had a closed relationship with SXAB10-SXAB13 strains, suggesting the transmission happened in these two hospitals and other hospital in China. In addition, the 4300STDY7045869 strain, which was collected from Thailand, possessed near genetic relationship with our isolates in this study, suggesting the possible spread among various countries. Additionally, 3-237 single nucleotide polymorphisms were observed among these strains. In conclusion, this study conducted a genome-based study for A. baumannii strains collected from two hospitals in China and revealed their epidemiological and molecular features. Clone spreading occurred in these two hospitals. Hence, there is an urgent need for increased surveillance in hospitals and other clinical settings to prevent and control CRAB spreading.

A panel of genotypically and phenotypically diverse clinical Acinetobacter baumannii strains for novel antibiotic development

Acinetobacter baumannii is one of the most important pathogens worldwide. The intrinsic and acquired resistance of A. baumannii, coupled with the slow pace of novel antimicrobial drug development, poses an unprecedented and enormous challenge to clinical anti-infective therapy of A. baumannii. Recent studies in the field of pathogenicity, antibiotic resistance, and biofilms of A. baumannii have focused on the model strains, including ATCC 17978, ATCC 19606, and AB5075. However, these model strains represent only a limited portion of the heterogeneity in A. baumannii. Furthermore, variants of these model strains have emerged that show significant diversity not only at the genotypic level but also reflected in differences at the phenotypic levels of capsule, virulence, pathogenicity, and antibiotic resistance. Research on A. baumannii, a key pathogen, would benefit from a standardized approach, which characterizes heterogeneous strains in order to facilitate rapid diagnosis, discovery of new therapeutic targets, and efficacy assessment. Our study provides and describes a standardized, genomically and phenotypically heterogeneous panel of 45 different A. baumannii strains for the research community. In addition, we performed comparative analyses of several phenotypes of this panel. We found that the sequence type 2 (ST2) group showed significantly higher rates of resistance, lower fitness cost for adaptation, and yet less biofilm formation. The Macrocolony type E (MTE, flat center and wavy edge phenotype reported in the literature) group showed a less clear correlation of resistance rates and growth rate, but was observed to produce more biofilms. Our study sheds light on the complex interplay of resistance fitness and biofilm formation within distinct strains, offering insights crucial for combating A. baumannii infection.

IMPORTANCE

Acinetobacter baumannii is globally notorious, and in an effort to combat the spread of such pathogens, several emerging candidate therapies have already surfaced. However, the strains used to test these therapies vary across studies (the sources and numbers of test strains are varied and often very large, with little heterogeneity). The variation complicates the studies. Furthermore, the limited standardized resources of A. baumannii strains have greatly restricted the research on the physiology, pathogenicity, and antibiotic resistance. Therefore, it is crucial for the research community to acquire a standardized and heterogeneous panel of A. baumannii. Our study meticulously selected 45 diverse A. baumannii strains from a total of 2,197 clinical isolates collected from 64 different hospitals across 27 provinces in China, providing a scientific reference for the research community. This assistance will significantly facilitate scientific exchange in academic research.

Genotypic and phenotypic characteristics of Acinetobacter baumannii isolates from the people's hospital of Qingyang City, Gansu province

BACKGROUND

Acinetobacter baumannii (A. baumannii) is a common opportunistic pathogen in hospitals that causes nosocomial infection. In order to understand the phenotypic and genotypic characteristics of A. baumannii isolates, we sequenced and analyzed 62 A. baumannii isolates from a hospital in Gansu province.

RESULTS

Non-repeated 62 A. baumannii isolates were collected from August 2015 to November 2021. Most isolates (56/62) were resistant to multiple drugs. All the 62 A. baumannii isolates were resistant to aztreonam and contained blaADC-25 gene which exists only on chromosome contigs. The 62 isolates in this study were not clustered in a single clade, but were dispersed among multiple clades in the common genome. Seven sequence types were identified by Multilocus sequence type (MLST) analysis and most isolates (52/62) belonged to ST2. The plasmids were grouped into 11 clusters by MOB-suite.

CONCLUSIONS

This study furthers the understanding of A. baumannii antimicrobial-resistant genotypes, and may aid in prevention and control nosocomial infection caused by drug-resistant A. baumannii.

The Distribution of Carbapenem-Resistant Acinetobacter Species and High Prevalence of CC92 OXA-23-Producing Acinetobacter Baumannii in Community Hospitals in South Korea

Background

Clinical isolates of Acinetobacter species in South Korea are continuously exhibiting high rates of antimicrobial resistance to carbapenems, indicating that there are public health concerns among both healthcare-associated infections and community-associated infections. The aim of this study was to describe the prevalence and characteristics of carbapenem-resistant Acinetobacter isolates originating from community hospitals.

Materials and Methods

A total of 817 non-duplicated Acinetobacter species were isolated from December 2022 to July 2023 at long-term care facilities and general hospitals in 16 regions geographically distributed throughout South Korea. Bacterial identification and antimicrobial susceptibility testing were performed using the VITEK-2 system. The bacteria were identified as Acinetobacter baumannii by blaOXA-51 PCR and as non-baumannii Acinetobacter species by rpoB sequence analysis. The carbapenem resistance genes (OXA-23, OXA-48, OXA-58, IMP, VIM, NDM, GES, and KPC) were identified via PCR and sequencing. The genetic relatedness of carbapenem-resistant A. baumannii (CRAB) isolates was assessed by multilocus sequence typing.

Results

A total of 659 A. baumannii and 158 non-baumannii Acinetobacter isolates, comprising 19 different species, were identified in all 16 regions. The carbapenem resistance rate was 87.4% (n=576) for the A. baumannii isolates, and all the strains produced blaOXA-23. For non-baumannii Acinetobacter, the rate of carbapenem resistance was 8.9% (n=14); this resistance was primarily caused by blaOXA-23 (n=9), followed by blaNDM-1 (n=3) and blaVIM-2 (n=2). Of the 576 CRAB isolates, clonal complex 92 (CC92) was the predominant genotypes, followed by sequence type 229 (ST229), ST373, ST397, ST447, and ST620.

Conclusion

Our results showed the distribution of Acinetobacter species and showed that CC92 CRAB clinical isolates with widespread production of blaOXA-23 were predominant in community hospitals. Our findings suggest that there is a need for urgent and effective methods to reduce carbapenem resistance in A. baumannii in South Korea.

Co-production of metallo-β-lactamase and OXA-type β-lactamases in carbapenem-resistant Acinetobacter baumannii clinical isolates in North East India

Carbapenem-resistant Acinetobacter baumannii poses a significant threat to public health globally, especially due to its ability to produce multiple carbapenemases, leading to treatment challenges. This study aimed to investigate the antibiotic resistance pattern of carbapenem-resistant A. baumannii isolates collected from different clinical settings in North East India, focusing on their genotypic and phenotypic resistance profiles. A total of 172 multidrug-resistant A. baumannii isolates were collected and subjected to antibiotic susceptibility test using the Kirby-Bauer disk diffusion method. Various phenotypic tests were performed to detect extended-spectrum β-lactamase (ESBL), metallo-β-lactamase (MBL), class C AmpC β-lactamase (AmpC), and carbapenem hydrolyzing class D β-lactamase (CHDL) production among the isolates. Overexpression of carbapenemase and cephalosporinase genes was detected among the isolates through both phenotypic and genotypic investigation. The antibiotic resistance profile of the isolates revealed that all were multidrug-resistant; 25% were extensively drug-resistant, 9.30% were pan-drug-resistant, whereas 91.27% were resistant to carbapenems. In the genotypic investigation, 80.81% of isolates were reported harbouring at least one metallo-β-lactamase encoding gene, with blaNDM being the most prevalent at 70.34%, followed by blaIMP at 51.16% of isolates. Regarding class D carbapenemases, blaOXA-51 and blaOXA-23 genes were detected in all the tested isolates, while blaOXA-24, blaOXA-48, and blaOXA-58 were found in 15.11%, 6.97%, and 1.74% isolates respectively. Further analysis showed that 31.97% of isolates co-harboured ESBL, MBL, AmpC, and CHDL genes, while 31.39% of isolates co-harboured ESBL, MBL, and CHDL genes with or without ISAba1 leading to extensively drug-resistant or pan drug-resistant phenotypes. This study highlights the complex genetic profile and antimicrobial-resistant pattern of the isolates circulating in North East India, emphasizing the urgent need for effective infection control measures and the development of alternative treatment strategies to combat these challenging pathogens.

Machine learning and feature extraction for rapid antimicrobial resistance prediction of Acinetobacter baumannii from whole-genome sequencing data

Background

Whole-genome sequencing (WGS) has contributed significantly to advancements in machine learning methods for predicting antimicrobial resistance (AMR). However, the comparisons of different methods for AMR prediction without requiring prior knowledge of resistance remains to be conducted.

Methods

We aimed to predict the minimum inhibitory concentrations (MICs) of 13 antimicrobial agents against Acinetobacter baumannii using three machine learning algorithms (random forest, support vector machine, and XGBoost) combined with k-mer features extracted from WGS data.

Results

A cohort of 339 isolates was used for model construction. The average essential agreement and category agreement of the best models exceeded 90.90% (95%CI, 89.03-92.77%) and 95.29% (95%CI, 94.91-95.67%), respectively; the exceptions being levofloxacin, minocycline and imipenem. The very major error rates ranged from 0.0 to 5.71%. We applied feature selection pipelines to extract the top-ranked 11-mers to optimise training time and computing resources. This approach slightly improved the prediction performance and enabled us to obtain prediction results within 10 min. Notably, when employing these top-ranked 11-mers in an independent test dataset (120 isolates), we achieved an average accuracy of 0.96.

Conclusion

Our study is the first to demonstrate that AMR prediction for A. baumannii using machine learning methods based on k-mer features has competitive performance over traditional workflows; hence, sequence-based AMR prediction and its application could be further promoted. The k-mer-based workflow developed in this study demonstrated high recall/sensitivity and specificity, making it a dependable tool for MIC prediction in clinical settings.

Carbapenemase genes distribution in clonal lineages of Acinetobacter baumannii: a comprehensive study on plasmids and chromosomes

Background

The global spread of plasmids carrying carbapenemase genes within carbapenem resistant Acinetobacter baumannii (CRAB) strains poses a worldwide public health issue. In this study, we conducted a comprehensive genetic analysis of plasmids and chromosomes harboring the major carbapenemase genes (bla NDM, bla KPC, bla VIM, bla IMP, bla GES, bla OXA-58-like, bla OXA-24/40-like, bla OXA-143-like, and bla OXA-23-like) in CRAB strains using bioinformatic tools.

Methods

We retrieved plasmids and chromosomes carrying the major carbapenemase genes from GenBank. The size, replicon type, and conjugal apparatus of the plasmids were also determined. Furthermore, allele types, co-existence of other antimicrobial resistance genes alongside carbapenemases in plasmids or chromosomes, co-occurrence of carbapenemase genes, gene repetition, and sequence types (ST) of whole genomes were characterized.

Results

The database contained 113 plasmids and 38 chromosomes harboring carbapenemase genes. This investigation revealed that bla NDM and bla OXA-58-like were the predominant allele types in both the plasmids and chromosomes. Nine (7.96%) plasmids with bla NDM-1 were potentially conjugative. The most common replicon types of the plasmids were R3-T1, R3-T8, R3-T2, R3-T23, and RP-T1. The analysis revealed that bla NDM-1 and bla OXA-58-like genes possessed the highest variety of co-existence with other antibiotic resistance genes. The co-occurrence of dual carbapenemases was identified in 12 plasmids and 19 chromosomes. Carbapenemase gene repetitions were identified in 10 plasmids and one chromosome. Circular alignment revealed that the plasmids carrying the co-occurrence of bla NDM-1 and bla OXA-58 were more homogeneous. However, there was heterogeneity in certain regions of these plasmids. According to the minimum spanning tree (MST) results, the majority of the plasmids belonged to the genomes of ST2Pas, ST1Pas, ST422Pas, ST622Pas, and ST85Pas.

Conclusion

A. baumannii appears to have a strong ability for genome plasticity to incorporate carbapenemase genes on its plasmids and chromosomes to develop resistance against carbapenems. Mobilizable plasmids harboring carbapenemases significantly contribute to the dissemination of these genes. The genetic structure of the plasmids revealed a strong associations of class I integrons, ISAba-like structures, Tn4401 elements, and aac (6')-Ib with carbapenemases. Furthermore, gene repetition may also be associated with carbapenem heteroresistance.