Emergence of carbapenem-resistant Acinetobacter baumannii ST787 in clinical isolates from blood in a tertiary teaching hospital in Northern Taiwan

Isolation and Characterization of a Novel Siphoviridae Phage, vB_AbaS_TCUP2199, Infecting Multidrug-Resistant Acinetobacter baumannii

Multidrug-resistant Acinetobacter baumannii (MDRAB) is a pathogen recognized as antimicrobial-resistant bacteria involved in healthcare-associated infections. Resistance to antibiotics has made alternative therapies necessary. Bacteriophage therapy is considered a potential solution to treat MDRAB. In this study, we isolated and characterized the phage vB_AbaS_TCUP2199 (TCUP2199), which can infect MDRAB. Morphological analysis revealed that TCUP2199 belongs to the Siphoviridae family. TCUP2199 has a wide host range, can adsorb rapidly (68.28% in 2 min), and has a burst size of 196 PFU/cell. At least 16 distinct structural proteins were visualized by SDS polyacrylamide gel electrophoresis. A stability test showed that TCUP2199 was stable at 37 °C and pH 7. Genome analysis of TCUP2199 showed that it consists of a double-stranded DNA genome of 79,572 bp with a G+C content of 40.39%, which contains 98 putative open reading frames, none of which is closely related to the bacteriophage genome sequence that was found in the public database. TCUP2199 shows similarity in genomic organization and putative packaging mechanism with Achromobacter phage JWF and Pseudoalteromonas phage KB12-38 based on protein BLAST and phylogenetic analysis. Because of those unique characteristics, we consider TCUP2199 to be a novel phage that is suitable for inclusion in a phage cocktail to treat A. baumannii infection.

Epidemiological Molecular Analysis of Acinetobacter baumannii isolates using a multilocus sequencing typing and Global lineage

The Multilocus sequence typing MLST method was used to recognize outbreaks of hospitals distinct clonal lineages of A. baumannii; these schemes appeared to provide largely concordant classifications that have been tools to evaluate the population structures of bacterial pathogens. One hundred fifty samples were collected from different specimens of patients within Baghdad hospitals (blood 40%, CSF 5%, urine 5%) between July 2019 to February 2020. Then identification all isolated as phenotypic detection and performed using PCR amplification of 16srRNA and blaOXA-51-like as genotypic detections. According to clinical and laboratory standards institute (CLSI) guidelines, Susceptibility testing was performed. Clonally analysis was performed by global lineage ICs correlated with multilocus sequence typing (MLST) when our data showed a very high rate of antimicrobial resistance in all hospital isolates, especially against colistin (8%) which determined the PDR isolates from other types also recorded 70% of isolates standing for carbapenems antibiotics (IMI 32%, MER70%& DOR 64%). Then already clustered into four groups according to multiplex PCR for two groups of three genes (ompA, csuE & blaOXA-51-like) where IC II was predominant in Iraq but in our strains founding ICI (38%) more prevalence one followed by IC0 (26%) then ICII and ICIII (20% &16% respectively). MLST used for detected the common sequence types (STs) of our selected 8 A. baumannii strains (IC0/A11, ICI/A6,48, ICII/A33,50,19 and ICIII/A1,36) were performed by using 7 housekeeping genes than were submitted in the MLST Pasteur scheme dataset (ID 5098, 5099, 5100, 5101, 5102, 5103, 5482 & 5483) followed by statistical eBurst analysis was done to study Clonal complexes (CCs). Identified 5 new STs (8, 444, 346, 1587 & 621) within Iraq and new one ST (1830) worldwide.

Mechanism Underlying the Role of LuxR Family Transcriptional Regulator abaR in Biofilm Formation by Acinetobacter baumannii

Our study attempted to explore the mechanism underlying the role of LuxR family transcriptional regulator abaR in biofilm formation by Acinetobacter baumannii. The abaR gene was knocked out in ATCC 17978 strain using homologous recombination method. The growth curve and biofilm formation were measured in the wild type and abaR gene knockdown strains. Transcriptome sequencing was performed in the wild type and abaR gene knockdown strains following 8 h of culture. The growth curve in the abaR gene knockdown strain was similar to that of the wild-type strain. Biofilm formation significantly declined in the abaR gene knockdown strain at 8 and 48 h after culture. A total of 137 differentially expressed genes (DEGs) were obtained including 20 downregulated DEGs and 117 upregulated DEGs. Genes with differential expression were closely related to viral procapsid maturation (GO:0046797), acetoin catabolism (GO:0045150), carbon metabolism (ko01200), and the glycolysis/gluconeogenesis (ko00010)-related pathways. The results of the eight verified expression DEGs were consistent with the results predicted by bioinformatics. AbaR gene knockdown significantly affected biofilm formation by A. baumannii ATCC 17978 strain. The glycolysis/gluconeogenesis pathways were significantly dysregulated and induced by abaR gene knockdown in A. baumannii.

In Vitro and In Vivo Activity of AS101 against Carbapenem-Resistant Acinetobacter baumannii

The increasing trend of carbapenem-resistant Acinetobacter baumannii (CRAB) worldwide has become a concern, limiting therapeutic alternatives and increasing morbidity and mortality rates. The immunomodulation agent ammonium trichloro (dioxoethylene-O,O′-) tellurate (AS101) was repurposed as an antimicrobial agent against CRAB. Between 2016 and 2018, 27 CRAB clinical isolates were collected in Taiwan. The in vitro antibacterial activities of AS101 were evaluated using broth microdilution, time-kill assay, reactive oxygen species (ROS) detection and electron microscopy. In vivo effectiveness was assessed using a sepsis mouse infection model. The MIC range of AS101 for 27 CRAB isolates was from 0.5 to 32 µg/mL, which is below its 50% cytotoxicity (approximately 150 µg/mL). Bactericidal activity was confirmed using a time-kill assay. The antibacterial mechanism of AS101 was the accumulation of the ROS and the disruption of the cell membrane, which, in turn, results in cell death. The carbapenemase-producing A. baumannii mouse sepsis model showed that AS101 was a better therapeutic effect than colistin. The mice survival rate after 120 h was 33% (4/12) in the colistin-treated group and 58% (7/12) in the high-dose AS101 (3.33 mg/kg/day) group. Furthermore, high-dose AS101 significantly decreased bacterial population in the liver, kidney and spleen (all p < 0.001). These findings support the concept that AS101 is an ideal candidate for further testing in future studies.

Rapid typing of carbapenem-resistant Acinetobacter baumannii and Acinetobacter nosocomialis by multiplex Pan- and OXA-PCR assays

Introduction. Outbreaks of carbapenem-resistant A. baumannii and A. nosocomialis have occurred worldwide in healthcare settings. Rapid and reliable molecular typing of bacterial isolates is vital for the effective surveillance of institutional outbreaks. The Pan-PCR and OXA-PCR assays are two multiplex PCR-based assays for the molecular typing of Acinetobacter species.Gap statement. However, few studies have investigated the discriminatory power of two multiplex PCR assays in in the genotyping of Acinetobacter species.Aim. We aimed to evaluate the efficacies of the Pan-PCR and OXA-PCR assays for molecular typing of A. baumannii and A. nosocomialis.Methodology. A total of 105 carbapenem-resistant A. baumannii isolates (CRABs) and 93 carbapenem-resistant A. nosocomialis isolates (CRANs) obtained from blood cultures were used for molecular typing by the Pan-PCR and OXA-PCR assays and two multilocus sequence typing (MLST) schemes.Results. The isolates were individually divided into 12 and 21 different sequence types via the Pasteur and Oxford MLST schemes, respectively. Additionally, these isolates were distinguished into 18 different types by the Pan-PCR and OXA-PCR assays. The results of the Pan-PCR and OXA-PCR assays distinguished CRABs and CRANs with a sensitivity of 98.13 % and a specificity of 100 %.Conclusion. The Pan-PCR and OXA-PCR assays are promising alternative methods for rapid molecular typing of CRABs and CRANs in a routine laboratory setting.

Molecular characterization & epidemiology of carbapenem-resistant Acinetobacter baumannii collected across India

Background & objectives

Acinetobacter baumannii is an opportunistic pathogen responsible for causing nosocomial infections. A. baumannii develops resistance to various antimicrobial agents including carbapenems, thereby complicating the treatment. This study was performed to characterize the isolates for the presence of various β-lactamases encoding genes and to type the isolates to compare our clones with the existing international clones across five centres in India.

Methods

A total 75 non-repetitive clinical isolates of A. baumannii from five different centres were included in this study. All the isolates were confirmed as A. baumannii by bl a_OXA-51-likePCR. Multiplex PCR was performed to identify the presence of extended spectrum β-lactamases (ESBL) and carbapenemases. Multilocus sequence typing was performed to find the sequence type (ST) of the isolates. e-BURST analysis was done to assign each ST into respective clonal complex.

Results

bla_OXA-51-likewas present in all the 75 isolates. The predominant Class D carbapenemase was bla_OXA-23-likefollowed by Class B carbapenemase, bla_NDM-like. Class A carbapenemase was not observed. bla_PER-likewas the predominant extended spectrum β-lactamase. ST-848, ST-451 and ST-195 were the most common STs. Eight-novel STs were identified. e-BURST analysis showed that the 75 A. baumannii isolates were clustered into seven clonal complexes and four singletons, of which, clonal complex 208 was the largest.

Interpretation & conclusions

Most of the isolates were grouped under clonal complex 208 which belongs to the international clonal lineage 2. High occurrence of ST-848 carrying bla_OXA-23-likegene suggested that ST-848 could be an emerging lineage spreading carbapenem resistance in India.

Acinetobacter baumannii and methicillin-resistant Staphylococcus aureus in long-term care facilities in eastern Taiwan

Objective:

The prevention of infections is crucial in long-term care programs. Investigations of the occurrence and sources of pathogens in long-term care facilities (LTCFs) are still lacking, especially in eastern Taiwan. In this study, we conducted a surveillance of two common pathogens, Acinetobacter baumannii (AB) and methicillin-resistant Staphylococcus aureus (MRSA), in LTCFs in Hualien.

Materials and Methods:

Pathogenic assays including isolation, identification, and antimicrobial susceptibility tests were conducted for AB and MRSA at LTCFs in Eastern Taiwan. Staphylococcal cassette chromosome mec typing assays were done to understand the relatedness of clonal strains of MRSA.

Results:

All AB-positive samples in the LTCFs were mainly from water-rich samples and were drug susceptible. Our data indicated that the AB strains from LTCFs were similar to those from Puzi River watersheds in Taiwan, which were not drug resistant to commonly used antibiotics. On the other hand, the drug resistance analysis of MRSA indicated that the genotypes from the LTCFs were similar to those from nearby hospitals. Eight strains of MRSA were isolated from four LTCFs, of which five were identified as hospital-acquired strains according to SSCmed typing assays.

Conclusion:

These findings suggest that MRSA in LTCFs might propagate from hospitals and could be transmitted between hospitals and LTCFs. Health authorities should be aware of this risk. The long-term follow-up of MRSA is recommended in local medical institutions as well as in LTCFs for correlative analysis.

In vitro activities of cefiderocol, ceftolozane/tazobactam, ceftazidime/avibactam and other comparative drugs against imipenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, and Stenotrophomonas maltophilia, all associated with bloodstream infections in Taiwan

Objectives

We investigated the in vitro activities of cefiderocol, ceftazidime/avibactam, ceftolozane/tazobactam and other related drugs against imipenem-resistant Pseudomonas aeruginosa, imipenem-resistant Acinetobacter baumannii and Stenotrophomonas maltophilia isolates.

Methods

Non-duplicated bacteraemia isolates (n = 300) of imipenem-resistant P. aeruginosa (n = 100), imipenem-resistant A. baumannii (n = 100) and S. maltophilia (n = 100) were evaluated. Imipenem-resistant P. aeruginosa and imipenem-resistant A. baumannii isolates were defined as isolates exhibiting imipenem MIC ≥8 mg/L, as determined using the VITEK 2 system. The MICs of 11 other antimicrobial agents for the isolates were determined by the broth microdilution method. Iron-depleted CAMHB was used to determine the MICs of cefiderocol.

Results

The rates of colistin resistance of imipenem-resistant P. aeruginosa and imipenem-resistant A. baumannii were 5% and 10%, respectively. The MIC90 values of cefiderocol, ceftolozane/tazobactam, ceftazidime/avibactam, tigecycline and colistin were as follows: imipenem-resistant P. aeruginosa: 1, 4, 16, >4 and 2 mg/L; imipenem-resistant A. baumannii: 8, >64, >64, 4 and 2 mg/L; and S. maltophilia: 0.25, >64, >64, 2 and >8 mg/L, respectively. For imipenem-resistant A. baumannii isolates, the MICs of cefiderocol, ceftolozane/tazobactam and ceftazidime/avibactam were ≤4 mg/L for 88%, 8% and 1% of the isolates, respectively. Cefiderocol MICs were ≤4 mg/L for the five colistin-resistant imipenem-resistant P. aeruginosa isolates and 70% of the 10 colistin-resistant imipenem-resistant A. baumannii isolates.

Conclusions

Cefiderocol exhibited more potent in vitro activity than ceftolozane/tazobactam and ceftazidime/avibactam against imipenem-resistant P. aeruginosa, imipenem-resistant A. baumannii and S. maltophilia isolates.

Clonal relationship and the association of the ST218 strain harboring blaOXA-72 gene to mortality in carbapenem-resistant Acinetobacter baumannii bacteremia

BACKGROUND/PURPOSE

In 2017, the World Health Organization categorized carbapenem-resistant Acinetobacter baumannii (CRAB) as a priority 1, critical antibiotic-resistant bacteria. This study analyzed the clinical outcomes and investigated the molecular epidemiology of CRAB bacteremia in a medical center in Northern Taiwan.

METHODS

We collected 62 blood isolates from patients with CRAB bacteremia from January 2014 to December 2015 at MacKay Memorial Hospital and determined the clonal relationship using the PCR-based technique for molecular epidemiology. Medical charts were reviewed for clinical outcomes.

RESULTS

Fifty-six isolates harbored the bla_OXA-51-like and bla_OXA-23-like carbapenemase genes, 4 isolates harbor the bla_OXA-51-like and bla_OXA-24-like carbapenemase genes and 2 isolates harbored only the bla_OXA-51-like gene. After sequencing, all four isolates of bla_OXA-24-like carbapenemase gene were confirmed to be isolates of bla_OXA-72 carbapenemase genes. In multivariate analysis in the 60 patients, the independent mortality risk factors of CRAB bacteremia included ≥65 years (elderly) (Odds ratio, 4.04, 95% CI, 1.10-14.83, p = 0.035), chronic kidney disease (4.36, 1.14-16.72, p = 0.032). Isolates harboring the bla_OXA-72 gene had the same sequence type (ST218) and PFGE pulsotype raising the possibility of intra-hospital transmission, and all infected patients died.

CONCLUSION

This study showed the clonal relationship of isolates harboring the carbapenemase gene in CRAB bacteremia. Patients with the ST218 strain harboring bla_OXA-72 gene had high mortality. This warrants further research to determine the mechanism of virulence and risk factors in order to reduce mortality.

In vitro activity of ceftazidime-avibactam, ceftolozane-tazobactam, and other comparable agents against clinically important Gram-negative bacilli: results from the 2017 Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART)

Objectives

We investigated the in vitro antimicrobial susceptibilities of clinically important Gram-negative bacteria (GNB) from 16 major teaching hospitals in Taiwan in 2017.

Materials and methods

Escherichia coli (n=686) and Klebsiella pneumoniae bloodstream isolates (n=673), non-typhoid Salmonella (NTS; n=221) from various sources, Shigella species (n=21) from fecal samples, and Neisseria gonorrhoeae (n=129) from the genitourinary tract were collected. Antibiotic minimum inhibitory concentrations (MICs) were determined using the broth microdilution method. Alleles encoding K. pneumoniae carbapenemases (KPCs), New Delhi metallo-β-lactamases (NDMs), Verona integron-encoded metallo-β-lactamase, imipenemase, _OXA-48-like, and mcr-1-5 genes were detected by molecular methods in Enterobacteriaceae isolates.

Results

Five (0.7%) E. coli isolates harbored mcr-1 alleles. Twenty-four (3.6%), seven (1.0%), four (0.6%), and one (0.15%) K. pneumoniae isolates contained bla_KPC, bla_OXA-48-like, mcr-1, and bla_NDM, respectively. Three (1.4%) NTS and no Shigella isolates harbored mcr-1 genes. Seventy-one (10.5%) K. pneumoniae isolates displayed non-susceptibility (NS) to carbapenem agent(s). Phenotypically extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates showed significantly higher rates of ertapenem, tigecycline, and ceftolozane–tazobactam (CLZ– TAZ) NS (40.2%, 16.3%, and 71%–80%, respectively) than E. coli isolates exhibiting ESBL phenotypes (5.4%, 0.7%, and 18%–28%, respectively). All phenotypically ESBL-producing E. coli isolates were ceftazidime–avibactam (CAZ–AVB) susceptible. Two (8.3%) KPC-producing K. pneumoniae isolates showed CAZ–AVB NS. Hospital-acquired K. pneumoniae isolates were significantly less susceptible to ertapenem and CLZ–TAZ than hospital-acquired E. coli isolates.

Conclusion

Third-generation cephalosporins remain the optimal choice for treating NTS, Shigella, and gonococcal infections in Taiwan. Hospital-acquired and phenotypically ESBL-producing K. pneumoniae are a heavy resistance burden in Taiwan.

Prevalence of different carbapenemase genes among carbapenem-resistant Acinetobacter baumannii blood isolates in Taiwan

Background

Although the prevalence of the carbapenem-resistant A. baumannii (CRAB) has increased in Taiwan, few studies have elucidated the prevalence of different carbapenemase genes in Taiwan. The first objective of this study was to identify the types and prevalence of different carbapenemase genes, and the second objective was to determine the carbapenem antimicrobial susceptibility of carbapenemase producing isolates.

Methods

In total, 269 CRAB blood isolates from four medical centres in Taiwan from 1/1/2009 to 31/12/2013 were analysed. Antimicrobial susceptibilities were determined using the Vitek 2 system. Carbapenemase genes were identified by polymerase chain reaction (PCR) and sequencing. Pulsed-field gel electrophoresis (PFGE) was used to identify the different pulsotypes.

Results

All 269 CRAB isolates had the bla_OXA-51-like gene, while 237 (88.1%) had the bla_OXA-23-like gene, and 11 (4.09%) had the bla_OXA-24-like gene. Twenty-one CRAB isolates (7.81%) contained only the bla_OXA-51-like gene. None of the isolates had the bla_OXA-58-like gene or the metallo-β-lactamases (MBL)-encoding genes. In 28.69% of isolates with the bla_OXA-23-like gene and 90.91% of isolates with the bla_OXA-24-like gene, the minimum inhibitory concentrations (MICs) for imipenem were 64 mg/L or more. In 37.55% of isolates with the bla_OXA-23-like gene and 100% of isolates with the bla_OXA-24-like gene, meropenem MICs were 64 mg/L or more. PFGE analyses indicated that six highly similar genomes which harbored the bla_OXA-24-like gene came from three different medical centres.

Conclusion

Our study determined the prevalence of CRAB, the types and prevalence of carbapenemase genes, carbapenem susceptibility among CRAB isolates, and documented that the bla_OXA-24-like gene had greater resistance to carbapenem than the bla_OXA-23-like gene. We also demonstrated inter-hospital transmission of the highly resistant bla_OXA-24-like gene.