Investigation of carbapenem-resistant Acinetobacter baumannii isolates in a district hospital in Taiwan

WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

Background

Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated.

Results

In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by bla_ADC.25 (38.6%) conferring resistance to cephalosporin, bla_OXA-23 (29%) and the bla_OXA-66 variant of the intrinsic bla_OXA-51-likes (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. bla_TEM variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic bla_OXA-51 carbapenemase gene, bla_OXA-510 and bla_ADC-25 genes were found in isolates obtained from dried milk samples.

Conclusion

The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02270-7.

Molecular Characterization and Antibiotic Susceptibility Pattern of Acinetobacter Baumannii Isolated in Intensive Care Unit Patients in Al-Hassa, Kingdom of Saudi Arabia

Background:

Acinetobacter baumannii, is an emerging nosocomial multidrug resistance pathogen with the rapid spread of clones being reported in health-care settings and hospitals worldwide. Carbapenem resistance in this bacterium has been attributed to D OXA β-lactamases with OXA-51-like β-lactamase, being present in all A. baumannii isolate. The present study looks into the antibiotics susceptibility and molecular characterization of clinical A. baumannii isolates from Intensive Care Unit (ICU) samples in Al-Hofuf, South-eastern region of Saudi Arabia.

Materials and Methods:

Eleven strains of ICU A. baumanni i isolates were used for the investigation. Bacteria isolation was by basic microbiological techniques. Organisms identification and antibiogram susceptibility testing was by the BioMerieux VITEK 2 compact automated system (BioMerieux, Marcy I'Etoile France), according to the manufacturers guidelines. Confirmation of A. baumannii was by the presence of the OX-51 gene, also, carbapenemase encoding resistant genesbla_OXA-23, bla_OXA-40, and bla_OXA-51, were analyzed using multiplex PCR. The Student's t test was used to analyze the obtained data for between group comparisons with statistically significance level set at P < 0.05.

Results:

Eight of the isolates were confirmed to be A. baumannii. Five of which were resistant to the carbapenems against which they had been tested. One isolate was resistant to tigecycline, whereas three tested intermediate to the drug. OXA-23 was detected in isolates 1, 4, 5, 6, and 7.

Conclusion:

It can, therefore, be concluded that the probable predominate carbapenems resistant genes in ICU isolates from the present investigation, are those associated with OXA-23.

Molecular characteristics of carbapenem-resistant gram-negative bacteria in southern China

A total of 368 nonreplicate gram-negative bacteria with resistance to imipenem or meropenem were collected to search for carbapenemase genes, class 1 integrons, and insertion sequence with common region 1 (ISCR1). The carbapenemase genes blaIMP-4, blaKPC-2, and blaNDM-1 were found in two Enterobacteriaceae and seven Pseudomonas aeruginosa isolates, nine Klebsiella pneumoniae isolates, and seven Enterobacteriaceae and two Acinetobacter spp. isolates. The class D OXA-type carbapenemase genes blaOXA-23-like, blaOXA-24-like, blaOXA-58, and blaOXA-51-like were detected in 59 (34.9%), 2 (1.2%), 16 (9.5%), and 126 (74.6%) Acinetobacter strains. This is the first description of blaNDM-1 in Enterobacter hormaechei and Acinetobacter genomic species 13TU. Of the integrase-positive strains, 135 (90.0%) Acinetobacter spp., 22 (61.1%) P. aeruginosa, and 14 (100%) Enterobacteriaceae isolates were identified by five, ten, and four different gene cassette arrays, respectively. Three novel gene cassette arrays aadB-aadA1, dfrA25, and dfrA16-aadA2 were reported for the first time in some species. Of the ISCR1-positive strains, the nonfermentative strains (102 Acinetobacter spp. and 13 P. aeruginosa. isolates) contained the same arrangement blaPER-1-putative glutathione-S-transferase-novel type ABC transporter, and three Enterobacteriaceae isolates harbored three different arrangements. Four distinct complex class 1 integron structures were observed. The complex class 1 integron detected in New Delhi, metallo-β-lactamase (NDM-1)-producing E. hormaechei, was found to coexist in the NDM-1-carrying plasmid. Our results suggested that we should pay more attention to the strict implementation of infection control measures and active antibiotic resistance surveillance to avoid the rapid spread or outbreak of carbapenemase-producing gram-negative bacteria.

The comparison of genotyping, antibiogram, and antimicrobial resistance genes between carbapenem-susceptible and -resistant Acinetobacter baumannii

This study was conducted to explore the epidemiological and molecular differences between carbapenem-susceptible Acinetobacter baumannii (CSAB) and carbapenem-resistant A. baumannii (CRAB) isolates. Thirty-two CSAB and 55 CRAB isolates were collected in 2010. By multilocus sequence typing analysis, 31 (56%) CRAB isolates and 11 (34%) CSAB isolates belonged to ST2. Twenty-one (38%) CRAB isolates, and 4 (13%) CSAB isolates belonged to a new type, ST129. The blaIMP, blaVIM, and blaOXA-58-like were not detected in our study isolates. blaOXA-23 and blaOXA-24/40-like were not detected in all CSAB isolates. On the contrary, blaOXA-23 was detected in 51 (93%) CRAB isolates. Class 1 integron was detected in 19 (35%) CRAB isolates and 8 (25%) CSAB isolates (p>0.05). In conclusion, the ST2 and ST129 were the major sequence types in both CSAB and CRAB isolates. The blaOXA-23 is the primary carbapenem-resistance gene in CRAB isolates from hospitalized patients and the specimens collected from hospital environment.

Types and prevalence of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex in Northern Taiwan

The frequency of the carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (CRACB) complex increases annually in our hospitals. However, the types and prevalence of carbapenemases among isolates still remain unclear. In this study, we identified and collected 672 carbapenem-resistant isolates from a medical center in Northern Taiwan between April and December of 2010. There were 577 genospecies 2 (Acinetobacter baumannii), 79 genospecies 13TU, and 16 genospecies 3 isolates. The isolates had an acquired blaOXA-24-like gene, which was confirmed by sequencing for the encoded OXA-72 carbapenemase, and were often associated with high-level carbapenem resistance. These CRACB complex isolates remained susceptible to colistin (100%). The genotyping of isolates was conducted using pulsed-field gel electrophoresis with ApaI digestion. In most clonally related groups, patients were from both branch hospitals. The results indicate that interhospital dissemination of clones occurred. This study provides updated data on the types and prevalence of the CRACB complex. In addition, it presents a warning on the emergence and spread of CRACB complex harboring blaOXA-24-like genes in northern Taiwan.

Molecular epidemiology, antimicrobial susceptibility and carbapenemase resistance determinants among Acinetobacter baumannii clinical isolates in Taiwan

BACKGROUND

Emerging carbapenem resistance among Acinetobacter baumannii clinical isolates is a worldwide problem. Infections caused by A. baumannii are increasing and demonstrate high mortality rates. This study aimed to establish a nationwide surveillance of antimicrobial susceptibility, carbapenemase genes, and clonal relationships of A. baumannii clinical isolates in Taiwan.

METHODS

Clinical isolates of Acinetobacter calcoaceticus-A. baumannii (ACB) complex collected by the Taiwan Surveillance of Antimicrobial Resistance-V program between July 2006 and September 2006 were used in this study. Genospecies identification was verified by 16S-23S rRNA intergenic-spacer sequences. Carbapenemase genes were detected by polymerase chain reaction. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) was applied for identification of clonal relationships.

RESULTS

Among the 151 ACB-complex isolates collected, 134 (88.7%) were A. baumannii, 12 (8.0%) were A. pittii, and five (3.3%) were A. nosocomialis. A. baumannii isolates showed higher resistance rates to ciprofloxacin, amikacin, and ampicillin/sulbactam than A. pittii or A. nosocomialis (all p < 0.001). The most commonly detected carbapenemase genes were bla(OxA-51) (n = 135), followed by bla(OxA-24) (n = 4), bla(OxA-23) (n = 2), and bla(OxA-58) (n = 1). Three major A. baumannii clones were found throughout Taiwan, and showed significantly higher resistance rates to ciprofloxacin, amikacin, and ampicillin/sulbactam than the other A. baumannii isolates (100% vs. 68.7%, p < 0.001; 98.4% vs. 61.5%, p < 0.001; and 66.7% vs. 39.8%, p = 0.004; respectively). MLST showed that these major clones were sequence type 2 and belonged to international clonal complex 2.

CONCLUSION

Our results demonstrate clonal spreading of A. baumannii in Taiwan hospitals and that these clones were more resistant to many antimicrobial agents. Efforts to prevent and control A. baumannii colonization/infections and prudent use of antibiotics to reduce antimicrobial selective pressure should be emphasized.

Repeated colonization by multi-drug-resistant Acinetobacter calcoaceticus-A. baumannii complex and changes in antimicrobial susceptibilities in surgical intensive care units

BACKGROUND

A nosocomial outbreak of multi-drug-resistant Acinetobacter calcoaceticus-A. baumannii (MDR-ACB) complex infection occurred in a newly constructed building at a 2,500-bed tertiary medical center in Taiwan.

METHODS

An investigation was carried out by molecular approaches to trace the bacteria. Antimicrobial susceptibilities, risk factors, and the occurrence of nosocomial MDR-ACB infections were investigated. From January to December 2009, 53 patients were infected with MDR-ACB, and 23 environmental surveys were performed in two surgical intensive care units (ICUs) within the new building. Forty-two clinical isolates were obtained from patients and 22 samples from nine environmental surveys.

RESULTS

Forty clinical isolates (95.2%) and 18 environmental samples (81.8%) were positive for MDR-ACB of type A, the predominant outbreak strain. This strain was identical to that isolated in an outbreak in the old hospital in 2006, as proved by repetitive extragenic palindromic-based polymerase chain reaction and pulsed-field gel electrophoresis. Although the outbreak isolates contained blaOXA-23-like and blaOXA-51-like genes, analysis of the antimicrobial susceptibilities demonstrated increases in resistance to cefepime and imipenem-cilastatin in MDR-ACB isolated in the later outbreak.

CONCLUSIONS

Not only patients or healthcare workers, but also medical equipment, might have carried the predominant outbreak strain from the old district to the new building. Therefore, even in a new environment, infection control programs must be enforced continually, and healthcare providers must be educated repeatedly to prevent recurrent outbreaks of MDR-ACB infection in the hospital setting.

Increase of carbapenem-resistant Acinetobacter baumannii infection in acute care hospitals in Taiwan: association with hospital antimicrobial usage

Objective

Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as an important pathogen causing healthcare-associated infections (HAIs) in Taiwan. The present study is aimed to investigate the epidemiology of HAIs caused by CRAB and the association of CRAB infection and hospital usage of different antimicrobials.

Methods

Two nationwide databases in the period 2003 to 2008, the Taiwan Nosocomial Infection Surveillance System and National Health Insurance claim data, were used for analysis. A total of 13,811 healthcare-associated A. baumannii infections and antimicrobial usage data from 121 hospitals were analyzed.

Results

There was a significant increase in the proportion of number of HAIs caused by CRAB over that by all A. baumannii (CRABpAB), from 14% in 2003 to 46% in 2008 (P<0.0001). The greatest increase was in central Taiwan, from 4% in 2003 to 62% in 2008 (P<0.0001). Use of anti-pseudomonal carbapenems, but not other classes of antibiotics, was significantly correlated with the increase of CRABpAB (r = 0.86, P<0.0001).

Conclusions

We suggested that dedicated use of anti-pseudomonal carbapenems would be an important intervention to control the increase of CRABpAB.

Molecular characterisation of multiple drug-resistant Acinetobacter baumannii isolates in southern Taiwan

The purpose of this study was to develop a multiplex polymerase chain reaction (mt-PCR) assay for synchronous detection of carbapenem resistance genes and/or pandrug resistance genes in clinical isolates of multidrug-resistant Acinetobacter baumannii (MDR-AB) and to investigate the association between the genetic make-up and a drug-resistant pattern. In total, 213 MDR-AB isolates were collected. All clinical isolates underwent antimicrobial susceptibility testing and were analysed for the presence of oxacillinase genes (bla(OXA-23), bla(OXA-24), bla(OXA-51)-like and bla(OXA-58)), class A and C β-lactamase genes (bla(TEM-1) and bla(AmpC), respectively), and an integron-associated antibiotic resistance gene (int1) by an in-house-designed mt-PCR assay. Of the 213 isolates, 73.87% harboured both bla(TEM-1) and bla(AmpC) and 83.92% carried at least three oxacillinase genes. Moreover, 64.82% of the isolates were significant in that they had two β-lactamase genes and three oxacillinase genes (P<0.001), indicating the complexity of the genetic make-up of carbapenem-resistant A. baumannii. The bla(OXA-51)-like allele was detected in the majority of these A. baumannii isolates (97.49%), whereas bla(OXA-23) was rarely prevalent in these isolates. In multivariate logistic regression, the presence of bla(OXA-23) and bla(TEM-1) had a statistically significant association with imipenem resistance [bla(OXA-23), P=0.004, odds ratio (OR)=10.52, 95% confidence interval (CI) 2.12-52.17; bla(TEM-1), P=0.005, OR=6.14, 95% CI 1.74-21.62]. These results suggest that detecting bla(OXA-23) and bla(TEM-1) genes could be used to predict imipenem resistance in MDR-AB isolates. A mt-PCR for detecting carbapenem resistance genes and pandrug resistance genes of A. baumannii isolates was developed to provide an assay to quickly screen for potential imipenem-resistant A. baumannii in the clinic.

Difference in imipenem, meropenem, sulbactam, and colistin nonsusceptibility trends among three phenotypically undifferentiated Acinetobacter baumannii complex in a medical center in Taiwan, 1997-2007

BACKGROUND

To determine whether the susceptibilities and the trends of nonsusceptibility of imipenem, meropenem, sulbactam, and colistin differed among Acinetobacter baumannii, Acinetobacter genomic species 3 (AGS 3), and Acinetobacter genomic species 13TU (AGS 13TU) over 11 years.

METHODS

A total of 1,039 nonduplicate blood isolates of A baumannii complex from bacteremic patients between 1997 and 2007 were collected at Taipei Veterans General Hospital and were identified to the species level using a multiplex polymerase chain reaction method and sequence analysis of 16S-23S intergenic spacer. The minimal inhibitory concentrations of antibiotics were determined by the agar dilution method.

RESULTS

The nonsusceptibility rates of carbepenems and sulbactam were highest in A baumannii, which also showed a trend toward increasing rate of carbapenems nonsusceptibility over the 11-year period of the study. AGS 13TU had the highest nonsusceptible rate to colistin, comparably increasing trend of carbapenem nonsusceptiblity as that of A baumannii, and is the only species with increasing sulbactam nonsusceptibility. AGS 3 had the lowest rate of nonsusceptibility to all four antimicrobial agents.

CONCLUSION

Although A baumannii had the highest nonsusceptibility rate to imipenem, meropenem, and sulbactam over the years, the higher rate of colistin nonsusceptibility and the emergence of nonsusceptibility of carbapenems and sulbactam in AGS 13TU suggested that this species might cause a great problem in the near future.

Emergence and dissemination of blaOXA-23-carrying imipenem-resistant Acinetobacter sp in a regional hospital in Taiwan

BACKGROUND

The distribution and characterization of OXA-type carbapenemases in Acinetobacter sp in Taiwan has less been reported. The aim of the study was to investigate the molecular epidemiology and OXA-type carbapenemase genes in a regional hospital in Taiwan.

METHODS

Imipenem-resistant Acinetobacter sp were collected between 2005 and 2007 in a regional hospital. Genotyping was performed by pulsed-field gel electrophoresis. OXA-type carbapenemase genes were determined by multiplex polymerase chain reaction (PCR) and gene sequencing.

RESULTS

A total of 136 isolates were collected. Fifty-six pulsotypes were identified. None of the pulsotypes established predominance throughout the 3-year period. Multiplex PCR of blaOXA genes showed that 99% (135/136) of the Acinetobacter sp possessed blaOXA51-like genes. The coexistences of blaOXA51-like/blaOXA-23-like and blaOXA51-like/blaOXA-24-like were detected in 19% (26/136) and 1% (2/136) of the isolates, respectively. Among blaOXA-23-like gene-carrying isolates, two isolates (Pulsotypes 18 and 20) were found in 2006 and the remainder (n=24), including Pulsotypes 27 (n=18), 29 (n=1), 52 (n=3), and 53 (n=2), were found in 2007. Sequencing performed on the 26 representative isolates confirmed the presence of the blaOXA-23 carbapenemase gene. Analysis of the genetic content of blaOXA-23 showed that these genes were presumably chromosomal and associated with the upstream-located insertion sequence ISAba1.

CONCLUSIONS

The emergence and imminent widespread of blaOXA-23-carrying imipenem-resistant Acinetobacter sp appeared in Taiwan during the period from 2006 to 2007.

Overexpression of the adeB gene in clinical isolates of tigecycline-nonsusceptible Acinetobacter baumannii without insertion mutations in adeRS

Thirteen clinical isolates of multidrug-resistant Acinetobacter baumannii resistant to carbapenems (MRAB-C) with tigecycline nonsusceptibility were collected from individual patients in this study. None of the 13 isolates shared the same strain characteristics in molecular typing. All of them showed increased adeB transcription, as predicted. However, none of these tigecycline-nonsusceptible MRAB-C isolates were found to possess previously known adeRS mutations. Upregulation of adeB transcription may result from cross stimulation by other mechanisms.

Distribution of blaOXA-carrying imipenem-resistant Acinetobacter spp. in 3 hospitals in Taiwan

We investigated the molecular epidemiology and OXA-type carbapenemase genes of 83 imipenem-resistant Acinetobacter spp. collected from 2 university hospitals (hospitals A and B) and a regional hospital (hospital C) during 2007 in Taiwan. Genotyping by pulsed-field gel electrophoresis identified 51 pulsotypes. None of the pulsotypes established predominance throughout the 3 hospitals. Multiplex polymerase chain reaction of blaOXA genes showed that 100% (18/18), 91%(31/34), and 100% (31/31) of the Acinetobacter spp. collected from hospital A, B, and C, respectively, possessed blaOXA-51-like genes. None of the strains carrying blaOXA-23-like and blaOXA-24-like genes were found in hospital A. The coexistences of blaOXA-51-like/blaOXA-23-like and blaOXA-51-like/blaOXA-24-like genes detected in hospitals B and C were 26% (9/34) and 12% (4/34) and 58% (18/31) and 3% (1/31), respectively. Among blaOXA-23-like gene-carrying isolates collected from hospitals, clonal spread of strains carrying the blaOXA-23 gene was detected in the regional hospital but not the other 2 university hospitals. The results suggest that interhospital dissemination of imipenem-resistant Acinetobacter spp. was not found in these hospitals. The increasing percentage of OXA-23 in OXA-type carbapenemases in Acinetobacter spp. from the regional hospitals to medical centers deserves further attention in Taiwan.