RAPD-PCR typing of Acinetobacter isolates from activated sludge systems designed to remove phosphorus microbiologically

Molecular Characterization of Acinetobacter baumannii Isolated from Ventilator-Associated Pneumonia and Burn Wound Colonization by Random Amplified Polymorphic DNA Polymerase Chain Reaction and the Relationship between Antibiotic Susceptibility and Biofilm Production

Background:

Multidrug-resistant Acinetobacter baumannii can cause complications in antibiotic therapy and increase the rate of morbidity and mortality in hospitalized patients. Patients with ventilator and burns are two specific groups at high risk for A. baumannii infections. This study aimed to determine antibiotic susceptibility patterns associated with biofilm production in A. baumannii and to assess its molecular epidemiology by random amplified polymorphic DNA polymerase chain reaction (RAPD PCR) in A. baumannii isolated from ventilator-associated pneumonia and burn wound colonization.

Materials and Methods:

In this study, 79 isolates of A. baumannii (32 ventilator-associated pneumonia [VAP] 47 burns) were collected in two teaching hospitals in Tehran, Iran, in 2018. Conventional biochemical and microbiological methods were used to identify bacteria. Antibiotic susceptibility was detected by disc diffusion methods according to the Clinical and Laboratory Standards Institute 2018. Tube test was examined for the detection of the biofilm formation rate in collected strains. The most prevalent carbapenemase genes were detected by PCR and molecular typing by RAPD PCR.

Results:

All of bacteria were extensively drug-resistant (XDR) except for two isolates. The results of tube test indicated that only 36% of XDR strains were in weak rate of biofilm formation group. Two major clonal genetic groups were found in VAP and burn strains. Oxa-23 was the most prevalent carbapenemase in collected A. baumannii.

Conclusion:

The presence of XDR strains of A. baumannii is considerable significant problem in hospitals. Further, similar genetic clonal identified in them indicated the nosocomial infection origin. Hence, these results are very important for control of nosocomial infection committee in health-care systems.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

Usefulness of phenotypic and genotypic methods for metallo-beta-lactamases detection in carbapenem-resistant Acinetobacter baumannii strains

BACKGROUND

Acinetobacter baumannii is an opportunistic microorganism with an increasing role in nosocomial outbreaks. For the last 2 decades, a growing number of carbapenem-resistant A. baumannii strains have been identified, including the metallo-beta-lactamases (MBLs) producers. The study aimed to investigate the genetic relatedness of, and MBLs production among, a collection of A. baumannii isolates from Poland.

MATERIAL/METHODS

This study involved 78 clinical isolates of carbapenem-resistant A. baumannii. Strain typing of the isolates was performed using PCR-RAPD. The presence of MBLs was phenotypically determined using different double disc synergy tests (DDST), the imipenem/EDTA combination disk test (CDT) and Etest MBL. blaIMP and blaVIM genes were detected using a duplex PCR assay.

RESULTS

The isolates were divided into 18 PCR-RAPD patterns. Among 18 examined isolates, 94.4% were MBL-positive by the phenotypic method relying on comparing the bacteria growth inhibition zones diameters between imipenem/EDTA and imipenem discs, 88.9% using Etest MBL, 66.7% using the double disc synergy test with ceftazidime, imipenem, meropenem and EDTA, and 88.9% using a corresponding method with 2-MPA. The existence of blaIMP was identified in 8 (10.3%) strains.

CONCLUSIONS

MBLs production was an important mechanism of carbapenem resistance among A. baumannii isolates in Poland. Laboratories should routinely screen for MBLs among A. baumannii isolates.

Outbreak of Acinetobacter baumannii producing the carbapenem-hydrolyzing oxacillinase OXA-58 in Rome, Italy

In this study 45 epidemic and sporadic isolates of Acinetobacter baumannii were investigated by antimicrobial resistance, integron identifications and genotyping. Isolates were genotyped by random amplified polymorphism (RAPD) DNA and pulsed-field gel electrophoresis (PFGE). Four different RAPD patterns were observed among the isolates of our collection, further discerned in six PFGE types. Two prevalent genotypes were identified, one corresponding to a carbapenem resistant epidemic clone, causing an outbreak at the intensive care unit of a hospital of Rome. Two class 1 integrons, carrying different gene cassette arrays, were identified among the two prevalent genotypes. Nucleotide analysis of the integron-variable regions revealed the presence of the aacA4, orfO, bla(OXA-20), and aacC1, orfX, orfX', aadA1 gene cassette arrays, respectively. All the carbapenem resistant strains analyzed in this study carried the bla (OXA-58) gene located on plasmids.

The rapid identification of Acinetobacter species using Fourier transform infrared spectroscopy

AIMS

Fourier transform infrared (FT-IR) was used to analyse a selection of Acinetobacter isolates in order to determine if this approach could discriminate readily between the known genomic species of this genus and environmental isolates from activated sludge.

METHODS AND RESULTS

FT-IR spectroscopy is a rapid whole-organism fingerprinting method, typically taking only 10 s per sample, and generates 'holistic' biochemical profiles (or 'fingerprints') from biological materials. The cluster analysis produced by FT-IR was compared with previous polyphasic taxonomic studies on these isolates and with 16S-23S rDNA intergenic spacer region (ISR) fingerprinting presented in this paper. FT-IR and 16S-23S rDNA ISR analyses together indicate that some of the Acinetobacter genomic species are particularly heterogeneous and poorly defined, making characterization of the unknown environmental isolates with the genomic species difficult.

CONCLUSIONS

Whilst the characterization of the isolates from activated sludge revealed by FT-IR and 16S-23S rDNA ISR were not directly comparable, the dendrogram produced from FT-IR data did correlate well with the outcomes of the other polyphasic taxonomic work.

SIGNIFICANCE AND IMPACT OF THE STUDY

We believe it would be advantageous to pursue this approach further and establish a comprehensive database of taxonomically well-defined Acinetobacter species to aid the identification of unknown strains. In this instance, FT-IR may provide the rapid identification method eagerly sought for the routine identification of Acinetobacter isolates from a wide range of environmental sources.

Seven novel species of Acinetobacter isolated from activated sludge

Thirteen isolates of Acinetobacter were obtained from activated sludge plants in Victoria, Australia. Earlier 16S-23S rDNA genomic fingerprinting and partial 16S rDNA sequence data had suggested that these isolates might contain previously undescribed species. This view was confirmed here. A polyphasic taxonomic approach involving phenotypic characterization, near-complete 16S rDNA sequence data and DNA-DNA hybridization analyses support the view that seven novel genomic species can be differentiated in this group of isolates. However, when fluorescence in situ hybridization (FISH) studies were performed with a 16S-rRNA-targeted probe specific for the genus Acinetobacter, used to identify Acinetobacter in activated sludge plants, all these strains responded positively. This suggests that these isolates would not have been missed in earlier FISH studies where their role as polyphosphate-accumulating bacteria has been questioned. This report describes these isolates and proposes that they be named Acinetobacter baylyi (type strain B2T = DSM 14961T = CIP 107474T), Acinetobacter bouvetii (type strain 4B02T = DSM 14964T = CIP 107468T), Acinetobacter grimontii (type strain 17A04T = DSM 14968T = CIP 107470T), Acinetobacter tjernbergiae (type strain 7N16T = DSM 14971T = CIP 107465T), Acinetobacter towneri (type strain AB1110T = DSM 14962T = CIP 107472T), Acinetobacter tandoii (type strain 4N13T = DSM 14670T = CIP 107469T) and Acinetobacter gerneri (type strain 9A01T = DSM 14967T = CIP 107464T).

Pyrolysis mass spectrometry (PyMS) and 16S-23S rDNA spacer region fingerprinting suggests the presence of novel acinetobacters in activated sludge

Screening of large numbers of Acinetobacter spp. from activated sludge systems with Pyrolysis Mass Spectrometry (PyMS) showed that many did not cluster tightly with the currently described genomic species which have been obtained mainly from clinical sources. Selected isolates were then genotypically fingerprinted using their 16S-23S rDNA spacer region, and again the data revealed considerable differences in the genomic fingerprints of many of these activated sludge isolates to the predominantly clinical genomic species. In fact, few could be identified from them. The possibility that the current speciation within this genus is not adequate to encompass all these environmental isolates is addressed in relation to the methods used to study the population dynamics of Acinetobacter in activated sludge.

DNA polynucleotide probes generated from representatives of the genus Acinetobacter and their application in fluorescence in situ hybridization of environmental samples

The application of rRNA directed polynucleotide probes carrying multiple labels facilitates the detection of target cells by fluorescence in situ hybridizations and allows specific enrichment by cell fishing. So far, exclusively RNA transcript probes have been used. To reduce the effort in the preparation of the polynucleotides and to enhance their stability, DNA probes matching a part of the highly variable domain III on the 23S rRNA were constructed by amplification of the target region using PCR. Fluorescent labeling was achieved by incorporation of Cy3-labeled desoxyribonucleotides in the amplification. DNA polynucleotide probes were constructed for the seven validly described Acinetobacter species. Amplified domain III rDNA of A. baumannii and A. calcoaceticus could be readily applied as species specific probe. In addition, rDNA fragments could be used to recognize two groups of species, one comprising A. haemolyticus, A. junii and A. radioresistens and the other one A. lwoffii and A. johnsonii. Acinetobacter baumannii cells, some of them occurring in filaments, could be detected by in situ hybridization in native samples of activated sludge.