Identification of Acinetobacter species: Is Bruker biotyper MALDI-TOF mass spectrometry a good alternative to molecular techniques?

Molecular typing of reduced susceptibility of Acinetobacter calcoaceticus-baumannii complex to Chlorhexidine in Turkey by pulsed-field gel electrophoresis

Introduction. The global spread of Acinetobacter spp., particularly the Acinetobacter calcoaceticusbaumannii (ACB) complex, has led to its recognition as a significant pathogen by the World Health Organization (WHO). The increasing resistance of the ACB complex to multiple antibiotics presents a challenge for treatment, necessitating accurate antibiotic susceptibility profiling after isolation.Hypothesis or gap statement. There is limited understanding of the antimicrobial resistance and chlorhexidine, a biocide, susceptibility profiles of ACB complex strains, especially in clinical settings in Turkey.Aim. This study aimed to identify ACB complex strains recovered from various clinical specimens at Hacettepe University Hospitals in Ankara, Turkey, in 2019, and to assess identification, their antibiotic and chlorhexidine susceptibility profiles, and genomic relatedness.Methodology. Eighty-two ACB complex strains were identified using MALDI-TOF MS. Susceptibility testing to 12 antibiotics was conducted using the disc diffusion method, and colistin, chlorhexidine susceptibility was assessed using the broth microdilution technique, following the latest EUCAST and CLSI guidelines. ACB complex members with reduced chlorhexidine sensitivity were further analyzed by pulsed-field gel electrophoresis (PFGE) for bacterial typing.Results. Among the isolates, 1.2% were multidrug-resistant (MDR), 73.2% were extensively drug-resistant (XDR), and 12.2% were pandrug-resistant (PDR). Carbapenem resistance was found in 86.7% of MDR, PDR, and XDR strains. Colistin resistance was observed in 15.8% of isolates, and 18.2% exhibited decreased susceptibility to chlorhexidine. PFGE revealed seven different clones among strains with reduced chlorhexidine sensitivity, indicating vertical transmission within the hospital.Conclusion. This study highlights the reduced susceptibility to chlorhexidine in ACB complex members and provides epidemiological insights into their spread. The findings underscore the importance of screening for antimicrobial resistance and biocide susceptibility profiles to effectively manage healthcare-associated infections.

In vitro assessment of crude oil degradation by Acinetobacter junii and Alcanivorax xenomutans isolated from the coast of Ghana

This study was aimed at using in vitro microcosm experiments to assess crude oil degradation efficiency of Acinetobacter junii and Alcanivorax xenomutans isolated along Ghana's coast. Uncontaminated seawater from selected locations along the coast was used to isolate bacterial species by employing enrichment culture procedures with crude oil as the only carbon source. The isolates were identified by means of the extended direct colony transfer method of the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectroscopy (MALDI-TOF MS), as Acinetobacter junii, and Alcanivorax xenomutans. Remediation tests showed that Acinetobacter junii yielded degradation efficiencies of 27.59 %, 41.38 % and 57.47 %. Whereas efficiencies of 21.14 %, 32.18 % and 43.68 % were recorded by Alcanivorax xenomutans representing 15, 30 and 45 days respectively. Consortia of Acinetobacter junii, and Alcanivorax xenomutans also yielded 32.18 %, 48.28 % and 62.07 % for the selected days respectively. Phylogenetic characterization using ClustalW and BLAST of sequences generated from the Oxford Nanopore Sequencing technique, showed that the Ghanaian isolates clustered with Alcanivorax xenomutans and Acinetobacter junii species respectively. An analysis of the sequenced data for the 1394-bp portion of the 16S rRNA gene of the isolates revealed >99 % sequence identity with the isolates present on the GenBank database. The isolates of closest identity were Alcanivorax xenomutans and Acinetobacter junii with accession numbers, NR_133958.1 and KJ147060.1 respectively. Acinetobacter junii and Alcanivorax xenomutans isolated from Ghana's coast under pristine seawater conditions have therefore demonstrated their capacity to be used for the remediation of crude oil spills.

Phenotypical and molecular characterization of Acinetobacter spp. isolated from a pharmaceutical facility

Characterizing microorganisms according to different criteria is useful when investigating sources of microbiological contamination in the pharmaceutical industry. The aim of this study was to characterize 38 Acinetobacter baumannii complex strains isolated from a biopharmaceutical industry by 16S rRNA sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS), multilocus sequence typing (MLST), antimicrobial susceptibility profile, biofilm formation, and sensibility to disinfectants. Thirty-three (86.9%) strains were identified by 16S rRNA gene sequencing as A. seifertii/pitti/nosocomialis/lactucae, four (10.5%) as A. baumannii, and one (2.6%) as A. vivianii/courvalini. MALDI-TOF/MS did not identify one strain, and incorrectly identified 30/37 (81.1%) strains as A. baumannii. Strains were assigned to 12 different STs, of which nine were newly defined in this study (STs 2091-2099). Twenty-six (68.4%) strains showed resistance to amikacin and gentamicin. Thirty-three (86.8%) strains were classified as moderately or strongly adherent on polystyrene. Alcohol 70%/15 min and quaternary ammonium 0.08%/20 min were not able to eliminate the biofilm formed, but sodium hypochlorite 0.1%/15 min was efficient. In conclusion, improved methods are needed to improve the identification of Acinetobacter strains in pharmaceutical industries. This organism is of particular concern as it forms recalcitrant biofilms, leading to persistence in the manufacturing environment and increased risk of product contamination.

Rapid Identification of Aphid Species by Headspace GC-MS and Discriminant Analysis

Aphids are a ubiquitous group of pests in agriculture that cause serious losses. For sustainable aphid identification, it is necessary to develop a precise and fast aphid identification tool. A new simple chemotaxonomy approach to rapidly identify aphids was implemented. The method was calibrated in comparison to the established phylogenetic analysis. For chemotaxonomic analysis, aphids were crushed, their headspace compounds were collected through closed-loop stripping (CLS) and analysed using gas chromatography-mass spectrometry (GC-MS). GC-MS data were then subjected to a discriminant analysis using CAP12.exe software, which identified key biomarkers that distinguish aphid species. A dichotomous key taking into account the presence and absence of a set of species-specific biomarkers was derived from the discriminant analysis which enabled rapid and reliable identification of aphid species. As the method overcomes the limits of morphological identification, it works with aphids at all life stages and in both genders. Thus, our method enables entomologists to assign aphids to growth stages and identify the life history of the investigated aphids, i.e., the food plant(s) they fed on. Our experiments clearly showed that the method could be used as a software to automatically identify aphids.

Determination of Pathogens by Electrophoretic and Spectrometric Techniques

In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.

Genotypic characterization and clonal relatedness of metallo-β-lactamase-producing non-fermentative gram negative bacteria in the first 5 years of their circulation in Paraguay (2011-2015)

Pseudomonas aeruginosa and species of Acinetobacter calcoaceticus-baumanii complex are multiresistant intrahospital opportunistic pathogens, able to acquire carbapenemases and produce outbreaks with high morbidity and mortality. Pseudomonas putida has also emerged with similar characteristics. The aim of this research was to characterize the Metallo-β-lactamases (MBLs) detected by surveillance in Paraguay in the first 5 years of their circulation in hospitals. The coexistence of KPC and OXA-type carbapenemases was also investigated. 70 MBL-producing strains from inpatients were detected from clinical samples and rectal swab from 11 hospitals. The strains were identified by manual, automated, and molecular methods. Antimicrobial susceptibility was studied by Kirby-Bauer and automated methods, while colistin susceptibility was determined by broth macrodilution. MBLs were investigated by synergy with EDTA against carbapenems and PCR, and their variants by sequencing. KPC and OXA-carbapenemases were investigated by PCR. Clonality was studied by pulsed-field gel electrophoresis (PFGE). The results demonstrated the circulation of blaVIM-2 (60%), blaNDM-1 (36%), and blaIMP-18 (4%). The MBL-producing species were P. putida (45.7%), P. aeruginosa (17.2%), A. baumannii (24.3%), A. pittii (5.7%), A. nosocomialis, (4.3%) A. haemolyticus (1.4%), and A. bereziniae (1.4%). PFGE analysis showed one dominant clone for A. baumannii, a predominant clone for half of the strains of P. aeruginosa, and a polyclonal spread for P. putida. In the first 5 years of circulation in Paraguay, MBLs were disseminated as unique variants per genotype, appeared only in Pseudomonas spp. and Acinetobacter spp., probably through horizontal transmission between species and vertical by some successful clones.

Molecular and Physiological Diversity of Indigenous Yeasts Isolated from Spontaneously Fermented Wine Wort from Ilfov County, Romania

(1) Background: Wine yeast research offers the possibility of isolating new strains with distinct metabolic properties due to the geographical location of the vineyard and the processes used in winemaking. Our study deals with the isolation and identification of six yeasts from spontaneously fermented wine wort from Romania and their characterization as new potential starter culture for traditional beverages, for food industry or biomedicine. (2) Materials and methods: The isolates were identified using conventional taxonomy tests, phenotypic phylogeny analysis (Biolog YT), MALDI-TOF mass spectrometry, PCR-RFLP, and sequencing of the ITS1-5,8S-ITS2 rDNA region. The capacity of the yeasts to grow under thermal, ionic, and osmotic stress was determined. The safe status was confirmed by testing virulence and pathogenicity factors. Assays were performed in order to evaluate the growth inhibition of Candida strains and determine the antimicrobial mechanism of action. (3) Results and discussions: The yeast isolates were identified as belonging to the Metschinikowia, Hanseniaspora, Torulaspora, Pichia, and Saccharomyces genera. All the isolates were able to develop under the tested stress conditions and were confirmed as safe. With the exception of S. cerevisiae CMGB-MS1-1, all the isolates showed good antimicrobial activity based on competition for iron ions or production of killer toxins. (4) Conclusions: The results revealed the resistance of our yeasts to environmental conditions related to industrial and biomedical applications and their high potential as starter cultures and biocontrol agents, respectively.

Novel members of bacterial community during a short-term chilled storage of common carp (Cyprinus carpio)

This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation sequencing (NGS) and cultivation-dependent methods. Carp fillets were stored for 96 h at 2 °C and 6 °C with and without a vacuum package, and an additional frozen-thawed storage experiment was set for 120 days. Community profiles of the initial and stored fish samples were determined by amplicon sequencing. Conventional microbial methods were used parallelly for the enumeration and cultivation of the dominant members of the microbial community. Cultivated bacteria were identified with 16S rRNA sequencing and the MALDI-TOF MS method. Based on our results, the vacuum package greatly affected the diversity and composition of the forming microbial community, while temperature influenced the cell counts and consequently the microbiological criteria for shelf-life of the examined raw fish product. Next-generation sequencing revealed novel members of the chilled flesh microbiota such as Vagococcus vulneris or Rouxiella chamberiensis in the vacuum-packed samples. With traditional cultivation, 161 bacterial strains were isolated and identified at the species level, but the identified bacteria overlapped with only 45% of the dominant operational taxonomic units (OTUs) revealed by NGS. Next-generation sequencing is a promising and highly reliable tool recommended to reach a higher resolution of the forming microbial community of stored fish products. Knowledge of the initial microbial community of the flesh enables further optimization and development of processing and storage technology.

In Vitro Activity of Minocycline Against Multidrug-Resistant Acinetobacter baumannii Isolates-Evaluation of Clinical Breakpoints and Review of Literature

Therapeutic options for the treatment of infections by multidrug-resistant Acinetobacter baumannii strains are often limited. Minocycline (MIN) is an old antibiotic, with excellent activity against A. baumannii isolates, which can be administered orally. Currently, there is no single criterion regarding the breakpoints for MIN and A. baumannii. The activity of MIN was examined against a collection of A. baumannii isolates recovered from 15 hospitals of 6 countries of South America. A review of the literature was also performed. In our series and most of the studies, the percentages of MIN susceptible isolates exceeded 50%, regardless of the breakpoints utilized (4-2 or 1 μg/mL). However, a greater number of isolates not harboring Tet B were considered resistant with the breakpoints of 1 or 2 μg/mL, whereas isolates with tet(B) genes were still detected with minimum inhibitory concentration below all breakpoints considered. Tetracycline susceptibility may be used as a screening to discriminate the populations with and without acquired resistance mechanisms to MIN. In this study, MIN-resistant subpopulations were found in isolates harboring Tet B, with MIC ≤1 μg/mL, and their frequency increased after incubation with MIN. These subpopulations were not detected in isolates not harboring Tet B. The clinical correlation of these subpopulations should be evaluated in future studies.

In vitro synergistic activity of the sulbactam/avibactam combination against extensively drug-resistant Acinetobacter baumannii

Introduction. The therapeutic options to treat Acinetobacter baumannii infections are very limited.Aim. Our aim was to evaluate the activity of sulbactam combined directly with avibactam or the ampicillin-sulbactam/ceftazidime-avibactam combination against extensively drug-resistant A. baumannii isolates.Methodology. Extensively drug-resistant A. baumannii isolates (n=127) collected at several South American hospitals were studied. Synergy with the sulbactam/avibactam combination was assessed in all isolates using the agar dilution method. Avibactam was used at a fixed concentration of 4 mg l^-1. A disc diffusion synergy test was also performed. Synergy by a time-kill experiment was performed in a selected isolate.Results. Synergy with sulbactam/avibactam was demonstrated in 124 isolates and it showed MIC values ≤4 mg l^-1. This synergy was not detected in the three New Delhi metallo-β-lactamase-harbouring isolates. Similar results were observed with the disc diffusion synergy test of ampicillin-sulbactam/ceftazidime-avibactam. In the time-kill experiments, sulbactam/avibactam showed a rapid synergistic and bactericidal activity in ampicillin-sulbactam-resistant isolates.Conclusions. This study demonstrated that the sulbactam/avibactam combination displayed synergistic activity against A. baumannii isolates. This synergy was observed when both inhibitors were also used as part of the commercially available combinations: ampicillin-sulbactam and ceftazidime-avibactam.

Rapid screening and early precautions for carbapenem-resistant Acinetobacter baumannii carriers decreased nosocomial transmission in hospital settings: a quasi-experimental study

Background

Active surveillance has the potential to prevent nosocomial transmission of carbapenem-resistant Acinetobacter baumannii (CRAB). We assessed whether rapid diagnosis using clinical specimen-direct loop-mediated isothermal amplification (LAMP), a rapid molecular diagnostic assay, and subsequent intervention, could reduce CRAB nosocomial transmission in intensive care units (ICUs).

Methods

A before and after (quasi-experimental) study was conducted in two ICUs at the Mahidol University Faculty of Medicine Ramathibodi Hospital with 3 months of observational period followed by 9 months of interventional period. All patients were screened for CRAB using both the culture and LAMP method from rectal swab and/or bronchial aspirates (intubated patients only) upon admission, weekly thereafter, and upon discharge. During the pre-intervention period, we performed contact precautions based on culture results. In contrast, during the intervention period, we initiated contact precautions within a few hours after sample collection on the basis of LAMP results.

Results

A total of 1335 patients were admitted to the ICUs, of which 866 patients (pre-intervention period: 187; intervention period: 679) were eligible for this study. Incidence rate of CRAB infection decreased to 20.9 per 1000 patient-days in the intervention period from 35.2 in the pre-intervention period (P < 0.02). The calculated hazard ratio of CRAB transmission was 0.65 (95% confidence interval [CI], 0.44–0.97). Risk factors for CRAB acquisition included exposure to carbapenem (hazard ratio, 2.54 [95% CI: 1.61–5.57]).

Conclusions

LAMP screening for CRAB upon ICU admission proved feasible for routine clinical practice. Rapid screening using LAMP followed by early intervention may reduce CRAB transmission rates in ICUs when compared to conventional intervention.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0564-9) contains supplementary material, which is available to authorized users.

Accurate identification of clinically important Acinetobacter spp.: an update

Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of bla_OXA-51-like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex.

Acinetobacter species are considered to be one of the most important pathogens and associated with increased mortality. The species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex have emerged as high priority pathogens, especially in intensive care units, thereby posing a challenge to infection management practices. However, identification of Acinetobacter to the species level is difficult. Clear differentiation among various Acinetobacter species with available standard biochemical methods and automated systems is challenging. Although various molecular methods are available, they are not regularly used in diagnostic laboratories. The advantages and disadvantages of different methods useful in the accurate identification of Acinetobacter species are discussed in this review.

[Molecular epidemiology of carbapenem-resistant isolates of Acinetobacter baumannii in Argentina]

One hundred sequential, epidemiologically unrelated carbapenem-resistant- Acinetobacter baumannii isolates from 11 hospitals in 10 Argentine provinces were collected between January and August 2016. Genes coding for Ambler class D and B carbapenemases were investigated by PCR using specific primers. All isolates were typed using the 3-locus sequence typing and bla_OXA-51-like sequence-based typing techniques. The bla_OXA-23 gene was recovered in all isolates studied. The population of carbapenem-resistant- A. baumannii in Argentina was principally associated with ST1 (45%), ST25 (34%) and ST79 (15%). ST25 was recovered in all the regions studied and CC2 was not detected.

Limitations of routine MALDI-TOF mass spectrometric identification of Acinetobacter species and remedial actions

A set of 204 taxonomically well-defined strains belonging to 17 Acinetobacter spp., including 11 recently described species (A. albensis, A. bohemicus, A. colistiniresistens, A. courvalinii. A. dispersus, A. gandensis, A. modestus, A. proteolyticus, A. seifertii, A. variabilis, and A. vivianii) and six species of the so-called haemolytic clade (A. beijerinckii, A. gyllenbergii, A. haemolyticus, A. junii, A. parvus, and A. venetianus), were subjected to MALDI-TOF mass spectrometric profiling. The identification outputs were evaluated using the current version (8.0.0.0) of the commercially available Bruker Daltonics, Biotyper database, which does not contain reference entries for six of the species tested. Up to 29% of the strains were falsely identified as different Acinetobacter spp. present in the Biotyper database, resulting mostly from the close phylogenetic relationship of species of the haemolytic clade. To obtain more reliable identification, extending the commercial database showed only partial improvement, while the use of an alternative MALDI matrix solution (strongly acidified ferulic acid) allowed correct identification of nearly all problematic strains.

Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study

In recent years, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has become the standard for routine bacterial species identification due to its rapidity and low costs for consumables compared to those of traditional DNA-based methods. However, it has been observed that strains of some bacterial species, such as Acinetobacter baumannii strains, cannot be reliably identified using mass spectrometry (MS). Raman spectroscopy is a rapid technique, as fast as MALDI-TOF, and has been shown to accurately identify bacterial strains and species. In this study, we compared hierarchical clustering results for MS, genomic, and antimicrobial susceptibility test data to hierarchical clustering results from Raman spectroscopic data for 31 A. baumannii clinical isolates labeled according to their pulsed-field gel electrophoresis data for strain differentiation. In addition to performing hierarchical cluster analysis (HCA), multiple chemometric methods of analysis, including principal-component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), were performed on the MS and Raman spectral data, along with a variety of spectral preprocessing techniques for best discriminative results. Finally, simple HCA algorithms were performed on all of the data sets to explore the relationships between, and natural groupings of, the strains and to compare results for the four data sets. To obtain numerical comparison values of the clustering results, the external cluster evaluation criteria of the Rand index of the HCA dendrograms were calculated. With a Rand index value of 0.88, Raman spectroscopy outperformed the other techniques, including MS (with a Rand index value of 0.58).

Trends in the resistance profiles of Acinetobacter baumannii endemic clones in a university hospital of Argentina

A total of 925 Acinetobacter spp. isolates were collected from routine clinical samples of patients admitted to the university hospital of Buenos Aires city during the period 2004-2012. From this collection, 129 isolates identified as Acinetobacter baumannii were selected for molecular studies. Minimal inhibitory concentrations (MICs) of antimicrobials were determined by agar dilution method. Colistin (COL) heteroresistance was investigated by means of population analysis studies. PCR-based methods were used for epidemiological analysis and for the screening of carbapenemases and the bla(tetB) gene. We have observed a steady rise in the MIC50 of imipenem (IMI)-resistant isolates and an increment in the presence of bla(OXA-23)-like gene (74-100%) as well. A rapid increasing rate of minocycline (MIN) resistance and a rise of the MIC50 of the resistant isolates have been detected since the year 2008. All isolates harboured the tet (B) gene. An increase in the value of the tigecycline (TIG) MIC was seen from the year 2007 onwards. This loss of activity was observed among different clones. A rise of COL heteroresistance from 46.4% in 2004 to 95% in 2012 was detected. During this period, COL consumption also increased (11.1-fold). However, COL resistance remained sporadic.

Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS

Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.

MALDI-TOF/MS identification of species from the Acinetobacter baumannii (Ab) group revisited: inclusion of the novel A. seifertii and A. dijkshoorniae species

OBJECTIVES

Rapid identification of Acinetobacter species is critical as members of the A. baumannii (Ab) group differ in antibiotic susceptibility and clinical outcomes. A. baumannii, A. pittii, and A. nosocomialis can be identified by MALDI-TOF/MS, while the novel species A. seifertii and A. dijkshoorniae cannot. Low identification rates for A. nosocomialis also have been reported. We evaluated the use of MALDI-TOF/MS to identify isolates of A. seifertii and A. dijkshoorniae and revisited the identification of A. nosocomialis to update the Bruker taxonomy database.

METHODS

Species characterization was performed by rpoB-clustering and MLSA. MALDI-TOF/MS spectra were recovered from formic acid/acetonitrile bacterial extracts overlaid with α-cyano-4-hydroxy-cinnamic acid matrix on a MicroflexLT in linear positive mode and 2000-20 000 m/z range mass. Spectra were examined with the ClinProTools v2.2 software. Mean spectra (MSP) were created with the BioTyper software.

RESULTS

Seventy-eight Acinetobacter isolates representative of the Ab group were used to calculate the average spectra/species and generate pattern recognition models. Species-specific peaks were identified for all species, and MSPs derived from three A. seifertii, two A. dijkshoorniae, and two A. nosocomialis strains were added to the Bruker taxonomy database, allowing successful identification of all isolates using spectra from either bacterial extracts or direct colonies, resulting in a positive predictive value (PPV) of 99.6% (777/780) and 96.8% (302/312), respectively.

CONCLUSIONS

The use of post-processing data software identified statistically significant species-specific peaks to generate reference signatures for rapid accurate identification of species within the Ab group, providing relevant information for the clinical management of Acinetobacter infections.

Biotechnological tools to improve bioremediation of phenol by Acinetobacter sp. RTE1.4

The use of native bacteria is a useful strategy to decontaminate industrial effluents as well as the environment. Acinetobacter sp. RTE1.4 was previously isolated from polluted environments and constitutes a promising alternative for this purpose due to its capability to remove phenol from synthetic solutions and industrial effluents. In this work, this strain was identified at species level as A. tandoii RTE1.4. Phenol degradation pathway was studied and some reaction intermediates were detected, confirming that this strain degraded phenol through ortho-cleavage of the aromatic ring. Phenol removal assays were carried out in a stirred tank bioreactor and a complete degradation of the contaminant was achieved after only 7 h, at an aeration rate of 3 vvm and at agitation of 600 rpm. Moreover, this bacterium was immobilized into calcium alginate beads and an increase in phenol biodegradation with respect to free cells was observed. The immobilized cells were reused for four consecutive cycles and stored at 4°C for 9 months, during which phenol removal efficiency was maintained. Post-removal solutions were evaluated by Microtox® test, showing a toxicity reduction after bacterial treatment. These findings demonstrated that A. tandoii RTE1.4 might be considered as a useful biotechnological tool for an efficient treatment of different solutions contaminated with phenol in bioreactors, using either free or immobilized cells.

Rapid detection of Acinetobacter baumannii and molecular epidemiology of carbapenem-resistant A. baumannii in two comprehensive hospitals of Beijing, China

Acinetobacter baumannii is an important opportunistic pathogen associated with a variety of nosocomial infections. A rapid and sensitive molecular detection in clinical isolates is quite needed for the appropriate therapy and outbreak control of A. baumannii. Group 2 carbapenems have been considered the agents of choice for the treatment of multiple drug-resistant A. baumannii. But the prevalence of carbapenem-resistant A. baumannii (CRAB) has been steadily increasing in recent years. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of A. baumannii in clinical samples by using high-specificity primers of the bla OXA-51 gene. Then we investigated the OXA-carbapenemases molecular epidemiology of A. baumannii isolates in two comprehensive hospitals in Beijing. The results showed that the LAMP assay could detect target DNA within 60 min at 65°C. The detection limit was 50 pg/μl, which was about 10-fold greater than that of PCR. Furthermore, this method could distinguish A. baumannii from the homologous A. nosocomialis and A. pittii. A total of 228 positive isolates were identified by this LAMP-based method for A. baumannii from 335 intensive care unit patients with clinically suspected multi-resistant infections in two hospitals in Beijing. The rates of CRAB are on the rise and are slowly becoming a routine phenotype for A. baumannii. Among the CRABs, 92.3% harbored both the bla OXA-23 and bla OXA-51 genes. Thirty-three pulsotypes were identified by pulsed-field gel electrophoresis, and the majority belonged to clone C. In conclusion, the LAMP method developed for detecting A. baumannii was faster and simpler than conventional PCR and has great potential for both point-of-care testing and basic research. We further demonstrated a high distribution of class D carbapenemase-encoding genes, mainly OXA-23, which presents an emerging threat in hospitals in China.

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.

Clinical Specimen-Direct LAMP: A Useful Tool for the Surveillance of blaOXA-23-Positive Carbapenem-Resistant Acinetobacter baumannii

Healthcare-associated infections are a leading cause of morbidity and mortality worldwide. Treatment is increasingly complicated by the escalating incidence of antimicrobial resistance. Among drug-resistant pathogens, carbapenem-resistant Acinetobacter baumannii (CRAb) is of increasing concern because of the limited applicable therapies and its expanding global distribution in developed countries and newly industrialized countries. Therefore, a rapid detection method that can be used even in resource-poor countries is urgently required to control this global public health threat. Conventional techniques, such as bacterial culture and polymerase chain reaction (PCR), are insufficient to combat this threat because they are time-consuming and laborious. In this study, we developed a loop-mediated isothermal amplification (LAMP) method for detecting bla_OXA-23-positive CRAb, the most prevalent form of CRAb in Asia, especially in Thailand, and confirmed its efficacy as a surveillance tool in a clinical setting. Clinical samples of sputum and rectal swabs were collected from patients in a hospital in Bangkok and used for LAMP assays. After boiling and centrifugation, the supernatants were used directly in the assay. In parallel, a culture method was used for comparison purposes to evaluate the specificity and sensitivity of LAMP. As a first step, a total of 120 sputum samples were collected. The sensitivity of LAMP was 88.6% (39/44), and its specificity was 92.1% (70/76) using the culture method as the “gold standard”. When surveillance samples including sputum and rectal swabs were analyzed with the LAMP assay, its sensitivity was 100.0%. This method enables the direct analysis of clinical specimens and provides results within 40 minutes of sample collection, making it a useful tool for surveillance even in resource-poor countries.

Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes

BACKGROUND

Acinetobacter spp. is a diverse group of Gram-negative bacteria which are ubiquitous in soil and water, and an important cause of nosocomial infections. The purpose of this study was to identify a collection of Acinetobacter spp. clinical isolates accurately and to investigate their antibiotic susceptibility patterns.

MATERIALS AND METHODS

A total of 197 non-duplicate clinical isolates of Acinetobacter spp. isolates identified using conventional biochemical tests. The molecular technique of PCR-RFLP and sequence analysis of rpoB and 16S rRNA genes was applied for species identification. Antimicrobial susceptibility test was performed with a disk diffusion assay.

RESULTS

Based on 16S rRNA and rpoB genes analysis separately, most of clinical isolates can be identified with high bootstrap values. However, the identity of the isolate 555T was uncertain due to high similarity of A. grimontii and A. junii. Identification by concatenation of 16S rRNA and rpoB confirmed the identity of clinical isolates of Acenitobacer to species level confidently. Accordingly, the isolate 555T assigned as A. grimontii due to 100% similarity to A. grimontii. Moreover, this isolate showed 98.64% to A. junii. Besides, the identity of the isolates 218T and 364T was confirmed as Genomic species 3 and A. calcoaceticus respectively. So, the majority of Acinetobacter spp. isolates, were identified as: A. baumannii (131 isolates, 66%), A. calcoaceticus (9 isolates, 4.5%), and A. genomosp 16 (8 isolates, 4%). The rest of identified species showed the lower frequencies. In susceptibility test, 105 isolates (53%), presented high antibiotic resistance of 90% to ceftriaxone, piperacillin, piperacillin tazobactam, amikacin, and 81% to ciprofloxacin.

CONCLUSION

Sequence analysis of the 16S rRNA and rpoB spacer simultaneously was able to do identification of Acinetobacter spp. to species level. A.baumannii was identified as the most prevalent species with high antibiotic resistance. Other species showed lower frequencies ranged from 4 to 9 strains.

Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for species identification of nonfermenting Gram-negative bacilli

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to identify 396 Nonfermenting Gram-Negative Bacilli clinical isolates was evaluated in comparison with conventional phenotypic tests and/or molecular methods. MALDI-TOF MS identified to species level 256 isolates and to genus or complex level 112 isolates. It identified 29 genera including uncommon species.

[Frequency and antimicrobial resistance of Acinetobacter species in a university hospital of Buenos Aires City]

Two-hundred Acinetobacter isolates belonging to 200 patients admitted to Hospital de Clínicas José de San Martín during the period March 2013-June 2014 were analyzed. The identification was performed by mass spectrometry and was confirmed by molecular methods. Susceptibility to antimicrobials was studied by the Vitek-2 system. A 94% correlation of both identification methods was found. Multidrug resistant Acinetobacter baumannii was the predominant genomic species (92.6%) in hospital-acquired infections, whereas Acinetobacter pitti and Acinetobacter nosocomialis accounted for 3.5% and 0.5% of the isolates recovered, respectively. In community-acquired infections a major predominance of the different genomic species was observed. Acinetobacter johnsonii and A. baumannii are the most frequent species, accounting for 45.9% of the isolates recovered. Resistance to carbapenems and minocycline was only observed in A. baumannii. Mass spectrophotometry was an effective tool for the identification of the different genomic species.

Characterization and plasmid elimination of NDM-1-producing Acinetobacter calcoaceticus from China

The presence of multidrug-resistant bacterial pathogens in the environment poses a serious threat to public health. The opportunistic Acinetobacter spp. are among the most prevalent causes of nosocomial infections. Here, we performed complete genome sequencing of the Acinetobacter calcoaceticus strain XM1570, which was originally cultivated from the sputum of a patient diagnosed with pneumonia in Xiamen in 2010. We identified carbapenem resistance associated gene bla_NDM-1 located on a 47.3-kb plasmid. Three methods – natural reproduction, sodium dodecyl sulfate treatment and nalidixic acid treatment – were used to eliminate the bla_NDM-1-encoding plasmid, which achieved elimination rates of 3.32% (10/301), 83.78% (278/332), and 84.17% (298/354), respectively. Plasmid elimination dramatically increased antibiotic sensitivity, reducing the minimum bacteriostatic concentration of meropenem from 256 µg/ml in the clinical strain to 0.125 µg/ml in the plasmid-eliminated strain. Conjugation transfer assays showed that the bla_NDM-1-containing plasmid could be transferred into Escherichia coli DH5α:pBR322 in vitro as well as in vivo in mice. The bla_NDM-1 genetic environment was in accordance with that of other bla_NDM-1 genes identified from India, Japan, and Hong-Kong. The multilocus sequence type of the isolate was identified as ST-70. Two novel genes encoding intrinsic OXA and ADC were identified and named as OXA-417 and ADC-72. The finding of bla_NDM-1 in species like A. calcoaceticus demonstrates the wide spread of this gene in gram-negative bacteria which is possible by conjugative plasmid transfer. The results of this study may help in the development of a treatment strategy for controlling NDM-1 bacterial infection and transmission.

MALDI-TOF: A useful tool for laboratory identification of uncommon glucose non-fermenting Gram-negative bacteria associated with cystic fibrosis

The predisposition of patients with cystic fibrosis (CF) for recurrent pulmonary infections can result in poor prognosis of the disease. Although the clinical significance in CF of micro-organisms, such as Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa, is well established, the implication of uncommon glucose non-fermenting Gram-negative bacilli (UGNF-GNB) in respiratory samples from CF patients is still unclear. Because of limitations of traditional methods used in most clinical laboratories, the accurate identification of these microbes is a challenge. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) is an alternative tool for efficient identification of bacteria. This was a retrospective study to evaluate different identification methods in a collection of UGNF-GNB isolated from children with CF during a period of three years. The performance of MALDI-TOF was compared to that of 16S rDNA gene sequencing and to a conventional and automated phenotypic identification. The discriminatory power of MALDI-TOF (75.0 % agreement) was superior to automated techniques (67.1 % agreement) and to conventional phenotypical identification (50.0 % agreement). MALDI-TOF also demonstrated high accuracy in identifying Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Chryseobacterium indologenes, but had limited utility in identifying Pandoraea spp. and some species of Acinetobacter and Chryseobacterium (other than C. indologenes). Although MALDI-TOF identified only 75 % of the isolates in comparison with 16S rDNA gene sequencing, the prompt identification and high discriminatory power exhibited by MALDI-TOF make it a useful tool for the characterization of micro-organisms that are difficult to identify using routine methods.

Species distribution of clinical Acinetobacter isolates revealed by different identification techniques

A total of 2582 non-duplicate clinical Acinetobacter spp. isolates were collected to evaluate the performance of four identification methods because it is important to identify Acinetobacter spp. accurately and survey the species distribution to determine the appropriate antimicrobial treatment. Phenotyping (VITEK 2 and VITEK MS) and genotyping (16S rRNA and rpoB gene sequencing) methods were applied for species identification, and antimicrobial susceptibility test of imipenem and meropenem was performed with a disk diffusion assay. Generally, the phenotypic identification results were quite different from the genotyping results, and their discrimination ability was unsatisfactory, whereas 16S rRNA and rpoB gene sequencing showed consistent typing results, with different resolution. Additionally, A. pittii, A. calcoaceticus and A. nosocomialis, which were phylogenetically close to A. baumannii, accounted for 85.5% of the non-A. baumannii isolates. One group, which could not be clustered with any reference strains, consisted of 11 isolates and constituted a novel Acinetobacter species that was entitled genomic species 33YU. None of the non-A. baumannii isolates harbored a bla_OXA-51-like gene, and this gene was disrupted by ISAba19 in only one isolate; it continues to be appropriate as a genetic marker for A. baumannii identification. The resistance rate of non-A. baumannii isolates to imipenem and/or meropenem was only 2.6%, which was significantly lower than that of A. baumannii. Overall, rpoB gene sequencing was the most accurate identification method for Acinetobacter species. Except for A. baumannii, the most frequently isolated species from the nosocomial setting were A. pittii, A. calcoaceticus and A. nosocomialis.

Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Acinetobacter species

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker Biotyper) was able to accurately identify 98.6% (142/144) of Acinetobacter baumannii isolates, 72.4% (63/87) of A. nosocomialis isolates, and 97.6% (41/42) of A. pittii isolates. All Acinetobacter junii, A. ursingii, A. johnsonii, and A. radioresistens isolates (n = 28) could also be identified correctly by Bruker Biotyper.

MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species

MALDI-TOF MS is becoming the technique of choice for rapid bacterial identification at species level in routine diagnostics. However, some drawbacks concerning the identification of closely related species such as those belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex lead to high rates of misidentifications. In this work we successfully developed an approach that combines MALDI-TOF MS and chemometric tools to discriminate the six Acb complex species (A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, A. calcoaceticus, genomic species "Close to 13TU" and genomic species "Between 1 and 3"). Mass spectra of 83 taxonomically well characterized clinical strains, reflecting the breadth of currently known phenetic diversity within the Acb complex, were achieved from intact cells and cell extracts and analyzed with hierarchical cluster analysis (HCA) and partial least squares discriminant analysis (PLSDA). This combined approach lead to 100% of correct species identification using mass spectra obtained from intact cells. Moreover, it was possible to discriminate two Acb complex species (genomic species "Close to 13TU" and genomic species "Between 1 and 3") not included in the MALDI Biotyper database.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Rapid identification and discrimination of bacterial strains by laser induced breakdown spectroscopy and neural networks

Identification and discrimination of bacterial strains of same species exhibiting resistance to antibiotics using laser induced breakdown spectroscopy (LIBS) and neural networks (NN) algorithm is reported. The method has been applied to identify 40 bacterial strains causing hospital acquired infections (HAI), i.e. Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Salmonella typhimurium, Salmonella pullurum and Salmonella salamae. The strains analyzed included both isolated from clinical samples and constructed in laboratory that differ in mutations as a result of their resistance to one or more antibiotics. Small changes in the atomic composition of the bacterial strains, as a result of their mutations and genetic variations, were detected by the LIBS-NN methodology and led to their identification and classification. This is of utmost importance because solely identification of bacterial species is not sufficient for disease diagnosis and identification of the actual strain is also required. The proposed method was successfully able to discriminate strains of the same bacterial species. The optimized NN models provided reliable bacterial strain identification with an index of spectral correlation higher than 95% for the samples analyzed, showing the potential and effectiveness of the method to address the safety and social-cost HAI-related issue.

Comparison of rpoB gene sequencing, 16S rRNA gene sequencing, gyrB multiplex PCR, and the VITEK2 system for identification of Acinetobacter clinical isolates

Since accurate identification of species is necessary for proper treatment of Acinetobacter infections, we compared the performances of 4 bacterial identification methods using 167 Acinetobacter clinical isolates to identify the best identification method. To secure more non-baumannii Acinetobacter (NBA) strains as target strains, we first identified Acinetobacter baumannii in a total of 495 Acinetobacter clinical isolates identified using the VITEK 2 system. Because 371 of 495 strains were identified as A. baumannii using gyrB multiplex 1 PCR and blaOXA51-like PCR, we performed rpoB gene sequencing and 16S rRNA gene sequencing on remaining 124 strains belonging to NBA and 52 strains of A. baumannii. For identification of Acinetobacter at the species level, the accuracy rates of rpoB gene sequencing, 16S rRNA gene sequencing, gyrB multiplex PCR, and the VITEK 2 were 98.2%, 93.4%, 77.2%, and 35.9%, respectively. The gyrB multiplex PCR seems to be very useful for the detection of ACB complex because its concordance rates to the final identification of strains of ACB complex were 100%. Both the rpoB gene sequencing and the 16S rRNA gene sequencing may be useful in identifying Acinetobacter.

Multi-center evaluation of the VITEK® MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli

Studies have demonstrated that matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate method for the identification of clinically relevant bacteria. The purpose of this study was to evaluate the performance of the VITEK MS v2.0 system (bioMérieux) for the identification of the non-Enterobacteriaceae Gram-negative bacilli (NEGNB). This multi-center study tested 558 unique NEGNB clinical isolates, representing 18 genera and 33 species. Results obtained with the VITEK MS v2.0 were compared with reference 16S rRNA gene sequencing and when indicated recA sequencing and phenotypic analysis. VITEK MS v2.0 provided an identification for 92.5 % of the NEGNB isolates (516 out of 558). VITEK MS v2.0 correctly identified 90.9 % of NEGNB (507 out of 558), 77.8 % to species level and 13.1 % to genus level with multiple species. There were four isolates (0.7 %) incorrectly identified to genus level and five isolates (0.9 %), with one incorrect identification to species level. The remaining 42 isolates (7.5 %) were either reported as no identification (5.0 %) or called "mixed genera" (2.5 %) since two or more different genera were identified as possible identifications for the test organism. These findings demonstrate that the VITEK MS v2.0 system provides accurate results for the identification of a challenging and diverse group of Gram-negative bacteria.

Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry

During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry in clinical microbiology

Despite widespread application of nucleic acid diagnostics, cultures remain integral in modern laboratories. Because cultures detect a large number of organism types, it is unlikely that they will disappear from clinical practice in the near future. Their downside is slow turn-around time, impacted by time to growth and identification of that growth. The latter is expedited using a new proteomic technology, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

Optimized method for Acinetobacter species carbapenemase detection and identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry

The use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid detection and identification of the enzymes responsible for carbapenem resistance in Acinetobacter spp. appears as a promising option, but it will be necessary to have a standardized protocol that facilitates routine use. Based on the results reported herein and comparisons of several previously published reports, we identified the significant peaks for imipenem detection. Optimal bacterial inoculum and incubation time were established, and results obtained with and without dipicolinic acid (DPA) and Zn(2+) allowed us to distinguish between metallo-beta-lactamases and oxacillinases.