Identification of Acinetobacter Species Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Optimizing Treatment for Carbapenem-Resistant Acinetobacter baumannii Complex Infections: A Review of Current Evidence

Carbapenem-resistant Acinetobacter baumannii complex (CRAB) poses a significant global health challenge owing to its resistance to multiple antibiotics and limited treatment options. Polymyxin-based therapies have been widely used to treat CRAB infections; however, they are associated with high mortality rates and common adverse events such as nephrotoxicity. Recent developments include numerous observational studies and randomized clinical trials investigating antibiotic combinations, repurposing existing antibiotics, and the development of novel agents. Consequently, recommendations for treating CRAB are undergoing significant changes. The importance of colistin is decreasing, and the role of sulbactam, which exhibits direct antibacterial activity against A. baumannii complex, is being reassessed. High-dose ampicillin-sulbactam-based combination therapies, as well as combinations of sulbactam and durlobactam, which prevent the hydrolysis of sulbactam and binds to penicillin-binding protein 2, have shown promising results. This review introduces recent advancements in CRAB infection treatment based on clinical trial data, highlighting the need for optimized treatment protocols and comprehensive clinical trials to combat the evolving threat of CRAB effectively.

A novel major facilitator superfamily-type tripartite efflux system CprABC mediates resistance to polymyxins in Chryseobacterium sp. PL22-22A

Background

Polymyxin B (PMB) and polymyxin E (colistin, CST) are polymyxin antibiotics, which are considered last-line therapeutic options against multidrug-resistant Gram-negative bacteria in serious infections. However, there is increasing risk of resistance to antimicrobial drugs. Effective efflux pump inhibitors (EPIs) should be developed to help combat efflux pump-mediated antibiotic resistance.

Methods

Chryseobacterium sp. PL22-22A was isolated from aquaculture sewage under selection with 8 mg/L PMB, and then its genome was sequenced using Oxford Nanopore and BGISEQ-500 platforms. Cpr (Chryseobacterium Polymyxins Resistance) genes encoding a major facilitator superfamily-type tripartite efflux system, were found in the genome. These genes, and the gene encoding a truncation mutant of CprB from which sequence called CprBc was deleted, were amplified and expressed/co-expressed in Escherichia coli DH5α. Minimum inhibitory concentrations (MICs) of polymyxins toward the various E. coli heterologous expression strains were tested in the presence of 2-128 mg/L PMB or CST. The pumping activity of CprABC was assessed via structural modeling using Discovery Studio 2.0 software. Moreover, the influence on MICs of baicalin, a novel MFS EPI, was determined, and the effect was analyzed based on homology modeling.

Results

Multidrug-resistant bacterial strain Chryseobacterium sp. PL22-22A was isolated in this work; it has notable resistance to polymyxin, with MICs for PMB and CST of 96 and 128 mg/L, respectively. A novel MFS-type tripartite efflux system, named CprABC, was identified in the genome of Chryseobacterium sp. PL22-22A. Heterologous expression and EPI assays indicated that the CprABC system is responsible for the polymyxin resistance of Chryseobacterium sp. PL22-22A. Structural modeling suggested that this efflux system provides a continuous conduit that runs from the CprB funnel through the CprC porin domain to pump polymyxins out of the cell. A specific C-terminal α-helix, CprBc, has an activation function on polymyxin excretion by CprB. The flavonoid compound baicalin was found to affect the allostery of CprB and/or obstruct the substrate conduit, and thus to inhibit extracellular polymyxin transport by CprABC.

Conclusion

Novel MFS-type tripartite efflux system CprABC in Chryseobacterium sp. PL22-22A mediates resistance to polymyxins, and baicalin is a promising EPI.

An efflux pump in genomic island GI-M202a mediates the transfer of polymyxin B resistance in Pandoraea pnomenusa M202

BACKGROUND

Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious infections. However, the risk of antimicrobial resistance and its spread to the environment should be brought to the forefront.

METHODS

Pandoraea pnomenusa M202 was isolated under selection with 8 mg/L polymyxin B from hospital sewage and then was sequenced by the PacBio RS II and Illumina HiSeq 4000 platforms. Mating experiments were performed to evaluate the transfer of the major facilitator superfamily (MFS) transporter in genomic islands (GIs) to Escherichia coli 25DN. The recombinant E. coli strain Mrc-3 harboring MFS transporter encoding gene FKQ53_RS21695 was also constructed. The influence of efflux pump inhibitors (EPIs) on MICs was determined. The mechanism of polymyxin B excretion mediated by FKQ53_RS21695 was investigated by Discovery Studio 2.0 based on homology modeling.

RESULTS

The MIC of polymyxin B for the multidrug-resistant bacterial strain P. pnomenusa M202, isolated from hospital sewage, was 96 mg/L. GI-M202a, harboring an MFS transporter-encoding gene and conjugative transfer protein-encoding genes of the type IV secretion system, was identified in P. pnomenusa M202. The mating experiment between M202 and E. coli 25DN reflected the transferability of polymyxin B resistance via GI-M202a. EPI and heterogeneous expression assays also suggested that the MFS transporter gene FKQ53_RS21695 in GI-M202a was responsible for polymyxin B resistance. Molecular docking revealed that the polymyxin B fatty acyl group inserts into the hydrophobic region of the transmembrane core with Pi-alkyl and unfavorable bump interactions, and then polymyxin B rotates around Tyr43 to externally display the peptide group during the efflux process, accompanied by an inward-to-outward conformational change in the MFS transporter. Additionally, verapamil and CCCP exhibited significant inhibition via competition for binding sites.

CONCLUSIONS

These findings demonstrated that GI-M202a along with the MFS transporter FKQ53_RS21695 in P. pnomenusa M202 could mediate the transmission of polymyxin B resistance.

Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods

Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).

Role of Feeding and Novel Ripening System to Enhance the Quality and Production Sustainability of Curd Buffalo Cheeses

The buffalo dairy sector is extending its boundaries to include new buffalo cheese productions beyond mozzarella, overcoming some barriers that make cheeses expensive and unsustainable. This study aimed to evaluate the effects of both the inclusion of green feed in the diet of Italian Mediterranean buffaloes and an innovative ripening system on buffalo cheese quality, providing solutions capable of guaranteeing the production of nutritionally competitive and sustainable products. For this purpose, chemical, rheological, and microbiological analyses were carried out on cheeses. Buffaloes were fed with or without the inclusion of green forage. Their milk was used to produce dry ricotta and semi-hard cheeses, ripened according to both respective traditional (MT) and innovative methods (MI); these are based on automatic adjustments of climatic recipe guided by the continuous control of pH. Green feed enhances the nutritional profile of the final products (high content of MUFAs and PUFAs). As far as the ripening method is concerned, to our knowledge, this is the first study that tests aging chambers, commonly used for meat, for the maturing of buffalo cheeses. Results pointed out the MI validity also in this field of application, as it shortens the ripening period without negatively compromising any of desirable physicochemical properties and the safety and hygiene of the final products. Conclusively, this research highlights the benefits of diets rich in green forage on productions and provides support for the ripening optimization of buffalo semi-hard cheeses.

Community-Acquired Acinetobacter radioresistens Bacteremia in an Immunocompetent Host

Acinetobacter species are gram-negative coccobacilli ubiquitous in nature and widely distributed in the environment. Acinetobacter baumannii is a bacteria commonly seen in the hospital setting, responsible for causing a wide range of bloodstream infections, urinary tract infections, secondary meningitis, infective endocarditis, and wound infections, and is the cause of outbreaks mainly due to its antimicrobial resistance patterns. The use of broad-spectrum antibiotic coverage with carbapenems is essential in the hospital setting. Therefore, carbapenem-resistant Acinetobacter baumannii (CRAB) poses as a very challenging pathogen. Acinetobacter radioresistens, a rare species in comparison to the more prevalent Acinetobacter baumannii, is an underestimated agent in causing nosocomial infections and also is a potential disseminator of resistance genes. It is also resistant to gamma radiation at 4-8 times higher than other Acinetobacter spp. and is the source of the class D OXA-23 carbapenemase that can confer carbapenem resistance. Therefore, immediate and precise identification of A. radioresistens is crucial for the clinical management of multidrug-resistant bacteremia.

Emergence and multi-lineages of carbapenemase-producing Acinetobacter baumannii-calcoaceticus complex from canine and feline origins

The carbapenemase-producing Acinetobacter baumannii is an important opportunistic bacterium and frequently causes hospital-acquired infections in humans. It also has increasingly been reported in veterinary medicine. This study illustrates multiple clones of carbapenemase-producing A. baumannii disseminating and causing diseases in dogs and cats in Thailand. Between 2016 and 2020, 44 A. baumannii and two A. pittii isolates exhibiting imipenem resistance (MIC≥16 μg/mL) from diagnostic samples were characterized by Pasteur multilocus sequence typing (MLST), sequence grouping (SG), repetitive extragenic palindromic element (rep)-PCR fingerprint analysis and antimicrobial resistance (AMR) profiling. All isolates contained bla_OXA-23 in the Tn2006 family, and A. baumannii showed the sequence type (ST) 16 (14/44), ST149 (12/44), ST25 (6/44), ST2 (4/44), ST1581 (3/44), ST23 (2/44), ST1575 (1/44) and ST1576 (1/44). DNA fingerprint analysis and SG illustrated clonal relationships in the STs and its single locus variants, and AMR gene profiles, including tetracycline and aminoglycoside resistance genes, showed minor variations in the clones. The findings suggest that bla_OXA-23 has been spread in multiple clones of A. baumannii and A. pittii from canine and feline hosts. With the collection of multiple AMR genes and intrinsic resistance, antimicrobial options are limited for treatment, and pets can be a potential reservoir of extensively drug-resistant, carbapenemase-producing A. baumannii in the community. Epidemiological tracking by passive and active surveillance in animals, veterinary personnel and hospital environment and preventive measurements should be promoted to decrease the risk of infection and transmission to humans.

Characterization of Microbiological Quality of Whole and Gutted Baltic Herring

There is growing interest in Baltic herring (Clupea harengus membras) and other undervalued, small-sized fish species for human consumption. Gutting or filleting of small-sized fish is impractical; hence, the aim of this study was to explore the suitability of the whole (ungutted) herring for food use. The microbiological quality of commercially fished whole and gutted herring was analysed with culture-dependent methods combined with identification of bacterial isolates with MALDI-TOF Mass Spectrometry and culture-independent 16S rRNA gene amplicon sequencing. Whole and gutted herring had between 2.8 and 5.3 log₁₀ CFU g⁻¹ aerobic mesophilic and psychrotrophic bacteria and between 2.2 and 5.6 log₁₀ CFU g⁻¹ H₂S-producing bacteria. Enterobacteria counts remained low in all the analysed herring batches. The herring microbiota largely comprised the phyla Proteobacteria, Firmicutes, and Actinobacteria (71.7% to 95.0%). Shewanella, Pseudomonas, and Aeromonas were the most frequently isolated genera among the viable population; however, with the culture-independent approach, Shewanella followed by Psychrobacter were the most abundant genera. In some samples, a high relative abundance of the phylum Epsilonbacteraeota, represented by the genus Arcobacter, was detected. This study reports the bacterial diversity present in Baltic herring and shows that the microbiological quality was acceptable in all the analysed fish batches.

Evaluation of a Rapid and Simplified Protocol for Direct Identification of Microorganisms From Positive Blood Cultures by Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

Early and rapid identification of microorganisms is critical for reducing the mortality rate caused by bloodstream infections (BSIs). The accuracy and feasibility of directly identifying pathogens in positive blood cultures by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been intensely confirmed. In this study, we combined density centrifugation and extra chemical lysis-extraction to develop an optimized method in the blood culture process, which significantly improved the effectiveness of direct identification by MALDI-TOF MS. The accuracy was evaluated by 2,032 positive blood culture samples (115 species of microorganism). The overall MALDI-TOF MS based identification rate with scores ≥ 1.700 was 87.60%. 94.06% of gram-negative bacteria were identified consistently to the genus level, followed by anaerobes (93.33%), gram-positive bacteria (84.46%), and fungi (60.87%). This protocol could obtain results within 10–20 min at a cost of less than $0.1 per sample, which saved up to 24 h in identifying 87.60% of the microorganism from positive blood cultures. This rapid and simplified protocol facilitates the direct identification of microorganism in positive blood cultures, and exhibits the advantages of cost-effective, time-saving, and easy-to-use. It could provide the causative organism of the patient to clinicians in time for targeted treatment and reduce mortality.

Acinetobacter baumannii: Its Clinical Significance in Human and Veterinary Medicine

Acinetobacter baumannii is a Gram-negative, opportunistic pathogen, causing severe infections difficult to treat. The A. baumannii infection rate has increased year by year in human medicine and it is also considered as a major cause of nosocomial infections worldwide. This bacterium, also well known for its ability to form biofilms, has a strong environmental adaptability and the characteristics of multi-drug resistance. Indeed, strains showing fully resistant profiles represent a worrisome problem in clinical therapeutic treatment. Furthermore, A. baumannii-associated veterinary nosocomial infections has been reported in recent literature. Particularly, carbapenem-resistant A. baumannii can be considered an emerging opportunistic pathogen in human medicine as well as in veterinary medicine.

Acinetobacter baumannii as a community foodborne pathogen: Peptide mass fingerprinting analysis, genotypic of biofilm formation and phenotypic pattern of antimicrobial resistance

Acinetobacter baumannii (A. baumannii) is one of the most common Gram-negative pathogens that represent a major threat to human life. Because the prevalence of Multidrug-resistant biofilm-forming A. baumannii is increasing all over the world, this may lead to outbreaks of hospital infections. Nonetheless, the role of raw meat as a reservoir for A. baumannii remains unclear. Here our research was aimed to exhibit the frequency, precise identification, and genotyping of biofilm-related genes as well as antimicrobial resistance of A. baumannii isolates of raw meat specimens. Fifty-five A. baumannii strains were recovered from 220 specimens of different animal meat and then identified by Peptide Mass Fingerprinting Technique (PMFT). All identified isolates were genotyped by the qPCR method for the existence of biofilm-related genes (ompA, bap, blaPER-1, csuE, csgA, and fimH). In addition, the antimicrobial resistance against A. baumannii was detected by the Kirby-Bauer method. Based on our findings, the frequency rate of 55 A. baumannii isolates was 46.55%, 32.50%, 15.00%, and 9.68% of sheep, chicken, cow, and camel raw meat samples, respectively. The PMFT was able to identify all strains by 100%. the percentages of csuE, ompA, bla_PER-1, bap, and csgA genes in biofilm and non-biofilm producer A. baumannii were 72.73%, 60%, 58.2%, 52.74%, and 25.45%, respectively. In contrast, the fimH was not detected in all non-biofilm and biofilm producer strains. The ompA, bap, blaPER-1, csgA were detected only in biofilm-producing A. baumannii isolates. The maximum degree of resistance was observed against amoxicillin/clavulanic acid (89.10%), gentamicin (74.55%), tetracycline (72.73%), ampicillin (65.45%), and tobramycin (52.73%). In conclusion, our investigation demonstrated the high incidence of multi-drug resistant A. baumannii in raw meat samples, with a high existence of biofilm-related virulence genes of ompA, bap, blaPER-1, csgA. Therefore, it has become necessary to take the control measures to limit the development of A. baumannii.

The carbapenem resistance gene blaOXA-23 is disseminated by a conjugative plasmid containing the novel transposon Tn6681 in Acinetobacter johnsonii M19

Background

Carbapenem resistant Acinetobacter species have caused great difficulties in clinical therapy in the worldwide. Here we describe an Acinetobacter johnsonii M19 with a novel bla_OXA-23 containing transposon Tn6681 on the conjugative plasmid pFM-M19 and the ability to transferand carbapenem resistance.

Methods

A. johnsonii M19 was isolated under selection with 8 mg/L meropenem from hospital sewage, and the minimum inhibitory concentrations (MICs) for the representative carbapenems imipenem, meropenem and ertapenem were determined. The genome of A. johnsonii M19 was sequenced by PacBio RS II and Illumina HiSeq 4000 platforms. A homologous model of OXA-23 was generated, and molecular docking models with imipenem, meropenem and ertapenem were constructed by Discovery Studio 2.0. Type IV secretion system and conjugation elements were identified by the Pathosystems Resource Integration Center (PATRIC) server and the oriTfinder. Mating experiments were performed to evaluate transfer of OXA-23 to Escherichia coli 25DN.

Results

MICs of A. johnsonii M19 for imipenem, meropenem and ertapenem were 128 mg/L, 48 mg/L and 24 mg/L, respectively. Genome sequencing identified plasmid pFM-M19, which harbours the carbapenem resistance gene bla_OXA-23 within the novel transposon Tn6681. Molecular docking analysis indicated that the elongated hydrophobic tunnel of OXA-23 provides a hydrophobic environment and that Lys-216, Thr-217, Met-221 and Arg-259 were the conserved amino acids bound to imipenem, meropenem and ertapenem. Furthermore, pFM-M19 could transfer bla_OXA-23 to E. coli 25DN by conjugation, resulting in carbapenem-resistant transconjugants.

Conclusions

Our investigation showed that A. johnsonii M19 is a source and disseminator of bla_OXA-23 and carbapenem resistance. The ability to transfer bla_OXA-23 to other species by the conjugative plasmid pFM-M19 raises the risk of spread of carbapenem resistance.

Graphic abstract

The carbapenem resistance gene bla_OXA-23 is disseminated by a conjugative plasmid containing the novel transposon Tn6681 in Acinetobacter johnsonii M19.

Evaluation of microbial contamination of different pork carcass areas through culture-dependent and independent methods in small-scale slaughterhouses

Routine evaluation of the slaughter process is performed by the enumeration of the aerobic colony count, Enterobacteriaceae and Salmonella spp. on the carcass through destructive or non-destructive methods. With non-destructive methods, bacteria are counted from a minimum area of 100 cm² in different sampling sites on the pork carcasses, and the results of these investigated areas are pooled to one value for the complete carcass evaluation (a total of 400 cm²). However, the composition of the bacterial community present on the different sampling areas remains unknown. The aim of the study was to characterize the microbial population present on four areas (ham, back, jowl and belly) of eight pork carcasses belonging to two different slaughterhouses through culture-dependent (Matrix-assisted laser desorption/ionization time-of-flight Mass Spectrometry MALDI-TOF MS, combined with 16S rRNA gene sequencing) and complementary culture-independent (16S rRNA amplicon sequencing) methods. The presence of Salmonella spp. and Y. enterocolitica was additionally assessed. Using MALDI-TOF MS, Staphylococcus, Pseudomonas, and Escherichia coli were found to dominate the bacterial cultures isolated from the 8 carcasses. Based on the 16S rRNA amplicon sequencing analyses however, no specific genus clearly dominated the bacterial community composition. By using this culture-independent method, the most abundant genera in microbial populations of the ham, back, jowl and belly were found to be similar, but important differences between the two slaughterhouses were observed. Thus, present data suggests that the indigenous bacterial population of individual animals is overruled by the microbial population of the slaughterhouse in which the carcass is handled. Also, our data suggests that sampling of only one carcass area by official authorities may be appropriate for the evaluation of the hygienic status of the carcasses and therefore of the slaughter process.

Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex

Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.

Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus

Acinetobacter haemolyticus is a Gammaproteobacterium that has been involved in serious diseases frequently linked to the nosocomial environment. Most of the strains causing such infections are sensitive to a wide variety of antibiotics, but recent reports indicate that this pathogen is acquiring very efficiently carbapenem-resistance determinants like the blaNDM-1 gene, all over the world. With this work we contribute with a collection set of 31 newly sequenced nosocomial A. haemolyticus isolates. Genome analysis of these sequences and others collected from RefSeq indicates that their chromosomes are organized in 12 syntenic blocks that contain most of the core genome genes. These blocks are separated by hypervariable regions that are rich in unique gene families, but also have signals of horizontal gene transfer. Genes involved in virulence or encoding different secretion systems are located inside syntenic regions and have recombination signals. The relative order of the synthetic blocks along the A. haemolyticus chromosome can change, indicating that they have been subject to several kinds of inversions. Genomes of this microorganism show large differences in gene content even if they are in the same clade. Here we also show that A. haemolyticus has an open pan-genome.

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.

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing

Wild boars (Sus scrofa) are the most widely distributed large mammals and recent increase in consumption of wild boar meat urges the need of microbiological quality criteria. The aim of the study was to characterize the initial bacterial contamination on freshly-killed wild boar meat using a culture-dependent approach with ISO-methods combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification and 16S rRNA amplicon sequencing. Moreover, the presence of foodborne pathogens was examined using Real-Time-PCR and confirmed by classical isolation. Analysing 22 unrelated wild boar meat samples showed a higher bacterial contamination level compared to pork, with Salmonella present in almost one third of the samples. A great variability of the microbial contamination between the samples was recorded, as well as complementary results between culturing and 16S rRNA amplicon sequencing as frequently isolated genera were not always detected, and vice versa. Furthermore, the foodborne pathogen Salmonella was never detected with 16S rRNA amplicon sequencing, demonstrating the necessity for a cautious approach in the implementation of new analysis techniques in food safety. The present work determines that attention should be paid to the trade of non-inspected meat directly to retail or consumers.

Assessment of food microbiological indicators applied on poultry carcasses by culture combined MALDI-TOF MS identification and 16S rRNA amplicon sequencing

Examination of the bacterial contamination on food products is still largely performed by standardized culture methods, though culture-independent methods are suggested as a more reliable approach. Knowledge of the diversity of bacteria isolated from food as well as the impact of the plate incubation conditions applied are still understudied. The impact of incubation at 7 °C and 30 °C on total aerobic bacterial count and diversity, and the performance of ISO methods generally applied in microbiological quality examination were assessed by culture combined MALDI-TOF MS identification and 16S rRNA amplicon sequencing. Examining breast skin of 16 chicken carcasses, no significant impact of the incubation temperature on the total aerobic bacteria level and diversity was detected, limiting the usefulness of additional psychrophilic examination. Bacteria phenotypically similar to Pseudomonas, were identified on selective CFC plates, and on MRS agar plates for lactic acid bacteria, Escherichia coli and Staphylococcus were commonly present. Application of 16S rRNA amplicon sequencing revealed a higher bacterial diversity, but the impact of the DNA extraction kit applied, and the detection of non-viable bacteria should be taken into account to interpret the final outcome.

Acinetobacter radioresistens infection with bacteremia and pneumonia

Acinetobacter species are non-fermentative Gram-negative coccobacilli that are ubiquitous in the environment. The archetype pathogen within the genus is Acinetobacter baumannii, however, other species have the potential to cause human infection, especially in the hospital setting. We describe a patient with infection due to Acinetobacter radioresistens, a rare agent of human disease, which is often misidentified using biochemical methods. Acinetobacter radioresistens is the source of the Class D OXA-23 carbapenemase that can confer carbapenem resistance in A. baumannii. Therefore, accurate identification of A. radioresistens is important for clinical management and to potentially prevent the spread of carbapenem resistance.

Molecular mechanisms of antimicrobial resistance in Acinetobacter baumannii, with a special focus on its epidemiology in Lebanon

Acinetobacter baumannii is an opportunistic bacterium involved in several types of infection with high mortality and morbidity, especially in intensive care units. Treatment of these infections remains a challenge due to the worldwide emergence of broad-spectrum resistance to many antibiotics. Following the implementation of molecular techniques to study A. baumannii outbreaks, it has been shown that they are mainly caused by specific clones such as international clones I, II and III. The present work aims to review the available data on the mechanisms underlying antimicrobial resistance in A. baumannii, with a special focus on the molecular epidemiology of this species in Lebanon.

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.

Acinetobacter in veterinary medicine, with an emphasis on Acinetobacter baumannii

Acinetobacter spp. are aerobic, rod-shaped, Gram-negative bacteria belonging to the Moraxellaceae family of the class Gammaproteobacteria and are considered ubiquitous organisms. Among them, Acinetobacter baumannii is the most clinically significant species with an extraordinary ability to accumulate antimicrobial resistance and to survive in the hospital environment. Recent reports indicate that A. baumannii has also evolved into a veterinary nosocomial pathogen. Although Acinetobacter spp. can be identified to species level using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) coupled with an updated database, molecular techniques are still necessary for genotyping and determination of clonal lineages. It appears that the majority of infections due to A. baumannii in veterinary medicine are nosocomial. Such isolates have been associated with several types of infection such as canine pyoderma, feline necrotizing fasciitis, urinary tract infection, equine thrombophlebitis and lower respiratory tract infection, foal sepsis, pneumonia in mink, and cutaneous lesions in hybrid falcons. Given the potential multidrug resistance of A. baumannii, treatment of diseased animals is often supportive and should preferably be based on in vitro antimicrobial susceptibility testing results. It should be noted that animal isolates show high genetic diversity and are in general distinct in their sequence types and resistance patterns from those found in humans. However, it cannot be excluded that animals may occasionally play a role as a reservoir of A. baumannii. Thus, it is of importance to implement infection control measures in veterinary hospitals to avoid nosocomial outbreaks with multidrug-resistant A. baumannii.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ² = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.

Acinetobacter baumannii Resistance Trends in Children in the United States, 1999-2012

BACKGROUND

Acinetobacter baumannii is a common cause of healthcare-associated infections. Carbapenem-resistant (CR) A baumannii is a significant threat globally. We used a large reference laboratory database to study the epidemiology of A baumannii in children in the United States.

METHODS

Antimicrobial susceptibility data from The Surveillance Network were used to phenotypically identify antibiotic resistance in A baumannii isolates in children 1-17 years of age between January 1999 and July 2012. Logistic regression analysis was used to calculate trends in the prevalence of antibiotic resistance in A baumannii. Isolates from infants (<1 year old) were excluded.

RESULTS

The crude proportion of cephalosporin-resistant (CephR) A baumannii increased from 13.2% in 1999 to 23.4% in 2012 with a peak of 32.5% in 2008, and the proportion of CR A baumannii increased from 0.6% in 1999 to 6.1% in 2012 with a peak of 12.7% in 2008. From 1999 to 2012, the proportion of CephR and CR A baumannii increased each year by 3% and 8%, respectively (CephR odds ratio [OR] = 1.03, 95% confidence interval [CI], 1.01-1.04; CR OR = 1.08, 95% CI, 1.05-1.12); however, after 2008, a significant decrease in trend was observed (CephR OR = 0.78, 95% CI, 0.71-0.87; CR OR = 0.73, 95% CI, 0.62-0.86), but resistance remained higher than baseline (1999).

CONCLUSIONS

Overall, between 1999 and 2012, CephR and CR A baumannii isolates increased in children; however, a decreasing trend was observed after 2008.There is a need for ongoing surveillance of A baumannii infections and continued assessment of effective prevention strategies in vulnerable populations.

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).