Method For Bacterial Identification Research Articles

Multiple skin abscesses due to Nocardia neocaledoniensis: a case report and literature review

N. neocaledoniensis is a very rare infectious pathogen that causes human disease, particularly in immunocompromised individuals. In this case report, we describe the successful diagnosis of N. neocaledoniensis in a patient confirmed by mNGS and the treatment of multiple skin abscesses due to N. neocaledoniensis infection. mNGS is an important diagnostic method complementary to routine bacterial culture and identification methods, especially for rare, novel, co-infected pathogens, and pathogens that are difficult to culture. This report may provide a reference for the clinical treatment and diagnosis of N. neocaledoniensis infection in humans.

Myroides species, pathogenic spectrum and clinical microbiology sight in Mexican isolates.

Myroides is a bacterial genus of opportunistic bacteria responsible for diverse infections including in the skin and soft tissues, urinary tract, cardiovascular system, and bacteremia, although the incidence of its reported infections is low, it is increasing, likely due the use of better bacterial identification methods, but also perhaps due an increase in its prevalence. In addition, their pathogenic role is limited in terms of reporting their microbial physiology, so the present work provides information in this regard in addition to the information that is available in the international literature. To describe the microbiological and genetic characteristics of seven different Myroides spp. clinical strains and comment on their phylum, pathogenic and resistance characteristics. Seven Myroides spp., strains associated with infections were included from 1/January/2012 to 1/January/20 and identified by miniaturized biochemistry and MALDI-ToF. Susceptibility tests were performed according to CLSI recommendations by broth microdilution. Whole genome sequencing was performed for each strain and bioinformatics analysis were performed. Strains were identified at genus level by two methodologies. Our results revealed that likely four strains belong to the species Myroides odoratimimus, while the other two may be undescribed ones. Remarkably, all isolates harbored several genes encoding antibiotic resistance determinants for ß-lactams, aminoglycosides and glycopeptides and in concordance, presented high levels of resistance, against these antibiotics (AK and GN both 100%, ATM, CAZ and FEP 100%, e.g.); moreover, the presences of carbapenemases were evidenced by meropenem (mCIM) and imipenem (CARBA NP) degrading activity in six isolates and two strains possessed plasmids harboring mainly ribosomal RNA genes, tRNAs and genes encoding proteins with unknown functions. Our study increases the knowledge about the biology of this understudied genus and highlights the potential of Myroides to emerge as a broader cause of recalcitrant opportunistic infections.

Evaluation of Geh gene expression in Staphylococcus aureus isolated from acne patients

Acne vulgaris is a chronic skin disease that affects the hair follicle and sebaceous glands. Staphylococcus aureus colonizes human skin and causes infections ranging from local skin infections to systemic infections that may threaten human life due to its ability to produce many virulence factors and antibiotic resistance. The objective of this study is to measure the genetic expression of Geh gene responsible for producing the lipase enzyme from S. aureus isolated from acne patients. This study was conducted by collecting 130 swabs from acne patients at Tikrit Teaching Hospital. Using routine bacterial isolation and identification methods, 50 samples (38.4%) of the total samples were identified as S. aureus through its ability to grow in mannitol salt agar medium, the fermentation of mannitol sugar, and the change of the medium color to yellow. The Geh gene expression of ten S. aureus isolates from acne patients was examined using RT-PCR. The results showed that Geh gene was expressed in all isolates, with an expression ranging from 1.5 to 7.2, and that the mean folding of the Geh gene for ten samples was 4.2. This indicates the presence of high gene expression of the Geh gene in S. aureus isolates. Therefore, it is concluded that Lipase enzyme plays an important role in the pathogenesis of S. aureus in acne patients.

Impact of direct identification of bacteria in blood culture–positive specimens by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry on physician selection of antimicrobial therapy

BackgroundRapid identification of the causative organism in blood stream infections is essential for early initiation of appropriate antimicrobial therapy. Direct identification of bacteria in positive blood culture bottles using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry is a promising application. A variety of direct identification methods have been reported; however, few studies have evaluated the impact of these methods on physician decision making regarding antimicrobial therapy. MethodsWe developed a simple method for direct bacterial identification and applied it to daily clinical practice to investigate the impact of direct identification of bacteria in positive blood culture bottles on physicians’ choice of antimicrobial agents for treatment. ResultsFrom January 2016 to December 2022, we attempted direct identification in 98 cases and successfully acquired identification results in 88 cases. In three cases, no empiric antimicrobial agents were initiated at the time of venipuncture for blood culture but later initiated based on the direct identification results. In the remaining 85 cases, empiric antimicrobial therapy was initiated at the time blood cultures were performed, and in 29 cases, empiric antimicrobial therapy was changed after direct identification. In 17 of these 29 cases, the antimicrobial therapy was changed based on the direct identification of bacterial genus/species, resulting in a change to an effective antimicrobial therapy before the antimicrobial susceptibility testing results were available. ConclusionsDirect identification of bacteria from positive blood culture bottles could contribute to earlier selection of or changes to antimicrobial therapies by attending physicians.

Utility of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Periprosthetic Joint Infection Diagnosis.

One of the most feared complications of arthroplasty surgery is septic loosening. Periprosthetic joint infection (PJI) requires an accurate and fast diagnosis, and identification of pathogen microorganisms is essential for successful treatment. While standard bacteriological cultures can identify bacteria in seven to 14 days with sensitivity ranging from 35% to 70% that could further be increased by sonication of the explanted prosthesis, we would like to review a more novel and faster method of PJI detection and bacterial identification. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is a technique that identifies bacteria based on peptides and protein ions from the cell surface, comparing the obtained results within a database. While MALDI-TOF/MS is not a novel method, being already successfully used in microbiology, its role in PJI is still being researched. With this paper, we would like to reveal the current state of development in implementing MALDI-TOF/MS as an alternative or auxiliary test to classic bacterial cultures in orthopedic implant infectious pathology to increase the accuracy of detecting and identifying bacteria.

Comparison of commercial next-generation sequencing assays to conventional culture methods for bacterial identification and antimicrobial susceptibility of samples obtained from clinical cases of canine superficial bacterial folliculitis.

Bacterial identification and antimicrobial susceptibility testing is an important step in timely therapeutic decisions for canine superficial bacterial folliculitis (SBF), commonly caused by Staphylococcus pseudintermedius. Next-generation sequencing (NGS) offers the appeal of potentially expedited results with complete detection of bacterial organisms and associated resistance genes compared to culture. Limited studies exist comparing the two methodologies for clinical samples. To compare and contrast genotypic and phenotypic methods for bacterial identification and antimicrobial susceptibility from cases of canine SBF. Twenty-four client-owned dogs with lesions consistent with SBF were enrolled. A sterile culturette swab was used to sample dogs with SBF lesions. The swab was rinsed in 0.9 mL of sterile phosphate-buffered saline and vortexed to create a homogenous solution. Two swabs for NGS laboratories (Labs) and one swab for culture (Culture Lab) were randomly sampled from this solution and submitted for bacterial identification and antimicrobial susceptibility. No statistical difference regarding turnaround time for NGS Labs compared to Culture Lab was found. NGS Lab 1 identified more organisms than NGS Lab 2 and Culture Lab, which were both statistically significant. There was no statistical difference in detection frequency for Staphylococcus spp. among all laboratories. There was poor agreement for the presence of meticillin resistance and most antimicrobials among all laboratories. Utilisation of NGS as a replacement for traditional culture when sampling canine SBF lesions is not supported at this time.

Validation of short culture method for rapid bacterial identification of blood cultures via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Development of rapid bacterial identification from blood cultures has been an area of intense study in diagnostic microbiology. Shortened turnaround time coupled with antimicrobial stewardship interventions have been shown to improve patient outcomes and decrease healthcare-associated costs. We report the validation of a short incubation method for Gram-positive and Gram-negative bacterial identification utilizing MALDI-TOF MS without additional instrumentation, processing or cost compared with current practice. Prospective, observational, single-centre study in a quaternary care academic hospital encompassing 376 blood cultures subjected to bacterial identification after short incubation periods of 3-4 and 6-8 h. There was 97.5% species-level identification agreement with tests undertaken after 3-4 h incubation with 83.6% isolates identified, and 99.7% species-level identification agreement after 6-8 h incubation with 96.7% isolates identified. The short incubation method provides a rapid MALDI-TOF MS bacterial identification method, reducing turnaround time by 10-18 h compared with standard practice without additional cost, processing or instrumentation.

Bacterial Pesticides: Mechanism of Action, Possibility of Food Contamination, and Residue Analysis Using MS.

As Sustainable Development Goals (SDGs) and the realities of climate change become widely accepted around the world, the next-generation of integrated pest management will become even more important for establishing a sustainable food production system. To meet the current challenge of food security and climate change, biological control has been developed as one sustainable crop protection technology. However, most registered bacteria are ubiquitous soil-borne bacteria that are closely related to food poisoning and spoilage bacteria. Therefore, this review outlined (1) the mechanism of action of bacterial pesticides, (2) potential concerns about secondary contamination sources associated with past food contamination, and, as a prospective solution, focused on (3) principles and methods of bacterial identification, and (4) the possibility of identifying residual bacteria based on mass spectrometry.

Exploring oral bacterial compositional network in two oral disease groups using a convergent approach of NGS-molecular diagnostics.

Since most of the commonly known oral diseases are explained in link with balance of microbial community, an accurate bacterial taxonomy profiling for determining bacterial compositional network is essential. However, compared to intestinal microbiome, research data pool related to oral microbiome is small, and general 16S rRNA screening method has a taxonomy misclassification issue in confirming complex bacterial composition at the species level. Present study aimed to explore bacterial compositional networks at the species level within saliva of 39 oral disease patients (Dental Caries group: n = 26 and Periodontitis group: n = 13) through comparison with public Korean-specific healthy oral microbiome data. Here, we applied comprehensive molecular diagnostics based on qRT-PCR and Sanger sequencing methods to complement the technical limitations of NGS-based 16S V3-V4 amplicon sequencing technology. As a result of microbiome profiling at the genus level, relative frequencies of many nitrate-reducing bacteria within each oral disease group were found to be significantly low compared to the healthy group. In addition, the molecular diagnostics-based bacterial identification method allowed the determination of the correct taxonomy of screened primary colonizers (Streptococcus and Actinomyces unclassification clusters) for each oral disease. Finally, as with the results of microbiome profiling at the genus level, many core-species classified within the saliva of each oral disease group were also related to nitrate-reduction, and it was estimated that various pathogens associated with each disease formed a bacterial network with the core-species. Our study introduced a novel approach that can compensate for the difficulty of identifying an accurate bacterial compositional network at the species level due to unclear taxonomy classification by using the convergent approach of NGS-molecular diagnostics. Ultimately, we suggest that our experimental approach and results could be potential reference materials for researchers who intend to prevent oral disease by determining the correlation between oral health and bacterial compositional network according to the changes in the relative frequency for nitrate-reducing species.

Evaluation of phenotypic and genotypic methods for the identification and characterization of bacterial isolates recovered from catheter-associated urinary tract infections.

Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital. We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design. This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.

Rapid Bacterial Identification from Positive Blood Cultures by MALDI-TOF MS Following Short-Term Incubation on Solid Media.

This study aimed to assess the performance of the MALDI-TOF MS short incubation method for bacterial identification at short-term incubation times to improve the reporting of blood cultures. MALDI-TOF MS analysis was conducted at intervals of 2, 4, and 6 hours during the development of microbial biomass on solid media until successful identification was achieved, with a final assessment at 24 hours for conventional identification. Species-level identification rates at the 2nd, 4th, 6th, and 24th hours were 57.5%, 83.6%, 93.1%, and 93.1% for Gram-negative bacilli; 12.5%, 42.7%, 76.1%, 97.8% for Gram-positive cocci and 0%, 11.8%, 17.6%, 58.8% for Gram-positive bacilli, respectively. The species-level identification rate was 76.5% for all monomicrobial cultures at the 6th hour. Our results have led us to implement this method into our routine laboratory workflow, and we have started to report rapid identification results for Gram-negative bacteria on the day of blood culture positivity.

Water physicochemical quality as driver of spatial and temporal patterns of microbial community composition in lake ecosystems

This study aimed at monitoring and management of the surface water and potentially pathogenic microbes of Lake Tonga (Algeria) with respect to. It characterized the main bacterial diversity patterns of Lake Tonga and predicted from water physicochemical parameters and water quality index (WQI) the distribution of bacterial species and the main indicator groups of faecal water contamination. Water samples were taken monthly at three sampling sites of different water depths. Several physicochemical parameters were measured; of which some were included in computing WQI to characterize the water quality of the lake. Counting, isolation and bacterial identification methods were used to characterize the existing aerobic heterotrophic bacteria. The composition of the microbial community of the waterbody of Lake Tonga included an abundant culturable bacterial flora belonging to several bacterial families and whose specific richness varied between water depths of the sites sampled. Species richness of the bacteria identified phenotypically varied between 7 and 11 per sample. The site with shallow water was the richest in bacterial species, compared to moderate and deep waters. The redundancy analysis showed the main physicochemical drivers of the microbial community composition. Our findings showed that high WQI scores indicated the water quality deterioration which triggered the increase in total load of faecal indicator bacterial groups. This study identified in Lake Tonga an important culturable aerobic bacterial flora whose specific richness and distribution varied spatially following the effects of water physicochemical parameters. Lake Tonga needs an integrated management plan to mitigate human disturbances declining water quality.

Topical issues of antibiotic resistance: modern methods of identification of bacterial pathogens and determination of their qualities

One of the most urgent problems in medicine today is the problem of antibiotic resistance. Why this problem? After all, scientists around the world proclaimed victory over microorganisms in the 50-60s of the last century? And since the 70s already began to appear information about resistant strains. Everything turned out to be not so simple. Due to uncontrolled and irrational use of antibiotics, mankind is rapidly approaching the so-called "post-antibiotic era". How to stop this "approach"? It is necessary to clearly follow the principles of rational antibiotic therapy.
 Rational antibiotic therapy requires identifying the bacterial nature of the disease, determining the sensitivity of the microorganisms to the antibiotic and starting treatment as soon as possible. To comply with these principles, rapid and accurate methods of identification of microorganisms are necessary, because it is on the basis of these methods that the most effective antimicrobial agent is selected.
 There are standard methods of identification, which include the disk-diffusion method and the serial dilution method. The main disadvantage of these methods is the length of time it takes to obtain results.
 So what are the alternative methods available? There are many methods of microbial identification, but not all of them are suitable for widespread use due to the high cost, the need for expensive equipment.
 Of all the current methods, three methods are emphasized in this review: 16S rRNA gene sequencing, MALDI-TOF MS and EUCAST RAST. Sequencing of the 16S rRNA gene is based on decoding the region of the gene, which in bacteria carries information on resistance mechanisms and structure features. MALDI-TOF MS is a desorption method of "soft" ionization caused by exposure of the matrix with the analyzed substance to pulses of laser radiation. The EUCAST RAST method is an accelerated disk-diffusion method.
 This review describes the problem of antibiotic resistance, mechanisms of bacterial resistance, as well as modern and standard methods of bacterial identification and antibiotic sensitivity.
 The aim of this review was to compare routine methods of identification of species and qualitative properties of microorganisms, causative agents of nosocomial infections, with modern technologies of microbiological testing as an important step in solving the problem of priority selection of effective antimicrobial agents.
 So, the main question of this review is: can modern methods displace standard methods of microorganism identification?

Rapid detection of Pseudomonas syringae pv. actinidiae by electrochemical surface-enhanced Raman spectroscopy

Bacterial cancer caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to kiwifruit in the world, and there is still a lack of effective control measures. The field of bacterial detection needs a fast, easy-to-use and sensitive identification platform. The current bacterial identification methods are lack of time efficiency, which brings problems to many sectors of society. Surface-enhanced Raman spectroscopy (SERS) and electrochemistry (EC) have been studied as possible candidates for bacterial detection because of their high sensitivity for the detection of biomolecules. In this work, SERS, EC and electrochemical surface-enhanced Raman spectroscopy (EC-SERS) were used for the first time to study the adsorption and EC behavior of Psa on the surface of nanostructured silver electrodes. Two different Raman spectra of a single analyte were obtained, and this dual detection was realized. Silver nanoparticles with iodide and calcium ions (Ag@ICNPs) were synthesized as SERS substrates significantly enhanced the characteristic signal peaks of Psa, and the limit of detection (LOD) is as low as 1.0 × 102 cfu/mL. Chemical imaging results show that the application of negative voltage can significantly improve the spectrum quality, showing a higher signal at −0.8 V, indicating that Psa molecules may have potential-induced reorientation on the electrode surface. Therefore, EC-SERS has the ability to greatly improve the SERS performance of bacteria in terms of peak intensity and spectral richness.

Presence of blaCTXM-1, blaCTXM-9, and blaTEM-1 Genes in Extended-spectrum β-lactamase-producing Escherichia coli Isolates from Hospital Wastewater

BACKGROUND: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) are selectively proliferated in the human gut, excreted through feces, and deposited through wastewater lines, with hospital wastewater acting as a major reservoir of antibiotic resistance genes and resistant bacteria, thus pose adverse effects to human health. This study aimed to determine the presence of blaCTXM-1, blaCTXM-9, blaTEM-1, and blaSHV-1 genes in ESBL-EC in wastewater from selected hospitals in Manila and Quezon City, the Philippines.METHODS: Influent and effluent in twelve hospital wastewater treatment plants were collected, screened for cefotaxime-resistant E. coli, and examined for the ESBL production through phenotypic characterization using conventional bacterial identification, disk diffusion method, and VITEK® 2 Compact system and genotypic identification of ESBL-EC blaCTXM-1, blaCTXM-9, blaTEM-1, blaSHV-1 genes using multiplex polymerase chain reaction (PCR).RESULTS: Conventional bacterial identification methods and the VITEK® 2 Compact system results showed that both influent and effluent samples were positive for ESBL-EC at 33.3% and 16.7%, respectively. Multiplex PCR results revealed that various E. coli isolates were of ESBL-EC blaCTXM-1, blaCTXM-9, and blaTEM-1 genes. Multi-drug resistance was observed among all ESBL-EC isolates with resistance being highest against ampicillin, cefuroxime, ceftazidime, ceftriaxone, cefepime, piperacillin, and aztreonam.CONCLUSION: As the study revealed the presence of ESBL-producing bacteria, efforts must be made to ensure the prudent antimicrobial use with possible emphasis on antibiotic rotation accompanied by intensified infection prevention and control in hospital settings.KEYWORDS: antimicrobial resistance, beta-lactams, blaCTXM, blaTEM, extended-spectrum beta-lactamase, E. coli, hospital wastewater

Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer.

The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was onlyobtained in 63% of the cases.

Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis.

The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity.

Bacteria detection and species identification at the single-cell level using super-resolution fluorescence imaging and AI analysis

The skin microbiome is thought to play a critical role in maintaining skin health and protecting against infection. While most microorganisms that live on the skin are harmless or even beneficial, some can cause skin infections or other health problems, emphasizing the importance of diagnosis of the composition and diversity of the skin flora. However, conventional diagnostic methods for evaluation of the skin microbiome are not sensitive enough to detect bacteria at low concentrations and suffer from poor specificity, thus limiting early diagnosis of bacterial infections. In this study, we developed novel approaches for bacterial species detection and identification methods with single-cell sensitivity using super-resolution microscopy and AI-based image analysis: a protein quantification-based method and an AI-based bacterial image analysis method. We demonstrate that these methods can differentiate between common bacterial members of the skin flora, including Staphylococcus aureus and Staphylococcus epidermidis, and different ribotypes of Cutibacterium acnes, both in purified bacterial samples and in scaling skin samples. The advantages of these methods, including the lack of time-consuming amplification or purification steps and single-cell level detection sensitivity, allow early diagnosis of bacterial infections, even from bacterial samples at extremely low concentrations, thus showing promise as a next-generation platform for microbiome detection as single-cell diagnostics.

Multi-resistant Bacteria to Antibiotics in Hospitals: The Case of Neonatology Services of the University Hospitals Centers of Abidjan, Côte d'Ivoire

Background: Multidrug-resistant bacteria (MDR) represent a global health scourge. Their emergence in hospital services complicates the clinical management of infections caused in particular in immunocompromised persons. The objective of our work was to evaluate the prevalence of MDR in the neonatal services of the University Hospitals Centers of Abidjan.
 Materials and Methods: The present study took place from September to November 2020 and from January to June 2021. The samples collected consisted of venous blood samples for blood cultures, rectal swabs from newborns, nasal and hand swabs from health care workers, and swabs from inert surfaces and neonatal care equipment. Bacterial identification methods, antibiotic susceptibility testing, and Chi-square testing were performed.
 Results: A total of 513 samples were obtained from which 215 organisms were isolated and identified. These bacteria consisted of 52.1% Gram-negative bacilli, of which 77.7% were Enterobacteriaceae and 47.9% Gram-positive cocci. Klebsiella pneumoniae (K. pneumoniae) (25.6%), coagulase-Negative Staphylococcus (CoNS) (24.6%), and Staphylococcus aureus (S. aureus) (23.2%) were the most isolated bacteria. The overall prevalence of MDR was 73.9%. The main antibiotic resistance phenotypes described were the production of Broad Spectrum β-lactamases (ESBL) in 71.9% of Enterobacteriaceae and methicillin resistance (Meti-R) in 75.6% of Staphylococcus. ESBL-producing Enterobacteriaceae (E-ESBL) were mainly observed in rectal carriage and Meti-R strains in blood cultures in newborns in the respective proportions of 45.6% and 56.4%.
 Conclusion: In our work, the results obtained showed a high prevalence of MDR in neonatal services and newborns are the most affected subjects. Improving hygiene rules and control and rationalizing the use of antibiotics are highly recommended control strategies to reduce the hospital dissemination of MDR.

Characterization and in vitro assessment of probiotic potential of Lactiplantibacillus plantarum BXM2 from fermented honey passion fruit beverage

AbstractA potential probiotic strain BXM2 was isolated from naturally fermented honey passion fruit beverage, and identified as Lactiplantibacillus plantarum using 16S rDNA sequence analysis, rpoA gene sequence analysis combined with API bacterial identification method. BXM2 was evaluated for its probiotic and technological properties, such as growth efficiency, gastrointestinal tolerance, antibacterial activity and antibiotic resistance. The results showed that the optimum growth efficiency of BXM2 was achieved under the fermentation temperature ranged from 30°C to 37°C. The initial content of BXM2 (8.50 log CFU/mL) was decreased to 7.53 log CFU/mL after 3 h treatment in simulated gastric fluid (pH = 3.0) and 8.12 log CFU/mL after 6 h treatment in simulated intestinal fluid (pH = 8.0) (p < .05). BXM2 showed active antibacterial activity against oral pathogens (Streptococcus mutans, Prevotella intermedia) and foodborne pathogens (Escherichia coli, Staphylococcus aureus, Shigella sonnei, Salmonella Typhimurium, Proteus mirabilis) with average diameters of inhibition zones ranging from 11.00 to 21.67 mm. Autoaggregation rate of BXM2 was 55.41% and coaggregation rates with the tested pathogens ranged from 34.05% to 86.42%. The antibiotic resistance test showed that BXM2 was safe and sensitive to most of the antibiotics. This study provides valuable information for future investigation and industrial application of this selected strain BXM2.