Rapid and Accurate Detection of the SARS-CoV-2 Omicron Variant with a CRISPR-Cas12a Reaction in the RT-qPCR Pot.

Gene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consuming step, which hinders the deployment of a very fast response during a pandemic. Here, we propose to run a CRISPR-Cas12a reaction after completing the RT-qPCR and in the very same pot to detect with high specificity genetic marks characterizing variants of concern. A crRNA was appropriately designed to detect the S gene of the SARS-CoV-2 Omicron BA.1 variant. A significant response with >20-fold dynamic range was obtained for the Omicron BA.1 S gene, while the Delta S gene did not produce any detectable signal. The sensitivity of the method was analyzed with a series of diluted samples and different Cas12a nucleases. A correlation between the RT-qPCR CT values and the CRISPR-Cas12a reaction signals was observed. Variant discrimination with the CRISPR-Cas12a reaction was possible in some minutes with high accuracy from patient samples. In conclusion, CRISPR-Cas systems seem ready to be exploited in the clinic to boost personalized diagnoses and accelerate epidemiological surveillance in a cost-effective way.

The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum.

Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.

Pan-genomic analysis of Corynebacterium amycolatum gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype.

Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.

Activity of Essential Oils Against Multidrug-Resistant Salmonella enteritidis.

We have investigated the antibacterial, anti-biofilm, and anti-quorum sensing potencies of six Essential Oils (EOs) obtained from cinnamon (Cinnamomum verum), thyme (Thymus vulgaris), clove (Eugenia caryophyllata), curcuma (Curcuma longa L.), rosemary (Rosmarinus officinalis L.), and sage (Salvia officinalis). The study was conducted on 20 multidrug-resistant (MDR) S. enteritidis clinical strains. Minimum inhibitory concentrations and minimum bactericide concentrations were displayed by microdilution. The effect on biofilm formation was tested on polystyrene plates. The anti-quorum sensing effect was determined by measuring the inhibition of violacein production by Chromobacterium violaceum CV026. The influence of EOs on the adhesion of Salmonella strains to HT-29 cells was studied. The potency of S. enteritidis to infect and kill Caenorhabditis elegans was evaluated. The cinnamon, thyme, and clove EOs showed remarkable antibacterial properties. Biofilm formation was significantly reduced by the six EOs: 99.10% for cinnamon, 97.64% for clove, 95.90% for thyme, 79.84% for rosemary, 28.98% for curcuma, and 15.55% for sage. The MIC/2 of clove EO exhibited the highest percentage of inhibition of violacein production (99.03%), followed by thyme (91.68%) and cinnamon (84.13%) EOs. Thyme extracts exhibited an important anti-adhesive potency. Clove EO behaves as an effective regulator of Salmonella virulence in nematodes.

Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates.

Acinetobacter baumannii is a Gram-negative coccoid rod species, clinically relevant as a human pathogen, included in the ESKAPE group. Carbapenem-resistant A. baumannii (CRAB) are considered by the World Health Organization (WHO) as a critical priority pathogen for the research and development of new antibiotics. Some of the most relevant features of this pathogen are its intrinsic multidrug resistance and its ability to acquire rapid and effective new resistant determinants against last-resort clinical antibiotics, mostly from other ESKAPE species. The presence of plasmids and mobile genetic elements in their genomes contributes to the acquisition of new antimicrobial resistance determinants. However, although A. baumannii has arisen as an important human pathogen, information about these elements is still not well understood. Current genomic analysis availability has increased our ability to understand the microevolution of bacterial pathogens, including point mutations, genetic dissemination, genomic stability, and pan- and core-genome compositions. In this work, we deeply studied the genomes of four clinical strains from our hospital, and the reference strain ATCC®19606TM, which have shown a remarkable ability to survive and maintain their effective capacity when subjected to long-term stress conditions. With that, our aim was presenting a detailed analysis of their genomes, including antibiotic resistance determinants and plasmid composition.

Virulence of clinically relevant multidrug resistant Corynebacterium striatum strains and their ability to adhere to human epithelial cells and inert surfaces.

Corynebacterium striatum is a nosocomial pathogen which is increasingly associated with serious infections in both immunocompetent and immunocompromised patients. However, little is known about virulence factors and mechanisms that may enhance the establishment and long-term survival of Corynebacterium striatum. in the hospital environment. In this study, we investigated the ability of 22 multidrug-resistant C. striatum clinical isolates to adhere to human epithelial cells and to produce biofilm on polystyrene plates, glass and various tracheostomy tubes. We also tested the virulence of these strains on the nematode Caenorhabditis elegans. They showed good adhesion to epithelial human cells after 180 min of infection. The 22 C. striatum were able to produce biofilms on positively and negatively charged abiotic surfaces at 37 °C. They were also able to infect and to kill Caenorhabditis elegans after 5 days of infection. The virulence condition was associated with the presence of SpaDEF operon encoding pili in all strains. This study provides new insights on virulence mechanisms that may contribute to the persistence of C. striatum in the hospital environment, increasing the probability of causing nosocomial infections.

Anticoagulation Therapy in Patients With Coronavirus Disease 2019: Results From a Multicenter International Prospective Registry (Health Outcome Predictive Evaluation for Corona Virus Disease 2019 [HOPE-COVID19]).

OBJECTIVES: No standard therapy, including anticoagulation regimens, is currently recommended for coronavirus disease 2019. Aim of this study was to evaluate the efficacy of anticoagulation in coronavirus disease 2019 hospitalized patients and its impact on survival. DESIGN: Multicenter international prospective registry (Health Outcome Predictive Evaluation for Corona Virus Disease 2019). SETTING: Hospitalized patients with coronavirus disease 2019. PATIENTS: Five thousand eight hundred thirty-eight consecutive coronavirus disease 2019 patients. INTERVENTIONS: Anticoagulation therapy, including prophylactic and therapeutic regimens, was obtained for each patient. MEASUREMENTS AND MAIN RESULTS: Five thousand four hundred eighty patients (94%) did not receive any anticoagulation before hospitalization. Two-thousand six-hundred one patients (44%) during hospitalization received anticoagulation therapy and it was not associated with better survival rate (81% vs 81%; p = 0.94) but with higher risk of bleeding (2.7% vs 1.8%; p = 0.03). Among patients admitted with respiratory failure (49%, n = 2,859, including 391 and 583 patients requiring invasive and noninvasive ventilation, respectively), anticoagulation started during hospitalization was associated with lower mortality rates (32% vs 42%; p < 0.01) and nonsignificant higher risk of bleeding (3.4% vs 2.7%; p = 0.3). Anticoagulation therapy was associated with lower mortality rates in patients treated with invasive ventilation (53% vs 64%; p = 0.05) without increased rates of bleeding (9% vs 8%; p = 0.88) but not in those with noninvasive ventilation (35% vs 38%; p = 0.40). At multivariate Cox' analysis mortality relative risk with anticoagulation was 0.58 (95% CI, 0.49-0.67) in patients admitted with respiratory failure, 0.50 (95% CI, 0.49-0.67) in those requiring invasive ventilation, 0.72 (95% CI, 0.51-1.01) in noninvasive ventilation. CONCLUSIONS: Anticoagulation therapy in general population with coronavirus disease 2019 was not associated with better survival rates but with higher bleeding risk. Better results were observed in patients admitted with respiratory failure and requiring invasive ventilation.

Plant-Derivatives Small Molecules with Antibacterial Activity.

The vegetal world constitutes the main factory of chemical products, in particular secondary metabolites like phenols, phenolic acids, terpenoids, and alkaloids. Many of these compounds are small molecules with antibacterial activity, although very few are actually in the market as antibiotics for clinical practice or as food preservers. The path from the detection of antibacterial activity in a plant extract to the practical application of the active(s) compound(s) is long, and goes through their identification, purification, in vitro and in vivo analysis of their biological and pharmacological properties, and validation in clinical trials. This review presents an update of the main contributions published on the subject, focusing on the compounds that showed activity against multidrug-resistant relevant bacterial human pathogens, paying attention to their mechanisms of action and synergism with classical antibiotics.

Whole-genome sequencing reveals misidentification of a multidrug-resistant urine clinical isolate as Corynebacterium urealyticum.

OBJECTIVES: Corynebacterium urealyticum is a non-diphtherial urease-producing clinically relevant corynebacterium associated with urinary tract infections. Most clinical C. urealyticum isolates are multidrug-resistant. Whole-genome sequencing (WGS) of C. urealyticum VH4248 isolated from a clinical urine sample at Hospital Universitario Marqués de Valdecilla, Santander, Spain, was performed to predict its antimicrobial resistance profile and to compare it with results of culture-based phenotypic antimicrobial susceptibility testing. METHODS: Classical microbiological methods and VITEK® MS were used for isolation and initial identification of strain VH4248. Draft genome sequencing was performed on an Illumina HiSeq 2500 platform, followed by assembly and annotation using SPAdes and RAST. Resistance genes were identified through PATRIC, the Pathosystems Resource Integration Center. Average nucleotide identity (ANI) analysis was done using the EDGAR and OrthoANI databases. Antimicrobial susceptibility was determined by Etest. RESULTS: Isolate VH4248 was initially identified asC. urealyticum. Its genome size is 2 261 231 bp with 64.4% GC content. Genome-based identification tools showed an average 93.7% similarity between VH4248 and C. urealyticum genomes deposited in public databases. Therefore, this isolate must be classified as Corynebacterium sp. The blaA and ermX genes as well as a class 1 integron including the aadB and sul1 genes are present in the VH4248 genome. This isolate is highly resistant to ampicillin, erythromycin and trimethoprim/sulfamethoxazole, and moderately resistant to gentamicin and kanamycin. CONCLUSIONS: WGS is a powerful tool forCorynebacterium identification to species level and for detection of unusual resistance determinants, such as that encoded by the class 1 integron in isolate VH4248.

Antimicrobial Susceptibility and Characterization of Resistance Mechanisms of Corynebacterium urealyticum Clinical Isolates.

Corynebacterium urealyticum is a non-diphtherial urease-producing clinically relevant corynebacterial, most frequently involved in urinary tract infections. Most of the C. urealyticum clinical isolates are frequently resistant to several antibiotics. We investigated the susceptibility of 40 C. urealyticum isolated in our institution during the period 2005-2017 to eight compounds representative of the main clinically relevant classes of antimicrobial agents. Antimicrobial susceptibility was determined by the Epsilometer test. Resistance genes were searched by PCR. All strains were susceptible to vancomycin whereas linezolid and rifampicin also showed good activity (MICs90 = 1 and 0.4 mg/L, respectively). Almost all isolates (39/40, 97.5%) were multidrug resistant. The highest resistance rate was observed for ampicillin (100%), followed by erythromycin (95%) and levofloxacin (95%). Ampicillin resistance was associated with the presence of the blaA gene, encoding a class A ß-lactamase. The two rifampicin-resistant strains showed point mutations driving amino acid replacements in conserved residues of RNA polymerase subunit ß (RpoB). Tetracycline resistance was due to an efflux-mediated mechanism. Thirty-nine PFGE patterns were identified among the 40 C. urealyticum, indicating that they were not clonally related, but producing sporadic infections. These findings raise the need of maintaining surveillance strategies among this multidrug resistant pathogen.

Author Correction: Human neutrophils phagocytose and kill Acinetobacter baumannii and A. pittii.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Anti-oxidant, antibacterial, anti-biofilm, and anti-quorum sensing activities of four essential oils against multidrug-resistant bacterial clinical isolates.

PURPOSE OF THE STUDY: Outbreaks of multidrug-resistant bacteria are increasingly reported at the clinical setting. The antimicrobial, anti-biofilm, anti-quorum sensing, and anti-oxidant activities of four essential oils extracted from Cinnamomum verum, Origanum majorana, Thymus vulgaris, and Eugenia caryophyllata against Gram-positive and Gram-negative multidrug-resistant bacteria were evaluated in vitro. MATERIALS AND METHODS: This study was conducted on 105 multidrug resistant clinical strains. Inhibition diameter zone, minimum inhibitory concentration, and minimum bactericide concentration of the oils were determined using agar disc diffusion method and microdilution. The ability of the 4 essential oils to inhibit the production of bacterial biofilms was tested on polystyrene plates, as well as their inhibitory effect on the production of violacein by Chromobacterium violaceum CV026. The anti-oxidant activity was evaluated by the 2,2-diphenyl-1-picrylhydrazyl scavenging method. RESULTS: Essential oils of Cinnamomum verum, Thymus vulgaris and Eugenia caryophyllata showed an important antibacterial activity. The inhibition diameter zone was higher than 20 mm for 90.24 %, 85.71 % and 60.95 % of strains respectively. These essential oils have a remarkable anti-biofilm and anti-quorum sensing activities against almost all the species studied. Clove extract revealed the highest anti-oxidant activity (Pourcentage of inhibtion of DPPH = 90.3 %). CONCLUSION: These results supported the use of the 4 essential oils as alternative or complementary agents to treat infections caused by multidrug-resistant bacteria, and to prevent biofilm formation and quorum sensing signaling. They might be used as a safe anti-oxidants instead of harmful artificial ones.

Acinetobacter baumannii maintains its virulence after long-time starvation.

Acinetobacter baumannii is a cause of healthcare-associated infections. Although A. baumannii is an opportunistic pathogen, its infections are notoriously difficult to treat due to intrinsic and acquired antimicrobial resistance, often limiting effective therapeutic options. A. baumannii can survive for long periods in the hospital environment, particularly on inanimate surfaces. Such environments may act as a reservoir for cross-colonization and infection outbreaks and should be considered a substantial factor in infection control practices. Moreover, clothing of healthcare personnel and gadgets may play a role in the spread of nosocomial bacteria. A link between contamination of hospital surfaces and A. baumannii infections or between its persistence in the environment and its virulence has not yet been established. Bacteria under stress (i.e., long-term desiccation in hospital setting) could conserve factors that favor infection. To investigate whether desiccation and/or starvation may be involved in the ability of certain strains of A. baumannii to retain virulence factors, we have studied five well-characterized clinical isolates of A. baumannii for which survival times were determined under simulated hospital conditions. Despite a considerable reduction in the culturability over time (up to 88% depending on strain and the condition tested), some A. baumannii strains were able to maintain their ability to form biofilms after rehydration, addition of nutrients, and changing temperature. Also, after long-term desiccation, several clinical strains were able to grow in the presence of non-immune human serum as fine as their non-stressed homologs. Furthermore, we also show that the ability of bacterial strains to kill Galleria mellonella larvae does not change although A. baumannii cells were stressed by long-term starvation (up to 60 days). This means that A. baumannii can undergo a rapid adaptation to both the temperature shift and nutrients availability, conditions that can be easily found by bacteria in a new patient in the hospital setting.

Efficient differentiation of Corynebacterium striatum, Corynebacterium amycolatum and Corynebacterium xerosis clinical isolates by multiplex PCR using novel species-specific primers.

A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.

Occurrence of Corynebacterium striatum as an emerging antibiotic-resistant nosocomial pathogen in a Tunisian hospital.

Corynebacterium striatum is a nosocomial opportunistic pathogen increasingly associated with a wide range of human infections and is often resistant to several antibiotics. We investigated the susceptibility of 63 C. striatum isolated at the Farhat-Hached hospital, Sousse (Tunisia), during the period 2011-2014, to a panel of 16 compounds belonging to the main clinically relevant classes of antimicrobial agents. All strains were susceptible to vancomycin, linezolid, and daptomycin. Amikacin and gentamicin also showed good activity (MICs90 = 1 and 2 mg/L, respectively). High rates of resistance to penicillin (82.5%), clindamycin (79.4%), cefotaxime (60.3%), erythromycin (47.6%), ciprofloxacin (36.5%), moxifloxacin (34.9%), and rifampicin (25.4%) were observed. Fifty-nine (93.7%) out of the 63 isolates showed resistance to at least one compound and 31 (49.2%) were multidrug-resistant. Twenty-nine resistance profiles were distinguished among the 59 resistant C. striatum. Most of the strains resistant to fluoroquinolones showed a double mutation leading to an amino acid change in positions 87 and 91 in the quinolone resistance-determining region of the gyrA gene. The 52 strains resistant to penicillin were positive for the gene bla, encoding a class A ß-lactamase. Twenty-two PFGE patterns were identified among the 63 C. striatum, indicating that some clones have spread within the hospital.

Lisfranc Joint Ligament Complex Reconstruction: A Promising Solution for Missed, Delayed, or Chronic Lisfranc Injury Without Arthritis.

The current classifications of "Lisfranc injury" can be purely ligamentous (low-grade midfoot sprains) or involve the osseous and articular structures (high-grade Lisfranc fracture displacements). The first type is often difficult to detect. If these patients are not properly treated, long-term disability can result. The rate of missed or delayed diagnoses has ranged from 13% to 24%, primarily owing to the subtlety of the radiographic findings. This is relatively more common in cases of subtle ligamentous injury (19%). The aim of the present report was to provide a new technique for missed or delayed Lisfranc injury without degenerative local signs. The Lisfranc ligament complex reconstruction is performed with a gracilis tendon graft and is protected by temporary screw fixation. We performed this technique in 3 patients. All 3 patients obtained good results, have been able to resume their previous activities, and have stated they would undergo this type of procedure again. The minimum follow-up length was 2 years.

Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine.

Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.

Human neutrophils phagocytose and kill Acinetobacter baumannii and A. pittii.

Acinetobacter baumannii is a common cause of health care associated infections worldwide. A. pittii is an opportunistic pathogen also frequently isolated from Acinetobacter infections other than those from A. baumannii. Knowledge of Acinetobacter virulence factors and their role in pathogenesis is scarce. Also, there are no detailed published reports on the interactions between A. pittii and human phagocytic cells. Using confocal laser and scanning electron microscopy, immunofluorescence, and live-cell imaging, our study shows that immediately after bacteria-cell contact, neutrophils rapidly and continuously engulf and kill bacteria during at least 4 hours of infection in vitro. After 3 h of infection, neutrophils start to release neutrophil extracellular traps (NETs) against Acinetobacter. DNA in NETs colocalizes well with human histone H3 and with the specific neutrophil elastase. We have observed that human neutrophils use large filopodia as cellular tentacles to sense local environment but also to detect and retain bacteria during phagocytosis. Furthermore, co-cultivation of neutrophils with human differentiated macrophages before infections shows that human neutrophils, but not macrophages, are key immune cells to control Acinetobacter. Although macrophages were largely activated by both bacterial species, they lack the phagocytic activity demonstrated by neutrophils.