Prevalence of ESKAPE pathogens in the environment: Antibiotic resistance status, community-acquired infection and risk to human health

Characterization of a new lytic bacteriophage (vB_KpnM_KP1) targeting Klebsiella pneumoniae strains associated with nosocomial infections

A new bacteriophage, vB_KpnM_KP1, was identified and characterized, exhibiting a strong lytic effect on Klebsiella pneumoniae. Host range analysis revealed its effectiveness against 77.4% of clinical strains, achieving complete lysis of those associated with urinary tract infections (UTIs). Phage stability tests demonstrated that vB_KpnM_KP1 remained stable at neutral pH and across all tested temperatures. However, inactivation was observed at high ethanol concentrations and extreme pH levels. Transmission electron microscopy (TEM) analysis identified vB_KpnM_KP1 as a Myo-type phage with an icosahedral head and a contractile tail. Moreover, genome annotation of vB_KpnM_KP1 revealed a linear DNA genome of 174,802 bp, containing 307 open reading frames. Functional predictions suggest the presence of genes involved in DNA replication, transcription, morphogenesis, and cell lysis. Phylogenetic analysis classified vB_KpnM_KP1 within the Slopekvirus genus of the Straboviridae family, showing high sequence identity with phages that infect Enterobacter, Escherichia and Klebsiella species. These findings highlight the potential of phage vB_KpnM_KP1 as an alternative treatment for multidrug-resistant K. pneumoniae infections, particularly in UTIs, while offering valuable insights into its stability and genetic composition.

Novel circular antimicrobial peptides to combat a critical listed bacterial pathogen multi drug resistant Acinetobacter baumannii

Acinetobacter baumannii, acritical nosocomial pathogen, is one of the leading causes of human mortality, globally. The extraordinary genetic plasticity of A. baumannii leads to a high propensity antimicrobial resistance trait that demands urgent attention for alternative therapeutics. The current study involves synthesis and purification of two synthetic antimicrobial peptides, i.e., Cyclized melittin (CMEL) and its analog CMEL-M1, to investigate their minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and mechanism of action on the ultrastructural alteration using scanning and transmission electron microscopy (SEM/TEM) against the clinical strains of multidrug-resistant A. baumannii. Mass spectrometry and Kaiser test was employed to assess the effect of cyclization and substitution of polar amino acids with basic amino acids, that created cyclic melittin and its analogue replacing threonine with arginine and lysine. By using broth dilution method, CMEL-M1 demonstrated 70 % strains had MIC value of 31.25 μg/mL, while in case of CMEL, only 20 % isolates exhibited MIC value of 31.25 μg/mL which suggested that CMEL-M1 is significantly effective against MDR- A. baumannii. Action mechanism of synthetic peptides using SEM/TEM depicted the altered cellular morphology leading to the disruption of membranes and the impairment of essential A. baumannii cellular functions. Hence, present findings clearly indicate the potential of CMEL and CMEL-M1 as therapeutic agents for the management of MDR- A. baumannii infections.

Cephalosporin-based combination therapies for combating ESKAPE pathogens: a patent review

ESKAPE (namely Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) pathogens pose a major threat to global health. The World Health Organization highlights the need for new antimicrobial strategies, including combination therapies, to address their resistance. Cephalosporins, due to their broad-spectrum activity and safety profile, are widely used in hospitals and serve as strong candidates for such regimens. While many studies explore cephalosporin combinations, there is a lack of systematic reviews focused on patent literature. This study analyses patent filings related to cephalosporin-based combination therapies targeting ESKAPE pathogens. The Espacenet database was thoroughly searched using the keywords "combination," "antibiotics," and "cephalosporin" yielding 666 patent applications filed up to June 2024. Based on the inclusion criteria, 30 patents were selected for further analysis. Notably, most patents were filed in China and the USA, accounting for up to 30% and 17%, respectively. Most patents were filed by private companies and classified under the International Patent Classification code A61K, indicating their pharmaceutical applications. Additionally, in 2022, the highest number of patents were filed in this area. However, clinical data were included in only two patents, reflecting a broader challenge: the high cost of development limits real-world validation of these combinations. Despite this, the patent landscape offers valuable insights into emerging strategies for combating ESKAPE pathogens with cephalosporin-based therapies.

Ampicillin Exposure and Glutathione Deficiency Synergistically Promote Conjugative Transfer of Plasmid-Borne Antibiotic Resistance Genes

Plasmid-mediated conjugation is an important pathway for the spread of antibiotic resistance genes (ARGs), posing a significant risk to global public health. It has been reported that the conjugative transfer of ARGs could be enhanced by oxidative stress. Whether endogenous glutathione (GSH), a major non-protein thiol compound involved in cellular redox homeostasis, influences conjugative transfer is unknown. In this study, we show that the deletion of the GSH biosynthesis gene gshA and ampicillin exposure synergistically promoted the conjugative transfer of plasmid RP4 bearing multiple ARGs from the soil bacterium Enterobacter sp. CZ-1 to Escherichia coli S17-1λπ in co-culture experiments and to diverse soil bacteria belonging to eight phyla, including some potential human pathogens, in a soil incubation experiment. The deletion of gshA increased ROS generation and cell membrane permeability, and upregulated the expression of the genes involved in intracellular oxidative stress regulation, membrane permeability, plasmid replication, and the SOS response process, especially under ampicillin exposure. These results suggest that endogenous GSH is an important factor affecting the spread of plasmid-borne ARGs. Exposure to antibiotics and environmental stresses that cause a depletion of endogenous GSH in vivo are likely to increase the risk of ARG dissemination in the environment.

Expanding the Variety of Pyridinium-Based Bis-QACs with Antimicrobial Properties: Investigation into Linker Structure-Activity Correlation

For decades quaternary ammonium compounds (QACs) have served as main component of a top antiseptic and disinfectant compositions. Among them, bis-QACs are the most prominent and effective class of biocides. Although mono-QACs still dominate the antiseptic market, their activity against Gram-negative bacteria is largely inferior to bis-QACs. Moreover, the new wave of bacterial resistance during the COVID-19 pandemic is threatening the efficiency of popular antiseptics. Therefore, the requirement for novel biocides is urgent. Reported here is a unified and simple two-step synthesis to achieve novel biocide's architectures with aromatic linkers. Thus, a series of 14 bis-QACs have been prepared using an Ullman-type reaction following by N-alkylation. The most prominent compounds showed strong bioactivity against a panel of nineteen microbial pathogens, multi-resistant bacterial ESKAPEE strains, fungi and biofilms, including strains, which acquired resistance during COVID-19 in 2021. Moreover, significant improvements in antibiofilm action were observed, where bis-QACs 5 c and 6 a outperformed gold standard pyridinium antiseptic octenidine. These findings will serve as a good basis for further studies of bis-QACs architectures as highly effective biocides.

Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks

The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.

Spread of antimicrobial-resistant clones of the ESKAPEE group: From the clinical setting to hospital effluent

Antimicrobial resistance is a public health concern affecting human, animal, and environmental health. Antimicrobial-resistant pathogens, such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE), the most important microorganisms involved in healthcare-related infections, can be excreted by patients into hospital effluent which then becomes a reservoir for these pathogens. In this context, we characterized and compared resistant microorganisms of the ESKAPEE group, isolated from hospital effluent and clinical samples from patients of the Pequeno Príncipe Hospital, located at Curitiba, Paraná. Out of 345 microorganisms isolated, 208 from the ESKAPEE group were obtained from hospital effluent and 18 were from clinical samples. Among them, K. pneumoniae was the most frequently identified microorganism in both clinical and environmental settings. The genomic context of the resistance of 52 single-clone isolates with satisfactory genome assembly parameters was analyzed. The identified carbapenem resistance genes were blaKPC-2,blaGES-5, and blaNDM-1. Two Enterobacter kobei isolates co-produced the carbapenemases blaKPC-2 and blaGES-5. The samples were defined as polyclonal for K. pneumoniae and E. cloacae complexes and clonal for E. coli isolates. ST392 and ST11 were identified in both clinical and environmental samples of K. pneumoniae that produces Klebsiella pneumoniae carbapenemase (KPC) or New Delhi metallo-β-lactamase (NDM), suggesting the persistence of these microorganisms in hospital effluents. The ESKAPEE group is present in hospitals, and its dissemination through hospital effluents is a significant concern due to its capacity to transfer antimicrobial resistance genes, which poses a risk to public health and food safety.

Multi-scale wastewater surveillance at a Bangkok tertiary care hospital: A potential sentinel site for real-time COVID-19 surveillance at hospital and national levels

Wastewater-based epidemiology is a valuable tool for population-level pathogen surveillance, complementing clinical methods. While most sampling focuses on municipal wastewater treatment plants, emerging evidence suggests wastewater collected from hospital settings can lead to targeted clinical interventions. To investigate wastewater pathogen surveillance in hospital settings further, we tracked the presence and concentration of SARS-CoV-2 RNA in wastewater across multi-scale sample sites within a large, public tertiary care hospital in Bangkok, Thailand. From July 2022 to May 2023, weekly wastewater samples (n=392) were collected from various sample sites including clinical and non-clinical facilities, as well as the hospital's wastewater treatment plant. Influent wastewater at the hospital's wastewater treatment center yielded the most consistent SARS-CoV-2 RNA detection across all sample sites, with detection in all 26 samples. Despite varied building usage patterns, significant moderate negative correlations were found in 90% (9/10) of sample sites between wastewater RT-PCR cycle threshold values and clinical case data from hospital and national reports. Targeting specific buildings yielded distinct data trends, indicating their potential to offer complementary insights into viral shedding and transmission among clinical and non-clinical sub-populations within a hospital campus. Our findings suggest that hospital wastewater-based epidemiology reflects broader community disease trends, which may be especially useful in regions with limited municipal wastewater treatment coverage. Large tertiary care hospitals could serve as effective and cost-efficient sentinel surveillance sites for future pathogen monitoring, guiding public health actions.

Frog Skin Peptides Hylin-a1, AR-23, and RV-23: Promising Tools Against Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae Infections

BACKGROUND/OBJECTIVES

One of the pressing challenges in global public health is the rise in infections caused by carbapenem-resistant Enterobacteriaceae. Growing bacterial drug resistance, coupled with the slow development of new antibiotics, highlights the critical need to explore and develop new broad-spectrum antimicrobial agents able to inhibit bacterial growth efficiently. In recent years, antimicrobial peptides (AMPs) have gained significant attention as a promising alternative to conventional drugs, owing to their antimicrobial potency, low toxicity, and reduced propensity for fostering resistance. Our research aims to investigate the antibacterial ability of three amphibian AMPs, namely Hylin-a1, AR-23, and RV-23, against both antibiotic-sensitive and carbapenem-resistant strains of Escherichia coli and Klebsiella pneumoniae.

METHODS

A 3-(4,5 dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay (MTT) was performed to identify non-cytotoxic concentrations of peptides. A microdilution assay evaluated the antibacterial effect, determining the peptides' minimum inhibitory concentration (MIC). In addition, the checkerboard test analyzed the compounds' synergistic effect with meropenem.

RESULTS

We demonstrated that peptides with low toxicity profile and resistance to proteolytic activity exhibited strong antibacterial activity, with MIC ranging from 6.25 to 25 μM. The antibiofilm mechanism of action of peptides was also investigated, suggesting that they had a crucial role during the biofilm formation step by inhibiting it. Finally, we highlighted the synergistic effects of peptides with meropenem.

CONCLUSIONS

Our study identifies Hylin-a1, AR-23, and RV-23 as promising candidates against Gram-negative bacterial infections with a favorable therapeutic profile. This effect could be related to their great flexibility, as evidenced by circular dichroism data, confirming that the peptides could assume an α-helical conformation interacting with bacterial membranes.

Current Antibiotic Resistance Profile of ESKAPE Pathogens in a Nepalese Hospital: A Cross-Sectional Study

Background: Antimicrobial-resistant Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter (ESKAPE) species pathogens pose a threat to global health by limiting available treatments, escalating the burden of disease, and raising mortality rates. This study investigated the prevalence of ESKAPE pathogens in different infections in a Nepalese hospital and studied their antibiotic resistance pattern. Methodology: The study was performed from September 2022 to February 2023 at Tribhuvan University Teaching Hospital (TUTH), Kathmandu, Nepal. ESKAPE pathogens were isolated in accordance with standard procedures and subjected to antimicrobial susceptibility testing (AST). Identification was done via biochemical testing. The rates of multidrug resistance (MDR), production of extended-spectrum beta-lactamase (ESBL), and methicillin resistance were studied and statistically compared in terms of the type of pathogen, infection, and hospital admission. Result: Altogether, 7429 different clinical samples were cultured and ESKAPE pathogens were isolated from 503/1564 (32.1%) positive samples. The prevalence of these pathogens was significantly higher in admitted patients (p < 0.001). Higher rates of isolation were from urine and sputum samples. Klebsiella pneumoniae was the most prevalent organism while Enterobacter was the least. A total of 52.3% and 7.4% of the isolates were MDR and ESBL producers, respectively. A significant proportion of MDR isolates were from patients admitted to the Intensive Care Unit (ICU). The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) was 36.8%. AST revealed comparatively lower resistance of Gram-negative rods to tigecycline, polymyxin B, and colistin sulfate. Likewise, lower resistance rates to vancomycin and teicoplanin were observed in S. aureus. Conclusion: In various clinical samples, we discovered that ESKAPE pathogens were more prevalent. In order to escape the ESKAPE's torment of antibiotic resistance, our findings urge the urgent implementation of sensible antibiotic use, training healthcare professionals in antibiotic stewardship, developing effective infection control strategies, and conducting effective surveillance.

Identification of cross-reactive vaccine antigen candidates in Gram-positive ESKAPE pathogens through subtractive proteome analysis using opsonic sera

The Gram-positive pathogens of the ESKAPE group, Enterococcus faecium, and Staphylococcus aureus, are well-known to pose a serious risk to human health because of their high virulence and numerous drug resistances. To narrow down the list of previously identified promising protein vaccine candidates, a combination of several antigen discovery approaches was performed, in particular a "false positive analysis" of peptides generated by trypsin shaving with a subtractive proteome analysis. The final list of nine potential antigens included AdcAau, a protein performing the same function as AdcAfm, an already discovered antigen in enterococci. Bioinformatic analyses revealed that AdcAau and AdcAfm share a sequence identity of 41.2% and that the conserved regions present a high antigenicity. AdcAau was selected for further investigation and the results reported in this manuscript demonstrate the opsonic properties of AdcAau-specific antibodies against the Staphylococcus aureus strain MW2, as well as their cross-binding and cross-opsonic activity against several S. aureus, E. faecium, and E. faecalis strains. The experimental design revealed several promising vaccine candidates, including the newly identified S. aureus antigen, AdcAau. The study shows its potential as a vaccine candidate to prevent infections by dangerous Gram-positive ESKAPE pathogens.

Novel Species-Specific Primers Enable Accurate Detection and Quantification of Pseudomonas aeruginosa via qPCR

Pseudomonas aeruginosa, a notable pathogen in nosocomial infections, also emerges as a significant and often underestimated foodborne pathogen, frequently identified in diverse food categories, including meat, milk, fruits, vegetables, and water. Its resilience, virulence, and ability to form biofilms necessitate the development of novel methods for early detection of its presence in food products. This study aims to identify, design, and validate specific genetic markers for P. aeruginosa detection through quantitative PCR (qPCR) analysis. In this study, 816 publicly available genome sequences of P. aeruginosa strains were compared to identify a conserved and specific gene encoding a hypothetical protein (WP_003109295.1) in P. aeruginosa DSM 50071. Primers targeting this gene region were designed and validated for their ability to detect P. aeruginosa using qPCR, demonstrating a high level of sensitivity and specificity for P. aeruginosa among various Pseudomonas species. Further validation through standard curve analysis using three different templates such as cloned DNA, genomic DNA, and cell suspension confirmed the exceptional sensitivity and specificity of the designed primers in quantifying P. aeruginosa via qPCR. Additionally, the on-site application of these primers was validated on P. aeruginosa-inoculated carrot samples, highlighting their reliability and accuracy. The proposed direct qPCR method offers substantial advantages for the rapid, simple, and specific detection of P. aeruginosa, enhancing the efficiency of diagnostic and monitoring processes for this pathogen in food and vegetable distribution systems.

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii

The proliferation of multi-drug resistant (MDR) bacteria is driven by the global spread of epidemic lineages that accumulate antimicrobial resistance genes (ARGs). Acinetobacter baumannii, a leading cause of nosocomial infections, displays resistance to most frontline antimicrobials and represents a significant challenge to public health. In this study, we conduct a comprehensive genomic analysis of over 15,000 A. baumannii genomes to identify a predominant epidemic super-lineage (ESL) accounting for approximately 70% of global isolates. Through hierarchical classification of the ESL into distinct lineages, clusters, and clades, we identified a stepwise evolutionary trajectory responsible for the worldwide expansion and transmission of A. baumannii over the last eight decades. We observed the rise and global spread of a previously unrecognized Clade 2.5.6, which emerged in East Asia in 2006. The epidemic of the clade is linked to the ongoing acquisition of ARGs and virulence factors facilitated by genetic recombination. Our results highlight the necessity for One Health-oriented research and interventions to address the spread of this MDR pathogen.

Bacterial burden and drug-resistant bacteria in healthcare workers' mobile phones: a study in Puerto Rican outpatient clinics

Background

Mobile phones used by healthcare workers (HCWs) in hospitals are significant reservoirs of drug-resistant bacteria responsible for hospital-acquired infections (HAIs).

Aim

The objective of this study was to assess the level of contamination with such bacteria in outpatient clinics.

Methods

Swabs from 83 HCWs' mobile phones were processed using standard biochemical and enzymatic procedures to identify pathogenic bacteria. β-Lactamase tests, antimicrobial susceptibility tests, screening for extended-spectrum β-lactamase (ESBL), and carbapenemase production were performed according to CLSI guidelines. Molecular detection of multi-drug-resistant genes (mecA in Staphylococcus aureus and kpc/ndm carbapenemases in Klebsiella pneumoniae and Acinetobacter spp.) was performed using multiplex real-time polymerase chain reaction.

Findings

The overall prevalence of mobile phone contamination with one or more bacteria was 100%. A total of 51 Gram-positive and 44 Gram-negative isolates, including 20 coagulase-negative staphylococci (CoNS), 20 S. aureus (0 meticillin-resistant S. aureus), 11 Acinetobacter spp. and 10 K. pneumoniae were isolated. β-Lactamase production was detected in 45% of CoNS and 30% of S. aureus. Panton-Valentine Leukocidin (PVL) toxin gene in S. aureus was found in 20% (4/20) of the isolates. Twenty (20%) and 13% of the Acinetobacter spp. and K. pneumoniae isolates, respectively, were ESBL but not carbapenemase producers.

Conclusions

The presence of HAI-causing organisms on mobile phones used by HCWs in outpatient clinics necessitates the implementation of infection control measures to mitigate the risk of cross-contamination in critical healthcare settings.

Integrating machine learning and multitargeted drug design to combat antimicrobial resistance: a systematic review

Antimicrobial resistance (AMR) is a critical global health challenge, undermining the efficacy of antimicrobial drugs against microorganisms like bacteria, fungi and viruses. Multidrug resistance (MDR) arises when microorganisms become resistant to multiple antimicrobial agents. The World Health Organisation classifies AMR bacteria into priority list - I (critical), II (high) and III (medium), prompting action from nearly 170 countries. Six priority bacterial strains account for over 70% of AMR-related fatalities, contributing to more than 1.3 million direct deaths annually and linked to over 5 million deaths globally. Enterobacteriaceae, including Escherichia coli, Salmonella enterica and Klebsiella pneumoniae, significantly contribute to AMR fatalities. This systematic literature review explores how machine learning (ML) and multitargeted drug design (MTDD) can combat AMR in Enterobacteriaceae. We followed PRISMA guidelines and comprehensively analysed current prospects and limitations by mining PubMed and Scopus literature databases. Innovative strategies integrating AI algorithms with advanced computational techniques allow for the analysis of vast datasets, identification of novel drug targets, prediction of resistance mechanisms, and optimisation of drug molecules to overcome resistance. Leveraging ML and MTDD is crucial for both advancing our fight against AMR in Enterobacteriaceae, and developing combination therapies that target multiple bacterial survival pathways, reducing the risk of resistance development.

Antibiotic resistance and biofilm formation in Klebsiella spp. isolates from Intensive Care Units in the Brazilian Amazon

Klebsiella spp. is an opportunistic pathogen which poses a significant threat to public health, especially due to antimicrobial resistance and biofilm formation. This study aimed to determine the antibiotic resistance profile, biofilm formation and β-lactamases production in Klebsiella spp. strains from clinical samples obtained from hospitalized patients, health professionals and hospital environment of intensive care units (ICUs) in Brazilian Amazon. The strains were obtained from clinical samples in different hospitals and identified using molecular techniques. The antimicrobial susceptibility was investigated via disk diffusion and microdilution. Biofilm formation was evaluated using a microtiter plate assay, while the extended-spectrum β-lactamases (ESBL) and carbapenemases production was assessed via disk approximation tests and combined disk tests, respectively. A total of 226 Klebsiella spp. strains were identified, with 141 coming from patients hospitalized in ICUs, 54 from healthcare workers, and 31 from hospital structures. Collection sites that showed the highest frequencies of isolated bacteria were the armpit (43,3%), oral cavity (42.6%), nasal cavity (70.4%), beds (54.8%) and mechanical ventilation (19.4%). Klebsiella spp. isolates from hospitalized patients and hospital ICU environments showed a high frequency of resistance (>50%) to the antibiotics, cefuroxime, cefotaxime, ceftriaxone, ciprofloxacin and aztreonam, and greater sensitivity (>70%) to carbapenems, amikacin and polymyxin B. Samples obtained from hospital structures (74.2%) and patients (51.8%) exhibited a high rate of multidrug resistant (MDR) isolates. In addition, 29% of Klebsiella isolates were found to produce ESBL and 15.5% carbapenemases. Biofilm formation was observed in 58.4% (132/226) of the isolates, with percentages of 64.5% (91/141) in hospitalized patients, 51.6% (16/31) on hospital structures, and 46.3% (25/54) among healthcare professionals. These results indicated a high percentage of antibiotics resistance and MDR in isolates from hospital structures and patients, which also showed ability to produce biofilms, ESBL and carbapenemases. Our findings reinforce the need to monitor resistance and adopt measures aimed at preventing the spread of MDR bacteria in ICUs.

Yearlong analysis of bacterial diversity in hospital sink drains: culturomics, antibiotic resistance and implications for infection control

Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI's) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.

Synthesis, Antimicrobial Activities, and Model of Action of Indolyl Derivatives Containing Amino-Guanidinium Moieties

The objectives of the study were to design, synthesize, and evaluate the antibacterial activity of a series of novel aminoguanidine-indole derivatives. Thirty-seven new compounds were effectively synthesized through nucleophilic substitution reaction and guanidinylation reaction. Chemical structures of all the desired compounds were identified by NMR and HR-MS spectroscopy. Most of the synthesized compounds showed significant antibacterial activity against ESKAPE pathogens and clinical resistant Klebsiella pneumoniae (K. pneumoniae) isolates. K. pneumoniae is an important opportunistic pathogen that often threatens the health of immunocompromised people such as the elderly, children, and ICU patients. The most active compound 4P showed rapid bactericidal activity against resistant K. pneumoniae 2108 with MIC and MBC values that were 4 and 8 µg/mL, respectively. The hemolytic activity of 4P was low, with an HC50 value of 123.6 µg/mL. Compound 4P induced the depolarization of the bacterial membrane and disrupted bacterial membrane integrity and was not prone to antibiotic resistance. The dihydrofolate reductase (DHFR) activity was also notably inhibited by 4P in vitro. Molecular docking revealed that the aminoguanidine moiety and indole structure of 4P played an important role in binding to the target site of the K. pneumoniae dihydrofolate reductase (DHFR) receptor. In the mouse pneumonia model caused by K. pneumoniae, 4P improved the survival rate of mice, reduced bacterial loads, and alleviated tissues' pathological injuries at a dosage of 4 mg/kg. Therefore, compound 4P may be a promising lead compound or drug candidate for antibacterial purposes against K. pneumoniae.

A chionodracine-derived peptide, KHS-Cnd, as an anti-virulence agent against multidrug-resistant Acinetobacter baumannii clinical strains

About 71% of healthcare-associated infections are due to antibiotic-resistant bacteria, such as carbapenem-resistant A. baumannii, classified by World Health Organization into a critical priority group of pathogens. The antimicrobial resistance profile of A. baumannii relies on its ability to produce several virulence factors, including biofilm formation. Its ability to adhere and persist on surfaces as biofilm has contributed to its pathogenicity and drug resistance. In this study, the ability of an antimicrobial peptide (a chionodracine-derived peptide named KHS-Cnd) to inhibit or reduce biofilm formation was investigated as an example of a potential strategy to counteract infections caused by biofilm-forming pathogens. To this aim, the antimicrobial profiles were first analyzed in selected A. baumannii strains, two reference and six clinical strains, all biofilm-forming with different capability, regardless of whether they are drug resistant or sensitive. Successively, we investigated the bactericidal activity of the peptide that showed MIC values ranging from 5 to 10 µM and a significative antibiofilm activity on all tested strains at sub-inhibitory concentrations. In fact, KHS-Cnd can hinder biofilm A. baumannii strains formation with an inhibition percentage ranging between 65% and 10%. Also a statistically significant reduction of mature biofilm ranging from 20% to 50% was observed in four out of eight tested A. baumannii strains. KHS-Cnd impacts various stages of biofilm formation, including the inhibition of surface-associated and twitching motilities depending on the different strain. In particular, our results showed that only two strains possessed surface-associated motility that was strongly impaired by KHS-Cnd treatment; three clinical strains, instead, showed twitching motility, whose inhibition for two of them was evident after 24 h of incubation with peptide. Moreover, the invasion of pulmonary cells by A. baumannii was significantly impaired with a reduction of about 32% after treatment with 1.25 µM KHS-Cnd. Finally, when the peptide was used together with ceftazidime/avibactam against resistant A. baumannii strains, it was able to reduce the minimal inhibitory concentration of antibiotics needed to inhibit the microorganism growth.

Antimicrobial Resistance in ESKAPE Pathogens: A Retrospective Epidemiological Study at the University Hospital of Palermo, Italy

BACKGROUND

Antimicrobial resistance (AMR) is an escalating global health threat, projected to cause over 40 million deaths by 2050. ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are major contributors to nosocomial infections and AMR. We evaluated the epidemiology and AMR prevalence of ESKAPE pathogens at the University Hospital in Palermo between January 2018 and July 2023, analyzing factors associated with mortality in patients with positive blood cultures.

METHODS

Microbiological data from all specimen types were collected using the Business Intelligence system Biwer, excluding duplicates. We assessed the prevalence and trends of ESKAPE isolates and AMR over time. Clinical data from hospital discharge forms were used to evaluate factors associated with mortality in patients with ESKAPE-positive blood cultures. Differences in AMR prevalence between blood and non-blood isolates were examined.

RESULTS

A total of 11,607 specimens from 4916 patients were analyzed. Most patients were admitted to Internal Medicine (19.4%), the ICU (13.2%), and General Surgery (9.9%). Additionally, 21.5% of the specimens were collected from ICU-admitted patients. Blood cultures accounted for 14.3% of the specimens, urine for 25.3%, respiratory secretions for 22.1%, and skin and mucosal swabs for 20.9%. The prevalence of all isolates increased progressively, peaking in 2021. The vancomycin-resistant E. faecium prevalence was 19.4%, with a significant upward trend, while oxacillin-resistant S. aureus prevalence was 35.0%, showing a significant decline. A. baumannii exhibited high resistance to all antibiotics tested except for colistin and cefiderocol. Carbapenemase resistance was 55.0% in K. pneumoniae, 20.4% in P. aeruginosa, and 4.6% in Enterobacter spp. P. aeruginosa showed a significant decrease in meropenem resistance. K. pneumoniae and A. baumannii bloodstream infections were linked to higher mortality risk.

Whole-body Bacteriophage Distribution Characterized by a Physiologically based Pharmacokinetic Model

In 2019 there were over 2.8 million cases of antibiotic-resistant bacterial infection in the US with gram negative organisms having up to a 6% rate of mortality. Bacteriophage (phage) therapy holds great promise to treat such infections. However, the biologic features which influence the pharmacokinetics (PK) of phage have been difficult to characterize due to a lack of standardized protocols of phage purification, tissue assay, and labeling. Here we present robust methods for ultrapure phage preparation as well as non-destructive highly stable attachment of radio-iodide to phage using the well described Sulfo-SHPP linker. We purified and radiolabeled the phage strains, PAML-31-1, OMKO1, and Luz24 lytic to drug-resistant Pseudomonas aeruginosa for biodistribution assay in normal young adult CD-1 mice injected via penile vein. Groups of 5 mice were euthanized and tissues/organs removed for weighing and scintillation well counting of I-125 activity at 30 min, 1h, 2h, 4h, 8h, and 24h. A physiologically based PK (PBPK) model was then constructed focusing on compartments describing blood, lung, muscle, bone, liver, stomach, spleen, small intestines, large intestines, and kidney. Model permeability coefficient (PS) was estimated across all organs as being 0.0227. Tissue partition coefficients (KP) were estimated for high perfusion organs (lung and kidney) as 0.000138, GI organs (liver, spleen, and stomach) as 0.627, and all other organs as 0.220. Elimination was governed by MPS-mediated elimination (TMPS,deg) and active secretion at epithelial barriers (CLActive), which were estimated as 0.00301 h and 0.0145 L/h/kg, respectively. Monte Caro simulations showed that the rapid elimination phage in humans is expected, resulting in phage blood concentrations being lower than 102 PFU/mL (limit of quantification by plaque assay) by 12 hours. As such, multi-dose regimens and continuous infusion regimens were the only strategies that allowed continuously detectible phage concentrations. Evaluation of different dose levels showed that at a maximum dose of 1012 PFU, phage concentrations are expected to be approximately 107 PFU/g. Our physiologically based PK model of phage represents the first rigorous pre-clinical assessment of phage PK utilizing contemporary pharmacometric approaches amenable to both pre-clinical and clinical study design.

Antimicrobial peptides: An alternative strategy to combat antimicrobial resistance

Antimicrobial peptides (AMPs) are a diverse group of naturally occurring molecules produced by eukaryotes and prokaryotes. They have an important role in innate immunity via their direct microbicidal properties or immunomodulatory activities against pathogens. With the widespread occurrence of antimicrobial resistance (AMR), AMPs are considered as viable alternatives for the treatment of multidrug-resistant microbes, inflammation, and, wound healing. The broad-spectrum antibacterial activity of AMPs is predominantly attributed to membrane disruption, leading to the formation of transmembrane pores and, eventually, cell lysis. However, mechanisms related to inhibition of cell wall synthesis, nucleic acid synthesis, protein synthesis, or enzymatic activity are also associated with these peptides. In this review, we discuss our current understanding, therapeutic uses and challenges associated with the clinical applications of AMPs.

NIAID Workshop Report: Systematic Approaches for ESKAPE Bacteria Antigen Discovery

On 14-15 November 2023, the National Institute of Allergy and Infectious Diseases (NIAID) organized a workshop entitled "Systematic Approaches for ESKAPE Bacteria Antigen Discovery". The goal of the workshop was to engage scientists from diverse relevant backgrounds to explore novel technologies that can be harnessed to identify and address current roadblocks impeding advances in antigen and vaccine discoveries for the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The workshop consisted of four sessions that addressed ESKAPE infections, antigen discovery and vaccine efforts, and new technologies including systems immunology and vaccinology approaches. Each session was followed by a panel discussion. In total, there were over 260 in-person and virtual attendees, with high levels of engagement. This report provides a summary of the event and highlights challenges and opportunities in the field of ESKAPE vaccine discovery.

Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates

Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa .

Importance

Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.

Innovative epitopes in Staphylococcal Protein-A an immuno-informatics approach to combat MDR-MRSA infections

Background

Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant challenge in clinical environments due to its resistance to standard antibiotics. Staphylococcal Protein A (SpA), a crucial virulence factor of MRSA, undermines host immune responses, making it an attractive target for vaccine development. This study aimed to identify potential epitopes within SpA that could elicit robust immune responses, ultimately contributing to the combat against multidrug-resistant (MDR) MRSA.

Methods

The SpA protein sequence was retrieved from the UniProt database, with various bioinformatics tools employed for epitope prediction. T-cell epitopes were identified using the Tepitool server, focusing on high-affinity interactions with prevalent human leukocyte antigens (HLAs). B-cell epitopes were predicted using the BepiPred tool. Predicted epitopes underwent docking studies with HLA molecules to evaluate binding properties. In-silico analyses confirmed the antigenicity, promiscuity, and non-glycosylated nature of the selected epitopes.

Results

Several T and B cell epitopes within SpA were identified, showcasing high binding affinities and extensive population coverage. A multi-epitope vaccine construct, linked by synthetic linkers and an adjuvant, was modelled, refined, and validated through various bioinformatics assessments. The vaccine candidate was subsequently docked with Toll-like receptor 4 (TLR-4) to evaluate its potential for immunogenicity.

Conclusion

This study lays the groundwork for developing epitope-based vaccines targeting SpA in MRSA, identifying promising candidates for experimental validation and contributing to innovative immunotherapeutic strategies against MRSA infections.

Microbial Colonization and Antibiotic Resistance Profiles in Chronic Wounds: A Comparative Study of Hidradenitis Suppurativa and Venous Ulcers

Background/Objectives: Chronic wounds, including hidradenitis suppurativa (HS) and venous ulcers (VU), are commonly associated with complex microbial communities that may influence wound healing and treatment outcomes. Understanding microbial diversity and antibiotic resistance patterns is essential in order to optimize therapeutic strategies. This study aimed to investigate the microbial populations and antibiotic resistance profiles in HS and VU patients, comparing the prevalence of common pathogens and their antimicrobial resistance profiles. Methods: We conducted a cross-sectional analysis that included a total of 112 individuals (24 with the diagnosis of hidradenitis suppurativa and 88 diagnosed with venous ulcer). Wound swabs were cultured to identify bacterial species, and antibiotic resistance was assessed using a standard panel of antibiotics. Prevalence rates of key pathogens, such as Staphylococcus aureus, Pseudomonas aeruginosa, and Enterococcus faecalis, were compared between the two groups. Resistance patterns were analyzed using statistical methods to identify significant differences. Results: Staphylococcus aureus was the most common pathogen in both groups (45.8% in HS; 38.6% in VU), with a notable prevalence of methicillin-resistant S. aureus (MRSA). Pseudomonas aeruginosa was exclusively identified in VU patients (27.3%), while beta-hemolytic Streptococcus and Corynebacterium amycolatum were identified in HS cases only. Antibiotic resistance was moderate, notably in S. aureus and Proteus mirabilis, while one case of multidrug-resistant Pseudomonas aeruginosa was identified. Conclusions: This study highlights the distinctive microbial profiles and antibiotic resistance patterns in HS and VU chronic wounds. The predominance of S. aureus in both groups underscores the need for targeted therapies, while the absence of P. aeruginosa in HS wounds and the higher prevalence of other species emphasizes wound-specific microbial variations. These findings underscore the importance of personalized treatment strategies and continuous surveillance of antimicrobial resistance.

Forecasting the development of antimicrobial resistance of S. aureus

Today, about 15.0% of odontogenic pathology is caused by Staphylococcus aureus (S. aureus). The aim of the study was to predict the development of antimicrobial resistance of S. aureus based on retrospective data.

Methods

A total of 425 patients undergoing treatment for odontogenic infectious diseases of the facial area during 2019-2023 were involved in the study. The object of the study was 106 clinical isolates of S. aureus that were isolated and identified from patients. Determining the sensitivity of the obtained isolates to antimicrobial drugs was carried out using Vitek antimicrobial susceptibility testing (Biomerioux, France) and analyzed according to the breackpoint tables of the EUCAST. Prediction of the development of antimicrobial resistance of S. aureus to various antibiotics was carried out on the basis of the received sensitivity data of the studied isolates in 2019-2023 using the exponential smoothing method.

Results

The antimicrobial resistance of S. aureus isolates to various antibiotics changed annually during 2019-2023. The level of resistance of S. aureus isolates to benzylpenicillin wavered between 40%-50% from 2019 to 2023 with the trend of an 18.0% increase over the next five years. A uniform plateau of antimicrobial resistance of S. aureus to cefoxitin is predicted at the level of 32.0% during 2024-2028. We recorded the highest portions of S. aureus resistant to norfloxacin (33.3%) and ciprofloxacin (16.7%) in 2023 with prediction of its increasing in the next five years within the range of 20.0%. It was established that S. aureus may reach 100.0% resistance to gentamicin in 2027. According to exponential smoothing, the level of S. aureus resistance to amikacin will increase by 22.7% over the next five-year period. Moreover, representatives of this species of bacteria can develop complete (100.0%) resistance to tetracycline as early as 2027.

Conclusions

Mathematical prediction of the development of antimicrobial sensitivity of S. aureus isolates showed a high probability of its development to antibiotics of all groups in the next five years.

Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Klebsiella pneumoniae

BACKGROUND

The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the 'global clones of high risk'. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is more and more often used for these purposes, including the epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations.

DESCRIPTION

In this database, we provide the results of a thorough genomic analysis of 61,857 genomes of a highly dangerous bacterial pathogen Klebsiella pneumoniae. Important isolate typing information including multilocus sequence typing (MLST) types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, the presence of CRISPR-Cas systems, and cgMLST profiles are given, and the information regarding the presence of AMR, virulence genes and plasmid replicons within the genomes is provided.

CONCLUSION

This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.11069018 . The database will facilitate selection of the proper reference isolate sets for any types of genome-based investigations. It will be helpful for investigations in the field of K. pneumoniae genomic epidemiology, as well as antimicrobial resistance analysis and the development of prevention measures against this important pathogen.

Bacteriophage and Phage-Encoded Depolymerase Exhibit Antibacterial Activity Against K9-Type Acinetobacter baumannii in Mouse Sepsis and Burn Skin Infection Models

Acinetobacter baumannii is a widely distributed nosocomial pathogen that causes various acute and chronic infections, particularly in immunocompromised patients. In this study, the activities of the K9-specific virulent phage AM24 and phage-encoded depolymerase DepAPK09 were assessed using in vivo mouse sepsis and burn skin infection models. In the mouse sepsis model, in the case of prevention or early treatment, a single K9-specific phage or recombinant depolymerase injection was able to protect 100% of the mice after parenteral infection with a lethal dose of A. baumannii of the K9-type, with complete eradication of the pathogen. In the case of delayed treatment, mouse survival decreased to 70% when injected with the phage and to 40% when treated with the recombinant enzyme. In the mouse burn skin infection model, the number of A. baumannii cells on the surface of the wound and in the deep layers of the skin decreased by several-fold after treatment with both the K9-specific phage and the recombinant depolymerase. The phage and recombinant depolymerase were highly stable and retained activity under a wide range of temperatures and pH values. The results obtained contribute to expanding our understanding of the in vivo therapeutic potential of specific phages and phage-derived depolymerases interacting with A. baumannii of different capsular types.

Antibiofilm activities of lactoferricin-related Trp- and Arg-rich antimicrobial hexapeptides against pathogenic Staphylococcus aureus and Pseudomonas aeruginosa strains

Recently, several antimicrobial peptides (AMPs), varying in length from 12 to 37 residues, have been shown to act as antibiofilm agents. Here, we report a study of 23 hexapeptides modeled after four different Trp- and Arg-rich AMPs, including the RRWQWR-NH2 peptide, derived from bovine lactoferrin. They were tested against the pathogenic Gram-negative Pseudomonas aeruginosa PAO1 strain and a Gram-positive Staphylococcus aureus MRSA strain. Both strains were engineered to express the green fluorescent protein (GFP) protein, and fluorescence detection was used to measure the ability of the peptides to prevent biofilm formation (minimum biofilm inhibitory concentration (MBIC)) or to cause the breakdown of established biofilms (minimum biofilm eradication concentration (MBEC)). Similar antibiofilm activities were obtained with the standard crystal violet dye assay. Most Trp- and Arg-rich hexapeptides displayed a potent antibiofilm activity against the Gram-positive S. aureus MRSA strain. In particular, hexapeptides with 3 Arg and 3 Trp were very effective, especially when they contained the three Trp in sequence. Somewhat unexpectedly, the antimicrobial (MIC) values correlated with the MBIC and MBEC values, which has not been seen for several other AMP/antibiofilm peptides. Our results demonstrate that short Trp- and Arg-rich peptides merit further studies as antibiofilm agents that could be deployed to address part of the antimicrobial resistance problem.

Influence of critical micelle concentration of choline-based long chain fatty acid soaps on their antibacterial activity against Methicillin resistant Staphylococcus aureus

HYPOTHESIS

Antimicrobial resistance (AMR) is a pressing global health concern. ESKAPEE pathogens, such as Methicillin-resistant Staphylococcus aureus (MRSA) are notable of concern in healthcare settings due to their resistance to critical antibiotics. To combat AMR, the development of alternatives such as bacterial membrane-active agents is crucial. Fatty acids (FAs) have emerged as a sustainable, antibiotic-free solution with inherent antibacterial activity. However, long chain saturated fatty acids (LCFAs) sodium soaps exhibit poorly antibacterial properties in comparison to short chain FAs, believed to be linked to limited solubility in aqueous media.

EXPERIMENTS

We employed choline as a chaotropic organic counter-ion to enhance the solubility of LCFAs and investigated their antibacterial effects against MRSA. The optimal medium conditions for micelle formation for LCFAs was first investigated. Then, we determined the critical micelle concentration (CMC), micellar morphology, and aggregation number through surface tension measurements and small angle neutron scattering experiments. Antimicrobial activity was assessed using minimum bactericidal concentration (MBC) assays and time-kill experiments.

FINDINGS

We have identified conditions where LCFAs are effective against MRSA for the first time, providing valuable insights for developing new antibacterial agents to fight AMR. LCFAs need to be used above their Krafft temperatures and CMC to exhibit antibacterial efficacy.

Comparison of Phenotypic and Genotypic Detection of Drug Resistance in Acinetobacter baumannii in a Tertiary Care Hospital

Background Acinetobacter baumannii (A. baumannii) is a common cause of nosocomial infection. Multidrug-resistant A. baumannii is a life-threatening and therapeutic challenge, especially in critically ill and vulnerable patients. Drug resistance in A. baumannii is conferred by various underlying mechanisms. This prospective cross-sectional study aims to study the comparison of the phenotypic MBL-E test and molecular tests conferring drug resistance to A. baumannii. Materials and methods Different clinical samples were collected in a time period of two years. Isolated A. baumannii strains were studied for the drug-resistance profile by the Kirby disc method. These drug-resistant isolates were further subjected to metallo-beta-lactamase (MBL) production by molecular detection of OXA-48, NDM, and VIM genes and phenotypic methods by the double-disk synergy test, modified Hodge test, and MBL-E test.  Results A total of 104 A. baumannii isolates were obtained from 3965 samples. Ninety-three (89.4%) of these 104 isolates were found to be drug-resistant which were further analyzed by phenotypic methods for MBL production which showed a detection range of 36.54%-89.42% as compared to a molecular method where detection was observed as 56 (60%).  Conclusion Molecular detection of drug-resistance conferring genes can be a time-effective method as compared to phenotypic detection. However, genetic methods have their own limitation and additional research empaneling in a single test is required.

Mitigating Health Risks Through Environmental Tracking of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a prevalent nosocomial pathogen and a significant reservoir of antimicrobial resistance genes in residential and built environments. It is also widespread in various indoor and outdoor settings, including sewage, surface waters, soil, recreational waters (both treated and untreated), and industrial effluents. Surveillance efforts for P. aeruginosa are primarily focused on hospitals rather than built environments. However, evidence links multidrug-resistant P. aeruginosa of human origin with activity in built environments and hospital settings. Consequently, tracking this pathogen across all environments is crucial for understanding the mechanisms of reverse transmission from built environments to humans. This review explores public health hygiene by examining the prevalence of P. aeruginosa in various environments, its sequence types, the factors contributing to multidrug resistance, and the identification methods through global surveillance. Whole-genome sequencing with sequence typing and real-time quantitative PCR are widely used to identify and study antimicrobial-resistant strains worldwide. Additionally, advanced techniques such as functional metagenomics, next-generation sequencing, MALDI-TOF, and biosensors are being extensively employed to detect antimicrobial-resistant strains and mitigate the ongoing evolution of bacterial resistance to antibiotics. Our review strongly underscores the importance of environmental monitoring of P. aeruginosa in preventing human infections. Furthermore, strategic planning in built environments is essential for effective epidemiological surveillance of P. aeruginosa and the development of comprehensive risk assessment models.

Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review

The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.

Hot spots of resistance: Transit centers as breeding grounds for airborne ARG-carrying bacteriophages

The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in urban air poses a significant threat to public health. While prevailing research predominantly focuses on the airborne transmission of ARGs by bacteria, the potential influence of other vectors, such as bacteriophages, is often overlooked. This study aims to investigate the characteristics of phages and ARGs in aerosols originating from hospitals, public transit centers, wastewater treatment plants, and landfill sites. The average abundance of ARGs carried by phages in the public transit centers was 8.81 ppm, which was 2 to 3 times higher than that at the other three sites. Additionally, the abundance of ARGs across different risk levels at this site was also significantly higher than at the other three sites. The assembled phage communities bearing ARGs in public transit centers are chiefly governed by homogeneous selection processes, likely influenced by human movement. Furthermore, observations at public transit sites revealed that the average abundance ratio of virulent phages to their hosts was 1.01, and the correlation coefficient between their auxiliary metabolic genes and hosts' metabolic genes was 0.59, which were 20 times and 3 times higher, respectively, than those of temperate phages. This suggests that virulent phages may enhance their survival by altering host metabolism, thereby aiding the dispersion of ARGs and bacterial resistance. These revelations furnish fresh insights into phage-mediated ARG transmission, offering scientific substantiation for strategies aimed at preventing and controlling resistance within aerosols.

Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells

Acinetobacter baumannii, classified as priority number one by the World Health Organization (WHO), is an opportunistic pathogen responsible for infection and is able to develop antibiotic resistance easily. Membranes are bacteria's first line of defense against external aggression, such as antibiotics. A chemical modification of a lipid family or a change in lipid composition can lead to resistance to antibiotics. In this work, we analyzed different A. baumannii strains from various environments with different antibiotic resistance profiles, using matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS). This study shows that it is possible to describe the main lipidome (phospholipids and lipid A) from the simple preparation of lysed cells, and that despite the complexity of the mixture. This ultra-high resolution mass spectrometry technique enables the separation of isobaric ion, to report a new class of lipids. Given its performance, this technique can be used to quickly and reliably characterize the lipidome of clinical strains from different environments.

Antimicrobial Activity of ZnS and ZnO-TOP Nanoparticles Againts Pathogenic Bacteria

This study aims to synthesize ZnS nanoparticles (NPs) and investigate their biocidal effects, along with those of ZnO-Trioctylphosphine (ZnO-TOP) NPs, on various pathogenic microbes. The NPs were synthesized via the polyol method using the forced hydrolysis of zinc acetate. They were characterized by XRD and TEM. The average sizes of ZnS and ZnO-TOP are 3.63 nm and 16.28 nm, respectively. The antimicrobial activities were assessed using agar-well diffusion, minimum inhibitory concentration (MIC), and biofilm inhibition. The results showed that ZnS and ZnO-TOP NPs have potent antimicrobial activity against all tested pathogen microbes. A zone of maximum inhibition (ZMI) of 20±0.54 and 22±0.26 was observed in the case of ZnS for Acinetobacter baumannii and Candida albicans, respectively. For ZnO-TOP, a ZMI of 20±0.15 and 20±0.19 is obtained for Pseudomonas. aeruginosa ATCC 27853 and A. baumannii, respectively. Percentages of biofilm inhibition at 128 μg/ml were notably high for Enterococcus faecalis (96.83 % with ZnO-TOP and 91.17 % with ZnS) and Staphylococcus aureus (87.27 % with ZnO-TOP and 76.37 % with ZnS). The results suggest that ZnS and ZnO-TOP nanoparticles have promising potential as effective antimicrobial agents, especially against biofilm-forming pathogens, indicating their potential for future use in treating microbial infections.

Changes in microbial communities across the whole A2/O wastewater treatment process and their drivers-Reduced community diversity but increased proportion of certain pathogens

Microorganisms play a crucial role in pollutant removal and water quality stabilizing. However, limited research exists on the microbial variability and the factors driving it at different stages of wastewater treatment. In this study, the physicochemical properties of water and the composition of bacterial communities were thoroughly investigated across the entire A2/O wastewater treatment process, encompassing 3 stages (12 steps). The results revealed a significant reduction in alpha diversity, whereas the beta diversity remained largely unchanged across stages. Alpha diversity was primarily influenced by dissolved oxygen (DO) and pH, with DO having the most notable influence, while beta diversity was mainly constrained by nutrient conditions such as COD, BOD5, NH4-N, TN, and TP. Additionally, analyses of relative abundance, LEfSe, variance, and functional prediction indicated a significant increase in the relative abundance of certain pathogenic bacteria (e.g., Legionella, Leptospira), exhibiting different removal characteristics compared to Escherichia coli across various treatment steps. Even after UV disinfection, these pathogens persist, highlighting a potential pathogenic risk, which deserves more attention. In addition, this study helps explore the relatively under-researched area of microbial variability at different stages (steps) of wastewater treatment, especially in terms of how microbial communities respond to operational processes and environmental conditions. This will offer valuable guidance for addressing water treatment safety challenges encountered in real-world processes.

Investigating the changing taxonomy and antimicrobial resistance of bacteria isolated from door handles in a new infectious disease ward pre- and post-patient admittance

Healthcare-associated infections (HAIs) are a significant burden to health systems, with antimicrobial resistance (AMR) further compounding the issue. The hospital environment plays a significant role in the development of HAIs, with microbial surveillance providing the foundation for interventions. We sampled 40 door handles at a newly built hospital prior to patients being admitted and then 6 and 12 months after this date. We utilized 16S rDNA sequencing to identify unique colonies, disc diffusion assays to assess the antibiotic resistance of Staphylococcus spp., and whole-genome sequenced (WGS) multidrug-resistant (MDR) isolates. Before patient admission, 43% of sites harbored Staphylococcus spp., increasing to 55% and 65% at six and 12 months, respectively, while Bacillus spp. saw a large increase from 3% to 68% and 85%, respectively. No ESKAPE pathogens were identified. Staphylococcus spp. showed relatively low resistance to all antibiotics except cefoxitin (56%) before patient admittance. Resistance was highest after 6 months of ward use, with an increase in isolates susceptible to all antibiotics after 12 months (11% and 54% susceptibility, respectively). However, MDR remained high. WGS revealed blaZ (25/26), and mecA (22/26) and aac6-aph2 (20/26) were the most abundant resistance genes. Two Staphylococcus hominis isolates identified at the first two time points, respectively, and three Staphylococcus epidermidis isolates identified at all three time points, respectively, were believed to be clonal. This study highlighted the prevalence of a resistant reservoir of bacteria recoverable on high-touch surfaces and the long-term persistence of Staphylococcus spp. first introduced prior to patient admission.

IMPORTANCE

Healthcare-associated infections (HAIs) are a significant burden to health systems, conferring increased morbidity, mortality, and financial costs to hospital admission. Antimicrobial resistance (AMR) further compounds the issue as viable treatment options are constrained. Previous studies have shown that environmental cleaning interventions reduced HAIs. To ensure the effectiveness of these, it is important to analyze the hospital environment at a microbial level, particularly high-touch surfaces which see frequent human interaction. In addition to identifying infectious microorganisms, it is also beneficial to assess typically non-infectious organisms, as traits including AMR can be transferred between the two. Our study identified that there were high levels of antibiotic resistance in typically non-infectious organisms found on high touch surfaces on a hospital ward. However, the organisms identified suggested that the cleaning protocols in place were sufficient, with their presence being due to repeated recolonization events through human interaction after cleaning had taken place.

Synthesis of the pentasaccharide repeating unit with a conjugation-ready linker corresponding to the O-antigenic polysaccharide of Acinetobacter junii strain 65

A straightforward synthesis of the pentasaccharide with a readily available linker arm corresponding to the O-antigenic polysaccharide of Acinetobacter junii strain 65 has been achieved in good yield. The synthesis has been carried out using thioglycosides as glycosyl donor in the presence of a combination of N-iodosuccinimide (NIS) and trifluoromethanesulfonic acid (TfOH) as thiophilic activator. The yields of the glycosylation steps were very good with satisfactory stereochemistry at the glycosidic linkages. The pentasaccharide derivative has also been obtained using a one-pot iterative glycosylation strategy.

Agricultural Soil as a Reservoir of Pseudomonas aeruginosa with Potential Risk to Public Health

Pseudomonas aeruginosa is an opportunistic pathogen with a high capacity to adapt to different factors. The aim of this study is to analyze the pathogenicity in P. aeruginosa strains and their resistance to heavy metals and antibiotics, in agricultural soil of the state of Tamaulipas, Mexico. Susceptibility to 16 antibiotics was tested using the Kirby-Bauer method (CLSI). Eight virulence factors (FV) and six genes associated with heavy metal resistance were detected by PCR. As a result, P. aeruginosa was detected in 55% of the samples. The eight virulence factors were identified in ≥80% of the strains. The strains showed some level of resistance to only three antibiotics: 32.8% to ticarcillin, 40.8% to ticarcillin/clavulanic acid and 2.4% to aztreonam. The most frequent heavy metal resistance genes were arsC (92.8%) and copA (90.4%). However, copB and arsB genes were also identified in a percentage greater than 80%, and the least frequent genes were merA in 14.4% and czcA in 7.2%. Although P. aeruginosa strains showed a high percentage of factor virulence (potential ability to cause infections), their high levels of susceptibility to antibiotics lead to the assumption that infections are easily curable.

High prevalence of carbapenem-resistant Enterobacter cloacae complex in a tertiary hospital over a decade

The aim of this study was to explore the mechanisms and molecular epidemiology of carbapenem resistance in the carbapenem-resistant Enterobacter cloacae complex (CRECC) over a decade in a tertiary hospital in Zhejiang, China. From January 2011 to December 2021, we collected a total of 931 Enterobacter cloacae complex (ECC) isolates from a tertiary hospital in Zhejiang, China. Antimicrobial susceptibility tests were performed. Whole-genome sequencing was used to analyze the molecular characteristics of the CRECC isolates. For carbapenem-resistant strains, efflux inhibitor assay and quantitative real-time PCR (qRT-PCR) were performed to evaluate the function of efflux pumps. A total of 82 CRECC isolates were detected, and the rate of resistance for carbapenems was 8.8%, increasing from 5.5% in 2011 to 18.3% in 2019, with an overall increasing trend, with Enterobacter hormaechei subsp. hoffmannii being the predominant species. Among the CRECC, 24 (24/931) isolates were found to produce carbapenemases, including NDM-1, NDM-5, IMP-4, and KPC-2. Among all carbapenemases, NDM-1 was the most prevalent, accounting for 62.5% (15/24) of carbapenemases, followed by NDM-5 (5/24). Genes encoding extended-spectrum beta-lactamases (47/82) and AmpC (76/82) were also identified, with blaSHV-12 and blaACT being the predominant ones, respectively. Multilocus sequence typing revealed 28 different sequence types, among which ST78 was the predominant, followed by ST93 and ST177. IncFIB was the most common type of plasmid replicon. Efflux inhibitor assay and qRT-PCR indicated that the overexpression of efflux pumps was involved in carbapenem resistance mechanisms. Additionally, disrupted outer membrane proteins also contribute to carbapenem resistance. The detection rate of CRECC was rising in the tertiary hospital. BlaNDM-1 and blaNDM-5 were the main carbapenem resistance genes. Our study revealed the presence of carbapenem-resistant ECC strains, emphasizing the need for effective infection prevention approaches to reduce the prevalence of CRECC.

IMPORTANCE

The emergence and spread of the carbapenem-resistant Enterobacter cloacae complex (CRECC) have become a significant public health problem. CRECC strains frequently harbor multiple drug resistance genes and can be epidemic within healthcare facilities. The study explored the characteristics and prevalence of CRECC strains in the same hospital over a decade, which provides a theoretical basis for epidemiologic surveillance and clinical treatment.

Comparative genome analysis reveals putative and novel antimicrobial resistance genes common to the nosocomial infection pathogens

The 21st century has witnessed several clinical outcomes regarding AMR. One health concept has been foreseen as a standard global public health initiative in ensuring human, animal and environmental health. The present study explores critical Gram-negative ESKAPE pathogens encompassing Acinetobacter baumannii (ACB), Klebsiella pneumoniae (KPX) and Pseudomonas aeruginosa (PAE). A comparative genomic analysis approach was utilized for identifying novel and putative genes coercing global health consequences stressing the significance of the above iatrogenic and nosocomial pathogens. O findings reveal that Pseudomonas aeruginosaPAO1 (PAE) possesses the largest genome, measuring 62,64,404 base pairs, containing 14,342 protein-coding genes and an elevated count of ORFs, surpassing other organisms. Notably, P. aeruginosa PAO1 exhibits a comprehensive metabolic landscape with 355 pathways and 1659 metabolic reactions, encompassing 200 biosynthesis and 132 degradation pathways. Transferases are the predominant enzyme category across all three genomes, followed by oxidoreductases and hydrolases. The pivotal role of beta-lactamase in conferring resistance against antibiotics is also evident in all three microbes. This investigation underscores the PAE genome harbours genes and enzymes associated with heightened virulence in antibiotic resistance. The holistic review combined with comparative genomics underlines the significance of delving into the genomes of these antimicrobial-resistant organisms. In silico methodologies are increasingly stressed in aiding the successful accomplishment of the United Nations Sustainable Development Goal -3: Good Health and Well-being. The prominent findings establish Carbapenem resistance and evolutionary lineages of the MCR-1 gene conferring AMR landscapes for future research.

Overview of Antimicrobial Resistant ESKAPEE Pathogens in Food Sources and Their Implications from a One Health Perspective

Antimicrobial resistance is an increasing societal burden worldwide, with ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species and Escherichia coli) pathogens overwhelming the healthcare sectors and more recently becoming predominantly a concern for their persistence in food and food industries, including agricultural settings and animal husbandry environments. The aim of this review is to explore the mechanisms by which the ESKAPEE group gained its multidrug resistance profiles, to analyse their occurrence in different foods and other related reservoirs, including water, and to address the current challenges due to their spread within the food production chain. Moreover, the repertoire of surveillance programmes available focused on monitoring their occurrence, common reservoirs and the spread of antimicrobial resistance are described in this review paper. Evidence from the literature suggests that restricting our scope in relation to multidrug resistance in ESKAPEE pathogens to healthcare and healthcare-associated facilities might actually impede unveiling the actual issues these pathogens can exhibit, for example, in food and food-related reservoirs. Furthermore, this review addresses the need for increasing public campaigns aimed at addressing this challenge, which must be considered in our fight against antimicrobial resistance shown by the ESKAPEE group in food and food-related sectors.

Critical review on plant-derived quorum sensing signaling inhibitors in pseudomonas aeruginosa

Pseudomonas aeruginosa, a biofilm-forming organism with complex quorum mechanisms (Las, Rhl, PQS, and IQS), poses an imminent danger to the healthcare sector and renders current treatment options for chemotherapy ineffectual. The pathogen's diverse pathogenicity, antibiotic resistance, and biofilms make it difficult to eradicate it effectively. Quorum sensing, a complex system reliant on cell density, controls P. aeruginosa's pathogenesis. Quorum-sensing genes are key components of P. aeruginosa's pathogenic arsenal, and their expression determines how severe the spread of infection becomes. Over the past ten years, there has been a noticeable increase in the quest for and development of new antimicrobial medications. Quorum sensing may be an effective treatment for infections triggered by bacteria. Introducing quorum-sensing inhibitors as an anti-virulent strategy might be an intriguing therapeutic method that can be effectively employed along with current medications. Amongst the several speculated processes, a unique anti-virulence strategy using anti-quorum sensing and antibiofilm medications for targeting pseudomonal infestations seems to be at the forefront. Due to their noteworthy quorum quenching capabilities, biologically active phytochemicals have become more well-known in the realm of science in this context. Recent research showed how different phytochemical quorum quenching actions affect P. aeruginosa's QS-dependent pathogenicity. This review focuses on the most current data supporting the implementation of plant bio-actives to treat P.aeruginosa-associated diseases, as well as the benefits and future recommendationsof employing them in anti-virulence therapies as a supplementary drug development approach towards conventional antibiotic approaches.

An innovative approach to decoding genetic variability in Pseudomonas aeruginosa via amino acid repeats and gene structure profiles

Pseudomonas aeruginosa, a common pathogen in nosocomial infections, presents significant global health challenges due to its high prevalence and mortality rates. However, the origins and distribution of this bacterium remain unclear, partly due to the lack of effective gene typing methods. This situation necessitates the establishment of trustworthy and high-resolution protocol for differentiating closely related P. aeruginosa strains. In this context, the present study attempted to undertake a comparative genomic analysis of multiple P. aeruginosa strains available in the public database NCBI, with the goal of identifying potential genetic markers for measuring the genetic diversity. The preliminary comparative analysis of 816 P. aeruginosa strains revealed notable variations in two genes-specifically, the CDF family iron/cobalt efflux transporter AitP and the protease modulator HflC-across 44 strains. These variations were associated with single amino acid repeats (SHRs) that responsible for encoding histidine residue. Additionally, comparative gene map analysis revealed differential clustering patterns in the Rsx and TAXI genes among 16 strains. Interestingly, the gene structure pattern observed in TAXI groups displayed a strong correlation with the SHRs pattern in the CDF and HflC groups. In addition, the SHRs pattern of CDF and HflC were strongly correlated with MLST sequence type number. Overall, the study present a novel genetic markers based on SHRs and gene cluster patterns, offering a reliable method for genotyping of P. aeruginosa.

Targeting the phosphatidylglycerol lipid: An amphiphilic dendrimer as a promising antibacterial candidate

The rapid emergence and spread of multidrug-resistant bacterial pathogens require the development of antibacterial agents that are robustly effective while inducing no toxicity or resistance development. In this context, we designed and synthesized amphiphilic dendrimers as antibacterial candidates. We report the promising potent antibacterial activity shown by the amphiphilic dendrimer AD1b, composed of a long hydrophobic alkyl chain and a tertiary amine-terminated poly(amidoamine) dendron, against a panel of Gram-negative bacteria, including multidrug-resistant Escherichia coli and Acinetobacter baumannii. AD1b exhibited effective activity against drug-resistant bacterial infections in vivo. Mechanistic studies revealed that AD1b targeted the membrane phospholipids phosphatidylglycerol (PG) and cardiolipin (CL), leading to the disruption of the bacterial membrane and proton motive force, metabolic disturbance, leakage of cellular components, and, ultimately, cell death. Together, AD1b that specifically interacts with PG/CL in bacterial membranes supports the use of small amphiphilic dendrimers as a promising strategy to target drug-resistant bacterial pathogens and addresses the global antibiotic crisis.