Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study

Antibiotic resistance genes in aquatic systems: Sources, transmission, and risks

The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.

Metagenomic analysis reveals differences in antibiotic resistance and transmission risks across various poultry farming models

As living standards in rural areas continue to improve, farmers are increasingly seeking to diversify their farming models beyond monoculture farming. However, the differences in bacterial resistance and the associated transmission risks between monoculture poultry farming and integrated poultry farming remain poorly understood. This study utilizes metagenomic methods to examine the distribution and transmission of antibiotic resistance across three types of farms in Zhejiang Province, as well as to investigate the horizontal transmission mechanisms of plasmid-mediated blaNDM within these agricultural systems. An analysis of 26 environmental samples and 12 saliva samples from six poultry farms with different models has revealed that integrated poultry farms exhibit a more complex microbial composition and more severe resistance compared to monoculture farms. Furthermore, a blaNDM positive plasmid pndm-CD with complex conjugation transfer region was found in the integrated farms. The insertion sequence (IS) ISCR1 present in the upstream of blaNDM has the potential to promote its spread, while the downstream complex structure IS26-blaCTX-M-IS2-qnrB-TinR-ΔISKrA14 enhances the resistance of the host to β-lactam antibiotics, and improves the competition potential of the host bacteria in the anti-antibiotic environment. This research offers the first metagenomic analysis of the differences in bacterial resistance and transmission risks between various poultry farming models. These results offer a solid theoretical basis for managing the spread of antibiotic resistance in mixed chicken and duck farming operations. Additionally, they are significant for ensuring the health of agricultural workers and the hygiene safety of the poultry meat supply chain.

Antimicrobial Resistance - The 'Real' Pandemic We Are Unaware Of, Yet Nearby

Antimicrobial resistance (AMR) represents a persistent and escalating public health crisis, often overlooked despite its severe global impact. Unlike acute infectious diseases, AMR progresses silently but relentlessly, posing long-term threats to health systems worldwide. This review examines the historical evolution and current epidemiology of multidrug-resistant organisms (MDROs), emphasizing the global and Korean burden of MDROs. While the development of new antibiotics remains limited, alternative therapies such as bacteriophage treatment have re-emerged as potential solutions. However, challenges in access to novel agents persist, particularly in Korea, due to regulatory, economic, and market-related barriers. To counter AMR, comprehensive strategies are essential. These include infection control, antibiotic stewardship programs (ASPs), and the development and proper allocation of new drugs. The One Health approach must integrate human, animal, and environmental health perspectives. Notably, infectious disease specialists play a central role in this fight: leading ASPs, shaping policy, engaging in public education, supporting research, and coordinating multidisciplinary collaboration. The AMR pandemic is unlikely to subside without systemic reform, sustained investment, and international cooperation. Urgent efforts must be made to address this hidden but growing threat. Recognizing AMR as a true pandemic is the first step toward containing its spread and securing the efficacy of antibiotics for future generations.

Past, present, and future perspectives on aztreonam and avibactam

INTRODUCTION

Aztreonam is a monobactam antibiotic approved in 1986 to treat infections caused by aerobic Gram-negative bacteria, but, together with cephalosporins, lost clinical utility due to the emergence of extended-spectrum β-lactamases (ESBLs) and novel (serine) carbapenemases. Avibactam was the first in a novel non-β-lactam β-lactamase inhibitor class to effectively inhibit these enzymes. It has been approved in combination with ceftazidime to treat Gram-negative infections caused by bacteria that produce AmpC, ESBLs and serine carbapenemases, and with aztreonam to treat patients infected with metallo-β-lactamase-producing enteric bacteria. Combinations of avibactam with ceftazidime and/or aztreonam have been used successfully to treat enteric pathogens producing multiple classes of β-lactamases.

AREAS COVERED

Development of aztreonam, avibactam, and avibactam combinations are placed into a historical perspective, based on both preclinical and clinical data. A search of MEDLINE (Ovid) was used to identify relevant literature.

EXPERT OPINION

Avibactam combined with ceftazidime and aztreonam in either dual or triple combinations provides the opportunity to treat previously untreatable Gram-negative infections that produce multiple β-lactamases. Aztreonam combinations should be particularly attractive, due to stability to metallo-β-lactamase hydrolysis and its safety advantage in treating penicillin-allergic patients. Other inhibitor combinations in development may challenge these combinations.

Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.

Use of a national repository of Fourier-transform infrared spectroscopy spectra enables fast detection of silent outbreaks and prevention of spread of new antibiotic-resistant sequence types

BACKGROUND

The reference microbiology laboratory of Israel's National Institute for Antibiotic Resistance and Infection Control has established a national repository of isolates analyzed by Fourier-transform infrared (FTIR) spectroscopy and their spectra. Healthcare institutions send antibiotic-resistant isolates as part of outbreak investigation, periodic nation-wide collection of specific species, or point prevalence studies. Here, we describe the use of a national FTIR repository to detect the emergence and spread of new sequence types and resistance mechanisms.

METHODS

Using FTIR, we produced dendrograms of outbreaks and periodic country-level dendrograms of isolates from selected species. When FTIR identified new clusters that were distinct from previously characterized clusters, they were investigated further by whole genome sequencing.

RESULTS

FTIR analysis uncovered two clones new to Israel: NDM-5-producing E. coli ST650 harboring a novel plasmid, and NDM-producing K. pneumoniae ST307.

CONCLUSIONS

Establishing regional or national FTIR repositories could serve as a simple and effective tool for early detection of new antibiotic-resistant clones.

Revisiting therapeutic options against resistant klebsiella pneumoniae infection: Phage therapy is key

Multi-drug resistant and carbapenem-resistant hypervirulent Klebsiella pneumoniae strains are spreading globally at an alarming rate, emerging as one of the most serious threats to global public health. The formidable challenges posed by the current arsenal of antimicrobials highlight the urgent need for novel strategies to combat K. pneumoniae infections. This review begins with a comprehensive analysis of the global dissemination of virulence factors and critical resistance profiles in K. pneumoniae, followed by an evaluation of the accessibility of novel therapeutic approaches for treating K. pneumoniae in clinical settings. Among these, phage therapy stands out for its considerable potential in addressing life-threatening K. pneumoniae infections. We critically examine the existing preclinical and clinical evidence supporting phage therapy, identifying key limitations that impede its broader clinical adoption. Additionally, we rigorously explore the role of genetic engineering in expanding the host range of K. pneumoniae phages, and discuss the future trajectory of this technology. In light of the 'Bad Bugs, No Drugs' era, we advocate leveraging artificial intelligence and deep learning to optimize and expand the application of phage therapy, representing a crucial advancement in the fight against the escalating threat of K. pneumoniae infections.

Antibiotics in the global river system arising from human consumption

The presence of antibiotics in surface waters poses risks to aquatic ecosystems and human health due to their toxicity and influence on antimicrobial resistance. After human consumption and partial metabolism, antibiotic residues are excreted and undergo complex accumulation and decay processes along their pathway from wastewater to natural river systems. Here, we use a global contaminant fate model to estimate that of the annual human consumption of the 40 most used antibiotics (29,200 tonnes), 8,500 tonnes (29%) are released into the river system and 3,300 tonnes (11%) reach the world's oceans or inland sinks. Even when only domestic sources are considered (i.e. not including veterinary or industrial sources), we estimate that 6 million km of rivers worldwide are subject to total antibiotic concentrations in excess of thresholds that are protective of ecosystems and resistance promotion during low streamflow conditions, with the dominant contributors being amoxicillin, ceftriaxone, and cefixime. Therefore, it is of concern that human consumption alone represents a significant risk for rivers across all continents, with the largest extents found in Southeast Asia. Global antibiotic consumption has grown rapidly over the last 15 years and continues to increase, particularly in low- and middle-income countries, requiring new strategies to safeguard water quality and protect human and ecosystem health.

Distribution patterns and ecological risks of antibiotic resistance genes in the Yap Trench

Antibiotic resistance genes (ARGs) are a global environmental concern, yet their vertical distribution in pristine marine ecosystems remains poorly understood. This study investigated the distribution of ARG distribution in both the water column and sediments of the Yap Trench, which reaches depths over 6500 m Results revealed significant variations in ARG diversity and abundance across depths and habitats. The deep-water (DW) zones exhibited the highest diversity (291-472 subtypes) and abundance (1.79 copies/cell), followed by upper-water (UW) zones (240-314 subtypes, 0.31 copies/cell), while sediments had the lowest diversity (72-236 subtypes) and abundance (0.03 copies/cell). The most prevalent resistance genes included those conferring resistance to multidrug, polymyxin, and beta-lactam in the Yap Trench. ARG distribution closely correlated with microbial hosts, including Pseudomonadota, Chloroflexota, Bacteroidota, and Planctomycetota. Risk assessment showed high-risk ARGs were most abundant in DW zones, with pathogenic groups capable of spreading multiple ARGs (e.g., macAB, mexDJKW, mdtE, muxC). This study provides a systematic understanding of the distribution patterns and potential risks of ARGs in the water column and sediments of pristine marine ecosystems, underscoring the penetration of antibiotic pollution into the deep ocean and offering new insights for marine pollution control strategies.

Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes

Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.

Assessing the threat of Yersinia pestis harboring a multi-resistant IncC plasmid and the efficacy of an antibiotic targeting LpxC

Self-transmissible IncC plasmids rapidly spread multidrug resistance in many medically important pathogens worldwide. A large plasmid of this type (pIP1202, ~80 Kb) has been isolated in a clinical isolate of Yersinia pestis, the agent of plague. Here, we report that pIP1202 was highly stable in Y. pestis-infected mice and fleas and did not reduce Y. pestis virulence in these animals. Although pIP1202 inflicted a fitness cost in fleas (but not in mice) when the insects fed on blood containing a mixture of plasmid-free and plasmid-bearing strains, such a co-infection scenario has never been reported in nature, indicating that pIP1202 could persist in Y. pestis strains. Despite being resistant to commonly used antibiotic treatments, we show that plague caused by Y. pestis harboring the pIP1202 plasmid is effectively cured by LPC-233-a potent inhibitor of the essential LpxC enzyme in the lipid A biosynthetic pathway. Taken as a whole, our data highlight the alarming threat posed by Y. pestis harboring multidrug-resistant IncC plasmids that may persist in wild animals as a reservoir for long periods without antibiotic pressure and illuminate the impact of antibiotics with a novel mode of action against such a biothreat.

Comprehensive analysis of Enterobacteriaceae IncX plasmids reveals robust conjugation regulators PrfaH, H-NS, and conjugation-fitness tradeoff

Conjugative IncX plasmids are vital for spreading clinically significant antibiotic resistance genes. We identified key factors governing the conjugative process of IncX plasmids, the plasmid encoded activator PrfaH and inhibitor H-NS. Deletion of prfaH completely abolishes conjugative transfer, and the PrfaH binding site is an ops-like sequence located downstream of the prfaH promoter. We solved the crystal structure of PrfaH and identified the residues that likely mediate interactions with its target. The IncX3 plasmid-encoded H-NS inhibits conjugation by directly repressing PrfaH expression, while simultaneously enhancing host fitness. This tradeoff between plasmid conjugation and fitness is indispensable for plasmid persistence in nutrient-deprived environments. The presence of PrfaH paralogs in various antibiotic resistance plasmids suggests its fundamental role in regulating plasmid transfer. Our study not only elucidates the regulatory mechanisms behind the horizontal transfer of IncX plasmids but also highlights PrfaH as a potential target for strategies aimed at combating antimicrobial resistance.

Epidemiology and Resistance Profiles of Bacteria Isolated From Blood Samples in Septic Patients at Emergency Department Admission: A 6-Year Single Centre Retrospective Analysis From Northern Italy

OBJECTIVE

This study aimed to investigate the microbiological and clinical heterogeneity of community-onset bloodstream infections (BSIs) and identify features to support targeted empirical antibiotic therapy in the Emergency Department (ED).

METHODS

Clinical and microbiological data from 992 BSI cases (1,135 isolates) diagnosed within 24 h of ED admission at IRCCS Humanitas Research Hospital, Milan, Italy (January 2015-June 2022), were analysed. Drug resistance was interpreted using EUCAST-2023. Clinical features included age, sex, comorbidities (e.g., cancer, diabetes), infection source, presence of central venous catheters (CVC), ongoing therapies, and sepsis severity. Microbiological data included pathogen identification and antimicrobial susceptibility.

RESULTS

Antibiotic-susceptible Escherichia coli (29.5%) was the most common isolate, including extended-spectrum beta-lactamase (ESBL)-producing strains (11.3%), followed by methicillin-susceptible Staphylococcus aureus (MSSA, 8.4%). BSIs due to E. coli were more frequent in patients >60 years (43.9% vs. 27.3%, P < 0.001) and associated with ESBL production (OR = 2.202, P = 0.031) and urosepsis (OR = 1.688, P = 0.006). Younger patients (≤60 years) had more S. aureus-associated BSIs (22.4% vs. 10.8%, P < 0.001) and methicillin resistance (7.9% vs. 3.6%, P = 0.021). Carbapenem-resistant Enterobacterales were rare (2.1%-2.8%), predominantly involving Klebsiella pneumoniae. Onco-hematological patients had a lower multidrug-resistance prevalence (9.5% vs. 21.1%, P < 0.001).

CONCLUSIONS

Community-onset BSIs demonstrated substantial prevalence of resistant pathogens, including ESBL and MRSA, emphasizing the need for robust surveillance systems. Age is a critical factor in guiding empirical antibiotic therapy in the ED.

Hexane extract from Lindera communis roots: wound healing properties and membrane-disruptive activities against methicillin-resistant Staphylococcus aureus

Introduction

The extensively used Lindera communis Hemsl. (Lauraceae) in traditional Chinese medicine has been specifically employed for wound healing and treating skin diseases in cattle and horses, suggesting its potential antibacterial properties. To explore the antibacterial activities of L. communis plants, we investigated the chemicals, antibacterial activities and wound healing and of the n-hexane fraction of L. communis roots (LCH).

Methods

Our study included detecting phytochemical constituents, determining minimum inhibitory concentration (MIC) for different extract fractions, analyzing growth curves, assessing membrane integrity, monitoring potential changes in the membrane using scanning electron microscopy, and evaluating wound healing in rat excisional wounds.

Results

Based on our findings, humulene-type sesquiterpenes, guaiane-type sesquiterpenes, and lauric acid were identified from the LCH, responsible for antibacterial and wound healing activities. The results are that LCH affected the growth of methicillin-resistant Staphylococcus aureus (MIC: 0.1 mg/mL) through morphological alterations and disrupting cell surface structures, causing membrane hyperpolarization and altering membrane integrity. This result was subsequently validated through SEM analysis and cytotoxicity against HaCaT cells (IC50 1.83 ± 0.21 mg/mL). LCH also has exhibited remarkable effectiveness in healing rat excisional wounds, reinforcing its traditional use as a wound-healing agent.

Discussion

The findings substantiate the scientific essence of traditional applications, while also exhibiting significant potential as a promising candidate for the development of innovative and readily accessible wound healing agents.

One Health distribution of beta-lactamases in Enterobacterales in the United States: A systematic review and meta-analysis

BACKGROUND

The study aimed to review the beta-lactamase resistance genes detected in Enterobacterales from humans, animals, and the environment in the United States.

METHODS

We conducted a comprehensive search on PubMed, Web of Science, and Google Scholar for articles reporting beta-lactamase genes in the United States from 1981 to 22 April 2022, following the PRISMA protocol. Studies were evaluated based on predefined eligibility criteria, and both qualitative and quantitative analyses were conducted on the selected studies.

RESULTS

Of the 335 articles, a total of 169 different beta-lactamase genes, including narrow-spectrum, extended-spectrum, AmpC, and carbapenemase have been detected and reported in the United States, with human (137), animal (53), and environment (47). 22 genes (blaCMY-2, blaCTX-M-(1, 2, 9, 14, 15, 27, 32, 65), blaFOX-5, blaIMP-27, blaKPC-2, blaNDM-(1, 5), blaOXA-(1, 48), blaPSE-1, blaSHV-(1, 12), blaTEM-(1, 1A, 1B)) have been reported across animals, humans, and environment. Notably, blaCTX-M-15 was prevalent in E. coli isolates, with an overall pooled proportion of 10.7 %, varying between animals (8.6 %), humans (13.1 %), and the environment (0.8 %). Similarly, blaCMY-2 in E. coli isolates had an overall pooled proportion of 10.6 %, with distinctions in proportion among animals (1.6 %), humans (41.3 %), and the environment (16.2 %). The sequence type (ST131) was detected as the predominant, mainly associated with the blaCTX-M-15, with a pooled proportion of 56.9 %, varying from 14.3 % to 90 % across studies.

CONCLUSION

This study highlights the distribution of beta-lactamases in the United States, essential for understanding One Health and the molecular epidemiology of key beta-lactamases, especially extended-spectrum beta-lactamases and carbapenemases.

Whole genome sequencing characterization and comparative genome analysis of Acinetobacter baumannii JJAB01: A comprehensive insights on antimicrobial resistance and virulence genotype

The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individuals. Whole-Genome Sequencing studies are efficient in providing accurate genetic information, aiding in detecting outbreaks, surveillance of resistance, and controlling infection transmission. In this study, we investigated the whole genome of a clinical isolate A. baumannii JJAB01 which sourced from a urine sample of an Intensive Care Unit (ICU) patient. This strain showed resistance to 24 available antibiotics, signifying Extremely Drug Resistant (XDR) and high potential for pathogenicity. Whole Genome Sequencing was performed using Illumina, and the raw reads were evaluated using the FastQC tool. Genome assembly and annotation were performed with Unicycler and the RAST server. The JJAB01 genome is 4.07 Mb with a GC content of 38.9 %. A total of 51 and 31 virulence factors and antimicrobial-resistant (AMR) genes were predicted using the VFDB and CARD databases. Comparative genome studies were carried out on virulence factors, resistance genes, prophages, and Multi-Locus Sequence Typing (MLST) across twelve closely related A. baumannii genomes, including JJAB01, X4-584, X4-705, 2023CK-00423, 2023CK-00890, 2023CK-00127, 2022CK-00066, B20AB01, B20AB10, F20AB03, G20AB08, and X4-65. These computational investigations in this study emphasis the multidimensional nature of the ICU strain JJAB01 and its genetic similarity to other strains, thereby enhancing our understanding of drug resistance and the pathogenicity associated with A. baumannii infections.

Quinolone scaffolds as potential drug candidates against infectious microbes: a review

Prevalence of microbial infections and new rising pathogens are signified as causative agent for variety of serious and lethal health crisis in past years. Despite medical advances, bacterial and fungal infections continue to be a rising problem in the health care system. As more bacteria develop resistance to antibiotics used in therapy, and as more invasive microbial species develop resistance to conventional antimicrobial drugs. Relevant published publications from the last two decades, up to 2024, were systematically retrieved from the MEDLINE/PubMed, SCOPUS, EMBASE, and WOS databases using keywords such as quinolones, anti-infective, antibacterial, antimicrobial resistance and patents on quinolone derivatives. With an approach of considerable interest towards novel heterocyclic derivatives as novel anti-infective agents, researchers have explored these as essential tools in vistas of drug design and development. Among heterocycles, quinolones have been regarded extremely essential for the development of novel derivatives, even able to tackle the associated resistance issues. The quinolone scaffold with its bicyclic structure and specific functional groups such as the carbonyl and acidic groups, is indeed considered a valuable functionalities for further lead generation and optimization in drug discovery. Besides, the substitution at N-1, C-3 and C-7 positions also subjected to be having a significant role in anti-infective potential. In this article, we intend to highlight recent quinolone derivatives based on the SAR approach and anti-infective potential such as antibacterial, antifungal, antimalarial, antitubercular, antitrypanosomal and antiviral activities. Moreover, some recent patents granted on quinolone-containing derivatives as anti-infective agents have also been highlighted in tabular form. Due consideration of this, future research in this scaffold is expected to be useful for aspiring scientists to get pharmacologically significant leads.

Regional antimicrobial resistance gene flow among the One Health sectors in China

BACKGROUND

Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

RESULTS

In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.

CONCLUSIONS

Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.

Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression

Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

Preliminary insights on carbapenem resistance in Enterobacteriaceae in high-income and low-/middle-income countries

The emergence of carbapenem-resistant Enterobacteriaceae in the hospital sector as well as in the natural environment is a problem that affects both high-income countries (HICs) and low-/middle-income countries (LMICs). The observed differences in the prevalence of carbapenem-resistant strains between HICs and LMICs can be attributed mainly to antibiotic consumption in healthcare facilities and the quantity of treated wastewater. Hospital wastewater is a major hotspot for the spread of carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem resistance genes (CRGs) between the hospital sector and the environment. In this review article, attempts were made to describe and compare antibiotic consumption in hospitals, antimicrobial concentrations in both hospital and municipal wastewater, and the prevalence of CRE and CRGs in patients and in hospital and municipal wastewater in HICs and LMICs. A review of the literature has shown that carbapenems are more widely used in LMICs, but Saudi Arabia, an HIC, is a country with the highest carbapenem consumption in the world. The results of research conducted in both groups of countries indicate that Klebsiella sp./K. pneumoniae is the most common CRE in samples isolated from patients. Escherichia coli was the dominant pathogen in hospital and municipal wastewater in HICs, whereas Enterobacter spp. were most prevalent in LMICs. An analysis of the prevalence of CRGs demonstrated that the same genes are present in both groups of countries (blaKPC, blaKPC-2, blaVIM, blaVIM-1,2, blaNDM, blaIMP, blaIMP-8, blaOXA-48,181, blaNDM-1,5, blaGES, blaGES-5,6, blaIMI-1). The fact that the same CRGs are most prevalent in countries with different levels of economic development could suggest that these genes have a high potential to persist in the natural environment. These findings underscore the need for enhanced monitoring, effective control techniques, and a better understanding of carbapenem resistance pathways to mitigate public health hazards, notwithstanding the constraints of data analysis.

Increased risk of antibiotic resistance in surface water due to global warming

As the pace of global warming accelerates, so do the threats to human health, urgent priority among them being antibiotic-resistant infections. In the context of global warming, this review summarises the direct and indirect effects of rising surface water temperatures on the development of bacterial antibiotic resistance. First, the resistance of typical pathogens such as E. coli increased with average temperature. This is not only related to increased bacterial growth rate and horizontal gene transfer frequency at high temperatures but also heat shock responses and cumulative effects. Secondly, the acceleration of bacterial growth indirectly promotes antibiotic residues in surface water, which is conducive to the growth and spread of resistant bacteria. Furthermore, the cascading effects of global warming, including the release of nutrients into the water and the resulting increase of bacteria and algae, indirectly promote the improvement of resistance. Water treatment processes exposed to high temperatures also increase the risk of resistance in surface water. The fitness costs of antibiotic resistance under these dynamic conditions are also discussed, concluding the relationship between various factors and resistance persistence. It was expected to provide a comprehensive basis for mitigating antibiotic resistance in the face of global warming.

A systematic scoping review of antibiotic-resistance in drinking tap water

Environmental matrices have been considered of paramount importance in the spread of antibiotic-resistance; however, the role of drinking waters is still underexplored. Therefore, a scoping review was performed using a systematic approach based on PRISMA guidelines, with the aim of identifying and characterizing antibiotic-resistance in tap water, specifically, water treated at a potabilization plant and provided for drinking use through a water distribution system. The review included 45 studies, the majority of which were conducted in upper-middle-income economies (42.2%), mainly from the Western Pacific region (26.7%), followed by Europe (24.4%). Most of the papers focused on detecting antibiotic-resistant bacteria (ARB), either alone (37.8%) or in combination with antibiotic-resistant genes (ARGs) (26.7%). Multidrug-resistance profile was often identified in heterotrophic bacteria, including various species of nontuberculous mycobacteria, Pseudomonas spp., and Aeromonas spp., which were especially resistant to penicillins, cephalosporins (including 3rd-generation), and also to macrolides (erythromycin) and tetracyclines. Resistance to a wide range of antibiotics was also prevalent in fecal bacteria, e.g., the Enterobacteriaceae family, with common resistance to (fluoro)quinolones and sulfonamide groups. ARGs were investigated either in bacterial strains isolated from tap waters or directly in water samples, and the most frequently detected ARGs belonged to β-lactam, sulfonamide, and tetracycline types. Additionally, mobile genetic elements were found (i.e., int1 and tnpA). Sulfonamides and macrolides were the most frequently detected antibiotics across countries, although their concentrations were generally low (<10 ng/L) in Europe and the United States. From a health perspective, tap water hosted ARB of health concern based on the 2024 WHO bacterial priority pathogens list, mainly Enterobacteriaceae resistant to 3rd-generation cephalosporin and/or carbapenem. Despite the fact that tap water is treated to meet chemical and microbiological quality standards, current evidence suggests that it can harbor antibiotic-resistance determinants, thus supporting its potential role in environmental pathways contributing to antibiotic resistance.

Epidemiological and genomic analysis revealed the significant role of flies in dissemination of carbapenem-resistant Enterobacteriaceae (CRE) in China

While the role of flies as potential vectors for bacterial transmission is well recognized, the epidemiological features and genomic characteristics of associated antimicrobial-resistant strains remain underexplored. This study conducted a nationwide surveillance including 3689 flies and 838 isolates from sixteen human communities (HCs) and eight animal farms (AFs) across 21 provinces in China. Our findings revealed high carriage rates of carbapenem-resistant Enterobacteriaceae (CRE) in flies, with 27.0 % in AFs and 15.3 % in HCs. Among the 705 CRE strains identified, Providencia spp. (n = 356) and Escherichia coli (n = 231) were predominant, with 90.6 % attributed to the dissemination of the blaNDM gene. Phylogenetic tree analysis highlighted frequent clonal transmission events, with over 18 and 13 clonal evolutionary clades in Providencia spp. and E. coli, respectively. Notably, spearman analysis linked the increase of CRE prevalence in AFs flies to environmental factors like precipitation (p < 0.028) and temperature (p < 0.037), while in HCs, it positively corelated with the total meat production (p < 0.027) in each province except for Hainan. Despite significant differences in ciprofloxacin resistance (p ≤ 0.001) among E. coli strains from HCs and AFs, core genome cluster analysis and Uniform Manifold Approximation and Projection (UMAP) approach indicated these strains exhibiting close relatedness to clinical strains. This comprehensive study underscores the critical role of flies in the escalation of CRE spread within the ecosystem in China. Flies found in both HCs and AFs contribute to the dissemination of CRE, highlighting the need for urgent interventions to address this pressing issue.

Routine immunization against Streptococcus pneumoniae and Haemophilus influenzae type B and antibiotic consumption in India: a dynamic modeling analysis

Background

Childhood vaccinations can reduce disease burden and associated antibiotic use, in turn reducing the risk of antimicrobial resistance (AMR). We retrospectively estimated the population-level reductions in antibiotic use in India following the introduction of vaccines against Streptococcus pneumoniae and Haemophilius influenzae type B in the national immunization program for children in the mid-2010s and projected future gains to 2028 if vaccination coverage were to be increased.

Methods

Using IndiaSim, a dynamic agent-based microsimulation model (ABM) for India, we simulated the spread of Streptococcus pneumoniae and Haemophilius influenzae type B (Hib) among children to estimate reductions in antibiotic use under the scenarios of: (i) pneumococcal and Hib vaccine coverage levels equivalent to the national coverage of pentavalent diphtheria-pertussis-tetanus third dose (DPT3) compared to a baseline of no vaccination, and (ii) near-universal (90%) coverage of the vaccines compared to pre-COVID national DPT3-level coverage. Model parameters, including national DPT3 coverage rates, were based on data from the National Family Household Survey 2015-2016 and other published sources. We quantified reductions in antibiotic consumption nationally and by state and wealth quintiles.

Findings

We estimate that coverage of S. pneumoniae and Hib vaccines at the same level as DPT3 in India would translate to a 61.4% [95% UI: 43.8-69.5] reduction in attributable antibiotic use compared to a baseline of zero vaccination coverage. Increases in childhood vaccination coverage between 2004 and 2016 have likely reduced attributable antibiotic demand by as much as 93.4% among the poorest quintile. Increasing vaccination coverage by an additional 11 percentage points from 2016 levels results in mortality and antibiotic use across wealth quintiles becoming increasingly similar (p < 0.05), reducing in health inquities. We project that near-universal vaccine coverage would further reduce inequities in antibiotic demand and may eliminate of outbreak-associated antibiotic use from S. pneumoniae and Hib.

Interpretation

Though vaccination has a complex relationship with antibiotic use because both are modulated by socioeconomic factors, increasing vaccinations for S. pneumoniae and Hib may have a significant impact on reducing antibiotic use and improving health outcomes among the poorest individuals.

Funding

The Bill & Melinda Gates Foundation (grant numbers OPP1158136 and OPP1190803).

Antibiotic residues in poultry products and bacterial resistance: A review in developing countries

Antimicrobial resistance (AMR) is a growing global concern, particularly in poultry farming, where antibiotics are widely used for both disease prevention and growth promotion. This review examines the misuse of antibiotics in poultry production, especially in developing countries, and its contribution to the emergence of antibiotic-resistant bacteria. The findings highlight that factors such as increasing demand for poultry protein, the availability of inexpensive antibiotics, and weak regulatory oversight have led to widespread misuse, accelerating the spread of resistance genes. Although evidence links poultry farming to AMR, significant data gaps remain, especially regarding resistance transmission from poultry to humans. The review underscores the urgent need for stronger regulatory frameworks, phased-out use of antimicrobial growth promoters, and enhanced awareness campaigns to address this issue. Improving the capacity of regulatory bodies and developing more robust national data monitoring systems are essential steps to mitigate the threat of AMR in poultry farming and to protect both animal and human health.

Occurrence and distribution of emerging contaminants in wastewater treatment plants: A globally review over the past two decades

Emerging contaminants are pervasive in aquatic environments globally, encompassing pharmaceuticals, personal care products, steroid hormones, phenols, biocides, disinfectants and various other compounds. Concentrations of these contaminants are detected ranging from ng/L to μg/L. Even at trace levels, these contaminants can pose significant risks to ecosystems and human health. This article systematically summarises and categorizes data on the concentrations of 54 common emerging contaminants found in the influent and effluent of wastewater treatment plants across various geographical regions: North America, Europe, Oceania, Africa, and Asia. It reviews the occurrence and distribution of these contaminants, providing spatial and causal analyses based on data from these regions. Notably, the maximum concentrations of the pollutants observed vary significantly across different regions. The data from Africa, in particular, show more frequent detection of pharmaceutical maxima in wastewater treatment plants.

The longitudinal trend and influential factors exploring of global antimicrobial resistance in Klebsiella pneumoniae

Klebsiella pneumoniae (Kp) is a human symbiotic opportunistic pathogen capable of causing severe hospital-based infections and community-acquired infections. The problem of antimicrobial resistance (AMR) has become increasing serious over time, posing a major threat to socio-economic and human development. In this study, we explored the global trend of AMR in 1786 strains of Kp isolated between 1982 and 2023. The number of antibiotic resistance genes (ARGs) in Kp increased significantly from 24.29 ± 5.44 to 32.42 ± 8.52 over time. Mobile genetic elements (MGEs) were responsible for the ARGs horizontal transfer of Kp strains. The results of structural equation modeling (SEM) indicated a strong association between the human development index and the increase of antibiotic consumption, which indirectly affected the occurrence and development of antibiotic resistance in Kp. The results of Generalized Linear Models (GLM) indicated that the influence of environmental factors such as temperature on the development of Kp resistance could not be ignored. Overall, this study monitored the longitudinal trend of antimicrobial resistance in Kp, explored the factors influencing antibiotic resistance, and provided insights for mitigating the threat of antimicrobial resistance.

Carbapenem-Resistant Enterobacterales in the Western Balkans: Addressing Gaps in European AMR Surveillance Map

In the context of global efforts to combat antimicrobial resistance (AMR), the importance of comprehensive AMR data is more crucial than ever. AMR surveillance networks, such as the European Antimicrobial Resistance Surveillance Network (EARS-Net) and the Central Asian and European Surveillance of Antimicrobial Resistance (CAESAR), support member states in obtaining high-quality AMR data. Nevertheless, data gaps persist in some countries, including those in the Western Balkans (WBs), a region with high AMR rates. This review analyzed existing research on carbapenem-resistant Enterobacterales (CRE) to better understand the AMR landscape in the WB countries. The most prevalent CRE was Klebsiella pneumoniae, followed by Escherichia coli, Enterobacter cloacae, and Proteus mirabilis, with sporadic cases of Morganella morganii, Providencia spp., Klebsiella oxytoca, and Citrobacter sedlakii. Carbapenemase production was identified as the most common mechanism of carbapenem resistance, but other resistance mechanisms were not investigated. An increasing trend in carbapenem resistance has been observed over the last decade, alongside a shift in carbapenemase epidemiology from the NDM type in 2013-2014 to the OXA-48 type in recent years. Few studies have applied whole-genome sequencing for CRE analysis, which has demonstrated the spread of resistance determinants across different niches and over time, emphasizing the importance of molecular-based research. The overall low number of studies in the WB countries can be attributed to limited resources, highlighting the need for enhanced support in education, training, technology, and equipment to improve data collection and evaluation.

Pharmacophore-Based Study: An In Silico Perspective for the Identification of Potential New Delhi Metallo-β-lactamase-1 (NDM-1) Inhibitors

In the ongoing battle against antibiotic-resistant bacteria, New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a significant therapeutic challenge due to its ability to confer resistance to a broad range of β-lactam antibiotics. This study presents a pharmacophore-based virtual screening, docking, and molecular dynamics simulation approach for the identification of potential inhibitors targeting NDM-1, a critical enzyme associated with antibiotic resistance. Through the generation of a pharmacophore model and subsequent virtual screening of compound libraries, candidate molecules (ZINC29142850 (Z1), ZINC78607001 (Z2), and ZINC94303138 (Z3)) were prioritized based on their similarity to known NDM-1 binder (hydrolyzed oxacillin (0WO)). Molecular docking studies further elucidated the binding modes and affinities of the selected compounds towards the active site of NDM-1. These compounds demonstrated superior binding affinities to the enzyme compared to a control compound (-7.30 kcal/mol), with binding scores of -7.13, -7.92, and -8.10 kcal/mol, respectively. Binding interactions within NDM-1's active site showed significant interactions with critical residues such as His250, Asn220, and Trp93 for these compounds. Subsequent molecular dynamics simulations were conducted to assess the stability of the ligand-enzyme complexes, showing low root mean square deviation (RMSD) values between 0.5 and 0.7 nm for Z1, Z2, which indicate high stability. Z2's compactness in principal component analysis (PCA) suggests that it can stabilize particular protein conformations more efficiently. Z2 displays a very cohesive landscape with a notable deep basin, suggesting a very persistent conformational state induced by the ligand, indicating robust binding and perhaps efficient inhibition. Z2 demonstrates the highest binding affinity among the examined compounds with a binding free energy of -25.68 kcal/mol, suggesting that it could offer effective inhibition of NDM-1. This study highlights the efficacy of computational tools in identifying novel antimicrobial agents against resistant bacteria, accelerating drug discovery processes.

Isolation and Characterization of Extended-Spectrum β-Lactamase Producing Escherichia coli from Pig Farms and Slaughterhouse

Extended-spectrum β-lactamase (ESBL) producing Escherichia coli represents a formidable challenge in the field of microbiology and public health due to its resistance to commonly used antibiotics. These strains pose a serious threat to human and animal health, underscoring the urgency of comprehensive research and surveillance. The ongoing investigation seeks ESBL producing E. coli strains from pig farms and slaughterhouses in West Bengal and Assam, India. A total of 309 samples were collected: nasal swabs (25), rectal swabs (25) from healthy pigs, pig pen soil (45), faeces (55), slaughterhouse effluents (115), and cleaning water (44). In these samples, 154 tested positive for E. coli, indicating a 49.8% prevalence. Among 154 E. coli isolates, 23 (14.9%) produced ESBLs, sourced from pig rectal swabs (7.1%), faeces (10.7%), slaughterhouse effluents (26.1%), and cleaning water (11.7%). Significantly, 4 ESBL E. coli isolates (6.6%) exclusively emerged from pig slaughterhouse effluents, displaying imipenem-resistant properties. The majority of ESBL E. coli primarily produced CTX-M and CMY, with consistent genetic markers bla CTX-M (100%) and bla CMY (82.6%). Remarkably, 2 (8.6%) of 17 ESBL E. coli isolates from pig slaughterhouse effluents carried the genetic marker bla NDM1. These findings stress implementing thorough surveillance in pig farms and local slaughterhouses. This proactive approach is crucial to identify ESBL E. coli strains, enhancing public health protection.

Antimicrobial use in laboratory rodent facilities in Australia and New Zealand- a cross-sectional survey of veterinarians and facility managers

This cross-sectional study surveyed veterinarians and facility managers to characterise the use of antimicrobials in laboratory rodent facilities within Australia and New Zealand. Most facilities (71%) reported routine administration of antimicrobials. The indications for antibiotic use reflected those described in publications and differed significantly to reasons for use in non-laboratory animals. Antimicrobials used include those of critical importance to human health, and access to these drugs is unregulated, as prescription-only classes are ordered through research catalogues, without human or veterinary physician prescriptions. The ways in which antimicrobials are used in Australian and New Zealand rodent facilities are likely contributing to antimicrobial resistance within rodent populations, particularly as they are largely administered in drinking water, risking subtherapeutic dosing. Much antimicrobial use reported is unnecessary and could be replaced with changes to husbandry and handling. The generation of resistance in both pathogenic and commensal microbes may also represent a work health and safety issue for humans working with these animals. Reported disposal of antimicrobials included discharge into wastewater, without inactivation, and some respondents reported disposal of substrate, or soiled bedding, nesting material, and disposable enrichment items, from treated animals and medicated feed into landfill, without prior inactivation. Environmental contamination with resistant microbes and antimicrobials is a significant driver of antimicrobial resistance. As such, significant opportunities exist to implement judicious and responsible use of antimicrobials within research rodent facilities in Australia and New Zealand, with a particular focus on instituting aseptic surgery, optimising dosing regimens, and inactivation of medicated water and substrate before disposal.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Carbapenem Resistance in Acinetobacter calcoaceticus-baumannii Complex Isolates From Kathmandu Model Hospital, Nepal, Is Attributed to the Presence of bla OXA-23-like and bla NDM-1 Genes

The Acinetobacter calcoaceticus-baumannii (ACB) complex, also known as ACB complex, consists of four bacterial species that can cause opportunistic infections in humans, especially in hospital settings. Conventional therapies for susceptible strains of the ACB complex include broad-spectrum cephalosporins, β-lactam/β-lactamase inhibitors, and carbapenems. Unfortunately, the effectiveness of these antibiotics has declined due to increasing rates of resistance. The predominant resistance mechanisms identified in the ACB complex involve carbapenem-resistant (CR) oxacillinases and metallo-β-lactamases (MBLs). This research, conducted at Kathmandu Model Hospital in Nepal, sought to identify genes associated with CR, specifically blaNDM-1, blaOXA-23-like, and blaOXA-24-like genes in carbapenem-resistant Acinetobacter calcoaceticus-baumannii (CR-ACB) complex. Additionally, the study is aimed at identifying the ACB complex through the sequencing of the 16s rRNA gene. Among the 992 samples collected from hospitalized patients, 43 (approximately 4.334%) tested positive for the ACB complex. These positive samples were mainly obtained from different hospital units, including intensive care units (ICUs); cabins; and neonatal, general, and maternity wards. The prevalence of infection was higher among males (58.14%) than females (41.86%), with the 40-50 age group showing the highest infection rate. In susceptibility testing, colistin and polymyxin B exhibited a susceptibility rate of 100%, whereas all samples showed resistance to third-generation cephalosporins. After polymyxins, gentamicin (30.23%) and amikacin (34.88%) demonstrated the highest susceptibility. A substantial majority (81.45%) of ACB complex isolates displayed resistance to carbapenems, with respiratory and pus specimens being the primary sources. Polymerase chain reaction (PCR) revealed that the primary CR gene within the ACB complex at this hospital was bla OXA-23-like, followed by bla NDM-1. To ensure the accuracy of the phenotypic assessment, 12 samples were chosen for 16s rRNA sequencing using Illumina MiSeq™ to confirm that they are Acinetobacter species. QIIME 2.0 analysis confirmed all 12 isolates to be Acinetobacter species. In the hospital setting, a substantial portion of the ACB complex carries CR genes, rendering carbapenem ineffective for treatment.

Bacterial strain sharing between humans, animals, and the environment among urban households

Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low- and middle-income countries. In this study, we assessed bacterial strain-sharing and dissemination of antibiotic resistance across humans, domesticated poultry, canines, household soil, and drinking water in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households and performed Pooling Isolated Colonies-seq (PIC-seq) by sequencing pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and overlap of antibiotic-resistant genes (ARGs). Bacterial strains isolated from the household environment carried clinically relevant ARGs, reinforcing the role of the environment in antibiotic resistance dissemination. Strain-sharing rates and resistome similarities across sample types were strongly correlated within households, suggesting clonal spread of bacteria is a main driver of dissemination of ARGs in the domestic urban environment. Within households, E. coli strain-sharing was rare between humans and animals but more frequent between humans and drinking water. E. coli contamination in stored drinking water was also associated with higher strain-sharing between humans in the same household. Our study demonstrates that contaminated drinking water facilitates human to human strain sharing and water treatment can disrupt transmission.

An engineered prodrug selectively suppresses β-lactam resistant bacteria in a mixed microbial setting

The rise of β-lactam resistance necessitates new strategies to combat bacterial infections. We purposefully engineered the β-lactam prodrug AcephPT to exploit β-lactamase activity to selectively suppress resistant bacteria producing extended-spectrum-β-lactamases (ESBLs). Selective targeting of resistant bacteria requires avoiding interaction with penicillin-binding proteins, the conventional targets of β-lactam antibiotics, while maintaining recognition by ESBLs to activate AcephPT only in resistant cells. Computational approaches provide a rationale for structural modifications to the prodrug to achieve this biased activity. We show AcephPT selectively suppresses gram-negative ESBL-producing bacteria in clonal populations and in mixed microbial cultures, with effective selectivity for both lab strains and clinical isolates expressing ESBLs. Time-course NMR experiments confirm hydrolytic activation of AcephPT exclusively by ESBL-producing bacteria. In mixed microbial cultures, AcephPT suppresses proliferation of ESBL-producing strains while sustaining growth of β-lactamase-non-producing bacteria, highlighting its potential to combat β-lactam resistance while promoting antimicrobial stewardship.

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

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

Fish skin mucosal surface becomes a barrier of antibiotic resistance genes under apramycin exposure

Antibiotic resistance genes (ARGs) are a kind of emerging environmental contamination, and are commonly found in antibiotic application situations, attracting wide attention. Fish skin mucosal surface (SMS), as the contact interface between fish and water, is the first line of defense against external pollutant invasion. Antibiotics are widely used in aquaculture, and SMS may be exposed to antibiotics. However, what happens to SMS when antibiotics are applied, and whether ARGs are enriched in SMS are not clear. In this study, Zebrafish (Danio rerio) were exposed to antibiotic and antibiotic resistant bacteria in the laboratory to simulate the aquaculture situation, and the effects of SMS on the spread of ARGs were explored. The results showed that SMS maintained the stability of the bacterial abundance and diversity under apramycin (APR) and bacterial exposure effectively. Until 11 days after stopping APR exposure, the abundance of ARGs in SMS (mean value was 3.32 × 10-3 copies/16S rRNA copies) still did not recover to the initial stage before exposure, which means that enriched ARGs in SMS were persistently remained. Moreover, non-specific immunity played an important role in resisting infection of external contamination. Besides, among antioxidant proteins, superoxide dismutase showed the highest activity. Consequently, it showed that SMS became a barrier of antibiotic resistance genes under APR exposure, and ARGs in SMS were difficult to remove once colonized. This study provided a reference for understanding the transmission, enrichment process, and ecological impact of antibiotics and ARGs in aquatic environments.

Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors

Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.

Climate warming promotes collateral antibiotic resistance development in cyanobacteria

Both cyanobacterial blooms and antibiotic resistance have aggravated worldwide and posed a great threat to public health in recent years. As a significant source and reservoir of water environmental resistome, cyanobacteria exhibit confusing discrepancy between their reduced susceptibility and their chronic exposure to antibiotic mixtures at sub-inhibitory concentrations. How the increasing temperature affects the adaptive evolution of cyanobacteria-associated antibiotic resistance in response to low-level antibiotic combinations under climate change remains unclear. Here we profiled the antibiotic interaction and collateral susceptibility networks among 33 commonly detected antibiotics in 600 cyanobacterial strains isolated from 50 sites across four eutrophicated lakes in China. Cyanobacteria-associated antibiotic resistance level was found positively correlated to antibiotic heterogeneity across all sites. Among 528 antibiotic combinations, antagonism was observed for 62 % interactions and highly conserved within cyanobacterial species. Collateral resistance was detected in 78.5 % of pairwise antibiotic interaction, leading to a widened or shifted upwards mutant selection window for increased opportunity of acquiring second-step mutations. We quantified the interactive promoting effect of collateral resistance and increasing temperature on the evolution of both phenotypic and genotypic cyanobacteria-associated resistance under chronic exposure to environmental level of antibiotic combinations. With temperature increasing from 16 °C to 36 °C, the evolvability index and genotypic resistance level increased by 1.25 - 2.5 folds and 3 - 295 folds in the collateral-resistance-informed lineages, respectively. Emergence of resistance mutation pioneered by tolerance, which was jointly driven by mutation rate and persister fraction, was found to be accelerated by increased temperature and antibiotic switching rate. Our findings provided mechanic insights into the boosting effect of climate warming on the emergence and development of cyanobacteria-associated resistance against collateral antibiotic phenotypes.

Antimicrobial peptides as promising antibiotic adjuvants to combat drug-resistant pathogens

The widespread antimicrobial resistance (AMR) calls for the development of new antimicrobial strategies. Antibiotic adjuvant rescues antibiotic activity and increases the life span of the antibiotics, representing a more productive, timely, and cost-effective strategy in fighting drug-resistant pathogens. Antimicrobial peptides (AMPs) from synthetic and natural sources are considered new-generation antibacterial agents. Besides their direct antimicrobial activity, growing evidence shows that some AMPs effectively enhance the activity of conventional antibiotics. The combinations of AMPs and antibiotics display an improved therapeutic effect on antibiotic-resistant bacterial infections and minimize the emergence of resistance. In this review, we discuss the value of AMPs in the age of resistance, including modes of action, limiting evolutionary resistance, and their designing strategies. We summarise the recent advances in combining AMPs and antibiotics against antibiotic-resistant pathogens, as well as their synergistic mechanisms. Lastly, we highlight the challenges and opportunities associated with the use of AMPs as potential antibiotic adjuvants. This will shed new light on the deployment of synergistic combinations to address the AMR crisis.

Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes

Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.

Emergence and genomic chion of Proteus mirabilis harboring blaNDM-1 in Korean companion dogs

Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".

Expert opinion on antimicrobial therapies: is there enough scientific evidence to state that targeted therapies outperform non-targeted ones?

INTRODUCTION

Different active and passive strategies have been developed to fight against pathogenic bacteria. Those actions are undertaken to reduce the bacterial burden while minimizing the possibilities to develop not only antimicrobial resistance but also antimicrobial side-effects such as allergic or hypersensitivity reactions.

AREAS COVERED

We have reviewed preclinical results that evidence that targeted antimicrobial therapies outperform non-targeted ones. Active selective targeting against pathogenic bacteria has been achieved through the functionalization of antimicrobials, either alone or encapsulated within micro- or nanocarriers, with various recognition moieties. These moieties include peptides, aptamers, antibodies, carbohydrates, extracellular vesicles, cell membranes, infective agents, and other affinity ligands with specific bacterial tropism. Those selective ligands increase retention and enhance effectiveness reducing the side-effects and the required dose to exert the antimicrobial action at the site of infection.

EXPERT OPINION

When using targeted antimicrobial therapies not only reduced side-effects are observed, but also, compared to the administration of equivalent doses of the non-targeted drugs, a superior efficacy has been demonstrated against planktonic, sessile, and intracellular pathogenic bacterial persisters. The translation of those targeted therapies to subsequent phases of clinical development still requires the demonstration of a reduction in the probabilities for the pathogen to develop resistance when using targeted approaches.

The Clinical Efficacy of Adding Ceftazidime/Avibactam to Standard Therapy in Treating Infections Caused by Carbapenem-Resistant Klebsiella pneumonia with blaOXA-48-like Genes

Ceftazidime/avibactam (CAZ-AVI) is FDA-approved for managing infections caused by resistant gram-negative bacilli, particularly infections via carbapenem-resistant Enterobacterales pathogens. The clinical data are still limited, particularly those in Saudi Arabia. The present study is a retrospective cohort study that was carried out at the Armed Forces Hospital in the southern region of Saudi Arabia to compare the clinical and microbiological outcomes for CAZ-AVI-treated patients as monotherapy and as an add-on to standard therapy for carbapenem-resistant Klebsiella pneumonia (CRKP) OXA-48 infections to those treated with standard drugs. The study included CRKP OXA-48-like infected patients who were administered antibiotics for more than seven days from 1 August 2018 to May 2023. Patients' baseline characteristics and demography were extracted from the clinical records, and their clinical/microbiology efficiencies were assessed as per the corresponding definitions. Univariate and multivariate logistic regressions were conducted to identify the potential independent variable for CAZ-AVI efficiency. A total of 114 patient files were included for the evaluation. Among these patients, 64 used CAZ-AVI combined with standard therapy and were included in the intervention group, and 50 of them used standard therapy and were included in the comparative group. Following analysis, CAZ-AVI's clinical success was 42.2% (p = 0.028), while the intervention versus comparative groups showed decreased 30-day all-cause mortality (50.0% versus 70.0%; p = 0.036) and infection recurrence (7.8% versus 24.0%; p = 0.019), as well as substantially increased rates of microbial eradication (68.8% versus 42.0%; p = 0.007). CAZ-AVI add-on therapy rather than monotherapy showed statistically significant favored clinical and microbial outcomes over the standard therapy. Furthermore, sex (female %), ICU admission, and fever were negatively associated with patients' 30-day all-cause mortality, serving as independent negative factors. Only fever, CRP bio levels, inotropes, and ICU admissions were significant predictors influencing the CAZ-AVI's clinical efficiency. The duration of CAZ-AVI therapy positively influenced CAZ-AVI's microbial eradication, while both WBC counts and fever experiences were negative predictors. This study shows the effective usage of CAZ-AVI against CRKP OXA-48-like infections. The influencing independent variables depicted here should recommend that clinicians individualize the CAZ-AVI dose based on co-existing risk factors to achieve optimal survival and efficacy. Prospective multicenter and randomized control studies are recommended, with individualized CAZ-AVI precision administration implemented based on patients' characteristics.

The burden of antibiotic resistance of the main microorganisms causing infections in humans - review of the literature

One of the biggest threats to human well-being and public health is antibiotic resistance. If allowed to spread unchecked, it might become a major health risk and trigger another pandemic. This proves the need to develop antibiotic resistance-related global health solutions that take into consideration microdata from various global locations. Establishing positive social norms, guiding individual and group behavioral habits that support global human health, and ultimately raising public awareness of the need for such action could all have a positive impact. Antibiotic resistance is not just a growing clinical concern but also complicates therapy, making adherence to current guidelines for managing antibiotic resistance extremely difficult. Numerous genetic components have been connected to the development of resistance; some of these components have intricate paths of transfer between microorganisms. Beyond this, the subject of antibiotic resistance is becoming increasingly significant in medical microbiology as new mechanisms underpinning its development are identified. In addition to genetic factors, behaviors such as misdiagnosis, exposure to broad-spectrum antibiotics, and delayed diagnosis contribute to the development of resistance. However, advancements in bioinformatics and DNA sequencing technology have completely transformed the diagnostic sector, enabling real-time identification of the components and causes of antibiotic resistance. This information is crucial for developing effective control and prevention strategies to counter the threat.

The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC.

Biofilm-producing antibiotic-resistant bacteria in Indian patients: a comprehensive review

For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable impact in the field of infectious diseases, in particular healthcare-associated infections related to indwelling devices such as catheters, implants, artificial heart valves, and prosthetic joints. Bacterial biofilm potentially adheres to any biotic or abiotic surfaces that give specific shelter to the microbial community, making them less susceptible to many antimicrobial agents and even resistant to the immune cells of animal hosts. Around thirty clinical research reports available in PUBMED have been considered to establish the occurrence of biofilm-forming bacteria showing resistance against several regular antibiotics prescribed against infection by clinicians among Indian patients. After the extensive literature review, our observation exhibits a high predominance of biofilm formation among bacteria such as Escherichia sp., Streptococcus sp., Staphylococcus sp., and Pseudomonas sp., those are the most common biofilm-producing antibiotic-resistant bacteria among Indian patients with urinary tract infections and/or catheter-related infections, respiratory tract infections, dental infections, skin infections, and implant-associated infections. This review demonstrates that biofilm-associated bacterial infections constantly elevate in several pathological conditions along with the enhancement of the multi-drug resistance phenomenon.

Genomic surveillance for antimicrobial resistance - a One Health perspective

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.