Global Antimicrobial Resistance Research Articles

Progress of Implementation of World Health Organization Global Antimicrobial Resistance Surveillance System Recommendations on Priority Pathogen-Antibiotic Sensitivity Testing in Africa: Protocol for a Scoping Review.

Antimicrobial resistance (AMR) is a major global public health concern, particularly in low- and middle-income countries where resources and infrastructure for an adequate response are limited. The World Health Organization (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) was introduced in 2016 to address these challenges, outlining recommendations for priority pathogen-antibiotic combinations. Despite this initiative, implementation in Africa remains understudied. This scoping review aims to assess the current state of implementing WHO GLASS recommendations on antimicrobial sensitivity testing (AST) in Africa. The primary objective of this study is to determine the current state of implementing the WHO GLASS recommendations on AST for priority pathogen-antimicrobial combinations. The review will further document if the reporting of AST results is according to "susceptible," "intermediate," and "resistant" recommendations according to GLASS. Following the methodological framework by Arksey and O'Malley, studies published between January 2016 and November 2023 will be included. Search strategies will target electronic databases, including MEDLINE, Scopus, CINAHL, and Embase. Eligible studies will document isolates tested for antimicrobial sensitivity, focusing on WHO-priority specimens and pathogens. Data extraction will focus on key study characteristics, study context, population, and adherence to WHO GLASS recommendations on AST. Descriptive statistics involving summarizing the quantitative data extracted through measures of central tendency and variation will be used. Covidence and Microsoft Excel software will be used. This study will systematically identify, collate, and analyze relevant studies and data sources based on clear inclusion criteria to provide a clear picture of the progress achieved in the implementation of the WHO GLASS recommendations. Areas for further improvement will be documented to inform future efforts to strengthen GLASS implementation for enhanced AMR surveillance in Africa. The study results are expected in August 2024. To our knowledge, this scoping review will be the first to comprehensively examine the implementation of WHO GLASS recommendations in Africa, shedding light on the challenges and successes of AMR surveillance in the region. Addressing these issues aims to contribute to global efforts to combat AMR. PRR1-10.2196/58140.

Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health

Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.

Antimicrobial prescribing practices and factors associated with antimicrobial prescribing in hospitalized COVID-19 patients in Oyo state: A retrospective study.

Proportion of hospitalized COVID-19 patients receiving antimicrobial drug is significantly high despite evidence of low level of actual bacterial co-infection, potentially contributing to poor health outcome and global antimicrobial resistance. A retrospective study was performed on antimicrobial agents prescribed to adult patients with confirmed COVID-19 admitted across three isolation facilities between 1 March 2020 and 30 April 2021 in Ibadan, Oyo state, Nigeria. From individual records, we evaluated patient demographics, COVID-19 risk factors, diagnostic testing, disease severity and antimicrobial utilization. The primary aim was to determine the prevalence of antimicrobial prescription as well as factors associated with antimicrobial prescribing in hospitalized patients with COVID-19 in Oyo state. In total, 271 patients were included in this study. The median age of the population was 51 years (IQR; 32-62 years). The mean duration of hospital admission was 13 days (IQR: 10-14 days). Majority of participants were symptomatic (81.5%). All participants had a COVID-19 PCR test performed and none had bacterial culture performed. All patients received antimicrobial therapy across the entire cohort. The mean DOT per LOT across cohorts was 1.2 for mild cases, 1.4 for moderate cases and 1.3 for severe cases. Factors associated with the number of antimicrobials per prescription were being single (P = 0.02), being below 60 years of age (P = 0.04), mild COVID-19 symptoms (P < 0.001) and diabetes comorbidity (P = 0.03). Given the high rate of antimicrobial prescription and absence of bacteriological culture analysis in these patients, there is risk of development and spread of antimicrobial resistant. Continuous review of antimicrobial prescription is critical in the management of hospitalized COVID-19 patients.

Design characteristics of integrated surveillance of antimicrobial resistance at the human, animal, and environment interfaces

Abstract Efforts have been made to strengthen national and global antimicrobial resistance (AMR) surveillance programs by integrating data collection across the human, animal, and environmental sectors. We searched the literature to review published studies reporting the implementation of integrated AMR surveillance approaches, and we identified a total of 96 articles from 36 countries published from 2000 to 2022, which met our inclusion criteria. Standard review protocols were applied in our study. Out of 96 studies, 47 (49%) articles integrated AMR analysis from human and animal (HA) populations, 24 (25%) considered human, animal, and environmental (HAE) samples together, 11 (12%) studies included animal and environment (AE) samples, and 12 (13%) integrated human and environmental (HE) surveillance. Human isolate-based and animal isolate-based surveillance were the most common study designs (38, 52.8%), with the remainder applying human case-based and isolate-based for animal populations (32, 44.4%). Finally, our results demonstrate that AMR studies on E. coli revealed a lower correlation between human and animal AMR prevalence compared to Salmonella spp. and Campylobacter spp. studies. Different aspects of surveillance design were associated with the level of correlation of AMR prevalence between sectors. Our study found that while global efforts for integrated AMR surveillance have increased in the past 10 years, significant variation exists between studies with regard to the epidemiological and laboratory aspects of their surveillance designs. Our findings indicate that to enable the generation of comparable epidemiological data across countries and sectors, there is a need for the development of a global protocol to support the design of surveillance programs that aim to conduct integrated surveillance of AMR.

Strategy to develop and validate digital droplet PCR methods for global antimicrobial resistance wastewater surveillance.

According to World Health Organization (WHO), antimicrobial resistance (AMR) is currently one of the world's top 10 health threats, causing infections to become difficult or impossible to treat, increasing the risk of disease spread, severe illness, disability, and death. Accurate surveillance is a key component in the fight against AMR. Wastewater is progressively becoming a new player in AMR surveillance, with the promise of a cost-effective real-time tracking of global AMR profiles in specific regions. One of the most useful analytical methods for wastewater surveillance is currently based on real-time PCR (qPCR) and digital droplet PCR (ddPCR) technologies. As stated in the EU Wastewater Treatment Directive proposal, methodological standardization, including a workflow for method development and validation, will play a crucial role in global monitoring of AMR in wastewater. However, according to our knowledge, there are currently no qPCR and ddPCR methods for AMR surveillance available that have been validated according to international standard performance criteria. Therefore, this study proposes a workflow for the development and validation of PCR-based methods for a harmonized and global AMR surveillance, including the construction of specific sequence databases and microbial collections for an efficient method development and method specificity evaluation. Following this strategy, we have developed and validated four duplex ddPCR methods responding to international standard performance criteria, focusing on seven AMR genes (ARG's), including extended spectrum beta-lactam (blaCTX-M), carbapenem (blaKPC-2/3), tetracycline (tet(M)), erythromycin (erm(B)), vancomycin (vanA), sulfonamide (sul2), and aminoglycoside (aac(3)-IV), as well as one indicator of antibiotic (multi-) resistance and horizontal gene transfer, named the class I integron (intl1). The performance of these ddPCR methods was successfully assessed for their specificity, as no false-positive and false-negative results were observed. These ddPCR methods were also considered to be highly sensitive as showing a limit of detection below 25 copies of the targets. In addition, their applicability was confirmed using 14 wastewater samples collected from two Belgian water resource recovery facilities. The proposed study represents therefore a step forward to reinforce method harmonization in the context of the global AMR surveillance in wastewater. PRACTITIONER POINTS: In the context of wastewater surveillance, no PCR-based methods for global AMR monitoring are currently validated according to international standards. Consequently, we propose a workflow to develop and validate PCR-based methods for a harmonized and global AMR surveillance. This workflow resulted here in four duplex ddPCR methods targeting seven ARGs and one general indicator for mobilizable resistance genes. The applicability of these validated ddPCR methods was confirmed on 14 wastewater samples from two Belgian water resource recovery facilities.

Introducing innovative policy instrument to reduce antibiotics use. Relevant evidence from Bulgaria

Abstract Background of the public health challenge Excessive individual consumption of antibiotics (ABs) increases global antimicrobial resistance (AMR). Therefore, shaping consumers’ behaviors towards responsible ABs use is an essential strategy in the battle with the silent pandemic of AMR. The EU One Health (OH) Action Plan against AMR targets making Europe a best-practice region. Overall consumption of ABs in the EU decreased significantly, especially during the COVID-19 pandemic. Bulgaria is the only EU country that has reported an annual increase in ABs use during this period (ECDC data). A growing part of Bulgarians, believe that ‘ABs kill viruses’ and is unaware that ‘unnecessary use of ABs makes them ineffective’ (Eurobarometer 2022). This limited understanding of adequate ABs use resulted in counterproductive behaviors that demand change. Introducing innovative policy instrument as a tool for behavioral change: Undeniably, drug prescription monitoring has the potential to change consumers’ behaviors. In October 2023 mandatory electronic prescribing (e-Rx) for ABs was introduced in Bulgaria at a primary healthcare level. Consequently, there was an observed decline exceeding 30% in ABs sales (IQVIA Bulgaria data), evidencing a reduction in ABs consumption. However, there were negative reactions by the stakeholders, due to time-consuming procedures, nonoptimal IT infrastructure, etc., and that led to e-Rx-moratorium. Finally, in April 2024, the e-Rx is sustainably introduced. Conclusions Legislative measures, like e-Rx, can hinder the chaotic use of ABs. Moreover, Bulgarians need to reflect on their behaviors and values of solidarity which OH offers. Herewith, a multidisciplinary team of academic educators unite their OH efforts in raising awareness related to AMR and the rational use of ABs. Years of national endeavors toward healthcare digitalisation led to the introduction of e-Rx for ABs in Bulgaria. Research will prove its relevance for the rest of Europe. Key messages • To the European community: The introduction of the innovative policy tool (e-Rx for antibiotics) in Bulgaria is a significant national effort in making Europe a best-practice region regarding AMR. • To the Bulgarian society: Antibiotics are not bonbons! Responsible ABs use of every one of us can contribute to the EU efforts to manage AMR. In the context of AMR, every person is a stakeholder.

Point-Prevalence Survey of Antimicrobial Use and Healthcare-Associated Infections in Four Acute Care Hospitals in Kazakhstan.

Few studies have examined the prevalence of healthcare-associated infections (HAIs) and antimicrobial use (AMU) in acute care hospitals in Kazakhstan. This study aimed to address this gap by conducting a point-prevalence survey (PPS) of HAIs and AMU, as well as evaluating hospital antibiotic consumption via internationally recognized methodologies. PPS was conducted in four acute care hospitals in Kazakhstan on 11 May 2022, following the methodology of the European Center for Disease Prevention and Control, and included 701 patients. Antibiotic consumption in the same hospitals was assessed via the Global Antimicrobial Resistance and Use Surveillance System methodology. HAIs were observed in 3.8% of patients (27/701), with intensive care unit wards accounting for 48.1% of these cases (13/27). Pseudomonas aeruginosa was the most frequently identified pathogen (5 out of 14 documented cases, 35.7%). Resistance to carbapenems was the most common resistance, followed by resistance to glycopeptides and third-generation cephalosporins. The rate of AMU was 38.2%, with an average of 1.37 antibiotics administered per patient. Surgical prophylaxis lasting more than one day was the most common indication for antimicrobial prescription (44.8%). Ceftriaxone and cefazolin are the most commonly used antibiotics. The results of this study are important for understanding the current situation in Kazakhstan and for informing national antimicrobial stewardship and infection control strategies.

Natural compound-induced downregulation of antimicrobial resistance and biofilm-linked genes in wastewater Aeromonas species.

Addressing the global antimicrobial resistance (AMR) crisis requires a multifaceted innovative approach to mitigate impacts on public health, healthcare and economic systems. In the complex evolution of AMR, biofilms and the acquisition of antimicrobial resistance genes (ARGs) play a pivotal role. Aeromonas is a major AMR player that often forms biofilm, harbors ARGs and is frequently detected in wastewater. Existing wastewater treatment plants (WWTPs) do not have the capacity to totally eliminate antimicrobial-resistant bacteria favoring the evolution of ARGs in wastewater. Besides facilitating the emergence of AMR, biofilms contribute significantly to biofouling process within the activated sludge of WWTP bioreactors. This paper presents the inhibition of biofilm formation, the expression of biofilm-linked genes and ARGs by phytochemicals andrographolide, docosanol, lanosterol, quercetin, rutin and thymohydroquinone. Aeromonas species were isolated and purified from activated sludge samples. The ARGs were detected in the isolated Aeromonas species through PCR. Aeromonas biofilms were quantified following the application of biocompounds through the microtiter plate assay. qPCR analyses of related genes were done for confirmation. Findings showed that the natural compounds inhibited the formation of biofilms and reduced the expression of genes linked to biofilm production as well as ARGs in wastewater Aeromonas. This indicates the efficacy of these compounds in targeting and controlling both ARGs and biofilm formation, highlighting their potential as innovative solutions for combating antimicrobial resistance and biofouling.

ENOVAT: the European Network for Optimization of Veterinary Antimicrobial Treatment

The global antimicrobial resistance crisis has been the driver of several international strategies on antimicrobial stewardship. For their implementation at the field level, the veterinary sector encounters several specific challenges and in particular: (i) a shortage of experts in key disciplines related to antimicrobial stewardship, (ii) a lack of evidence-based antimicrobial treatment guidelines, and (iii) inferior diagnostic tests available compared to human medicine. The present white paper describes how the COST Action ENOVAT (the European Network for Optimization of Veterinary Antimicrobial Treatment, CA18217), comprising 332 persons from 51 countries, worked towards solutions to these challenges. Initially, surveys were conducted to explore the present state in Europe in terms of existing antimicrobial use guidelines and microbiology practices performed. Concurrently, various research activities were launched to optimize diagnostics, including development of epidemiological cut-offs, clinical breakpoints and matrix-assisted laser desorption ionization time of flight mass spectrometry interpretive criteria. Also, guidelines drafting groups working towards evidence-based antimicrobial treatment guidelines for six conditions in food-producing and companion animals were established. The processes and outcomes, also in terms of capacity building, are summarized in this white paper where emphasis is placed on sustainability of the activities. Although several ENOVAT initiatives and spin-off projects will continue beyond the Action, we recommend that a new European veterinary research agenda is launched focusing on research and funding leading to long-term impacts on veterinary antimicrobial use.

The United Nations' General Assembly High-Level Meeting on antimicrobial resistance: a joint statement from the Heads of Government and Chief Medical Officers of the United Kingdom's Overseas Territories.

The UK Overseas Territories (UKOTs) are small, often remote territories with historical and territorial links to the UK. They range from densely populated areas (Cayman, Bermuda, Gibraltar) to land with no permanent inhabitants (British Antarctic Territory, South Georgia). However, they are linked by ecosystem instability (the permacrisis) including antimicrobial resistance (AMR), climate change and biodiversity disruption. The Chief Medical Officers of the UKOTs met in June 2024 and were unanimous in their concerns about the threat of global AMR. They have issued this statement on their hopes and expectations for the United Nations' General Assembly High-Level Meeting, in September 2024. These may be summarized by the hope of achieving united and sustained global political will to reduce the threat of AMR by equitable access to treatments, prevention of AMR by sanitation and accurate diagnostics, and education in health care and the public.

New progress in laboratory detection of respiratory infectious diseases in children

Respiratory infectious disease has become ahead of all the children's diseases, with the trend of continuously increasing global incidence, antimicrobial resistance and simultaneous infection with multiple pathogens. Diagnosis of this disease is mainly based on clinical symptoms and pathogenic detection. However, there are some differences in clinical manifestations, progression and prognosis between pediatric patients and adults, which prompting clinical diagnosis mainly depending on clinical laboratory test. Therefore, fast, convenient and accurate methods are urgently needed to clarify the type of infectious pathogen and carry out differentiated treatment, and reduce the burden on families and public health-care systems in schools. This article aims to elaborate the laboratory methods of children's respiratory infectious diseases and explore the opportunities and challenges, which can provide ideas for prevention, early screening and diagnosis, prognosis and treatment monitoring.

Empowering Global AMR Research Community: Interactive GIS dashboards for AMR data analysis and informed decision-making

Background Antimicrobial Resistance (AMR) is a critical global public health concern, demanding effective tools for research, data analysis, and decision-making. This study proposes a groundbreaking approach to empower the global AMR research community by introducing interactive Geographic Information System (GIS) dashboards. These dashboards aim to facilitate comprehensive data analysis of AMR across multiple countries, providing insights into antimicrobial usage (AMU), resistance patterns, and geographic distribution. Methods The approach involves developing GIS dashboards that integrate and harmonize AMR data from diverse sources, including clinical laboratories, surveillance networks, and public health agencies. A comprehensive dashboard was created to encompass data from multiple countries, providing advanced analysis and visualization tools. Another dashboard was developed with a specific focus on Kenya and Uganda to enable comparative analysis of AMR within these regions. Additionally, a simulated dataset for Kampala, Uganda, was generated to address data gaps in this area. Results The GIS dashboards serve as powerful tools for visualizing and analyzing AMR-related datasets, providing stakeholders with a comprehensive view of the global AMR landscape. These dashboards offer valuable insights into antimicrobial usage, resistance patterns, and geographical distribution. The centralized platform facilitates data exploration and analysis, aiding researchers, policymakers, and healthcare professionals in making informed decisions to combat AMR. Conclusions In conclusion, the study demonstrates that the developed GIS dashboards empower stakeholders by providing valuable insights and informed decision-making capabilities. The dashboards serve as essential tools for addressing the global challenge of AMR, allowing for a deeper understanding of the problem and informing effective strategies. The approach outlined in this study has the potential to significantly contribute to the ongoing efforts to combat AMR on a global scale.

Impact of COVID-19 on Antibiotic Stewardship, Antimicrobial Resistance, and Prescribing Habits at Two General Hospitals in Abu Dhabi: A Retrospective Analysis.

Introduction The COVID-19 pandemic has overwhelmingly affected healthcare systems, particularly in the area of antibiotic management. The surge in antimicrobial use to address secondary bacterial infections in COVID-19 patients has heightened concerns about overuse and antimicrobial resistance (AMR). This study examined the pandemic's effect on the antibiotic stewardship program (ASP) at two general hospitals in Abu Dhabi, focusing on changes in prescribing practices, adherence to stewardship guidelines, resistance trends, and overall health system impact. The present retrospective study evaluated shifts in antibiotic consumption, compliance with stewardship practices, and broader healthcare implications. The aim is to assess the pandemic's impact, identify improvement areas, and provide insights to enhance the ASP in addressing the global AMR crisis. Methods This retrospective review assessed electronic medical records from two general hospitals in Abu Dhabi over a 24-month period, from January 2019 to December 2020. It included pre-COVID-19 data from 2019 and data from 2020 during the COVID-19 surge. The study focused on patients aged 25 to 40 years with respiratory tract infections, urinary tract infections, ventilator-associated pneumonia, and nosocomial infections, identified using predefined ICD-10-CM (International Classification of Diseases, Tenth Revision, Clinical Modification) codes. Patients with COVID-19 diagnoses and those undergoing surgical procedures were excluded. Key metrics compared data from 2019 and 2020 to assess changes in clinicians' prescribing practices, antibiotic usage, ASP interventions, and their impact on the healthcare system. Results The COVID-19 pandemic influenced antibiotic use and resistance trends, leading to longer hospital stays (3.86 days in 2019 vs. 4.29 days in 2020) and increased use of duplicate anaerobic therapy (4.58% in 2019 vs. 5.71%in 2020). From 2019 to 2020, the average duration of antibiotic therapy decreased from 6.23 days to 5.24 days, but empirical therapy without sufficient evidence rose. The average length of treatment increased (2.87 days in 2019 vs. 3.28 days in 2020), and there was a rise in the use of antibiotics for viral and fungal infections, with cases growing from 17.08%in 2019 to 22.38%in 2020. Despite modest improvements in stewardship practices in 2020, AMR challenges persisted. These results underscore the need for enhanced stewardship programs and continued research to address the ongoing impacton antibiotic prescribing and resistance. Conclusion The COVID-19 pandemic increased antibiotic use and altered resistance patterns. Although stewardship practices improved, AMR challenges remained. Enhanced stewardship programs and ongoing research are essential to mitigate these effects and improve antibiotic management. Recommendation To address changes in antibiotic use and resistance during the COVID-19 pandemic, it is recommended to strengthen ASPs to adapt to new prescribing trends, ensure adherence to evidence-based practices, provide ongoing education for clinicians, invest in research on long-term resistance impacts, and enhance data tracking and monitoring systems.

Comprehensive analysis of antibiotic and heavy metal resistance, and virulence factors in Aeromonas veronii CTe-01: Implications for global antimicrobial resistance

ObjectivesThis study aimed to characterize Aeromonas veronii CTe-01 focusing on its resistance to heavy metal and antibiotics. MethodsA. veronii CTe-01 was characterized using standard microbiological and molecular techniques. Antibiotic susceptibility and heavy metal resistance were tested per standard protocols. Genomic analysis, including plasmid characterization, was conducted in silico. ResultsA. veronii CTe-01 showed resistance to various heavy metals and antibiotics. Multiple resistance genes were identified, including those for beta-lactamases, heavy metal resistance, and type III secretion system components. The bacterium carries a 9 kb plasmid with repA/repB replication genes, parA/parB partitioning genes, and a type II toxin-antitoxin system for stability. ConclusionsA. veronii CTe-01 is a genetic reservoir for antibiotic resistance, heavy metal resistance genes, and virulence factors. The study offers insights into its dual role as a pathogen and heavy metal remediator in aquatic environments.

The global burden and trend of Clostridioides difficile and its association with world antibiotic consumption, 1990-2019.

To estimate the global trends and disease burden of Clostridioides difficile infection (CDI) and its correlation with worldwide antibiotic consumption. Clostridioides difficile infection and antibiotic consumption data were retrieved from the Global Burden of Disease 2019, ResistanceMap-AntibiocUse, Food and Drug Administration (FDA) Adverse Event Reporting System, and Global Antimicrobial Resistance and Use Surveillance System. Jointpoint regression and age-period-cohort model were developed to show the global trends and burden of CDI. Correlation tests were calculated to explore the relationship between CDI and antibiotics. Globally, CDI is the most significant one with a high-rocketing burden increase rate among 13 pathogens causing diarrheal deaths and disability-adjusted life years (DALYs). The age-standardised death rate (ASDR) increased from 0.19 in 1990 to 0.43 in 2019, in which the elderly and females are at higher risk. A rapid increase in ASDR in high to middle sociodemographic index (SDI) regions such as North America (average annual percentage change (AAPC) = 7.71%), Andean (AAPC = 7.82%), and Southern Latin America (AAPC = 11.08%) was identified. Antibiotic consumption has a significant positive correlation with CDI with different risk stratifications. The global burden of CDI has continuously increased for the past 30 years, especially in high to middle-SDI regions. World antibiotic consumption showed a strong positive correlation with CDI with different risk stratification. More effective prevention and control measures should be implemented in these critical regions, with a specific emphasis on vulnerable populations, to mitigate the spread of epidemics.

Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species

BackgroundEnterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing. AimTo characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs. MethodsStandard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain’s complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution. ResultsECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants. ConclusionE. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.

ENOVAT: the European Network for Optimization of Veterinary Antimicrobial Treatment.

The global antimicrobial resistance crisis has been the driver of several international strategies on antimicrobial stewardship. For their implementation on field level, the veterinary sector encounters several specific challenges and in particular: (i) a shortage of experts in key disciplines related to antimicrobial stewardship, (ii) a lack of evidence-based antimicrobial treatment guidelines, and (iii) inferior diagnostic tests available compared to human medicine. The present white paper describes how the COST Action ENOVAT (the European Network for Optimization of Veterinary Antimicrobial Treatment, CA18217), comprising 332 persons from 51 countries, worked towards solutions to these challenges. Initially, surveys were conducted to explore the present state in Europe in terms of existing antimicrobial use guidelines and microbiology practices performed. Concurrently, various research activities were launched to optimize diagnostics, including development of epidemiological cut-offs, clinical breakpoints and matrix-assisted laser desorption ionization time of flight mass spectrometry interpretive criteria. Also, guidelines drafting groups working towards evidence-based antimicrobial treatment guidelines for six conditions in food-producing and companion animals were established. The processes and outcomes, also in terms of capacity building, are summarized in this white paper where emphasis is placed on sustainability of the activities. Although several ENOVAT initiatives and spin-off projects will continue beyond the Action, we recommend that a new European veterinary research agenda is launched focusing on research and funding leading to long-term impacts on veterinary antimicrobial use.

Population genomics uncovers global distribution, antimicrobial resistance, and virulence genes of the opportunistic pathogen Klebsiella aerogenes

Klebsiella aerogenes is an understudied and clinically important pathogen. We therefore investigate its population structure by genome analysis aligned with metadata. We sequence 130 non-duplicated K. aerogenes clinical isolates and identify two inter-patient transmission events. We then retrieve all publicly available K. aerogenes genomes (n= 1,026, accessed by January 1, 2023) and analyze them with our 130 genomes. We develop a core-genome multi-locus sequence-typing scheme. We find that K. aerogenes is a species complex comprising four phylogroups undergoing evolutionary divergence, likely forming three species. We delineate remarkable clonal diversity and identify three worldwide-distributed carbapenemase-encoding clonal clusters, representing high-risk lineages. We uncover that K. aerogenes has an open genome equippedby a large arsenal of antimicrobial resistance genes. We identify two genetic regions specific for K. aerogenes, encoding a type VI secretion system and flagella/chemotaxis for motility, respectively, both contributing to the virulence. These results provide much-needed insights into the population structure and pan-genomes of K. aerogenes.

Advanced Vibrational Spectroscopy and Bacteriophages Team Up: Dynamic Synergy for Medical and Environmental Applications.

Bacteriophages are emerging as a promising alternative in combating antibiotic-resistant bacteria amidst the escalating global antimicrobial resistance crisis. Recently, there has been a notable resurgence of interest in phages, prompting extensive research into their therapeutic potential. Beyond conventional microbiology and virology techniques, such as genomics and proteomics, novel phenotypic and chemical characterization methods are being explored. Among these, there is a growing interest in vibrational spectroscopy, especially in advanced modalities such as surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), and atomic force microscopy-infrared spectroscopy (AFM-IR), which offer improved sensitivity and spatial resolution. This review explores the spectrum of uses of vibrational spectroscopy for bacteriophages, including its role in diagnostics, biosensing, phage detection, assistance in phage-based therapy, and advancing basic research.

Global trends of antimicrobial resistance rates in Neisseria gonorrhoeae: a systematic review and meta-analysis.

Antimicrobial resistance (AMR) of Neisseria gonorrhoeae (NG) is a significant public health concern. The objective of our study was to assess global AMR rates and test them both temporally and geographically. We conducted a systematic search of relevant reports from international databases up to 2021. The R statistical package was used for all statistical analyses. A total of 225 articles were analyzed, and 432,880 NG isolates were examined. The weighted pooled resistance (WPR) rate of different antibiotics was as follows: ciprofloxacin, 51.6%; tetracycline, 45.4%; trimethoprim/sulfamethoxazole, 42.4%; chloramphenicol, 4.1%; kanamycin, 2.1%; gentamicin, 0.6%; and spectinomycin, 0.3%. The resistance to spectinomycin, gentamicin, and kanamycin decreased over time. Significant differences in antibiotic resistance rates were found between the countries. Our findings reveal a continuous increase in resistance to some antibiotics (tetracycline and ciprofloxacin) historically used for gonorrhea, even after discontinuation. However, encouraging trends of decreasing resistance to spectinomycin, gentamicin, and kanamycin were observed. Continued global monitoring of AMR profiles in NG isolates is essential for informing appropriate treatment strategies and mitigating the threat of untreatable gonorrhea.