System Mapping of Antimicrobial Resistance to Combat a Rising Global Health Crisis

Association between antimicrobial use levels and meat inspection lesions in Danish finishers

In Denmark, the Yellow Card scheme enforces restrictions on pig herds exceeding official permitted limits for antimicrobial use (AMU). To assess if a Yellow Card is related to poor animal health, we examined the association between AMU and the health status of Danish finishers using meat inspection data as a proxy for pig health. We included meat inspection findings in 10.5 million finishers delivered to 9 Danish abattoirs between 2016 and 2020 from herds classified as having a low, medium, or high AMU (Yellow Card herds). The prevalence of meat inspection findings was calculated and analysed in mixed-effects logistic regression models to determine the associations between each of eight selected lesions and AMU level while also considering the effect of herd size, location (east or west) and herd type (indoor or outdoor). Despite differences in AMU, only minor differences in meat inspection lesions were present. The overall result of the multivariable modelling was that herds with a medium AMU level were associated with the lowest prevalence of meat inspection lesions - observed for five out of the eight lesions investigated. Moreover, large herds were associated with a lower prevalence of meat inspection lesions than small herds - observed for seven out of eight lesions. The prevalence of lung and tail lesions was higher for herds in the western region of Denmark compared to the eastern regions, and the prevalence of tail lesions, arthritis and osteomyelitis was higher in outdoor herds compared to indoor herds. Hence, both a high and a low AMU could be linked with health and welfare issues. The results indicate that the advisory role of the herd veterinarian is pivotal in preventing adverse effects of antimicrobial reduction measures on animal health and welfare, in particular, if the Yellow Card limits are reduced further.

Antimicrobial resistance in a protracted war setting: a review of the literature from Palestine

Antimicrobial resistance (AMR) is an escalating global health crisis. In war-affected regions, where healthcare systems are already compromised, AMR presents an even greater threat. The occupied Palestinian territories (oPt), subjected to chronic war-like conditions, have experienced extensive fragmentation, de-development, and destruction of healthcare. This review maps the existing knowledge regarding AMR carriage and infection in the oPt. We conducted a scoping review using PubMed, CINAHL, Embase, and Web of Science. Findings on the prevalence and suggested drivers of AMR were extracted and analyzed according to the One Health approach. From an initial 1,787 articles, 102 were included in the final analysis. Of these, 91 studies focused on AMR in humans, seven on animals, and four on water contamination. The findings reveal high rates of AMR, with 40% of Klebsiella pneumoniae producing extended-spectrum beta-lactamase (ESBL) and 55% of Streptococcus pneumoniae resistant to penicillin. Additionally, 45.6% of Staphylococcus aureus isolates from cow milk were methicillin-resistant, and 36% of chicken samples contained carbapenem-resistant gram negative bacteria. Significant gaps in the regulation of antibiotic prescription, dispensation, and consumption were reported. Despite the heterogeneity in reporting methods across studies and the inability to perform a meta-analysis, the evidence suggests alarmingly high AMR rates within the oPt. Notably, most studies attributed AMR to local practices, often overlooking broader structural and socio-political drivers. This review underscores the need to contextualize AMR within the environment, particularly under conditions of sustained warfare.IMPORTANCEThis study goes beyond merely reviewing and summarizing data on AMR in the occupied Palestinian territories (oPt), a region enduring chronic war-like conditions. Our work addresses critical gaps in knowledge about AMR in populations affected by war and siege. By contextualizing AMR through a socio-political lens, this study offers a novel perspective. It highlights deeper drivers, including the impact of war on the behaviors and education of patients and doctors, perceptions of antibiotics, the role of humanitarian interventions in fostering antibiotic anarchy, and the overall weakening of the Palestinian healthcare system. Importantly, this review also sets the stage for understanding the existing literature on AMR in the oPt within the context of the ongoing war in Gaza, emphasizing the immediate need for comprehensive strategies to address AMR under conditions of conflict. The insights can inform physicians and policymakers in designing and implementing effective AMR stewardship programs, not only in Palestine but also in other conflict-affected regions.

Evaluation of Antimicrobial Usage Supply Chain and Monitoring in the Livestock and Poultry Sector of Pakistan

Irrational use of antimicrobials in humans, livestock, and poultry is often cited as the key driver of the accelerated emergence of antimicrobial resistance (AMR) in humans and animals. In Pakistan, the use of antimicrobials in livestock and poultry is not well-regulated, owing to limited and/or ineffective implementation of existing legislations and lack of coordination amongst the key stakeholders. To gather data and information pertinent to the supply chain mapping and the usage of antibiotics in the livestock and poultry sectors of Pakistan, a national workshop for selected influential stakeholders was held in Islamabad, Pakistan during March 2020 to map the supply chain and the usage of antibiotics in the country. Participants from all relevant organizations identified the supply chain and discussed the status, challenges, and the way forward to enhance data collection and monitoring of antimicrobial usage (AMU) in livestock and poultry sectors to contain the emergence of AMR. The pre-workshop questionnaire was designed to gather relevant information on AMU and its distribution among diverse markets and users from the workshop participants, utilizing open-ended questions. A chart depicting the relative magnitude of an antimicrobial use (AMU) supply chain was constructed to illustrate the flow of antimicrobials from import and production to end-use at the farm level. This chart was shared with participants to gather their professional opinions and potential corrections. It also presented a list of agencies and their roles in regulating AMU, along with the types of AMU data available at each level. Specific recommendations were made at the end of the workshop to review and update legislation to cover the entire AMU supply chain, enhance regulations to restrict the use of antimicrobial growth promoters, build an integrated national AMU database system, and raise awareness about the responsible use of antimicrobials in the livestock and poultry sectors. It was concluded that the AMU supply chain in the veterinary sector of Pakistan is fragmented and is co-regulated by various federal and provincial stakeholders. There are some drugs, such as antibiotic growth promoters, which are not regulated at all. The approach and findings from this study can serve as a model to validate the use and management of antibiotics in other, similar countries currently grappling with serious antimicrobial resistance (AMR) crises.

Trouble on the horizon: anticipating biological invasions through futures thinking

Anticipating future biosecurity threats to prevent their occurrence is the most cost-effective strategy to manage invasive alien species. Yet, biological invasions are complex, highly uncertain processes. High uncertainty drives decision-making away from strategic preventative measures and towards operational outcomes aimed at post-invasion management. The limited success of preventative measures in curbing biological invasions reflects this short-term mindset and decision-makers should instead apply strategic foresight to imagine futures where biosecurity threats are minimised. Here, four major futures thinking tools (environmental scanning, driver-mapping, horizon scanning, and scenario planning) that describe probable, possible, plausible and preferable futures are assessed in terms of their potential to support both research and policy addressing biological invasions. Environmental scanning involves surveying existing data sources to detect signals of emerging alien species through knowledge of changes in either the likelihood or consequences of biological invasions. Several approaches are widely used for biosecurity including automated scans of digital media, consensus-based expert scoring, and prediction markets. Automated systems can be poor at detecting weak signals because of the large volume of 'noise' they generate while expert scoring relies on prior knowledge and so fails to identify unknown unknowns which is also true of prediction markets that work well for quite specific known risks. Driver-mapping uses expert consensus to identify the political, economic, societal, technological, legislative, and environmental forces shaping the future and is a critical component of strategic foresight that has rarely been applied to biological invasions. Considerable potential exists to extend this approach to develop system maps to identify where biosecurity interventions may be most effective and to explore driver complexes to determine megatrends shaping the future of biological invasions. Horizon scanning is a systematic outlook of potential threats and future developments to detect weak signals of emerging issues that exist at the margins of current thinking. Applications have been strongly focused on emerging issues related to research and technological challenges relevant to biosecurity and invasion science. However, most of these emerging issues are already well known in current-day research. Because horizon scanning is based on expert consensus, it needs to embrace a diversity of cultural, gender, and disciplinary diversity more adequately to ensure participants think intuitively and outside of their own subject boundaries. Scenario planning constructs storylines that describe alternative ways the political, economic, social, technological, legislative, and environmental situation might develop in the future. Biological invasion scenario planning has favoured structured approaches such as standardised archetypes and uncertainty matrices, but scope exists to apply more intuitive thinking by using incasting, backcasting, or causal layered analysis. Futures thinking in biological invasions has not engaged with decision-makers or other stakeholders adequately and thus outcomes have been light on policy and management priorities. To date, strategic foresight addressing biological invasions has applied each approach in isolation. Yet, an integrated approach to futures thinking that involves a diverse set of stakeholders in exploring the probable, possible, plausible, and preferable futures relating to biological invasions is crucial to the delivery of strategic biosecurity foresight at both national and global scales.

Investigating the occurrence of antimicrobial resistance in the environment in Canada: a scoping review

Antimicrobial resistance is an environmental, agricultural, and public health problem that is impacting the health of humans and animals. The role of the environment as a source of and transmission pathway for antibiotic resistant bacteria and antibiotic resistance genes is a topic of increasing interest that, to date, has received limited attention. This study aimed to describe the sources and possible pathways contributing to antimicrobial resistance dissemination through bioaerosols, water, and soil in Canada using a scoping review methodology and systems thinking approach. A systems map was created to describe the occurrence and relationships between sources and pathways for antimicrobial resistance dissemination through water, soil, and bioaerosols. The map guided the development of the scoping review protocol, specifically the keywords searched and what data were extracted from the included studies. In total, 103 studies of antimicrobial resistance in water, 67 in soil, and 12 in air were identified. Studies to detect the presence of antimicrobial resistance genes have mainly been conducted at wastewater treatment plants and commercial animal livestock facilities. We also identified elements in the systems map with little or no data available (e.g., retail) that need to be investigated further to have a better understanding of antimicrobial resistance dissemination through different Canadian environments.

Antimicrobial Potential of Scorpion-Venom-Derived Peptides

The frequent and irrational use of antibiotics by humans has led to the escalating rise of antimicrobial resistance (AMR) with a high rate of morbidity-mortality worldwide, which poses a challenge to the development of effective treatments. A large number of host defense peptides from different organisms have gained interest due to their broad antibacterial spectrum, rapid action, and low target resistance, implying that these natural sources might be a new alternative to antimicrobial drugs. As important effectors of prey capture, defense against other animal attacks, and competitor deterrence, scorpion venoms have been developed as important candidate sources for modern drug development. With the rapid progress of bioanalytical and high throughput sequencing techniques, more and more scorpion-venom-derived peptides, including disulfide-bridged peptides (DBPs) and non-disulfide-bridged peptides (NDBPs), have been recently identified as having massive pharmacological activities in channelopathies, pathogen infections, and cancer treatments. In this review, we summarize the molecular diversity and corresponding structural classification of scorpion venom peptides with antibacterial, antifungal, and/or antiparasitic activity. We also aim to improve the understanding of the underlying mechanisms by which scorpion-venom-derived peptides exert these antimicrobial functions, and finally highlight their key aspects and prospects for antimicrobial therapeutic or pharmaceutical application.

Prevalence of antibiotic-resistant Gram-negative bacteria having extended-spectrum β-lactamase phenotypes in polluted irrigation-purpose wastewaters from Indian agro-ecosystems

Antibiotic resistance in bacteria has emerged as a serious public health threat worldwide. Aquatic environments including irrigation-purpose wastewaters facilitate the emergence and transmission of antibiotic-resistant bacteria and antibiotic resistance genes leading to detrimental effects on human health and environment sustainability. Considering the paramount threat of ever-increasing antibiotic resistance to human health, there is an urgent need for continuous environmental monitoring of antibiotic-resistant bacteria and antibiotic resistance genes in wastewater being used for irrigation in Indian agro-ecosystems. In this study, the prevalence of antibiotic resistance in Gram-negative bacteria isolated from irrigation-purpose wastewater samples from Sirmaur and Solan districts of Himachal Pradesh was determined. Bacterial isolates of genera Escherichia, Enterobacter, Hafnia, Shigella, Citrobacter, and Klebsiella obtained from 11 different geographical locations were found to exhibit resistance against ampicillin, amoxyclav, cefotaxime, co-trimoxazole, tobramycin, cefpodoxime and ceftazidime. However, all the isolates were sensitive to aminoglycoside antibiotic gentamicin. Enterobacter spp. and Escherichia coli showed predominance among all the isolates. Multidrug-resistance phenotype was observed with isolate AUK-06 (Enterobacter sp.) which exhibited resistant to five antibiotics. Isolate AUK-02 and AUK-09, both E. coli strains showed resistant phenotypes to four antibiotics each. Phenotypic detection revealed that six isolates were positive for extended-spectrum β-lactamases which includes two isolates from Enterobacter spp. and E. coli each and one each from Shigella sp. and Citrobacter sp. Overall, the findings revealed the occurrence of antibiotic resistant and ESBL-positive bacterial isolates in wastewaters utilized for irrigation purpose in the study area and necessitate continuous monitoring and precautionary interventions. The outcomes of the study would be of significant clinical, epidemiological, and agro-environmental importance in designing effective wastewater management and environmental pollution control strategies.

Risk stratification for selecting empiric antibiotherapy during and after COVID-19

PURPOSE OF REVIEW

SARS-CoV-2 deeply modified the risk of bacterial infection, bacterial resistance, and antibiotic strategies. This review summarized what we have learned.

RECENT FINDINGS

During the COVID-19 pandemic, we observed an increase in healthcare-acquired infection and multidrug-resistant organism-related infection, triggered by several factors: structural factors, such as increased workload and ongoing outbreaks, underlying illnesses, invasive procedures, and treatment-induced immunosuppression. The two most frequently healthcare-acquired infections described in patients hospitalized with COVID-19 were bloodstream infection, related or not to catheters, health-acquired pneumonia (in ventilated or nonventilated patients). The most frequent species involved in bacteremia were Gram-positive cocci and Gram-negative bacilli in health-acquired pneumonia. The rate of Gram-negative bacilli is particularly high in late-onset ventilator-associated pneumonia, and the specific risk of Pseudomonas aeruginosa- related pneumonia increased when the duration of ventilation was longer than 7 days. A specificity that remains unexplained so far is the increase in enterococci bacteremia.

SUMMARY

The choice of empiric antibiotimicrobials depends on several factors such as the site of the infection, time of onset and previous length of stay, previous antibiotic therapy, and known multidrug-resistant organism colonization. Pharmacokinetics of antimicrobials could be markedly altered during SARS-CoV-2 acute respiratory failure, which should encourage to perform therapeutic drug monitoring.

Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens

Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.