The Mandate for a Global "One Health" Approach to Antimicrobial Resistance Surveillance

Barriers and pathways to environmental surveillance of antibiotic resistance in middle- and low-income settings: a qualitative exploratory key expert study

BACKGROUND

Local and global surveillance of antibiotic resistance (ABR) has proven a challenge to implement effectively in low- and middleincome (LMI) settings. Environmental surveillance solutions are increasingly highlighted as a strategy to help overcome such problems, and thus to promote global health as well as the local management of ABR in LMI countries. While technical and scientific aspects of such solutions are being probed continuously, no study has investigated their practical feasibility.

OBJECTIVE

Explore practical barriers for environmental surveillance of ABR in LMI countries, and pathways for surveillance experts to manage these.

METHODS

To start charting this unknown territory, we conducted an explorative, qualitative interview study with key informants, applying a constructivist grounded theory approach to analyze the results.

RESULTS

Barriers were identified across infrastructural, institutional and social dimensions, and pathways to manage them were mostly counterproductive from an ABR management perspective, including avoiding entire regions, applying substandard methods and failing to include local collaborators.

CONCLUSION

The research community as well as international agencies, organizations and states have key roles and responsibilities for improving the prospects of feasible environmental ABR surveillance in LMI-settings.

Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes

Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.

Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing

BACKGROUND

Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E. coli whole genome sequencing project.

RESULTS

Hybrid assembly (Illumina and Nanopore) combined with plasmid DNA extractions allowed for detection of the greatest number of plasmids in E. coli, as detected by MOB-suite software. In total, 79 plasmids were identified in 19 E. coli isolates. Hybrid assemblies were robust and consistent in quality regardless of sequencing kit used or if long reads were filtered or not. In contrast, long read only assemblies were more variable and influenced by sequencing and assembly parameters. Plasmid DNA extractions allowed for the detection of physically smaller plasmids, but when averaged over 19 isolates did not significantly change the overall number of plasmids detected.

CONCLUSIONS

Hybrid assembly can be reliably used to detect plasmids in E. coli, especially if researchers are focused on large plasmids containing antimicrobial resistance genes and virulence factors. If the goal is comprehensive detection of all plasmids, particularly if smaller sized vectors are desired for biotechnology applications, the addition of plasmid DNA extractions to hybrid assemblies is prudent. Long read sequencing is sufficient to detect many plasmids in E. coli, however, it is more prone to errors when expanded to analyze a large number of isolates.

Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain

Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.

Developing home cleaning intervention through community engagement to reduce infections and antimicrobial resistance in Ghanaian homes

Globally Antimicrobial Resistance (AMR) constitutes a health crisis, particularly in developing countries, where infectious disease are commonly fatal. There is clear evidence for microbial exposure and infection transmission within the home. Personal and environmental hygiene are the best ways of reducing household infections thus decreasing the need for antibiotics and consequently diminishing AMR. Despite this being an obvious step, research efforts to understand the home environment and its impact on AMR, cleaning and possible interventions on household cleaning are limited. We combined design and microbiology methods in an innovative mixed-method approach. A traditional survey design (n = 240), a design ethnography (n = 12), a co-design workshop and a pre-intervention microbiological dust sample analysis was undertaken to provide insights for codesign workshops in which new cleaning practices might be developed to minimise any AMR bacteria present in the household environments located in the Greater Accra Region of Ghana. Microbiological analysis of household dust showed that 36.6% of bacterial isolates detected were found to carry at least one resistance to the panel of antibiotics tested. Four scenarios were generated from an economic segmentation of the survey data. 50 ethnographic insights were 'presented' and descriptions of 12 bacteria species that showed resistance to one or more antibiotics (representing 176 bacterial isolates that showed resistance to one or more antibiotics found in the dust samples) were presented to the participants in a codesign workshop. An intervention, a new regime of cleaning practices agreed through the co-design workshop and practiced for thirty days, was made in (n = 7) households. The high prevalence of multidrug resistance observed in this study indicate the need for antibiotics surveillance program, not only in hospital settings but also in the household environment. There is, thus, an urgent need for targeting of interventions at the household level. Activating knowledge through community engagement in the research helps in increasing public perception and breaking down the scientist-public barrier.

Lessons from Dairy Farmers for Occupational Allergy and Respiratory Disease

PURPOSE OF REVIEW

Exposure to bioaerosols at dairies has long been associated with allergy, respiratory disease, and decreases in lung function. Recent advancements in exposure assessments have aided our understanding on the size distribution and composition of these bioaerosols, but investigations focusing solely on exposures may overlook important intrinsic factors impacting worker's susceptibility to disease.

RECENT FINDINGS

In our review, we discuss the most recent studies examining the exposures and genetic factors that contribute to occupational disease in dairy work. We also review more recent concerns in livestock work associated with zoonotic pathogens, antimicrobial resistant genes, and the role of the human microbiome. The studies highlighted in this review demonstrate the need for further research to better understand bioaerosol exposure-response relationships in the context of extrinsic and intrinsic factors, antibiotic-resistant genes, viral pathogens, and the human microbiome to help inform effective interventions that improve respiratory health among dairy farmers.

Land use as a critical determinant of faecal and antimicrobial resistance gene pollution in riverine systems

The WHO recognises antimicrobial resistance (AMR) as a global health threat. The environment can act as a reservoir, facilitating the exchange and the physical movement of resistance. Aquatic environments are at particular risk of pollution, with large rivers subject to pollution from nearby human, industrial or agricultural activities. The land uses associated with these activities can influence the type of pollution. One type of pollution and a likely contributor to AMR pollution that lowers water quality is faecal pollution. Both pose an acute health risk and could have implications for resistance circulating in communities. The effects of land use are typically studied using physiochemical parameters or in isolation of one another. However, this study aimed to investigate the impact of different land uses on riverine systems. We explored whether differences in sources of faecal contamination are reflected in AMR gene concentrations across agricultural and urban areas. Water quality from three rivers impacted by different land uses was assessed over one year by quantifying faecal indicator bacteria (FIB), microbial source tracking markers (MST) and AMR genes. In addition, a multiparametric analysis of AMR gene pollution was carried out to understand whether agricultural and urban areas are similarly impacted. Faecal indicators varied greatly, with the highest levels of FIB and the human MST marker observed in urban regions. In addition, these faecal markers correlated with AMR genes. Similarly, significant correlations between the ruminant MST marker and AMR gene levels in agriculture areas were observed. Overall, applying multiparametric analyses to include AMR gene levels, separation and clustering of sites were seen based on land use characterisation. This study suggests that differences in prescription of antimicrobials used in animal and human healthcare may influence environmental resistomes across agricultural and urban areas. In addition, public health risks due to exposure to faecal contamination and AMR genes are highlighted.

Testable Candidate Immune Correlates of Protection for Porcine Reproductive and Respiratory Syndrome Virus Vaccination

Porcine reproductive and respiratory syndrome virus (PRRSV) is an on-going problem for the worldwide pig industry. Commercial and experimental vaccinations often demonstrate reduced pathology and improved growth performance; however, specific immune correlates of protection (CoP) for PRRSV vaccination have not been quantified or even definitively postulated: proposing CoP for evaluation during vaccination and challenge studies will benefit our collective efforts towards achieving protective immunity. Applying the breadth of work on human diseases and CoP to PRRSV research, we advocate four hypotheses for peer review and evaluation as appropriate testable CoP: (i) effective class-switching to systemic IgG and mucosal IgA neutralizing antibodies is required for protective immunity; (ii) vaccination should induce virus-specific peripheral blood CD4+ T-cell proliferation and IFN-γ production with central memory and effector memory phenotypes; cytotoxic T-lymphocytes (CTL) proliferation and IFN-γ production with a CCR7- phenotype that should migrate to the lung; (iii) nursery, finishing, and adult pigs will have different CoP; (iv) neutralizing antibodies provide protection and are rather strain specific; T cells confer disease prevention/reduction and possess greater heterologous recognition. We believe proposing these four CoP for PRRSV can direct future vaccine design and improve vaccine candidate evaluation.

Association between Antimicrobial Consumption and the Prevalence of Nosocomial Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae in a Tertiary Hospital in Northern Taiwan

Carbapenem-resistant Enterobacteriales has become a threat in Taiwan. This is the first local study focusing on the association between carbapenem-resistant Enterobacteriales and antimicrobial consumption. From January 2012 to December 2020, data were collected in a tertiary care hospital in Taipei, Taiwan. Antimicrobial consumption was estimated by the defined daily dose/1,000 patient-days. During the same period, the prevalence of carbapenem-resistant Escherichia coli (CREC) and carbapenem-resistant Klebsiella pneumoniae (CRKP) were collected through routine surveillance data. The following retrospective analyses were conducted: 1) analysis of antimicrobial consumption over time, (2) analysis and forecast of CREC and CRKP prevalence over time, and 3) analysis of correlation between antimicrobial consumption and the prevalence of CREC and CRKP. The consumption of piperacillin/tazobactam (β = 0.615), fluoroquinolones (β = 0.856), meropenem (β = 0.819), and doripenem (β = 0.891) increased during the observation period (P < 0.001), and the consumption of aminoglycosides (β = -0.852) and imipenem/cilastatin (β = -0.851) decreased (P < 0.001). The prevalence of CRKP rose over time (β = 0.522, P = 0.001) and correlated positively with the consumption of fluoroquinolones, levofloxacin, penicillin/β-lactamase inhibitor, piperacillin/tazobactam, meropenem, and doripenem (P < 0.05). The prevalence of CRKP and CREC both correlated negatively with consumption of aminoglycosides (P < 0.01). The prevalence of CRKP in our hospital increased as the forecast predicted based on an autoregressive integrated moving average model. This study provides alarming messages for members participating in antimicrobial stewardship programs, including the increasing prevalence of CRKP, the increasing consumption of broad-spectrum antibiotics, and the positive correlation between them.

Veterinary Practitioners' Standpoints and Comprehension towards Antimicrobial Use-Are There Opportunities for Antimicrobial Stewardship Improvement?

The main subject of the research is the assessment of the knowledge, attitudes and behaviors of veterinarians regarding the use of antibiotics (AMU) and antimicrobial resistance (AMR) through a questionnaire conducted among veterinarians in the northern region of Serbia. A total of 62 respondents completed the questionnaire, which represents a response rate of 44.3%. Male veterinarians are less likely to be in the group of veterinarians with insufficient knowledge (p < 0.05). Veterinarians engaged in mixed practice (small and large animals) (p < 0.001) and veterinarians who have over 100 patients per month (p < 0.005) are also less likely to be in the group with insufficient knowledge of antimicrobial resistance. The proportion of those with insufficient knowledge is growing among veterinarians whose source is the Internet (p < 0.01), while the proportion of those with insufficient knowledge about antimicrobial resistance is declining among veterinarians whose source of information is continuous education (p < 0.05). The majority of the respondents (n = 59, 95.2%) completely agreed that AMR is a very big issue in the global health sector right now. Unfortunately, there are crucial gaps in the knowledge and attitudes of the surveyed participants. They do not appear to be aware of the importance of AMU in veterinary medicine and its influence on overall AMR, or the crucial part that non-prescribed antibiotics have in all of it. Positively, many veterinarians use good practice AMU guidelines in their everyday practice and in line with the global trend of AMU reduction, respondents have also decreased their AMU compared to the previous year.

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study

We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the bla_OXA-181, bla_OXA-48, bla_OXA-484, bla_NDM-1, and bla_GES-5 genes. Multiple species/clones carried bla_OXA-48 and bla_NDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.

Antibiotic Discovery and Resistance: The Chase and the Race

The history of antimicrobial resistance (AMR) evolution and the diversity of the environmental resistome indicate that AMR is an ancient natural phenomenon. Acquired resistance is a public health concern influenced by the anthropogenic use of antibiotics, leading to the selection of resistant genes. Data show that AMR is spreading globally at different rates, outpacing all efforts to mitigate this crisis. The search for new antibiotic classes is one of the key strategies in the fight against AMR. Since the 1980s, newly marketed antibiotics were either modifications or improvements of known molecules. The World Health Organization (WHO) describes the current pipeline as bleak, and warns about the scarcity of new leads. A quantitative and qualitative analysis of the pre-clinical and clinical pipeline indicates that few antibiotics may reach the market in a few years, predominantly not those that fit the innovative requirements to tackle the challenging spread of AMR. Diversity and innovation are the mainstays to cope with the rapid evolution of AMR. The discovery and development of antibiotics must address resistance to old and novel antibiotics. Here, we review the history and challenges of antibiotics discovery and describe different innovative new leads mechanisms expected to replenish the pipeline, while maintaining a promising possibility to shift the chase and the race between the spread of AMR, preserving antibiotic effectiveness, and meeting innovative leads requirements.

Environmental Biofilms as Reservoirs for Antimicrobial Resistance

Characterizing the response of microbial communities to a range of antibiotic concentrations is one of the strategies used to understand the impact of antibiotic resistance. Many studies have described the occurrence and prevalence of antibiotic resistance in microbial communities from reservoirs such as hospitals, sewage, and farm feedlots, where bacteria are often exposed to high and/or constant concentrations of antibiotics. Outside of these sources, antibiotics generally occur at lower, sub-minimum inhibitory concentrations (sub-MICs). The constant exposure to low concentrations of antibiotics may serve as a chemical "cue" that drives development of antibiotic resistance. Low concentrations of antibiotics have not yet been broadly described in reservoirs outside of the aforementioned environments, nor is the transfer and dissemination of antibiotic resistant bacteria and genes within natural microbial communities fully understood. This review will thus focus on low antibiotic-concentration environmental reservoirs and mechanisms that are important in the dissemination of antibiotic resistance to help identify key knowledge gaps concerning the environmental resistome.

On the Verge of a Catastrophic Collapse? The Need for a Multi-Ecosystem Approach to Microbiome Studies

While the COVID-19 pandemic has led to increased focus on pathogenic microbes that cross the animal-human species barrier, calls to include non-pathogenic interactions in our perspective on public health are gaining traction in the academic community. Over generations, the diversity of the human gut microbiota is being challenged by external perturbations and reduced acquisition of symbiotic species throughout life. When such reduced diversity concerns not only the microbial species, but also the higher taxonomic levels and even the guild level, adequate compensation for possible losses may be lacking. Shifts from a high-abundance to a low-abundance state, known as a tipping point, may result in simultaneous shifts in covarying taxa and ultimately to a catastrophic collapse in which the ecosystem abruptly and possibly irreversibly shifts to an alternative state. Here, we propose that co-occurrence patterns within and between microbial communities across human, animal, soil, water, and other environmental domains should be studied in light of such critical transitions. Improved mechanistic understanding of factors that shape structure and function is needed to understand whether interventions can sustainably remodel disease-prone microbiota compositions to robust and resilient healthy microbiota. Prerequisites for a rational approach are a better understanding of the microbial interaction network, both within and inter-domain, as well as the identification of early warning signs for a catastrophic collapse, warranting a timely response for intervention. We should not forget that mutualism and pathogenicity are two sides of the same coin. Building upon the planetary health concept, we argue that microbiome research should include system level approaches to conserve ecosystem resilience. HIGHLIGHTS 1. Non-pathogenic interactions between ecosystems play a key role in maintaining health. 2. The human gut microbiome may be on the verge of a catastrophic collapse. 3. Research should identify keystone taxa and guilds that interconnect different domains. 4. We should not forget that mutualism and pathogenicity are two sides of the same coin.

How animal agriculture stakeholders define, perceive, and are impacted by antimicrobial resistance: challenging the Wellcome Trust's Reframing Resistance principles

Humans, animals, and the environment face a universal crisis: antimicrobial resistance (AR). Addressing AR and its multi-disciplinary causes across many sectors including in human and veterinary medicine remains underdeveloped. One barrier to AR efforts is an inconsistent process to incorporate the plenitude of stakeholders about what AR is and how to stifle its development and spread-especially stakeholders from the animal agriculture sector, one of the largest purchasers of antimicrobial drugs. In 2019, The Wellcome Trust released Reframing Resistance: How to communicate about antimicrobial resistance effectively (Reframing Resistance), which proposed the need to establish a consistent and harmonized messaging effort that describes the AR crisis and its global implications for health and wellbeing across all stakeholders. Yet, Reframing Resistance does not specifically engage the animal agriculture community. This study investigates the gap between two principles recommended by Reframing Resistance and animal agriculture stakeholders. For this analysis, the research group conducted 31 semi-structured interviews with a diverse group of United States animal agriculture stakeholders. Participants reported attitudes, beliefs, and practices about a variety of issues, including how they defined AR and what entities the AR crisis impacts most. Exploration of Reframing Resistance's Principle 2, "explain the fundamentals succinctly" and Principle 3, "emphasis that this is universal issue; it can affect anyone, including you" reveals disagreement in both the fundamentals of AR and consensus of "who" the AR crisis impacts. Principle 2 may do better to acknowledge that animal agriculture stakeholders espouse a complex array of perspectives that cannot be summed up in a single perspective or principle. As a primary tool to combat AR, behavior change must be accomplished first through outreach to stakeholder groups and understanding their perspectives.

Mapping the scientific knowledge of antimicrobial resistance in food-producing animals

Antimicrobial resistance (AMR) can be highlighted as one of the most significant health concerns among the last decades, for which antimicrobial drug use in food-producing animals has contributed as one of the major drivers. Food-producing animals are one of the most important and rapidly expanding commercial agricultural sectors worldwide but there is currently limited knowledge on the temporal and geographical distribution of scientific research on antimicrobial resistance in food-producing animals. We provide a global overview of the spatial and temporal trends of scientific knowledge on AMR in food-producing animals. Peer-reviewed papers of AMR on food-producing animals were retrieved from the Web of Science, systemized and dissected. The final validated dataset contained 1341 occurrences observations covering the 1957-2018 period. There has been a shift of research efforts, both geographically and temporally, emphasizing regional differences in food animal production and changing practices in the food production industry. It becomes evident that many regions have been poorly surveyed, wherein intensified sampling and testing efforts should be most valuable. This systematization of knowledge will be crucial in helping to determine how to optimally allocate limited resources available for AMR monitor and control, aiding in the prediction where the threat of new resistant infections will be greatest. AMR research in food-producing animals in developing countries is markedly growing, reflecting changes in food animals production systems but also posing a particularly significant threat, not only due to intensive animal production, but also exacerbated by poor sanitation. We highlight that the use of antibiotics in food producing animals is pervasive, calling for urgent action. These findings raise the possibility to finetuning key priorities on AMR global issues.

Resistant bugs, porous borders and ecologies of care in India

As social science scholarship has routinely illustrated, professional practice is rarely as contained or coherent as it is often imagined to be. The increasing emphasis on the rise of antimicrobial resistance (AMR) has drawn renewed attention to the interconnectedness of clinic, community, environment and planet, and how proposed 'solutions' to major problems such as AMR require a broad, cross-cutting lens. In this study, set in Hyderabad, India, we draw on a series of interviews with hospital-based clinicians completed during 2019 and early 2020, to unpack the multidimensional, ecological acceleration of AMR and the implications for everyday practice. Their accounts make visible how practice operates in relation to industrial economies, community vulnerabilities, and ecologies. This in turn highlights the problem of epistemic bordering, where 'sites' of AMR are targeted but are prone to leakage and transgressions. We propose an ecological approach to conceptualising antimicrobial practices with implications for AMR interventions being rolled out in the sub-continent and beyond.

Next-Generation Antimicrobial Resistance Surveillance System Based on the Internet-of-Things and Microfluidic Technique

Antimicrobial resistance (AMR) of foodborne pathogens is a global crisis in public health and economic growth. A real-time surveillance system is key to track the emergence of AMR bacteria and provides a comprehensive AMR trend from farm to fork. However, current AMR surveillance systems, which integrate results from multiple laboratories using the conventional broth microdilution method, are labor-intensive and time-consuming. To address these challenges, we present the internet of things (IoT), including colorimetric-based microfluidic sensors, a custom-built portable incubator, and machine learning algorithms, to monitor AMR trends in real time. As a top priority microbe that poses risks to human health, Campylobacter was selected as a bacterial model to demonstrate and validate the IoT-assisted AMR surveillance. Image classification with convolution neural network ResNet50 on the colorimetric sensors achieved an accuracy of 99.5% in classifying bacterial growth/inhibition patterns. The IoT was used to carry out a small-scale survey study, identifying eight Campylobacter isolates out of 35 chicken samples. A 96% agreement on Campylobacter AMR profiles was achieved between the results from the IoT and the conventional broth microdilution method. The data collected from the intelligent sensors were transmitted from local computers to a cloud server, facilitating real-time data collection and integration. A web browser was developed to demonstrate the spatial and temporal AMR trends to end-users. This rapid, cost-effective, and portable approach is able to monitor, assess, and mitigate the burden of bacterial AMR in the agri-food chain.

To Push or To Pull? In a Post-COVID World, Supporting and Incentivizing Antimicrobial Drug Development Must Become a Governmental Priority

The COVID-19 pandemic has refocused attention worldwide on the dangers of infectious diseases, in terms of both global health and the effects on the world economy. Even in high income countries, health systems have been found wanting in dealing with the new infectious agent. However, the even greater long-term danger of antimicrobial resistance in pathogenic bacteria and fungi is still under-appreciated, especially among the general public. Although antimicrobial drug development faces significant scientific challenges, the gravest challenge at the moment appears to be economic, where the lack of a viable market has led to a collapse in drug development pipelines. There is therefore a critical need for governments across the world to further incentivize the development of antimicrobials. Most incentive strategies over the past decade have focused on so-called "push" incentives that bridge the costs of antimicrobial research and development, but these have been insufficient for reviving the pipeline. In this Perspective, we analyze the current incentive strategies in place for antimicrobial drug development, and focus on "pull" incentives, which instead aim to improve revenue generation and thereby resolve the antimicrobial market failure challenge. We further analyze these incentives in a broader "One Health" context and stress the importance of developing and enforcing strict protocols to ensure appropriate manufacturing practices and responsible use. Our analysis reiterates the importance of international cooperation, coordination across antimicrobial research, and sustained funding in tackling this significant global challenge. A failure to invest wisely and continuously to incentivize antimicrobial pipelines will have catastrophic consequences for global health and wellbeing in the years to come.

Role of soil in the regulation of human and plant pathogens: soils' contributions to people

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

A Call for One Health in Medical Education: How the COVID-19 Pandemic Underscores the Need to Integrate Human, Animal, and Environmental Health

During the early stages of the COVID-19 pandemic in 2020, the first author, then a fourth-year student at Harvard Medical School, was enrolled in a One Health clinical experience at Zoo New England where he was introduced to a transdisciplinary approach to integrate human, animal, and ecosystem health. Seeing the vast impact of the pandemic and knowing its roots as a zoonotic disease, he realized this approach was critical to his medical education and for preparation against future novel infectious diseases. Zoonotic diseases have been emerging into human populations with increasing frequency, leading to public health emergencies such as Ebola, avian influenza, and SARS. The SARS-CoV-2 narrative, starting in bats and then mutating through an intermediate host into humans, is another striking example of the interconnectedness between human, animal, and ecosystem health that underlies these infections. Preventing future pandemics will require a transdisciplinary One Health approach, and physicians should be prepared to participate in these discussions while advocating for One Health initiatives for the benefit of their current and future patients. Integration of One Health education into medical school curricula will also prepare future physicians for other complex and urgently important health issues such as climate change, antimicrobial resistance, and the impact of biodiversity loss. As the consequences of the COVID-19 pandemic persist, education in One Health must become a priority; it is essential to break down the conventional disciplinary silos of human medicine, veterinary medicine, environmental health, public health, and the social sciences, so that future health crises can be prevented and mitigated collaboratively.

Antimicrobial resistance and interspecies gene transfer in Campylobacter coli and Campylobacter jejuni isolated from food animals, poultry processing, and retail meat in North Carolina, 2018-2019

The Center for Disease Control and Prevention identifies antimicrobial resistant (AMR) Campylobacter as a serious threat to U.S. public health due to high community burden, increased transmissibility, and limited treatability. The National Antimicrobial Resistance Monitoring System (NARMS) plays an important role in surveillance of AMR bacterial pathogens in humans, food animals and retail meats. This study investigated C. coli and C. jejuni from live food animals, poultry carcasses at production, and retail meat in North Carolina between January 2018-December 2019. Whole genome sequencing and bioinformatics were used for phenotypic and genotypic characterization to compare AMR profiles, virulence factors associated with Guillain-Barré Syndrome (GBS) (neuABC and cst-II or cst-III), and phylogenic linkage between 541 Campylobacter isolates (C. coli n = 343, C. jejuni n = 198). Overall, 90.4% (489/541) Campylobacter isolates tested positive for AMR genes, while 43% (233/541) carried resistance genes for three or more antibiotic classes and were classified molecularly multidrug resistant. AMR gene frequencies were highest against tetracyclines (64.3%), beta-lactams (63.6%), aminoglycosides (38.6%), macrolides (34.8%), quinolones (24.4%), lincosamides (13.5%), and streptothricins (5%). A total of 57.6% (114/198) C. jejuni carried GBS virulence factors, while three C. coli carried the C. jejuni-like lipooligosaccharide locus, neuABC and cst-II. Further evidence of C. coli and C. jejuni interspecies genomic exchange was observed in identical multilocus sequence typing, shared sequence type (ST) 7818 clonal complex 828, and identical species-indicator genes mapA, ceuE, and hipO. There was a significant increase in novel STs from 2018 to 2019 (2 in 2018 and 21 in 2019, p<0.002), illustrating variable Campylobacter genomes within food animal production. Introgression between C. coli and C. jejuni may aid pathogen adaption, lead to higher AMR and increase Campylobacter persistence in food processing. Future studies should further characterize interspecies gene transfer and evolutionary trends in food animal production to track evolving risks to public health.

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial genomes from whole genome sequencing play an important role in source tracking. We aimed to determine the limits of detection and classification of STECs by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL933). We determined the limit of STEC detection by qPCR to be 30 CFU/reaction, which is equivalent to 105 CFU/ml in the enrichment. By using Oxford Nanopore's EPI2ME WIMP workflow and de novo assembly with Flye followed by taxon classification with a k-mer analysis software (Kraken2), E. coli O157:H7 could be detected at 103 CFU/ml (68 reads) and a complete fragmented E. coli O157:H7 metagenome-assembled genome (MAG) was obtained at 105-108 CFU/ml. Using a custom script to extract the E. coli reads, a completely closed MAG was obtained at 107-108 CFU/ml and a complete, fragmented MAG was obtained at 105-106 CFU/ml. In silico virulence detection for E. coli MAGs for 105-108 CFU/ml showed that the virulotype was indistinguishable from the spiked E. coli O157:H7 strain. We further identified the bacterial species in the un-spiked enrichment, including antimicrobial resistance genes, which could have important implications to food safety. We propose this workflow provides proof of concept for faster detection and complete genomic characterization of STECs from a complex microbial sample compared to current reporting protocols and could be applied to determine the limit of detection and assembly of other foodborne bacterial pathogens.

Antimicrobial uses for livestock production in developing countries

Antimicrobial is an indispensable part of veterinary medicine used for the treatment and control of diseases as well as a growth promoter in livestock production. Frequent use of antimicrobials in veterinary practices may lead to the residue in animal originated products and creates some potential problems for human health. The presence of antimicrobial residues in animal originated foods may induce serious health problems such as allergic reaction, antimicrobial resistance (AMR), and lead to carcinogenic and mutagenic effects in the human body. The misuse or abuse of antibiotics in human medicine is thought to be a principal cause of AMR but some antimicrobial-resistant bacteria and their resistant genes originating from animals are also responsible for developing AMR. However, the residual effect of antimicrobials in feed and food products of animal origin is undeniable. In developing countries, the community is unaware of this residual effect due to lack of proper information about antibiotic usage, AMR surveillance, and residue monitoring system. It is imperative to reveal the current situation of antimicrobial use in livestock production and its impacts on public health. Moreover, the safety levels of animal feeds and food products of animal origin must be strictly monitored and public awareness should be developed against the indiscriminate use of antimicrobial in animal production. Therefore, the current review summarizes the literature on antimicrobial use in livestock production and its hazardous residual impacts on the human body in developing countries.

Antimicrobial Resistance Profiles of Diarrheagenic E. coli (DEC) and Salmonella Species Recovered from Diarrheal Patients in Selected Rural Communities of the Amathole District Municipality, Eastern Cape Province, South Africa

Purpose

The emergence of multidrug-resistant bacteria remains as one of the major impediments towards the prevention and treatment of microbial infections and continues to be a serious threat to medicine. Henceforth, this study aimed at elucidating the antimicrobial resistance profiles of diarrheagenic E. coli (DEC) and Salmonella species recovered from diarrheal patients in selected rural communities of the Amathole District Municipality (ADM), Eastern Cape Province, South Africa (SA).

Methods

The antimicrobial resistance profiles of diarrheagenic E. coli (DEC) and Salmonella isolates were evaluated using antimicrobial susceptibility tests and the relevant antimicrobial resistance factors were elucidated by the Polymerase Chain Reaction technique.

Results

A sum of 324 diarrheagenic E. coli (DEC) and 62 Salmonella isolates were recovered from diarrheal stool specimens collected amongst diarrheal patients admitted in medical facilities/health-care centers within the ADM in the Eastern Cape Province, South Africa. Multiple antimicrobial resistance index mean values of 0.7 and 0.5 for DEC and Salmonella isolates, respectively, were observed in this study, indicating that these isolates were from sources where antimicrobials were frequently used. The antimicrobial resistance factors ampC, bla_TEM, SulI and II, tet A and aadA were detected among antimicrobial-resistant DEC pathotypes and Salmonella isolates recovered in this study.

Conclusion

The occurrence of the multiple antimicrobial-resistant DEC and Salmonella isolates with the relevant antimicrobial resistance factors in this study suggests a portentous human health threat associated with diarrhea and a major deterrent in medicine.

The frequency of virulent genes and antimicrobial resistance patterns of diarrheagenic Escherichia coli isolated from stools of children presenting with diarrhea in a tertiary hospital in Abakaliki, Nigeria

Aim: This study was aimed to determine the virulent genes and antibiotic resistance patterns among circulating diarrheagenic Escherichia coli (DEC) pathotypes in a tertiary care health center in east of Nigeria. Materials and Methods: Diarrheal stool samples were obtained from 80 children under 5 years and E. coli was isolated and identified using standard biochemical and molecular methods. Multiplex polymerase chain reaction (PCR) was used to detect eight virulent genes of DEC. Disk diffusion method was used to determine the antibiotic susceptibility of DEC. Results: DEC infection was observed in 54 (68%) children among which ial gene for enteroinvasive E. coli (EIEC) (40% [n=22]) was commonly detected followed by eltA/eltB for enterotoxigenic E. coli (ETEC) (30% [n=16]), pCVD for enteroaggregative E. coli (EAEC) (20% [n=11]), and eaeA/bfpA for typical enteropathogenic E. coli (EPEC) (10% [n=5]). The DEC isolates phenotypically exhibited resistance for ampicillin (AMP) (44 [81%]), followed by ciprofloxacin (CIP)/ levofloxacin (LEV) (28 [52%]), cefoxitin (FOX) (11 [20%]), and amoxicillin-clavulanic acid (AMC) (6 [11%]). About 60% isolates of stable toxins-ETEC were resistant to AMC, CIP, and LEV while all the labile toxin-ETEC exhibited resistance to AMP. About 60% (n=6) resistance were seen in EAEC against ampicillin, AMC, FOX, CIP, and LEV. In EIEC, all the isolates (n=22) were resistant to AMP while 50% (n=11) were resistant to both CIP and LEV. All EPEC (n=5) were resistant to AMP, FOX, CIP, and LEV. Conclusion: High frequency of virulent ial and eltA/eltB genes for EIEC and ETEC, respectively, suggests that they are the primary etiological agents of diarrhea in children among DEC pathotypes. Resistance of DEC to more than two classes of antibiotics indicate possible emergence of multidrug resistance.

The Effectiveness of Clinical Pharmacist-Led Consultation in the Treatment of Infectious Diseases: A Prospective, Multicenter, Cohort Study

Background

Antimicrobial resistance (AMR) is a serious global health threat and leads to a huge challenge to infectious diseases (ID) treatment. To tackle AMR, regional ‘Antimicrobial Stewardship Programs’ (ASP) have been implemented in many countries. Due to insufficient clinical pharmacy resources, a major intervention mode of ASP in China is through clinical pharmacist-led consultation (CPC). The current study aims to prospectively evaluate this intervention and compare the effectiveness of CPC served by ID and non-ID clinical pharmacists.

Methods

We conducted a prospective and multicenter cohort study based on a regional registry database in 17 hospitals in Western China, including consecutive patients with ID between April 2017 and December 2019. Baseline characteristics including sex, age, liver and kidney function, comorbidity, infection severity were prospectively collected and recorded. The main exposure of interest was whether the attending physician adopted recommendations of the clinical pharmacist in the therapeutic scheme. The outcome was the infection effective response, assessed during day 3–7 after completing CPC. Multivariate analyses were performed by generalized linear mixed models.

Results

A total of 2,663 ID patients were included in the final analysis according to the predesigned inclusion and exclusion criteria. The number of patients whose treatment followed and did not follow the pharmacists’ suggestion was 2,529 and 134, respectively. CPC intervention could improve the ID patient prognosis in the context of other confounders controlled (Adjusted Odds ratio(AOR)=1.838, 95%Confidence Interval(CI)=[1.212, 2.786]), and the effectiveness of CPC served by ID and non-ID clinical pharmacists might be equivalent (AOR=0.958, 95%CI[0.740, 1.240]). Special consultation (AOR=1.832, 95%CI[1.106, 3.035]) and surgical treatment of infectious sites (AOR=1.380, 95%CI[1.039, 1.834]) had positive influences on the patient prognosis, while hypoalbuminemia (AOR=0.694, 95%CI[0.523, 0.921]), liver dysfunction (AOR=0.705, 95%CI[0.559, 0.889]), presence of high-risk factors (AOR=0.775, 95%CI[0.613, 0.980]), and increased infection severity (AOR=0.631, 95%CI[0.529, 0.753])were associated with a decrease in effective response rate, independently.

Conclusion

This study suggests that CPC is a promising pharmacist-led intervention to improve ID treatment, and it can achieve standardization among clinical pharmacists with different backgrounds by some measures. Policy/decision-makers should promote this intervention mode in developing countries or regions where there is an insufficient number of clinical pharmacists.

Bibliometric analysis of global research output on antimicrobial resistance in the environment (2000-2019)

Background

Antimicrobial resistance (AMR) is a global health threat that requires a "One Health" approach. Of the One Health triad, the environmental component is the most dynamic and most neglected. Therefore, the objective of the current study was to assess and analyze global research activity on AMR in the environment.

Methods

This was a bibliometric descriptive study of publications on AMR in the environment. Publications were retrieved using SciVerse Scopus for the study period from 2000 to 2019. The search query was developed using terms and phrases related to the topic. The retrieved publications were analyzed for specific bibliometric indicators including annual growth, citation analysis, key players, research output for each world regions, research themes, and occurrences of different drug classes of antimicrobials. Visualization maps including research collaboration were created using VOSviewer program. The Hirsch (h) index was used to assess scientific impact.

Results

There were 2611 research articles based on the implemented research query. The retrieved documents had an average of 22 citations per document and an h-index of 122. The annual number of publications showed a steep increase from 2011 to 2019. The major research themes in the field were (1) dissemination and abundance of antibiotic-resistant genes and (2) detection of bacterial strains or antibiotic residues in various environmental isolates. The bulk of the retrieved articles (n = 899; 34.4%) originated from the European region. China led with 598 (22.9%) documents. Four of the top 10 active institutions were in China. The top 10 active countries had relatively inadequate international research collaboration. The most commonly encountered antibiotic drug classes in the retrieved articles were penicillin/cephalosporin (n = 1152 occurrences). The most frequently encountered pathogen in the retrieved publications was E. coli (n = 666). The Science of the Total Environment journal was the most prolific journal with 139 (5.3%) publications.

Conclusion

Scientific literature on the AMR in the environment has witnessed a steep growth lately with a leading role of China and Chinese institutions. Data on AMR in the environment need to be collected from all world regions including the Eastern Mediterranean and African regions through research collaboration and funding of research in this field.

Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was bla_TEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.

Veterinary informatics: forging the future between veterinary medicine, human medicine, and One Health initiatives-a joint paper by the Association for Veterinary Informatics (AVI) and the CTSA One Health Alliance (COHA)

Objectives

This manuscript reviews the current state of veterinary medical electronic health records and the ability to aggregate and analyze large datasets from multiple organizations and clinics. We also review analytical techniques as well as research efforts into veterinary informatics with a focus on applications relevant to human and animal medicine. Our goal is to provide references and context for these resources so that researchers can identify resources of interest and translational opportunities to advance the field.

Methods and Results

This review covers various methods of veterinary informatics including natural language processing and machine learning techniques in brief and various ongoing and future projects. After detailing techniques and sources of data, we describe some of the challenges and opportunities within veterinary informatics as well as providing reviews of common One Health techniques and specific applications that affect both humans and animals.

Discussion

Current limitations in the field of veterinary informatics include limited sources of training data for developing machine learning and artificial intelligence algorithms, siloed data between academic institutions, corporate institutions, and many small private practices, and inconsistent data formats that make many integration problems difficult. Despite those limitations, there have been significant advancements in the field in the last few years and continued development of a few, key, large data resources that are available for interested clinicians and researchers. These real-world use cases and applications show current and significant future potential as veterinary informatics grows in importance. Veterinary informatics can forge new possibilities within veterinary medicine and between veterinary medicine, human medicine, and One Health initiatives.

Zoonosis: An Emerging Link to Antibiotic Resistance Under "One Health Approach"

Current scenario in communicable diseases has generated new era that identifies the "One health" approach to understand the sharing and management of etiological agents with its impact on ecosystem. Under this context the relevance of zoonotic diseases generates major concern. The indiscriminate and higher use of antibiotics in animal husbandry creates substantial pressure on the gut microbiome for development of resistance due to shorter generation time and high density. Thus, gut works as a bioreactor for the breeding of ARBs in this scenario and are continuously released in different niches. These ARBs transfer resistance genes among native flora through horizontal gene transfer events, vectors and quorum sensing. About 60% of infectious diseases in human are caused by zoonotic pathogens have potential to carry ARGs which could be transmitted to humans. The well documented zoonotic diseases are anthrax cause by Bacillus anthracis, bovine tuberculosis by Mycobacterium tuberculosis, brucellosis by Brucella abortus, and hemorrhagic colitis by Escherichia coli. Similarly, most of the antibiotics are not completely metabolized and released in unmetabolized forms which enters the food chain and affect various ecological niches through bioaccumulation. The persistence period of antibiotics ranges from < 1 to 3466 days in environment. The consequences of misusing the antibiotic in livestock and their fate in various ecological niches have been discussed in this review. Further the light sheds on antibiotics persistence and it biodegradation through different abiotic and biotic approaches in environment. The knowledge on personnel hygiene and strong surveillance system for zoonotic disease including ARBs transmission, prevention and control measures should be established to regulate the spread of AMR in the environment and subsequently to the human being through a food web.

The Clinical Pharmacist-Led Consultation for Infectious Diseases in Guizhou Province, China: A Survey Among Hospital Pharmacies

BACKGROUND

As antimicrobial resistance became an increasing threat to global public health, Clinical Pharmacist-led Consultation (CPC) for Infectious Diseases (ID) was developed in China. We conducted a survey among hospital pharmacies to investigate the present situation and potential determinants of CPC for ID in China's Guizhou Province.

METHODS

The study was conducted by sending the questionnaire to the directors of hospital pharmacy who were members of Guizhou Province Pharmaceutical Administration Collaboration Network (GPPACN) from April to May 2019. We implemented the Firth's logistic regression model to analyze the factors that influence the implementation of CPC. The acceptance rate of consultation suggestions (ARCS) and effective response rate after acceptance of pharmacists' suggestions (ERRAPS) were pooled by meta-analysis using a random effect model, respectively. A pairwise meta-analysis was performed to compare the effective response rate between patients whose treatment followed the pharmacists' suggestions and those whose treatment did not.

RESULTS

A total of 83 hospitals covering 9 regions in Guizhou Province were included in this survey. The results showed that 50 hospitals (60.24%) developed the CPC for ID. Staffing ID, respiratory, or general clinical pharmacist had a significantly positive effect on the implementation of CPC [adjusted odds ratios = 7.298, 95% CI (confidence interval): 2.232 to 23.858]. The pooled ARCS and ERRAPS for secondary hospitals were 97.59% (95% CI: 94.27 to 100.00%) and 88.36% (95% CI: 84.71 to 92.17%), respectively. Importantly, CPC improved the prognosis of ID patients [risk ratio (RR) = 6.49, 95% CI: 2.84 to 14.82] in these hospitals.

CONCLUSION

CPC adoption is gradually increasing among hospitals and will be a promising intervention for ID treatment at grassroots medical institutions in Guizhou Province. Training more clinical pharmacists to specialize in ID, respiratory, or general diseases might be the most practical measure to promote the development of CPC for ID.

An overview of colistin resistance, mobilized colistin resistance genes dissemination, global responses, and the alternatives to colistin: A review

Colistin, also known as polymyxin E, is an antimicrobial agent that is effective against a variety of Gram-negative bacilli, especially the Enterobacteriaceae family. Recently, the wide dissemination of colistin-resistance has brought strong attention to the scientific society because of its importance as the last resort for the treatment of carbapenem-resistant Enterobacteriaceae infections and its possible horizontal transmission. The mobilized colistin resistance (mcr) gene was identified as the gene responsible for unique colistin resistance. Indeed, despite many studies that have revealed a pan variation in the existence of this gene, not only for the mcr genes main group but also for its many subgroups, the problem is growing and worsening day after day. In this regard, this review paper is set to review the updated data that has been published up to the end of 2019 third quarter, especially when related to colistin resistance by the mcr genes. It will include the present status of colistin resistance worldwide, the mcr gene dissemination in different sectors, the discovery of the mcr variants, and the global plan to deal with the threat of antimicrobial resistance. In line with global awareness, and to stop antibiotic misuse and overuse, especially in agricultural animals, the study will further discuss in detail the latest alternatives to colistin use in animals, which may contribute to the elimination of inappropriate antibiotic use and to the help in preventing infections. This review will advance our understanding of colistin resistance, while supporting the efforts toward better stewardship, for the proper usage of antimicrobial drugs in humans, animals, and in the environment.

Resistance Reservoirs and Multi-Drug Resistance of Commensal Escherichia coli From Excreta and Manure Isolated in Broiler Houses With Different Flooring Designs

Carriage of resistant bacteria and spread of antimicrobial resistance (AMR) in the environment through animal manure pose a potential risk for transferring AMR from poultry and poultry products to the human population. Managing this risk is becoming one of the most important challenges in livestock farming. This study focused on monitoring the prevalence of multi-drug resistance (MDR) bacteria and development of AMR depending on flooring. In two experiments (2 × 15,000 birds), broilers were always divided in two different stables. In the control group, the entire floor pen was covered with litter material and in the experimental group, the flooring system was partly modified by installing elevated slat platforms equipped with water lines and feed pans. Over the whole fattening period, excreta and manure samples were taken (days 2, 22, and 32). In total, 828 commensal E. coli isolates were collected. The development and prevalence of resistance against four different antibiotic classes (quinolones, β-lactams, tetracyclines, and sulfonamides) were examined by using broth microdilution. At the end of the trials, the amount of manure per square metre was twice as high below the elevated platforms compared to the control group. Approximately 58% of E. coli isolates from excreta showed resistance against at least one antibacterial agent at day 2. During and at the end of the fattening period, resistant E. coli isolates at least against one of the four antibacterial agents were observed in excreta (46 and 46%, respectively), and manure samples (14 and 42%, respectively), despite the absence of antibacterial agent usage. In spite of less contact to manure in the experimental group, the prevalence of resistant E. coli isolates was significantly higher. Birds preferred the elevated areas which inevitably led to a local high population density. Animal-to-animal contact seems to be more important for spreading antimicrobial resistant bacteria than contact to the litter-excreta mixture. Therefore, attractive areas in poultry housing inducing crowding of animals might foster transmission of AMR. In poultry farming, enrichment is one of the most important aims for future systems. Consequently, there is a need for keeping birds not carrying resistant bacteria at the start of life.

Use of synthesized double-stranded gene fragments as qPCR standards for the quantification of antibiotic resistance genes

Pollution of various environmental matrices by antibiotic resistance genes (ARGs) has become a growing threat to human health. For the quantitative analysis of the presence of ARGs, there is a need for sensitive and robust qPCR assays which can detect various genes from different types of DNA extracts. Fourteen ARGs were selected as target genes in this study including: bla_TEM, bla_OXA-1 and bla_CTX-M coded for resistance to β-lactams; ermB for macrolides; tetA, tetG, tetM, tetQ, tetW and tetX for tetracyclines; sul I and sul II for sulfonamides; drfA1 and drfA12 d for trimethoprim; and integron gene intI 1 and intI 2. Chemically synthesized double-stranded gene fragments were modified using molecular biology methods and used as real-time PCR standards as well as to establish in-house qPCR assays. The ermB gene from a naturally occurring plasmid was used to compare the performance of qPCR assay with the chemically synthesized ermB. Additionally, environmental water, soil and faeces samples were used to validate the established qPCR assays. Importantly, the study proves the usefulness of rapidly synthesized oligonucleotides serving as qPCR standards for ARG analysis and provides comparable sensitivity and reliability to a traditional amplicon standard.

Evaluation of the Effectiveness of Clinical Pharmacists' Consultation in the Treatment of Infectious Diseases: A Single-Arm, Prospective Cohort Study

Background: With the implementation of Antimicrobial Stewardship Program, clinical pharmacists’ consultation (CPC) for infectious diseases (ID) is gradually adopted by many hospitals in China. We conducted a cohort study to evaluate the effectiveness of CPC in ID treatment on patient outcomes and potential determinants.

Methods: Based on a registry database, a prospective cohort study was conducted in Guizhou Provincial People’s Hospital. The main exposure factor was whether clinician adopted the suggestion from clinical pharmacist. The outcome was effective response rate (ERR) of ID patients. The variables associated with the outcome (e.g., age, gender, severity of infection, liver function, and kidney function) were also prospectively recorded. A multilevel model was performed to analyze the factors related to ERR.

Results: A total of 733 ID inpatients were included in the final analysis according to the predesigned inclusion and exclusion criteria. The proportion of clinical pharmacists’ suggestions adopted by clinicians and ERR were 88.13 and 69.03%, respectively. Significant data aggregation (P < 0.05) for individuals at the level of department was observed. According to the two-level variance component model, liver dysfunction (Adjusted Odds Ratio (AOR) = 0.649, 95%Credible Interval (CI): 0.432–0.976), severity of infection (AOR = 0.602, 95%CI: 0.464–0.781), and adopting the suggestion from pharmacist (AOR = 1.738, 95%CI: 1.028–2.940) had significant association with ERR.

Conclusion: Our study suggests that the effect of CPC on ID treatment is significant. The policy/decision makers or hospital managers should be cognizant of the critical value of clinical pharmacists in ID treatment.