Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture

Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods

Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.

Antibiogram signatures of Vibrio species recovered from surface waters in South Western districts of Uganda: Implications for environmental pollution and infection control

Reports of vibriosis and other related gastrointestinal infections have remained a recurring concern in the diverse global continent. The safety of drinking surface water and associated environmental pollution has remained a public health concern in limited resource sittings. Seen in this light, we report the antibiogram signatures of Vibrio species recovered from surface waters in the South-Western districts of Uganda. Surface water samples were collected for four months for Vibrio species isolation in four districts (Bushenyi-B, Mitooma-M, Rubirizi-R, and Sheema-S) using bacteria culture procedures, disc diffusion and Polymerase Chain Reaction (PCR) technique. Isolates were characterised, and the antibiotic fingerprints were determined using PCR and nine selected antibiotics in routine use. A total of 392 Vibrio species were confirmed from the various districts (B: 172, M: 79. R: 60, S: 81), with 163 (94.77%) resistant to colistin (polymixin), 145 (84.3%) resistant to cefotaxime, 127 (73.84%) resistant to azithromycin, and 33 (19.19%) resistant to chloramphenicol among Bushenyi isolates. A similar high resistance to fluoroquinolones and carbapenem antibiotics were also recorded in other districts of the study area. A complete multiple antibiotic resistance phenotype ((M)ARPs) to the applied antibiotics (A-CTX-CXM-MEM-ATH-K-TM-C-PB-NI-CIP-NA) were also recorded among some isolates, which produced multiple antibiotic resistance indexes of 1, suggesting a high-risk source of contamination due to the usage of several antibiotics. The PCR reports also confirm ampC gene {20 (10.9%)}, beta-lactamase TEM gene (blaTEM2), {30 (10%)} and dihydropteroate synthase type-1 and 11 gene (sul 1 & 11) {16 (8%)}. The results present an implicated environmental pollution problem and a potential concern to public health, therefore there is the need for control of such infectious bacteria and environmental pollution monitoring. Hence, it is recommended various approaches crucial to monitoring of emerging trends in drug resistance at the local and international levels.

Multidrug-Resistant Infections in the Developing World

Antimicrobials are essential in reducing morbidity and mortality from infectious diseases globally. However, due to the lack of effective surveillance measures and widespread overuse, there is an increasing threat to the effectiveness of antimicrobials. Although there is a global increase in antimicrobial resistance, low- and middle-income countries share a much higher burden. Antimicrobial stewardship efforts such as effective surveillance and reduction in overuse can help combat the increase in antimicrobial resistance.

Disparity in socio-economic status explains the pattern of self-medication of antibiotics in India: understanding from game-theoretic perspective

The emergence of antimicrobial resistance has raised great concern for public health in many lower-income countries including India. Socio-economic determinants like poverty, health expenditure and awareness accelerate this emergence by influencing individuals' attitudes and healthcare practices such as self-medication. This self-medication practice is highly prevalent in many countries, where antibiotics are available without prescriptions. Thus, complex dynamics of drug- resistance driven by economy, human behaviour, and disease epidemiology poses a serious threat to the community, which has been less emphasized in prior studies. Here, we formulate a game-theoretic model of human choices in self-medication integrating economic growth and disease transmission processes. We show that this adaptive behaviour emerges spontaneously in the population through a self-reinforcing process and continual feedback from the economy, resulting in the emergence of resistance as externalities of human choice under resource constraints situations. We identify that the disparity between social-optimum and individual interest in self-medication is primarily driven by the effectiveness of treatment, health awareness and public health interventions. Frequent multiple-peaks of resistant strains are also observed when individuals imitate others more readily and self-medication is more likely. Our model exemplifies that timely public health intervention for financial risk protection, and antibiotic stewardship policies can improve the epidemiological situation and prevent economic collapse.

Electronic information systems for One Health surveillance of antimicrobial resistance: a systematic scoping review

INTRODUCTION

Electronic information systems (EIS) that implement a 'One Health' approach by integrating antimicrobial resistance (AMR) data across the human, animal and environmental health sectors, have been identified as a global priority. However, evidence on the availability, technical capacities and effectiveness of such EIS is scarce.

METHODS

Through a qualitative synthesis of evidence, this systematic scoping review aims to: identify EIS for AMR surveillance that operate across human, animal and environmental health sectors; describe their technical characteristics and capabilities; and assess whether there is evidence for the effectiveness of the various EIS for AMR surveillance. Studies and reports between 1 January 2000 and 21 July 2021 from peer-reviewed and grey literature in the English language were included.

RESULTS

26 studies and reports were included in the final review, of which 27 EIS were described. None of the EIS integrated AMR data in a One Health approach across all three sectors. While there was a lack of evidence of thorough evaluations of the effectiveness of the identified EIS, several surveillance system effectiveness indicators were reported for most EIS. Standardised reporting of the effectiveness of EIS is recommended for future publications. The capabilities of the EIS varied in their technical design features, in terms of usability, data display tools and desired outputs. EIS that included interactive features, and geospatial maps are increasingly relevant for future trends in AMR data analytics.

CONCLUSION

No EIS for AMR surveillance was identified that was designed to integrate a broad range of AMR data from humans, animals and the environment, representing a major gap in global efforts to implement One Health approaches to address AMR.

Global surveillance of antimicrobial resistance and hypervirulence in Klebsiella pneumoniae from LMICs: An in-silico approach

The global emergence of antimicrobial resistance (AMR) among pathogens is a major public health crisis that might soon lead to a post-antibiotic era. Klebsiella pneumoniae, included in the World Health Organization list of critical priority pathogens, is an emerging threat to global health owing to the rapid rise of convergent AMR and hypervirulent strains. Comprehensive epidemiology of AMR-hypervirulent determinants in K. pneumoniae from Low-and Middle-Income Countries (LMICs) is still lacking. As part of rapid risk assessment, an in-silico approach was employed to characterize the AMR and hypervirulence determinants in K. pneumoniae from LMICs. Genomic data of 2432 K. pneumoniae strains were obtained from 33 LMICs representing 4 continents; Asia (n = 12), Africa (n = 18), N. America (n = 2) and Europe (n = 1). All the analysed strains were multiple-drug resistant and 13.6% of them were hypervirulent as well. The co-existence of antibiotic resistant genes conferring concomitant resistance towards life-saving drugs (carbapenems, colistin, fluoroquinolones and fosfomycin) were also observed among the strains, thereby challenging the efficacy of current treatment strategies. The emergence of convergent strains of K. pneumoniae carrying both multi-drug resistance and hypervirulence-associated genes in 12 LMICs is highlighted in this study. Asian region was identified as the major hotspot for convergent strains, especially being confined to 3 countries (India, Pakistan and Vietnam), further exacerbating the situation. This represents a major challenge to disease treatment and public health management in the LMICs. Regular surveillance for emergence of convergence and necessary interventions in the high-risk regions are strongly recommended.

Antimicrobial Consumption in Latin American Countries: First Steps of a Long Road Ahead

Background:

Irrational antimicrobial consumption (AMC) became one of the main global health problems in recent decades.

Objective:

In order to understand AMC in Latin-American Region, we performed the present research in 6 countries.

Methods:

Antimicrobial consumption (J01, A07A, P01AB groups) was registered in Argentina, Chile, Colombia, Costa Rica, Paraguay, and Peru. Source of information, AMC type, DDD (Defined Daily Doses), DID (DDD/1000 inhabitants/day), population were variables explored. Data was analyzed using the Global Antimicrobial Resistance and Use Surveillance System (GLASS) tool.

Results:

Source of information included data from global, public, and private sectors. Total AMC was highly variable (range 1.91-36.26 DID). Penicillin was the most consumed group in all countries except in Paraguay, while macrolides and lincosamides were ranked second. In terms of type of AMC according to the WHO-AWaRe classification, it was found that for certain groups like “Reserve,” there are similarities among all countries.

Conclusion and Relevance:

This paper shows the progress that 6 Latin-American countries made toward AMC surveillance. The study provides a standardized approach for building a national surveillance system for AMC data analysis. These steps will contribute to the inclusion of Latin-America among the regions of the world that have periodic, regular, and quality data of AMC.

Review on Multiple Facets of Drug Resistance: A Rising Challenge in the 21st Century

With the advancements of science, antibiotics have emerged as an amazing gift to the human and animal healthcare sectors for the treatment of bacterial infections and other diseases. However, the evolution of new bacterial strains, along with excessive use and reckless consumption of antibiotics have led to the unfolding of antibiotic resistances to an excessive level. Multidrug resistance is a potential threat worldwide, and is escalating at an extremely high rate. Information related to drug resistance, and its regulation and control are still very little. To interpret the onset of antibiotic resistances, investigation on molecular analysis of resistance genes, their distribution and mechanisms are urgently required. Fine-tuned research and resistance profile regarding ESKAPE pathogen is also necessary along with other multidrug resistant bacteria. In the present scenario, the interaction of bacterial infections with SARS-CoV-2 is also crucial. Tracking and in-silico analysis of various resistance mechanisms or gene/s are crucial for overcoming the problem, and thus, the maintenance of relevant databases and wise use of antibiotics should be promoted. Creating awareness of this critical situation among individuals at every level is important to strengthen the fight against this fast-growing calamity. The review aimed to provide detailed information on antibiotic resistance, its regulatory molecular mechanisms responsible for the resistance, and other relevant information. In this article, we tried to focus on the correlation between antimicrobial resistance and the COVID-19 pandemic. This study will help in developing new interventions, potential approaches, and strategies to handle the complexity of antibiotic resistance and prevent the incidences of life-threatening infections.

Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases

The number of bacterial genomes deposited each year in public databases is growing exponentially. However, efforts to use these genomes to track trends in antimicrobial resistance (AMR) have been limited thus far. We used 22,102 genomes from public databases to track AMR trends in nontyphoidal Salmonella in food animals in the United States. In 2018, genomes deposited in public databases carried genes conferring resistance, on average, to 2.08 antimicrobial classes in poultry, 1.74 in bovines, and 1.28 in swine. This represents a decline in AMR of over 70% compared to the levels in 2000 in bovines and swine, and an increase of 13% for poultry. Trends in resistance inferred from genomic data showed good agreement with U.S. phenotypic surveillance data (weighted mean absolute difference ± standard deviation, 5.86% ± 8.11%). In 2018, resistance to 3rd-generation cephalosporins in bovines, swine, and poultry decreased to 9.97% on average, whereas in quinolones and 4th-generation cephalosporins, resistance increased to 12.53% and 3.87%, respectively. This was concomitant with a decrease of bla_CMY-2 but an increase in bla_CTX-M-65 and gyrA D87Y (encoding a change of D to Y at position 87). Core genome single-nucleotide polymorphism (SNP) phylogenies show that resistance to these antimicrobial classes was predominantly associated with Salmonella enterica serovar Infantis and, to a lesser extent, S. enterica serovar Typhimurium and its monophasic variant I 4,[5],12:i:−, whereas quinolone resistance was also associated with S. enterica serovar Dublin. Between 2000 and 2018, trends in serovar prevalence showed a composition shift where S. Typhimurium decreased while S. Infantis increased. Our findings illustrate the growing potential of using genomes in public databases to track AMR in regions where sequencing capacities are currently expanding.

IMPORTANCE Next-generation sequencing has led to an exponential increase in the number of genomes deposited in public repositories. This growing volume of information presents opportunities to track the prevalence of genes conferring antimicrobial resistance (AMR), a growing threat to the health of humans and animals. Using 22,102 public genomes, we estimated that the prevalence of multidrug resistance (MDR) in the United States decreased in nontyphoidal Salmonella isolates recovered from bovines and swine between 2000 and 2018, whereas it increased in poultry. These trends are consistent with those detected by national surveillance systems that monitor resistance using phenotypic testing. However, using genomes, we identified that genes conferring resistance to critically important antimicrobials were associated with specific MDR serovars that could be the focus for future interventions. Our analysis illustrates the growing potential of public repositories to monitor AMR trends and shows that similar efforts could soon be carried out in other regions where genomic surveillance is increasing.

Challenges to Antimicrobial Stewardship in the Countries of the Arab League: Concerns of Worsening Resistance during the COVID-19 Pandemic and Proposed Solutions

The COVID-19 pandemic is expected to worsen the global problem of antimicrobial resistance (AMR). There is a heightened interest in understanding this effect and to develop antimicrobial stewardship (AMS) interventions accordingly to curb this threat. Our paper aims to evaluate the potential magnitude of COVID-19 on AMR and AMS with a focus on the countries of the Arab league, given the social, political, and economic environments. We also evaluate obstacles in applying the rational use of antibiotics, monitoring resistance trends in the midst of the pandemic, and evaluating the impact of the economic crisis in some countries. We aim to raise awareness about the potential effects of antibiotic overuse during the pandemic and to propose practical approaches to tackle this issue.

Phages for Africa: The Potential Benefit and Challenges of Phage Therapy for the Livestock Sector in Sub-Saharan Africa

One of the world’s fastest-growing human populations is in Sub-Saharan Africa (SSA), accounting for more than 950 million people, which is approximately 13% of the global population. Livestock farming is vital to SSA as a source of food supply, employment, and income. With this population increase, meeting this demand and the choice for a greater income and dietary options come at a cost and lead to the spread of zoonotic diseases to humans. To control these diseases, farmers have opted to rely heavily on antibiotics more often to prevent disease than for treatment. The constant use of antibiotics causes a selective pressure to build resistant bacteria resulting in the emergence and spread of multi-drug resistant (MDR) organisms in the environment. This necessitates the use of alternatives such as bacteriophages in curbing zoonotic pathogens. This review covers the underlying problems of antibiotic use and resistance associated with livestock farming in SSA, bacteriophages as a suitable alternative, what attributes contribute to making bacteriophages potentially valuable for SSA and recent research on bacteriophages in Africa. Furthermore, other topics discussed include the creation of phage biobanks and the challenges facing this kind of advancement, and the regulatory aspects of phage development in SSA with a focus on Kenya.

Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance

Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.