Antimicrobial use and antimicrobial resistance: a population perspective

Association of infrastructure and operations with antibiotic resistance potential in the dairy environment in India

The dairy industry in developing countries is often associated with inappropriate use of antibiotics and the subsequent contamination of the environment with co-selectors of antibiotic resistance. However, the specific factors in dairy farm environments that influence antibiotic resistance levels and the subsequent exposure risks to farm workers are unknown. We examined the link between the infrastructure and operations of the dairy farm and the antibiotic resistance potential in India, which is the highest producer and consumer of dairy products globally. We sampled sixteen dairy farms in the Dehradun district, India, that varied in their herd size, infrastructure, and operational features during winter, summer, and monsoon. We collected samples of dung, manure, wastewater, manure-amended, and control soil from these farms. We quantified six antibiotic resistance genes (ARGs) (sul1, sul2, parC, mcr5, ermF, and tetW), an integron integrase gene cassette (intI1), and 16S rRNA gene copies as an indicator for total bacterial count. We observed that the infrastructure and the operations of the dairy farms were significantly associated with antibiotic resistance potential in the dairy environment. For example, with increased ventilation and exposure to external weather, the levels of sul2 (x͂=10-1.63) and parC (x͂=10-4.24) in manure increased. When farmers administered antibiotics without veterinary consultation, the relative levels of intI1 (x͂=10-2.36), sul2 (x͂=10-1.58), and tetW (x͂=10-3.04) in manure were lower than the cases where professional advice was sought. Small-scale farms had lower relative ARG levels than medium- and large-scale farms, except for mcr5 (x͂=10-3.98) in wastewater. In different sample types, the relative ARG levels trended as manure-amended soil (x͂=10-2.34) > wastewater (x͂=10-2.90)> manure (x͂=10-3.39)> dung (x͂=10-2.54). ARGs correlated with the marker for horizontal gene transfer, intI1, which exacerbates overall antibiotic resistance levels. Exposure assessment showed that the agriculture farm workers working in manure-amended agriculture farms are exposed to higher antibiotic resistance potential than dairy farm workers, who manually handle dung. Our study showed that the link between the dairy infrastructure (ventilation and floor type) and operations (scale of operation and veterinary consultation) and the antibiotic resistance potential in the dairy farm environment was statistically significant. This knowledge paves the way for designing interventions that can minimize the antibiotic resistance potential on dairy farms and in affected environments and thus reduce the public health burden of antibiotic-resistant infections in the dairy industry and dairy workers in India.

Characterizing antimicrobial selection pressure on resistance across four major causes of infections: Insights from the US Veterans Affairs Healthcare System, 2007-2021

Background There is conflicting evidence of the role of antibiotic in driving antimicrobial resistance. Existing studies asses use-resistance relationships typically only for few pathogens, for narrow time window, or only in one geographic space, and/or for few pathogen-antibiotic combinations and often only one pathogen and antibiotic (class) at a time. No systematic evidence of whether some antibiotics are more efficient at selecting for resistance than others. Here, we tested the hypothesis that each antibiotic class exerts selection for the antimicrobial susceptibility patterns resistant to it, using data on four major pathogens in the US Veterans Affairs Healthcare System. Methods We analysed clinical microbiology data from electronic health records from patients admitted to 138 Veterans Affairs Medical Centers with acute care wards across the USA from Feb 1, 2007, to Dec 31, 2021. We used clinical isolates classified as hospital-onset Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. We quantified inpatient antibiotic prescribing as days of therapy (DOT) per 1000 patient-days and the antibiogram incidence as the number of incident isolates with that antibiogram per 1,000 admissions. We performed time trend analyses for antibiogram incidence and antibiotic prescribing using generalized estimating equations and reported average annual percentage changes (AAPC). We performed hierarchical multinomial logistic regressions to estimate the effect of inpatient facility-level prescribing on antimicrobial susceptibility patterns. We included calendar time, facility characteristics, and community prevalence of a respective antibiogram as covariates to account for ecological confounding. Results From 2007 to 2021, the incidence of hospital-onset isolates declined for all four pathogens except E. coli isolates resistant to third-generation cephalosporins (3GC) and co-resistant to either fluoroquinolones or beta-lactam/beta-lactamase inhibitors (BL/BLI), or both. Over the same period, antibiotic prescribing generally remained stable or decreased, with the notable exception of 3GC prescribing, which increased from 2007 to 2019 (AAPC: 2.4%, 95% CI: 1.3%-3.5%). In general, higher facility-level use of a given antibiotic was associated with increased resistance to that antibiotic, although exceptions were observed. Fluoroquinolones consistently selected for resistance across the four pathogens. In S aureus, each additional 14-day course of fluoroquinolones (per 1,000 patient-days) was linked to a 5.9% (95% CI: 0.8%-11.2%) increase in the odds of isolating a fluoroquinolone-resistant, macrolide-susceptible, methicillin-resistant phenotype. Anti-staphylococcal beta-lactams were not associated with methicillin-resistant S aureus. In Enterobacterales, each additional 14-day course of 3GC treatment increased the odds of isolating 3GC- and BL/BLI-resistant E coli by 7.4% (95% CI: 1.8%-13.4%) and K pneumoniae by 4.1% (95% CI: 0.0%-8.7%). For P aeruginosa, antipseudomonal carbapenem use selected for carbapenem-resistant isolates; the largest effect was observed in carbapenem-resistant phenotypes susceptible to fluoroquinolones and 3GC, where each additional 14-day course increased the odds by 22.6% (95% CI: 13.4%-32.7%). Interpretation Our findings demonstrate that fluoroquinolones play a key role in selecting for resistance across multiple pathogens, underscoring their significance as a driver of AMR. Although these results highlight the importance of cautious fluoroquinolone use and targeted stewardship strategies, we also observed that reductions in fluoroquinolone prescribing were offset by increased 3GC prescribing and co-resistance in E coli. Consequently, effective AMR mitigation requires comprehensive stewardship approaches that address multiple antibiotic classes in tandem rather than in isolation.

Brief antibiotic use drives human gut bacteria towards low-cost resistance

Understanding the relationship between antibiotic use and the evolution of antimicrobial resistance is vital for effective antibiotic stewardship. Yet, animal models and in vitro experiments poorly replicate real-world conditions1. To explain how resistance evolves in vivo, we exposed 60 human participants to ciprofloxacin and used longitudinal stool samples and a new computational method to assemble the genomes of 5,665 populations of commensal bacterial species within participants. Analysis of 2.3 million polymorphic sequence variants revealed 513 populations that underwent selective sweeps. We found convergent evolution focused on DNA gyrase and evidence of dispersed selective pressure at other genomic loci. Roughly 10% of susceptible bacterial populations evolved towards resistance through sweeps that involved substitutions at a specific amino acid in gyrase. The evolution of gyrase was associated with large populations that decreased in relative abundance during exposure. Sweeps persisted for more than 10 weeks in most cases and were not projected to revert within a year. Targeted amplification showed that gyrase mutations arose de novo within the participants and exhibited no measurable fitness cost. These findings revealed that brief ciprofloxacin exposure drives the evolution of resistance in gut commensals, with mutations persisting long after exposure. This study underscores the capacity of the human gut to promote the evolution of resistance and identifies key genomic and ecological factors that shape bacterial adaptation in vivo.

Standard versus Pre-emptive Antibiotic Treatment to Reduce the Rate of Infectious Outcomes after Whipple resection (SPARROW): a study protocol for a multicentre, open-label, randomised controlled trial

BACKGROUND

Consensus and evidence on the impact of pre-emptive antibiotic treatment after pancreatoduodenectomy is lacking, which is reflected by contradictory recommendations in (inter)national guidelines and current clinical practice. Pre-emptive antibiotic treatment may reduce the risk of abdominal surgical site infections in patients with a high risk of contaminated bile undergoing pancreatoduodenectomy. This pertains mostly patients with preoperative biliary drainage or an ampullary malignancy. The SPARROW trial will evaluate the effect of pre-emptive antibiotic treatment in patients with preoperative biliary drainage or an ampullary malignancy undergoing pancreatoduodenectomy.

METHODS

The SPARROW trial is a multicentre, open-label, randomised controlled trial evaluating the effect of pre-emptive antibiotic treatment in patients with a high risk of contaminated bile undergoing pancreatoduodenectomy. A total of 366 evaluable patients will be included in twelve centres in the Netherlands. Patients will be randomly allocated to either the perioperative antibiotic prophylaxis and pre-emptive antibiotic treatment (intervention) arm and the perioperative antibiotic prophylaxis (control) arm. In both study arms, the perioperative antibiotic prophylaxis consists of cefazolin, metronidazole and a single-dose of gentamicin, which is discontinued after surgery. In the pre-emptive antibiotic treatment arm, an additional antibiotic course of 5 days of cefuroxime and metronidazole is started postoperatively. The primary outcome is a clinically relevant organ/space surgical site infection (OSI) up to 90 days after surgery. Secondary outcomes include other clinically relevant complications (such as isolated OSI, superficial incisional surgical site infections, postoperative pancreatic fistula, ICU admission, readmission, and in-hospital and 90-day mortality), use of therapeutic antibiotics, and concordance between perioperative obtained bile cultures and cultures obtained from infectious complications.

DISCUSSION

The SPARROW trial will provide evidence on the effect of pre-emptive antibiotic treatment in patients with a high risk of contaminated bile undergoing pancreatoduodenectomy to provide recommendations for an improved and standardised antimicrobial policy.

TRIAL REGISTRATION

ClinicalTrials.gov NCT0578431. Registered on March 23, 2023.

Comparing visual and automated urine dipstick analysis in a general practice population

INTRODUCTION

Urinary symptoms constitute the primary reason for female patients to consult their general practitioner. The urinary dipstick test serves as a cornerstone for diagnosing urinary tract infections (UTIs), yet traditional visual interpretation may be subject to variability. Automated devices for dipstick urinalysis are routinely used as alternatives, yet the evidence regarding their accuracy remains limited. Therefore we aimed to compare concordance between visual and automated urinary dipstick interpretation and determine their test characteristics for the prediction of bacteriuria.

MATERIAL AND METHODS

We conducted a prospective validation study including urine samples originating from adult patients in general practice that were sent to the Maastricht Medical Centre + for urinary culture. Urinary dipstick tests were performed on each sample, which were interpreted visually and automatically. We calculated Cohen's κ and percentage agreement and used 2 × 2 tables to calculate test characteristics.

RESULTS

We included 302 urine samples. Visual and automated analysis showed almost perfect agreement (κ = 0.82 and κ = 0.86, respectively) for both nitrite and leukocyte esterase, but moderate agreement for erythrocytes (κ = 0.51). Interpretation of clinically relevant (nitrite and/or leukocyte esterase positive) samples showed almost perfect agreement (κ = 0.88). Urinary dipsticks show similar test characteristics with urinary culture as gold standard, with sensitivities of 0.92 and 0.91 and specificities of 0.37 and 0.41 for visual and automated interpretation respectively.

CONCLUSION

Automated and visual dipstick analysis show near perfect agreement and perform similarly in predicting bacteriuria. However, automated analysis requires maintenance and occasionally measurement errors can occur.

Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data

Pathogenic bacteria are a major threat to patient health in hospitals. Here we leverage electronic health records from a major New York City hospital system collected during 2020-2021 to support simulation inference of nosocomial transmission and pathogenic bacteria detection using an agent-based model (ABM). The ABM uses these data to inform simulation of importation from the community, nosocomial transmission, and patient spontaneous decolonization of bacteria. We additionally use patient clinical culture results to inform an observational model of detection of the pathogenic bacteria. The model is coupled with a Bayesian inference algorithm, an iterated ensemble adjustment Kalman filter, to estimate the likelihood of detection upon testing and nosocomial transmission rates. We evaluate parameter identifiability for this model-inference system and find that the system is able to estimate modelled nosocomial transmission and effective sensitivity upon clinical culture testing. We apply the framework to estimate both quantities for seven prevalent bacterial pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus (both sensitive, MSSA, and resistant, MRSA, phenotypes), Enterococcus faecium and Enterococcus faecalis. We estimate that nosocomial transmission for E. coli is negligible. While bacterial pathogens have different importation rates, nosocomial transmission rates were similar among organisms, except E. coli. We also find that estimated likelihoods of detection are similar for all pathogens. This work highlights how fine-scale patient data can support inference of the epidemiological properties of micro-organisms and how hospital traffic and patient contact determine epidemiological features. Evaluation of the transmission potential for different pathogens could ultimately support the development of hospital control measures, as well as the design of surveillance strategies.

Penicillin allergy as an instrumental variable for estimating antibiotic effects on resistance

Antibiotic resistance is influenced by prior antibiotic use, but precise causal estimates are limited. This study uses penicillin allergy as an instrumental variable (IV) to estimate the causal effect of antibiotics on resistance. A retrospective cohort of 36,351 individuals with E. coli positive urine cultures and prior outpatient antibiotic use, with outcomes assessed up to one year post-exposure, was analyzed using data from Maccabi Healthcare Services (MHS), the second-largest non-profit health fund in Israel. IV methods estimated risk differences (RD) and numbers needed to harm (NNH) for penicillin versus other antibiotics. The RD for resistance was 11.4% (95% CI: 7.6%, 15.4%) for amoxicillin/clavulanic acid, 14.1% (95% CI: 9.0%, 19.4%) for ampicillin, and 0.8% (95% CI: 0.2%, 1.4%) for piperacillin/tazobactam, with NNHs of 8.8, 7.1, and 122.0, respectively. Risks declined over time since exposure. Gentamicin, used as a negative control, showed no effect (95% CI: -2.4%, 1.8%). When directly comparing penicillin and quinolone effects on their respective AMR, penicillin use within 180 days increased resistance to amoxicillin/clavulanic acid by an RD of 17.8% (95% CI: 2.1%, 35.2%; NNH: 5.6), while quinolones raised ciprofloxacin resistance by 43.9% (95% CI: 29.9%, 59.4%; NNH: 2.3). These findings provide quantitative evidence of the impact of prior penicillin use on resistance, with implications for clinical practice and prescription policies.

Assessment of Spillover of Antimicrobial Resistance to Untreated Children 7-12 Years Old After Mass Drug Administration of Azithromycin for Child Survival in Niger: A Secondary Analysis of the MORDOR Cluster-Randomized Trial

BACKGROUND

The risk of antibiotic resistance is complicated by the potential for spillover effects from one treated population to another. Azithromycin mass drug administration programs report higher rates of antibiotic resistance among treatment arms in targeted groups. This study aimed to understand the risk of spillover of antibiotic resistance to nontarget groups in these programs.

METHODS

Data were used from a cluster-randomized trial comparing the effects of biannual azithromycin and placebo distribution to children 1-59 months old on child mortality rates. Nasopharyngeal samples from untreated children 7-12 years old were tested for genetic determinants of macrolide resistance (primary outcome) and resistance to other antibiotic classes (secondary outcomes). Linear regression was used to compare the community-level mean difference in prevalence by arm at the 24-month time point, adjusting for baseline prevalence.

RESULTS

A total of 1103 children 7-12 years old in 30 communities were included in the analysis (15 azithromycin, 15 placebo). The adjusted mean differences in the prevalence of resistance determinants for macrolides, β-lactams, and tetracyclines were 3.4% (95% confidence interval, -4.1% to 10.8%; P = .37), -1.2% (-7.9% to 5.5%; P = .72), and -3.3% (-9.5% to 2.8%; P = .61), respectively.

CONCLUSIONS

We were unable to demonstrate a statistically significant increase in macrolide resistance determinants in untreated groups in an azithromycin mass drug administration program. While the result might be consistent with a small spillover effect, this study was not powered to detect such a small difference. Larger studies are warranted to better quantify the potential for spillover effects within these programs.

Versatile and Portable Cas12a-mediated Detection of Antibiotic Resistance Markers

Antimicrobial resistance (AMR) is a global public health problem particularly accentuated in low- and middle-income countries, largely due to a lack of access to sanitation and hygiene, lack of awareness and knowledge, and the inadequacy of molecular laboratories for timely and accurate surveillance programs. This study introduces a versatile molecular detection toolbox (C12a) for antibiotic resistance gene markers using CRISPR/Cas12a coupled to PCR. Our toolbox can detect less than 3×10-7 ng of DNA (100 attoMolar) or 102 CFU/mL. High concordance was observed when comparing the C12a toolbox with sequenced genomes and antibiotic susceptibility tests for the blaCTX-M-15 and floR antibiotic resistance genes (ARGs), which confer resistance to cefotaxime and other β-lactams, and amphenicols, respectively. C12aINT, designed to detect the Integrase 1 gene, confirmed a high prevalence of the integrase/integron system in E. coli containing multiple ARGs. The C12a toolbox was tested across a wide range of laboratory infrastructure including a portable setup. When combined with lateral flow assays (LFA), C12a exhibited competitive performance, making it a promising solution for on-site ARG detection. Altogether, this work presents a collection of molecular tools (primers, crRNAs, probes) and validated assays for rapid, versatile, and portable detection of antibiotic resistance markers, highlighting the C12a toolbox potential for applications in surveillance and ARG identification in clinical and environmental settings.

From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance

Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.

Predicting future hospital antimicrobial resistance prevalence using machine learning

BACKGROUND

Predicting antimicrobial resistance (AMR), a top global health threat, nationwide at an aggregate hospital level could help target interventions. Using machine learning, we exploit historical AMR and antimicrobial usage to predict future AMR.

METHODS

Antimicrobial use and AMR prevalence in bloodstream infections in hospitals in England were obtained per hospital group (Trust) and financial year (FY, April-March) for 22 pathogen-antibiotic combinations (FY2016-2017 to FY2021-2022). Extreme Gradient Boosting (XGBoost) model predictions were compared to the previous value taken forwards, the difference between the previous two years taken forwards and linear trend forecasting (LTF). XGBoost feature importances were calculated to aid interpretability.

RESULTS

Here we show that XGBoost models achieve the best predictive performance. Relatively limited year-to-year variability in AMR prevalence within Trust-pathogen-antibiotic combinations means previous value taken forwards also achieves a low mean absolute error (MAE), similar to or slightly higher than XGBoost. Using the difference between the previous two years taken forward or LTF performs consistently worse. XGBoost considerably outperforms all other methods in Trusts with a larger change in AMR prevalence from FY2020-2021 (last training year) to FY2021-2022 (held-out test set). Feature importance values indicate that besides historical resistance to the same pathogen-antibiotic combination as the outcome, complex relationships between resistance in different pathogens to the same antibiotic/antibiotic class and usage are exploited for predictions. These are generally among the top ten features ranked according to their mean absolute SHAP values.

CONCLUSIONS

Year-to-year resistance has generally changed little within Trust-pathogen-antibiotic combinations. In those with larger changes, XGBoost models can improve predictions, enabling informed decisions, efficient resource allocation, and targeted interventions.

The epidemiology of antibiotic-resistant clinical pathogens in Uganda

Background

Antibiotic resistance (ABR) is a global challenge, and its control depends on robust evidence primarily derived from surveillance systems.

Methods

We utilised a national surveillance data set to demonstrate how such evidence can be systematically generated. In doing so, we characterised the ABR profiles of priority clinical pathogens, identified associated factors, and drew inferences on antibiotic usage in Uganda.

Results

Of the 12 262 samples collected between 2019-21, we analysed 9033 with complete metadata. ABR was steadily increasing at a rate of 0.5% per year, with a surge in 2021 and the highest and lowest levels of penicillin and carbapenems detected in the northern (odds ratio (OR) = 2.26; P < 0.001) and the northeast (OR = 0.28; P < 0.001) regions of Uganda respectively. ABR was commonly observed with Escherichia coli (OR = 1.18; P < 0.001) and Klebsiella pneumoniae (OR = 1.25; P < 0.001) among older and male patients (61-70 years old) (OR = 1.88; P = 0.005). Multi-drug resistance (MDR) and ABR were disproportionately higher among bloodstream infections than respiratory tract infections and urinary tract infections, often caused by Acinetobacter baumannii. Co-occurrence of ABR suggests that cephalosporins such as ceftriaxone are in high use all over Uganda.

Conclusions

ABR is indeed a silent pandemic, and our results suggest it is increasing at 0.5% per year, with a notable surge in 2021 likely due to coronavirus disease 2019 (COVID-19). Of concern, ABR and MDR are mainly associated with bloodstream and surgical wound infections, with a gender and age dimension. However, it is encouraging that carbapenem resistance remains relatively low. Such evidence is critical for contextualising the implementation and evaluation of national action plans.

Electrically polarized nanoscale surfaces generate reactive oxygenated and chlorinated species for deactivation of microorganisms

Because of the decreasing supply of new antibiotics, recent outbreaks of infectious diseases, and the emergence of antibiotic-resistant microorganisms, it is imperative to develop new effective strategies for deactivating a broad spectrum of microorganisms and viruses. We have implemented electrically polarized nanoscale metallic (ENM) coatings that deactivate a wide range of microorganisms including Gram-negative and Gram-positive bacteria with greater than 6-log reduction in less than 10 minutes of treatment. The electrically polarized devices were also effective in deactivating lentivirus and Candida albicans. The key to the high deactivation effectiveness of ENM devices is electrochemical production of micromolar cuprous ions, which mediated reduction of oxygen to hydrogen peroxide. Formation of highly damaging species, hydroxyl radicals and hypochlorous acid, from hydrogen peroxide contributed to antimicrobial properties of the ENM devices. The electric polarization of nanoscale coatings represents an unconventional tool for deactivating a broad spectrum of microorganisms through in situ production of reactive oxygenated and chlorinated species.

Long-term antibiotic exposure landscapes and resistant Escherichia coli colonization in a densely populated setting

Antibiotic exposure is associated with resistant bacterial colonization, but this relationship can be obscured in community settings owing to horizontal bacterial transmission and broad distributions. Locality-level exposure estimates considering inhabitants' length of stay, exposure history, and exposure conditions of areas nearby could clarify these relationships. We used prescription data filled during 2010-2015 for 23 antibiotic types for members of georeferenced households in a population-based infectious disease surveillance platform. For each antibiotic and locality, we generated exposure estimates, expressed in defined daily doses (DDD) per 1000 inhabitant days of observation (IDO). We also estimated relevant environmental parameters, such as the distance of each locality to water, sanitation, and other amenities. We used data on ampicillin, ceftazidime, and trimethoprim-and-sulfamethoxazole resistant Escherichia coli colonization from stool cultures of asymptomatic individuals in randomly selected households. We tested exposure-colonization associations using permutation analysis of variance and logistic generalized linear mixed-effect models. Overall, exposure was highest for trimethoprim-sulfamethoxazole (1.8 DDD per 1000 IDO), followed by amoxicillin (0.7 DDD per 1000 IDO). Of 1,386 unique household samples from 195 locations tested between September 2015 and January 2016, 90%, 85% and 4% were colonized with E. coli resistant to trimethoprim and sulfamethoxazole, ampicillin, and ceftazidime, respectively. Ceftazidime-resistant E. coli colonization was common in areas with increased trimethoprim-sulfamethoxazole, cloxacillin, and erythromycin exposure. No association with any of the physical environmental variables was observed. We did not detect relationships between distribution patterns of ampicillin or trimethoprim-and-sulfamethoxazole resistant E. coli colonization and the risk factors assessed. Appropriate temporal and spatial scaling of raw antibiotic exposure data to account for evolution and ecological contexts of antibiotic resistance could clarify exposure-colonization relationships in community settings and inform community stewardship program.

Burden of bacterial antimicrobial resistance in low-income and middle-income countries avertible by existing interventions: an evidence review and modelling analysis

National action plans enumerate many interventions as potential strategies to reduce the burden of bacterial antimicrobial resistance (AMR). However, knowledge of the benefits achievable by specific approaches is needed to inform policy making, especially in low-income and middle-income countries (LMICs) with substantial AMR burden and low health-care system capacity. In a modelling analysis, we estimated that improving infection prevention and control programmes in LMIC health-care settings could prevent at least 337 000 (95% CI 250 200-465 200) AMR-associated deaths annually. Ensuring universal access to high-quality water, sanitation, and hygiene services would prevent 247 800 (160 000-337 800) AMR-associated deaths and paediatric vaccines 181 500 (153 400-206 800) AMR-associated deaths, from both direct prevention of resistant infections and reductions in antibiotic consumption. These estimates translate to prevention of 7·8% (5·6-11·0) of all AMR-associated mortality in LMICs by infection prevention and control, 5·7% (3·7-8·0) by water, sanitation, and hygiene, and 4·2% (3·4-5·1) by vaccination interventions. Despite the continuing need for research and innovation to overcome limitations of existing approaches, our findings indicate that reducing global AMR burden by 10% by the year 2030 is achievable with existing interventions. Our results should guide investments in public health interventions with the greatest potential to reduce AMR burden.

Prolonged mass azithromycin distributions and macrolide resistance determinants among preschool children in Niger: A sub-study of a cluster-randomized trial (MORDOR)

BACKGROUND

Randomized controlled trials found that twice-yearly mass azithromycin administration (MDA) reduces childhood mortality, presumably by reducing infection burden. World Health Organization (WHO) issued conditional guidelines for mass azithromycin administration in high-mortality settings in sub-Saharan Africa given concerns for antibiotic resistance. While prolonged twice-yearly MDA has been shown to increase antibiotic resistance in small randomized controlled trials, the objective of this study was to determine if macrolide and non-macrolide resistance in the gut increases with the duration of azithromycin MDA in a larger setting.

METHODS AND FINDINGS

The Macrolide Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) study was conducted in Niger from December 2014 to June 2020. It was a cluster-randomized trial of azithromycin (A) versus placebo (P) aimed at evaluating childhood mortality. This is a sub-study in the MORDOR trial to track changes in antibiotic resistance after prolonged azithromycin MDA. A total of 594 communities were eligible. Children 1 to 59 months in 163 randomly chosen communities were eligible to receive treatment and included in resistance monitoring. Participants, staff, and investigators were masked to treatment allocation. At the conclusion of MORDOR Phase I, by design, all communities received an additional year of twice-yearly azithromycin treatments (Phase II). Thus, at the conclusion of Phase II, the treatment history (1 letter per 6-month period) for the participating communities was either (PP-PP-AA) or (AA-AA-AA). In Phase III, participating communities were then re-randomized to receive either another 3 rounds of azithromycin or placebo, thus resulting in 4 treatment histories: Group 1 (AA-AA-AA-AA-A, N = 51), Group 2 (PP-PP-AA-AA-A, N = 40), Group 3 (AA-AA-AA-PP-P, N = 27), and Group 4 (PP-PP-AA-PP-P, N = 32). Rectal swabs from each child (N = 5,340) were obtained 6 months after the last treatment. Each child contributed 1 rectal swab and these were pooled at the community level, processed for DNA-seq, and analyzed for genetic resistance determinants. The primary prespecified outcome was macrolide resistance determinants in the gut. Secondary outcomes were resistance to beta-lactams and other antibiotic classes. Communities recently randomized to azithromycin (groups 1 and 2) had significantly more macrolide resistance determinants than those recently randomized to placebo (groups 3 and 4) (fold change 2.18, 95% CI 1.5 to 3.51, Punadj < 0.001). However, there was no significant increase in macrolide resistance in communities treated 4.5 years (group 1) compared to just the most recent 2.5 years (group 2) (fold change 0.80, 95% CI 0.50 to 1.00, Padj = 0.010), or between communities that had been treated for 3 years in the past (group 3) versus just 1 year in the past (group 4) (fold change 1.00, 95% CI 0.78 to 2.35, Padj = 0.52). We also found no significant differences for beta-lactams or other antibiotic classes. The main limitations of our study were the absence of phenotypic characterization of resistance, no complete placebo arm, and no monitoring outside of Niger limiting generalizability.

CONCLUSIONS

In this study, we observed that mass azithromycin distribution for childhood mortality among preschool children in Niger increased macrolide resistance determinants in the gut but that resistance may plateau after 2 to 3 years of treatment. Co-selection to other classes needs to be monitored.

TRIAL REGISTRATION

NCT02047981 https://classic.clinicaltrials.gov/ct2/show/NCT02047981.

Unleashing the promise of emerging nanomaterials as a sustainable platform to mitigate antimicrobial resistance

The emergence and spread of antibiotic-resistant (AR) bacterial strains and biofilm-associated diseases have heightened concerns about exploring alternative bactericidal methods. The WHO estimates that at least 700 000 deaths yearly are attributable to antimicrobial resistance, and that number could increase to 10 million annual deaths by 2050 if appropriate measures are not taken. Therefore, the increasing threat of AR bacteria and biofilm-related infections has created an urgent demand for scientific research to identify novel antimicrobial therapies. Nanomaterials (NMs) have emerged as a promising alternative due to their unique physicochemical properties, and ongoing research holds great promise for developing effective NMs-based treatments for bacterial and viral infections. This review aims to provide an in-depth analysis of NMs based mechanisms combat bacterial infections, particularly those caused by acquired antibiotic resistance. Furthermore, this review examines NMs design features and attributes that can be optimized to enhance their efficacy as antimicrobial agents. In addition, plant-based NMs have emerged as promising alternatives to traditional antibiotics for treating multidrug-resistant bacterial infections due to their reduced toxicity compared to other NMs. The potential of plant mediated NMs for preventing AR is also discussed. Overall, this review emphasizes the importance of understanding the properties and mechanisms of NMs for the development of effective strategies against antibiotic-resistant bacteria.

Four recent insights suggest the need for more refined methods to assess the resistogenicity of doxycycline post exposure prophylaxis

Two recently published randomized trials of doxycycline post exposure prophylaxis (PEP) have concluded that this intervention is highly effective at reducing the incidence of bacterial sexually transmitted infections (STIs) and has little or no risk of promoting the spread of antimicrobial resistance (AMR). In this perspective piece, we review four types of evidence that suggest that the risk of promoting AMR has been inadequately assessed in these studies. 1) The studies have all used proportion resistant as the outcome measure. This is a less sensitive measure of resistogenicity than MIC distribution. 2) These RCTs have not considered population-level pathways of AMR selection. 3) In populations with very high antimicrobial consumption such as PrEP cohorts, the relationship between antimicrobial consumption and resistance may be saturated. 4) Genetic linkage of AMR means that increased tetracycline use may select for AMR to not only tetracyclines but also other antimicrobials in STIs and other bacterial species. We recommend novel study designs to more adequately assess the AMR-inducing risk of doxycycline PEP.

45 years of tetracycline post exposure prophylaxis for STIs and the risk of tetracycline resistance: a systematic review and meta-analysis

There is considerable interest in the use of doxycycline post exposure prophylaxis (PEP) to reduce the incidence of bacterial sexually transmitted infections (STIs). An important concern is that this could select for tetracycline resistance in these STIs and other species. We searched PubMed and Google Scholar, (1948-2023) for randomized controlled trials comparing tetracycline PEP with non-tetracycline controls. The primary outcome was antimicrobial resistance (AMR) to tetracyclines in all bacterial species with available data. Our search yielded 140 studies, of which three met the inclusion criteria. Tetracycline PEP was associated with an increasedprevalence of tetracycline resistance in Neisseria gonorrhoeae, but this effect was not statistically significant (Pooled OR 2.3, 95% CI 0.9-3.4). PEP had a marked effect on the N. gonorrhoeae tetracycline MIC distribution in the one study where this was assessed. Prophylactic efficacy was 100% at low MICs and 0% at high MICs. In the one study where this was assessed, PEP resulted in a significant increase in tetracycline resistance in commensal Neisseria species compared to the control group (OR 2.9, 95% CI 1.5-5.5) but no significant effect on the prevalence of tetracycline resistance in Staphylococcus aureus. The available evidence suggests that PEP with tetracyclines could be associated with selecting tetracycline resistance in N. gonorrhoeae and commensal Neisseria species.

Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development

Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.

Lack of Association between Antimicrobial Consumption and Antimicrobial Resistance in a HIV Preexposure Prophylaxis Population: A Cross-Sectional Study

BACKGROUND

In antibiotic naïve populations, there is a strong association between the use of an antimicrobial and resistance to this antimicrobial. Less evidence is available as to whether this relationship is weakened in populations highly exposed to antimicrobials. Individuals taking HIV preexposure prophylaxis (PrEP) have a high intake of antimicrobials. We previously found that there was no difference in the prevalence of pheno- and genotypic antimicrobial resistance between two groups of PrEP clients who had, and had not, taken antimicrobials in the prior 6 months. Both groups did, however, have a higher prevalence of resistance than a sample of the general population.

METHODS

In the current study, we used zero-inflated negative binomial regression models to evaluate if there was an individual level association between the consumption of antimicrobials and 1. the minimum inhibitory susceptibilities of oral Neisseria subflava and 2. the abundance of antimicrobial resistance genes in the oropharynges of these individuals.

RESULTS

We found no evidence of an association between the consumption of antimicrobials and the minimum inhibitory susceptibilities of oral Neisseria subflava or the abundance of antimicrobial resistance genes in these individuals.

CONCLUSIONS

We conclude that in high-antimicrobial-consumption populations, the association between antimicrobial consumption and resistance may be attenuated. This conclusion would not apply to lower-consumption populations.

Perinatal colonization with extended-spectrum beta-lactamase-producing and carbapenem-resistant Gram-negative bacteria: a hospital-based cohort study

BACKGROUND

Antimicrobial resistance (AMR) is a growing global health threat that contributes to substantial neonatal mortality. Bangladesh has reported some of the highest rates of AMR among bacteria causing neonatal sepsis. As AMR colonization among newborns can predispose to infection with these bacteria, we aimed to characterize the frequency of and risk factors for colonization of mothers and newborns during hospitalization for delivery.

METHODS

We enrolled pregnant women presenting for delivery to a tertiary care hospital in Faridpur, Bangladesh. We collected vaginal and rectal swabs from mothers pre- and post-delivery, rectal swabs from newborns, and swabs from the hospital environment. Swabs were plated on agars selective for extended-spectrum-beta-lactamase producing bacteria (ESBL-PB) and carbapenem-resistant bacteria (CRB). We performed logistic regression to determine factors associated with ESBL-PB/CRB colonization.

RESULTS

We enrolled 177 women and their newborns during February-October 2020. Prior to delivery, 77% of mothers were colonized with ESBL-PB and 15% with CRB. 79% of women underwent cesarean deliveries (C-section). 98% of women received antibiotics. Following delivery, 98% of mothers and 89% of newborns were colonized with ESBL-PB and 89% of mothers and 72% of newborns with CRB. Of 290 environmental samples, 77% were positive for ESBL-PB and 69% for CRB. Maternal pre-delivery colonization was associated with hospitalization during pregnancy (RR for ESBL-PB 1.24, 95% CI 1.10-1.40; CRB 2.46, 95% CI 1.39-4.37). Maternal post-delivery and newborn colonization were associated with C-section (RR for maternal CRB 1.31, 95% CI 1.08-1.59; newborn ESBL-PB 1.34, 95% CI 1.09-1.64; newborn CRB 1.73, 95% CI 1.20-2.47).

CONCLUSIONS

In this study, we observed high rates of colonization with ESBL-PB/CRB among mothers and newborns, with pre-delivery colonization linked to prior healthcare exposure. Our results demonstrate this trend may be driven by intense use of antibiotics, frequent C-sections, and a contaminated hospital environment. These findings highlight that greater attention should be given to the use of perinatal antibiotics, improved surgical stewardship for C-sections, and infection prevention practices in healthcare settings to reduce the high prevalence of colonization with AMR organisms.

Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru

Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.

Changing Genotypic Distribution, Antimicrobial Susceptibilities, and Risk Factors of Urinary Tract Infection Caused by Carbapenemase-Producing Pseudomonas aeruginosa

Background

Carbapenem-resistant Pseudomonas aeruginosa (CrPA) is a leading cause of healthcare-associated urinary tract infections (UTIs). Carbapenemase production is an important mechanism that significantly alters the efficacy of frequently used anti-pseudomonal agents. Reporting the current genotypic distribution of carbapenemase-producing P. aeruginosa (CPPA) isolates in relation to antimicrobial susceptibility, UTI risk factors, and mortality is necessary to increase the awareness and control of these strains.

Methods

In total, 1,652 non-duplicated P. aeruginosa strains were isolated from hospitalized patients between 2015 and 2020. Antimicrobial susceptibility, carbapenemase genotypes, risk factors for UTI, and associated mortality were analyzed.

Results

The prevalence of carbapenem-non-susceptible P. aeruginosa isolates showed a decreasing trend from 2015 to 2018 and then increased in the background of the emergence of New Delhi metallo-β-lactamase (NDM)-type isolates since 2019. The CPPA strains showed 100.0% non-susceptibility to all tested antibiotics, except aztreonam (94.5%) and colistin (5.9%). Carbapenems were identified as a risk and common predisposing factor for UTI (odds ratio [OR]=1.943) and mortality (OR=2.766). Intensive care unit (ICU) stay (OR=2.677) and white blood cell (WBC) count (OR=1.070) were independently associated with mortality.

Conclusions

The changing trend and genetic distribution of CPPA isolates emphasize the need for relentless monitoring to control further dissemination. The use of carbapenems, ICU stay, and WBC count should be considered risk factors, and aggressive antibiotic stewardship programs and monitoring may serve to prevent worse outcomes.

Investigating the Role of Metabolism for Antibiotic Combination Therapies in Pseudomonas aeruginosa

Antibacterial resistance poses a severe threat to public health; an anticipated 14-fold increase in multidrug-resistant (MDR) bacterial infections is expected to occur by 2050. Contrary to antibiotics, combination therapies are the standard of care for antiviral and anticancer treatments, as synergistic drug-drug interactions can decrease dosage and resistance development. In this study, we investigated combination treatments of a novel succinate dehydrogenase inhibitor (promysalin) with specific inhibitors of metabolism and efflux alongside a panel of clinically approved antibiotics in synergy studies. Through these investigations, we determined that promysalin can work synergistically with vancomycin and antagonistically with aminoglycosides and a glyoxylate shunt pathway inhibitor at subinhibitory concentrations; however, these cooperative effects do not reduce minimum inhibitory concentrations. The variability of these results underscores the complexity of targeting metabolism for combination therapies in antibiotic development.

Antimicrobial consumption surveillance in Uganda: Results from an analysis of national import data for the human health sector, 2018-2021

BACKGROUND

The surveillance of antimicrobial consumption (AMC) is critical to developing appropriate antimicrobial stewardship interventions. It is a key component of World Health Organization's (WHO) Global Action Plan on Antimicrobial Resistance and the Uganda Antimicrobial Resistance National Action Plan 2018-2023. Our study's objective was to determine the national consumption of all antimicrobials.

METHODS

Data on all imported antimicrobials were retrieved from paper-based records and entered in the web-based National Drug Authority (NDA) management information system from 2021. The import data for the year is a proxy for nationwide consumption because they account for 95% of all medical products. The NDA authorizes all imports to the country regardless of final distribution in the supply chain. The data were analyzed in accordance with WHO Anatomical Therapeutic Chemical codes and defined daily dose (DDD) methodology. We also retrieved consumption data for 2018, 2019, and 2020 that were previously submitted by Uganda to WHO's Global Antimicrobial Resistance and Use Surveillance System.

RESULTS

In 2021, the average DDD per 1000 inhabitants was 29.02 for all antimicrobials; 80.7% of antimicrobials consumed were oral. Penicillins (27.6%) were the most consumed antimicrobial class, followed by sulfonamides and trimethoprim (15.5%). Based on WHO's Access, Watch, and Reserve (AWaRe) antibiotic classification, 62.91% of AMC was from the access class, with watch class averaging 14.51% in the period 2018-2021. Watch class AMC spiked in 2021 (34.2%) during COVID-19 pandemic compared to 2020 (24.29%). Azithromycin and ciprofloxacin were the most consumed watch class antimicrobials in 2021.

CONCLUSIONS

The relatively high consumption of injectable antimicrobials and year over year increase in watch class AMC requires urgent stewardship interventions. Further work is needed to establish a system for longitudinal AMC surveillance that is well resourced and funded to overcome the challenges of estimation and provide more accurate data on consumption and use patterns.

Appropriateness of antibiotic prescribing varies by clinical services at United States children's hospitals

OBJECTIVE

To describe patterns of inappropriate antibiotic prescribing at US children's hospitals and how these patterns vary by clinical service.

DESIGN

Serial, cross-sectional study using quarterly surveys.

SETTING

Surveys were completed in quarter 1 2019-quarter 3 2020 across 28 children's hospitals in the United States.

PARTICIPANTS

Patients at children's hospitals with ≥1 antibiotic order at 8:00 a.m. on institution-selected quarterly survey days.

METHODS

Antimicrobial stewardship physicians and pharmacists collected data on antibiotic orders and evaluated appropriateness of prescribing. The primary outcome was percentage of inappropriate antibiotics, stratified by clinical service and antibiotic class. Secondary outcomes included reasons for inappropriate use and association of infectious diseases (ID) consultation with appropriateness.

RESULTS

Of 13,344 orders, 1,847 (13.8%) were inappropriate; 17.5% of patients receiving antibiotics had ≥1 inappropriate order. Pediatric intensive care units (PICU) and hospitalists contributed the most inappropriate orders (n = 384 and n = 314, respectively). Surgical subspecialists had the highest percentage of inappropriate orders (22.5%), and 56.8% of these were for prolonged or unnecessary surgical prophylaxis. ID consultation in the previous 7 days was associated with fewer inappropriate orders (15% vs 10%; P < .001); this association was most pronounced for hospitalist, PICU, and surgical and medical subspecialty services.

CONCLUSIONS

Inappropriate antibiotic use for hospitalized children persists and varies by clinical service. Across 28 children's hospitals, PICUs and hospitalists contributed the most inappropriate antibiotic orders, and surgical subspecialists' orders were most often judged inappropriate. Understanding service-specific prescribing patterns will enable antimicrobial stewardship programs to better design interventions to optimize antibiotic use.

How to change the course: practical aspects of implementing shorter is better

BACKGROUND

Based on multiple randomized-controlled clinical trials, shorter antibiotic courses are equally effective as traditional longer courses for many types of infections. However, longer courses are still being used widely in the clinical practice.

OBJECTIVES

To describe four components involved in the successful implementation of shorter antibiotic courses in our health care institutions, including an academic, public hospital and a community hospital staffed primarily by private practitioners.

SOURCES

Clinical trials and peer-reviewed publications.

CONTENT

We provide practical advice on how to support the change in clinical practice to shorten antibiotic duration. Specifically, we list the steps that we have successfully used to develop and implement an institutional practice change regarding the duration of antibiotic therapy: (a) establishing consensus documents outlining a data-driven expected practice for using antibiotics, (b) antibiotic stewardship programme support, (c) provider education, and (d) reinforcing behaviour through psychological and other tools. The implementation of these processes has successfully led to shorter antibiotic courses and decreased antibiotic use in our diverse practice settings.

IMPLICATIONS

Intentional improvement in decreasing the duration of antibiotic therapy can be achieved by a specific antibiotic stewardship programme strategy and tactics. The implementation of shorter antibiotic courses has effects at individual and societal levels in an era of increasing antibacterial resistance and health care costs.

Plugging the leaks: antibiotic resistance at human-animal interfaces in low-resource settings

Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle-income country with substantial human-animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antibiotic resistance in low- and especially middle-income countries.

Prolonged antibiotic prophylaxis after pancreatoduodenectomy: systematic review and meta-analysis

BACKGROUND

Previous studies have reported conflicting results of prolonged antibiotic prophylaxis on infectious complications after pancreatoduodenectomy. This study evaluated the effect of prolonged antibiotics on surgical-site infections (SSIs) after pancreatoduodenectomy.

METHODS

A systematic review and meta-analysis was undertaken of SSIs in patients with perioperative (within 24 h) versus prolonged antibiotic (over 24 h) prophylaxis after pancreatoduodenectomy. SSIs were classified as organ/space infections or superficial SSI within 30 days after surgery. ORs were calculated using a Mantel-Haenszel fixed-effect model.

RESULTS

Ten studies were included in the qualitative analysis, of which 8 reporting on 1170 patients were included in the quantitative analysis. The duration of prolonged antibiotic prophylaxis varied between 2 and 10 days after surgery. Four studies reporting on 782 patients showed comparable organ/space infection rates in patients receiving perioperative and prolonged antibiotics (OR 1.35, 95 per cent c.i. 0.94 to 1.93). However, among patients with preoperative biliary drainage (5 studies reporting on 577 patients), organ/space infection rates were lower with prolonged compared with perioperative antibiotics (OR 2.09, 1.43 to 3.07). Three studies (633 patients) demonstrated comparable superficial SSI rates between patients receiving perioperative versus prolonged prophylaxis (OR 1.54, 0.97 to 2.44), as well as in patients with preoperative biliary drainage in 4 studies reporting on 431 patients (OR 1.60, 0.89 to 2.88).

CONCLUSION

Prolonged antibiotic prophylaxis is associated with fewer organ/space infection in patients who undergo preoperative biliary drainage. However, the optimal duration of antibiotic prophylaxis after pancreatoduodenectomy remains to be determined and warrants confirmation in an RCT.

The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance

Approximately 10% of antimicrobials used by humans in low- and middle-income countries are estimated to be substandard or falsified. In addition to their negative impact on morbidity and mortality, they may also be important drivers of antimicrobial resistance. Despite such concerns, our understanding of this relationship remains rudimentary. Substandard and falsified medicines have the potential to either increase or decrease levels of resistance, and here we discuss a range of mechanisms that could drive these changes. Understanding these effects and their relative importance will require an improved understanding of how different drug exposures affect the emergence and spread of resistance and of how the percentage of active pharmaceutical ingredients in substandard and falsified medicines is temporally and spatially distributed.

Effect on the Resistome of Dual vs Monotherapy for the Treatment of Neisseria gonorrhoeae: Results From a Randomized Controlled Trial (ResistAZM Trial)

Background

No randomized controlled trial (RCT) has compared the impact on the resistome of ceftriaxone (CRO) plus azithromycin (AZM) vs CRO for the treatment of Neisseria gonorrhoea (NG).

Methods

This was an open-label, single-center, RCT comparing the effect on the resistome of CRO plus AZM vs CRO for the treatment of NG. Men who have sex with men (MSM) with genital, anorectal, or pharyngeal NG infection were randomized into the CRO/AZM and CRO arms. Oral rinse and anorectal samples were taken for culture and resistome profiling at 2 visits (baseline and day 14). The primary outcome was the ratio of mean macrolide resistance determinants in anorectal samples from day 14 between arms.

Results

Twenty individuals were randomized into the CRO/AZM arm and 22 into the CRO arm. We found no significant difference in the mean macrolide resistance determinants in the day 14 anorectal samples between arms (ratio, 1.05; 95% CI, 0.55-1.83; P = .102). The prevalence of baseline macrolide resistance was high (CRO/AZM arm = 95.00%; CRO arm = 90.91%).

Conclusions

We could not demonstrate a significant effect of dual CRO/AZM therapy on the resistome compared with CRO alone, likely due to a high baseline resistance to AZM. Interventions to prevent the emergence of antimicrobial resistance in MSM are needed.

Healthcare-associated infections by multidrug-resistant bacteria in Andalusia, Spain, 2014 to 2021

BackgroundMultidrug-resistant (MDR) bacteria are among chief causes of healthcare-associated infections (HAIs). In Spain, studies addressing multidrug resistance based on epidemiological surveillance systems are lacking.AimIn this observational study, cases of HAIs by MDR bacteria notified to the epidemiological surveillance system of Andalusia, Spain, between 2014-2021, were investigated. Notified cases and their spatiotemporal distribution were described, with a focus on social determinants of health (SDoH).MethodsNew cases during the study period of HAIs caused by extended-spectrum β-lactamase (ESBL)-/carbapenemase-producing Enterobacterales, MDR Acinectobacter baumannii, MDR Pseudomonas aeruginosa or meticillin resistant Staphylococcus aureus were considered. Among others, notification variables included sex and age, while socio-economic variables comprised several SDoH. Cases' spatial distribution across municipalities was assessed. The smooth standardised incidence ratio (sSIR) was obtained using a Bayesian spatial model. Association between municipalities' sSIR level and SDoH was evaluated by bivariate analysis.ResultsIn total, 6,389 cases with a median age of 68 years were notified; 61.4% were men (n = 3,921). The most frequent MDR bacteria were ESBL-producing Enterobacterales (2,812/6,389; 44.0%); the main agent was Klebsiella spp. (2,956/6,389; 46.3%). Between 2014 and 2021 case numbers appeared to increase. Overall, up to 15-fold differences in sSIR between municipalities were observed. In bivariate analysis, there appeared to be an association between municipalities' sSIR level and deprivation (p = 0.003).ConclusionThis study indicates that social factors should be considered when investigating HAIs by MDR bacteria. The case incidence heterogeneity between Andalusian municipalities might be explained by SDoH, but also possibly by under-notification. Automatising reporting may address the latter.

Doxycycline PEP can induce doxycycline resistance in Klebsiella pneumoniae in a Galleria mellonella model of PEP

Background

Four randomized controlled trials have now established that doxycycline post exposure (sex) prophylaxis (PEP) can reduce the incidence of chlamydia and syphilis in men who have sex with men. These studies have concluded that the risk of selecting for antimicrobial resistance is low. We evaluated this risk in vitro and in vivo using a Galleria mellonella infection model.

Methods

We evaluated how long it took for doxycycline resistance to emerge during passage on doxycycline containing agar plates in 4 species - Escherichia coli, Klebsiella pneumoniae, Neisseria gonorrhoeae and Neisseria subflava. We then assessed if K. pneumoniae could acquire resistance to doxycycline (and cross resistance to other antimicrobials) during intermittent exposure to doxycycline in a Galleria mellonella model of doxycycline PEP.

Results

In our passage experiments, we found that resistance first emerged in K. pneumoniae. By day 7 the K. pneumoniae MIC had increased from 2 mg/L to a median of 96 mg/L (IQR 64-96). Under various simulations of doxycycline PEP in the G. mellonella model, the doxycycline MIC of K. pneumoniae increased from 2 mg/L to 48 mg/L (IQR 48-84). Ceftriaxone and ciprofloxacin MICs increased over ten-fold. Whole genome sequencing revealed acquired mutations in ramR which regulates the expression of the AcrAB-TolC efflux pump.

Conclusion

Doxycycline PEP can select for doxycycline, ceftriaxone and ciprofloxacin resistance in K. pneumoniae in a G. mellonella model. The emergent ramR mutations were similar to those seen in circulating strains of K. pneumoniae. These findings suggest that we need to assess the effect of doxycycline PEP on resistance induction on a broader range of bacterial species than has hitherto been the case.

Joining Forces against Antibiotic Resistance: The One Health Solution

Antibiotic resistance is a significant global health concern that affects both human and animal populations. The One Health approach acknowledges the interconnectedness of human health, animal health, and the environment. It emphasizes the importance of collaboration and coordination across these sectors to tackle complex health challenges such as antibiotic resistance. In the context of One Health, antibiotic resistance refers to the ability of bacteria to withstand the efficacy of antibiotics, rendering them less effective or completely ineffective in treating infections. The emergence and spread of antibiotic-resistant bacteria pose a threat to human and animal health, as well as to the effectiveness of medical treatments and veterinary interventions. In particular, One Health recognizes that antibiotic use in human medicine, animal agriculture, and the environment are interconnected factors contributing to the development and spread of antibiotic resistance. For example, the misuse and overuse of antibiotics in human healthcare, including inappropriate prescribing and patient non-compliance, can contribute to the selection and spread of resistant bacteria. Similarly, the use of antibiotics in livestock production for growth promotion and disease prevention can contribute to the development of antibiotic resistance in animals and subsequent transmission to humans through the food chain. Addressing antibiotic resistance requires a collaborative One Health approach that involves multiple participants, including healthcare professionals, veterinarians, researchers, and policymakers.

Effect of veterinary feed directive rule changes on tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the United States

BACKGROUND

Antimicrobial-resistant bacteria are a growing public health threat. In 2017 the U.S. Food and Drug Administration implemented Veterinary Feed Directive (VFD) rules changes to limit medically important antimicrobial use in food-producing animals, combating antimicrobial-resistant bacteria. The effect of the VFD rule changes on the occurrence of bacteria resistant to medically-important antimicrobials in retail meats is yet to be investigated in the U.S. This study investigates whether the VFD rule changes affected the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the U.S.

METHODS

Multivariable mixed effect logistic regression models were used to analyze 2002-2019 retail meats surveillance data from the National Antimicrobial Resistance Monitoring System (NARMS) in the U.S. Variables included VFD rule changes, meat type, quarter of year, and raising claims. A potential association between these variables and the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats was estimated.

RESULTS

Analysis included data regarding tetracycline-resistant Salmonella (n = 8,501), Escherichia (n = 20, 283), Campylobacter (n = 9,682), and erythromycin-resistant Campylobacter (n = 10,446) in retail meats. The odds of detecting tetracycline-resistant Escherichia (OR = 0.60), Campylobacter (OR = 0.89), and erythromycin-resistant Campylobacter (OR = 0.43) in chicken breast significantly decreased after the VFD rule changes, compared to the pre-VFD rule change period. The odds of detecting tetracycline-resistant Salmonella (0.66), Escherichia (OR = 0.56), and Campylobacter (OR = 0.33) in ground turkey also significantly decreased. However, the odds of detecting tetracycline-resistant Salmonella (OR = 1.49) in chicken breast and erythromycin-resistant Campylobacter (OR = 4.63) in ground turkey significantly increased. There was no significant change in the odds of detecting tetracycline-resistant Salmonella and Escherichia in ground beef or pork chops.

CONCLUSIONS

The implementation of VFD rule changes had a beneficial effect by reducing the occurrence of tetracycline-resistant and erythromycin-resistant bacteria in chicken and ground turkey. Ongoing surveillance of antimicrobial resistance and antimicrobial use could complement the implementation of stewardship such as VFD rule in food-producing animals in the U.S.

Evaluating the relationship between community water and sanitation access and the global burden of antibiotic resistance: an ecological study

BACKGROUND

Antibiotic resistance is a leading cause of death, with the highest burden occurring in low-resource settings. There is little evidence on the potential for water, sanitation, and hygiene (WASH) access to reduce antibiotic resistance in humans. We aimed to determine the relationship between the burden of antibiotic resistance in humans and community access to drinking water and sanitation.

METHODS

In this ecological study, we linked publicly available, geospatially tagged human faecal metagenomes (from the US National Center for Biotechnology Information Sequence Read Archive) with georeferenced household survey datasets that reported access to drinking water sources and sanitation facility types. We used generalised linear models with robust SEs to estimate the relationship between the abundance of antibiotic resistance genes (ARGs) in human faecal metagenomes and community-level coverage of improved drinking water and sanitation within a defined radii of faecal metagenome coordinates.

FINDINGS

We identified 1589 metagenomes from 26 countries. The mean abundance of ARGs, in units of log10 ARG fragments per kilobase per million mapped reads classified as bacteria, was highest in Africa compared with Europe (p=0·014), North America (p=0·0032), and the Western Pacific (p=0·011), and second highest in South-East Asia compared with Europe (p=0·047) and North America (p=0·014). Increased access to improved water and sanitation was associated with lower ARG abundance (effect estimate -0·22, [95% CI -0·39 to -0·05]) and the association was stronger in urban (-0·32 [-0·63 to 0·00]) than in rural (-0·16 [-0·38 to 0·07]) areas.

INTERPRETATION

Although additional studies to investigate causal effects are needed, increasing access to water and sanitation could be an effective strategy to curb the proliferation of antibiotic resistance in low-income and middle-income countries.

FUNDING

Bill & Melinda Gates Foundation.

Antibiotic prescription: Knowledge among physicians and nurses in western Sweden

Misuse and overuse of antibiotics are common in primary care. Guidelines for prescribing of antibiotics are often not followed We conducted a survey of 120 health centers in western Sweden to investigate to what extent physicians and nurses think they know and comply with the guidelines for prescribing of antibiotics. A large majority of the respondents answered that they know the guidelines well. However, many also believed that physicians/nurses in general know less about and are worse at following the guidelines than themselves, indicating optimism bias. According to the respondents the main reason for non-compliance with guidelines was patient expectations. The survey also showed that both physicians' and nurses' actual knowledge of when it is effective to prescribe antibiotics is incomplete. Interventions to reduce unnecessary antibiotic therapy in primary care should target the failing congruence between the perceived knowledge of guidelines for antibiotic therapy and actual knowledge.

‘Brave Enough’: A Qualitative Study of Veterinary Decisions to Withhold or Delay Antimicrobial Treatment in Pets

Veterinarians sometimes prescribe antimicrobials even when they know or suspect that they are unnecessary. The drivers of this behaviour must be understood to design effective antimicrobial stewardship interventions. Semi-structured interviews were conducted with 22 veterinarians who treated companion animals in Australia. The Theory of Planned Behaviour was used to organise interview themes, focusing on a decision to withhold antimicrobial therapy in the absence of a clear indication. Many background factors influenced antimicrobial-withholding decisions, including the veterinarian’s communication skills, general attitudes towards antimicrobial resistance (AMR), habits and energy levels. Client awareness of AMR and the veterinarian–client relationship were also important. Beliefs about the consequences of withholding antimicrobials (behavioural beliefs) were dominated by fears of the animal’s condition deteriorating and of failing to meet client expectations. These fears, weighed against the seemingly distant consequences of AMR, were major barriers to withholding antimicrobials. Normative beliefs were primarily focused on the expected approval (or disapproval) of the client and of other veterinarians. Control beliefs about the difficulty of withholding antimicrobials centred around client factors, most importantly, their capacity to adequately monitor their animal, to pay for further investigations, or to undertake non-antimicrobial management, such as wound care, at home. The use of antimicrobials by companion animal veterinarians in the absence of a clear indication is often powerfully driven by behavioural beliefs, chiefly, fears of clinical deterioration and of failing to meet client expectations.

A systematic review of fish adulteration and contamination in Bangladesh: A way forward to food safety

For decades, the world has been plagued by widespread food adulteration, and Bangladesh is no exception. Dishonest business people and fish farmers unlawfully utilize various preservatives to avoid rotting and extend the shelf life of fish. Although previous research has examined the level of formalin use in fish bodies, no studies focusing on all aspects of fish adulteration and contamination in Bangladesh have been carried out. In this context, the aim of this review is to explore the extent and magnitude of illegal fish adulteration and contamination in Bangladesh. Among the 37 reviewed studies, 11 of them highlighted formalin adulteration in fish samples and fish feed. The extent of formalin use varied between local and imported fish, and between large and small fish. Imported and large fish were substantially more formalin‐contaminated. Several investigations have discovered that antibiotic levels in farm water and fish feed exceed the permitted level. Farmers have used growth promoters incautiously. This study also identifies that certain metal substances, such as chromium, lead, arsenic, cadmium, iron, mercury and cobalt, have been frequently found in fish bodies and feed samples. Furthermore, a distinct type of fish adulteration caused by aromatic compounds has emerged recently. The findings and their ramifications are extremely concerning for human lives. However, since each study employed a different testing kit, the results were quite distinct. Thus, the adoption of a precise and sensitive kit is strongly recommended. The government should make it a top priority to solve the problem of fish adulteration by implementing appropriate food safety laws and policies.

Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data

Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen Staphylococcus aureus . The reported prevalence of these resistances vary, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures. We explored S. aureus AMR diversity in 70,000 isolates from a UK paediatric hospital between 2000-2020, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms, hospitalisation information, and antibiotic consumption. At the hospital-level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014-2020 from 25 to 50%, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible S. aureus . Ciprofloxacin resistance in MRSA decreased from 70% to 40% of tested isolates between 2007-2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4% of patients ever positive for S. aureus simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3% of patients ever positive for S. aureus . These changes equally represented gain and loss of resistance. Within this routinely collected dataset, we found that 65% of changes in resistance within a patient’s S. aureus population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single S. aureus clones.

The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study

BACKGROUND

Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.

METHODS

We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.

FINDINGS

ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.

INTERPRETATION

The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.

Antibiotic perceptions, adherence, and disposal practices among parents of pediatric patients

Antibiotics are frequently prescribed for children in the outpatient setting. Although sometimes necessary, antibiotic use is associated with important downstream effects including the development of antimicrobial resistance among human and environmental microorganisms. Current outpatient stewardship efforts focus on guiding appropriate antibiotic prescribing practices among providers, but little is known about parents' understanding of antibiotics and appropriate disposal of leftover antibiotics. To help bridge this gap, we conducted a qualitative study to assess parental understanding of their children's antibiotics, their adherence to antibiotic instructions, and their disposal practices. We conducted a semi-structured interview with parents of 13 children diagnosed with acute respiratory illnesses and prescribed antibiotics in an urban outpatient clinic. We found that parents had limited understanding of how antibiotics work. Although they received instructions about antibiotic use during the healthcare visit, adherence to the prescription and appropriate disposal of antibiotics was suboptimal. Limited baseline understanding of antibiotics, their prior experiences with antibiotics, perceptions about their social networks' antibiotic use, and information provided to them by healthcare providers may influence these behaviors. Our findings can inform educational efforts of outpatient stewardship programs to help optimize parental understanding of how to use and dispose of their children's antibiotics.

Appropriateness of antimicrobial selection for treatment of pneumonia in selected public hospitals of Eastern Ethiopia: A cross-sectional study

Objective

Inappropriate antimicrobial use leads to drug resistance and poor clinical outcomes. Considering the lack of data regarding the drug use patterns in the treatment of pneumonia in selected study areas, the authors felt compelled to assess the appropriateness of antimicrobial usage in the treatment of pneumonia at Hiwot Fana Specialized Comprehensive University Hospital and Jugal Hospital from May 1 to 31, 2021.

Methods

A cross-sectional retrospective study was conducted using the medical cards of 693 admitted patients with pneumonia. The collected data were analyzed using SPSS version 26. Bivariable and multivariable logistic regression analyses were used to identify the factors associated with an initial inappropriate antibiotic use. A p value of 0.05 was used to determine the statistical significance of the association using an adjusted odds ratio with 95% confidence interval.

Results

Of the total participants, 116 (16.74%, 95% confidence interval: 14.1-19.6) of them received an initial inappropriate antimicrobial regimen. Ceftriaxone plus azithromycin was the most prescribed antimicrobial agent. Patients who were younger than 5 years (adjusted odds ratio = 1.71; 95% confidence interval: 1.00-2.94), between 6 and 14 years (adjusted odds ratio = 3.14; 95% confidence interval: 1.64-6.00), and older than 65 years (adjusted odds ratio = 2.97; 95% confidence interval: 1.07-2.66), with comorbid conditions (adjusted odds ratio = 1.74; 95% confidence interval: 1.10-2.72) and prescribed by medical interns (adjusted odds ratio = 1.80; 95% confidence interval: 1.14-2.84) were associated with an initial inappropriate antimicrobial use.

Conclusion

Around one out of every six patients had received initial inappropriate treatments. Adherence to the recommendation of guidelines and attention to extreme-aged groups and comorbidity may improve antimicrobial use.

Carbapenem-resistant Acinetobacter baumannii: A challenge in the intensive care unit

Carbapenem-resistant Acinetobacter baumannii (CRAB) has become one of the leading causes of healthcare-associated infections globally, particularly in intensive care units (ICUs). Cross-transmission of microorganisms between patients and the hospital environment may play a crucial role in ICU-acquired CRAB colonization and infection. The control and treatment of CRAB infection in ICUs have been recognized as a global challenge because of its multiple-drug resistance. The main concern is that CRAB infections can be disastrous for ICU patients if currently existing limited therapeutic alternatives fail in the future. Therefore, the colonization, infection, transmission, and resistance mechanisms of CRAB in ICUs need to be systematically studied. To provide a basis for prevention and control countermeasures for CRAB infection in ICUs, we present an overview of research on CRAB in ICUs, summarize clinical infections and environmental reservoirs, discuss the drug resistance mechanism and homology of CRAB in ICUs, and evaluate contemporary treatment and control strategies.

A Threshold Logistic Modelling Approach for Identifying Thresholds between Antibiotic Use and Methicillin-Resistant Staphylococcus aureus Incidence Rates in Hospitals

The aim of this study was to demonstrate the utility of threshold logistic modelling, an innovative approach in identifying thresholds and risk scores in the context of population antibiotic use associated with methicillin-resistant Staphylococcus aureus (MRSA) incidence rates in hospitals. The study also aimed to assess the impact of exceeding those thresholds that resulted in increased MRSA rates. The study was undertaken in a 700-bed hospital in England between January 2015 and December 2021 (84 monthly observations). By employing the threshold logistic modelling approach, we: (i) determined the cut-off percentile value of MRSA incidence that defines a critical level of MRSA; (ii) identified thresholds for fluoroquinolone and co-amoxiclav use that would accelerate MRSA incidence rates and increase the probability of reaching critical incidence levels; (iii) enabled a better understanding of the effect of antibiotic use on the probability of reaching a critical level of resistant pathogen incidence; (iv) developed a near real-time performance monitoring feedback system; (v) provided risk scores and alert signals for antibiotic use, with the ability to inform hospital policies, and control MRSA incidence; and (vi) provided recommendations and an example for the management of pathogen incidence in hospitals. Threshold logistic models can help hospitals determine quantitative targets for antibiotic usage and can also inform effective antimicrobial stewardship to control resistance in hospitals. Studies should work toward implementing and evaluating the proposed approach prospectively, with the aim of determining the best counter-measures to mitigate the risk of increased resistant pathogen incidence in hospitals.

Identifying Antibiotic Use Targets for the Management of Antibiotic Resistance Using an Extended-Spectrum β-Lactamase-Producing Escherichia coli Case: A Threshold Logistic Modeling Approach

The aim of this study was to develop a logistic modeling concept to improve understanding of the relationship between antibiotic use thresholds and the incidence of resistant pathogens. A combined approach of nonlinear modeling and logistic regression, named threshold logistic, was used to identify thresholds and risk scores in hospital-level antibiotic use associated with hospital-level incidence rates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli). Threshold logistic models identified thresholds for fluoroquinolones (61.1 DDD/1000 occupied bed days (OBD)) and third-generation cephalosporins (9.2 DDD/1000 OBD) to control hospital ESBL-producing E. coli incidence. The 60th percentile of ESBL-producing E. coli was determined as the cutoff for defining high incidence rates. Threshold logistic analysis showed that for every one-unit increase in fluoroquinolones and third-generation cephalosporins above 61.1 and 9.2 DDD/1000 OBD levels, the average odds of the ESBL-producing E. coli incidence rate being ≥60th percentile of historical levels increased by 4.5% and 12%, respectively. Threshold logistic models estimated the risk scores of exceeding the 60th percentile of a historical ESBL-producing E. coli incidence rate. Threshold logistic models can help hospitals in defining critical levels of antibiotic use and resistant pathogen incidence and provide targets for antibiotic consumption and a near real-time performance monitoring feedback system.

Gut Resistome after Antibiotics among Children with Uncomplicated Severe Acute Malnutrition: A Randomized Controlled Trial

A broad-spectrum antibiotic, typically amoxicillin, is included in many country guidelines as part of the management of uncomplicated severe acute malnutrition (SAM) in children without overt clinical symptoms of infection. Alternative antibiotics may be beneficial for children with SAM without increasing selection for beta-lactam resistance. We conducted a 1:1 randomized controlled trial of single dose azithromycin versus a 7-day course of amoxicillin for SAM. Children 6-59 months of age with uncomplicated SAM (mid-upper arm circumference < 11.5 cm and/or weight-for-height Z-score < -3) were enrolled in Boromo District, Burkina Faso, from June through October 2020. Rectal swabs were collected at baseline and 8 weeks after treatment and processed using DNA-Seq. We compared the resistome at the class level in children randomized to azithromycin compared with amoxicillin. We found no evidence of a difference in the distribution of genetic antibiotic resistance determinants to any antibiotic class 8 weeks after treatment. There was no difference in genetic macrolide resistance determinants (65% azithromycin, 65% placebo, odds ratio, OR, 1.00, 95% confidence interval, CI, 0.43-2.34) or beta-lactam resistance determinants (82% azithromycin, 83% amoxicillin, OR 0.94, 95% CI, 0.33-2.68) at 8 weeks. Although presence of genetic antibiotic resistance determinants to macrolides and beta-lactams was common, we found no evidence of a difference in the gut resistome 8 weeks after treatment. If there are earlier effects of antibiotics on selection for genetic antibiotic resistance determinants, the resistome may normalize by 8 weeks.

Environmental impacts of mass drug administration programs: exposures, risks, and mitigation of antimicrobial resistance

Mass drug administration (MDA) of antimicrobials has shown promise in the reduction and potential elimination of a variety of neglected tropical diseases (NTDs). However, with antimicrobial resistance (AMR) becoming a global crisis, the risks posed by widespread antimicrobial use need to be evaluated. As the role of the environment in AMR emergence and dissemination has become increasingly recognized, it is likewise crucial to establish the role of MDA in environmental AMR pollution, along with the potential impacts of such pollution. This review presents the current state of knowledge on the antimicrobial compounds, resistant organisms, and antimicrobial resistance genes in MDA trials, routes of these determinants into the environment, and their persistence and ecological impacts, particularly in low and middle-income countries where these trials are most common. From the few studies directly evaluating AMR outcomes in azithromycin MDA trials, it is becoming apparent that MDA efforts can increase carriage and excretion of resistant pathogens in a lasting way. However, research on these outcomes for other antimicrobials used in MDA trials is sorely needed. Furthermore, while paths of AMR determinants from human waste to the environment and their persistence thereafter are supported by the literature, quantitative information on the scope and likelihood of this is largely absent. We recommend some mitigative approaches that would be valuable to consider in future MDA efforts. This review stands to be a valuable resource for researchers and policymakers seeking to evaluate the impacts of MDA.

Uses of mathematical modeling to estimate the impact of mass drug administration of antibiotics on antimicrobial resistance within and between communities

BACKGROUND

Antibiotics are a key part of modern healthcare, but their use has downsides, including selecting for antibiotic resistance, both in the individuals treated with antibiotics and in the community at large. When evaluating the benefits and costs of mass administration of azithromycin to reduce childhood mortality, effects of antibiotic use on antibiotic resistance are important but difficult to measure, especially when evaluating resistance that "spills over" from antibiotic-treated individuals to other members of their community. The aim of this scoping review was to identify how the existing literature on antibiotic resistance modeling could be better leveraged to understand the effect of mass drug administration (MDA) on antibiotic resistance.

MAIN TEXT

Mathematical models of antibiotic use and resistance may be useful for estimating the expected effects of different MDA implementations on different populations, as well as aiding interpretation of existing data and guiding future experimental design. Here, strengths and limitations of models of antibiotic resistance are reviewed, and possible applications of those models in the context of mass drug administration with azithromycin are discussed.

CONCLUSIONS

Statistical models of antibiotic use and resistance may provide robust and relevant estimates of the possible effects of MDA on resistance. Mechanistic models of resistance, while able to more precisely estimate the effects of different implementations of MDA on resistance, may require more data from MDA trials to be accurately parameterized.