Surveillance for control of antimicrobial resistance

Carbapenem-resistant Gram-negative bacteria (CR-GNB) in ICUs: resistance genes, therapeutics, and prevention - a comprehensive review

Intensive care units (ICUs) are specialized environments dedicated to the management of critically ill patients, who are particularly susceptible to drug-resistant bacteria. Among these, carbapenem-resistant Gram-negative bacteria (CR-GNB) pose a significant threat endangering the lives of ICU patients. Carbapenemase production is a key resistance mechanism in CR-GNB, with the transfer of resistance genes contributing to the extensive emergence of antimicrobial resistance (AMR). CR-GNB infections are widespread in ICUs, highlighting an urgent need for prevention and control measures to reduce mortality rates associated with CR-GNB transmission or infection. This review provides an overview of key aspects surrounding CR-GNB within ICUs. We examine the mechanisms of bacterial drug resistance, the resistance genes that frequently occur with CR-GNB infections in ICU, and the therapeutic options against carbapenemase genotypes. Additionally, we highlight crucial preventive measures to impede the transmission and spread of CR-GNB within ICUs, along with reviewing the advances made in the field of clinical predictive modeling research, which hold excellent potential for practical application.

Characterization of ES10 lytic bacteriophage isolated from hospital waste against multidrug-resistant uropathogenic E. coli

Escherichia coli is the major causative agent of urinary tract infections worldwide and the emergence of multi-drug resistant determinants among clinical isolates necessitates the development of novel therapeutic agents. Lytic bacteriophages efficiently kill specific bacteria and seems promising approach in controlling infections caused by multi-drug resistant pathogens. This study aimed the isolation and detailed characterization of lytic bacteriophage designated as ES10 capable of lysing multidrug-resistant uropathogenic E. coli. ES10 had icosahedral head and non-contractile tail and genome size was 48,315 base pairs long encoding 74 proteins. Antibiotics resistance, virulence and lysogenic cycle associated genes were not found in ES10 phage genome. Morphological and whole genome analysis of ES10 phage showed that ES10 is the member of Drexlerviridae. Latent time of ES10 was 30 min, burst size was 90, and optimal multiplicity of infection was 1. ES10 was stable in human blood and subsequently caused 99.34% reduction of host bacteria. Calcium chloride shortened the adsorption time and latency period of ES10 and significantly inhibited biofilm formation of host bacteria. ES10 caused 99.84% reduction of host bacteria from contaminated fomites. ES10 phage possesses potential to be utilized in standard phage therapy.

Siderophores promote cooperative interspecies and intraspecies cross-protection against antibiotics in vitro

The antibiotic cefiderocol hijacks iron transporters to facilitate its uptake and resists β-lactamase degradation. While effective, resistance has been detected clinically with unknown mechanisms. Here, using experimental evolution, we identified cefiderocol resistance mutations in Pseudomonas aeruginosa. Resistance was multifactorial in host-mimicking growth media, led to multidrug resistance and paid fitness costs in cefiderocol-free environments. However, kin selection drove some resistant populations to cross-protect susceptible individuals from killing by increasing pyoverdine secretion via a two-component sensor mutation. While pyochelin sensitized P. aeruginosa to cefiderocol killing, pyoverdine and the enterobacteria siderophore enterobactin displaced iron from cefiderocol, preventing uptake by susceptible cells. Among 113 P. aeruginosa intensive care unit clinical isolates, pyoverdine production directly correlated with cefiderocol tolerance, and high pyoverdine producing isolates cross-protected susceptible P. aeruginosa and other Gram-negative bacteria. These in vitro data show that antibiotic cross-protection can occur via degradation-independent mechanisms and siderophores can serve unexpected protective cooperative roles in polymicrobial communities.

Distribution characteristics of antibiotic resistance genes and microbial diversity in the inshore aquaculture area of Wenchang, Hainan, China

The rapid development of marine aquaculture has led to the increased use and release of antibiotics into the marine environment, consequently contributing to the emergence of antibiotic resistance. Information on antibiotic resistance in nearshore marine aquaculture areas remains limited, and research on the microbial composition and potential hosts of antibiotic resistance genes (ARGs) in marine aquaculture areas is scarce. This study used SmartChip real-time fluorescent quantitative PCR and qPCR to quantitatively analyze 44 ARGs and 10 mobile genetic elements (MGEs) genes in 12 sampling points in the nearshore aquaculture area of Wenchang. High-throughput sequencing of 16S rRNA was used to study microbial diversity in the study area, to clarify the correlation between ARGs, MGEs, and microbial diversity, and to determine the possible sources and potential hosts of ARGs. The results showed that a total of 37 ARGs and 8 MGEs were detected in the study area. The detection rate of 9 ARGs (aac(6')-Ib(aka aacA4)-02, catA1, cmlA, cfr, sul1, sul2, sulA/folP-01, tetC, tetX) was 100 %. The absolute abundance of ARGs in the 12 sampling points ranged from 2.75 × 107 to 3.79 × 1010 copies·L-1, and the absolute abundance of MGEs was 1.30 × 105 to 2.54 × 107 copies·L-1, which was relatively high compared to other research areas. ARGs and MGEs were significantly correlated, indicating that MGEs play an important role as a mediator in the spread of ARGs. At the phylum level, Proteobacteria and Cyanobacteria were the dominant bacteria in the study area, with HIMB11 and unidentifiedChloroplast being the dominant levels, respectively. Network analysis of ARGs and microorganisms (genus level) revealed that Cognatishimia, Thalassobius, Aestuariicoccus, Thalassotalea, and Vibrio were significantly correlated with multiple ARGs and were the main potential hosts of ARGs in the nearshore waters of Wenchang.

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

One Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019

BACKGROUND

Colistin serves as the last line of defense against multidrug resistant Gram-negative bacterial infections in both human and veterinary medicine. This study aimed to investigate the occurrence and spread of colistin-resistant Enterobacterales (ColR-E) using a One Health approach in Belgium and in the Netherlands.

METHODS

In a transnational research project, a total of 998 hospitalized patients, 1430 long-term care facility (LTCF) residents, 947 children attending day care centres, 1597 pigs and 1691 broilers were sampled for the presence of ColR-E in 2017 and 2018, followed by a second round twelve months later for hospitalized patients and animals. Colistin treatment incidence in livestock farms was used to determine the association between colistin use and resistance. Selective cultures and colistin minimum inhibitory concentrations (MIC) were employed to identify ColR-E. A combination of short-read and long-read sequencing was utilized to investigate the molecular characteristics of 562 colistin-resistant isolates. Core genome multi-locus sequence typing (cgMLST) was applied to examine potential transmission events.

RESULTS

The presence of ColR-E was observed in all One Health sectors. In Dutch hospitalized patients, ColR-E proportions (11.3 and 11.8% in both measurements) were higher than in Belgian patients (4.4 and 7.9% in both measurements), while the occurrence of ColR-E in Belgian LTCF residents (10.2%) and children in day care centres (17.6%) was higher than in their Dutch counterparts (5.6% and 12.8%, respectively). Colistin use in pig farms was associated with the occurrence of colistin resistance. The percentage of pigs carrying ColR-E was 21.8 and 23.3% in Belgium and 14.6% and 8.9% in the Netherlands during both measurements. The proportion of broilers carrying ColR-E in the Netherlands (5.3 and 1.5%) was higher compared to Belgium (1.5 and 0.7%) in both measurements. mcr-harboring E. coli were detected in 17.4% (31/178) of the screened pigs from 7 Belgian pig farms. Concurrently, four human-related Enterobacter spp. isolates harbored mcr-9.1 and mcr-10 genes. The majority of colistin-resistant isolates (419/473, 88.6% E. coli; 126/166, 75.9% Klebsiella spp.; 50/75, 66.7% Enterobacter spp.) were susceptible to the critically important antibiotics (extended-spectrum cephalosporins, fluoroquinolones, carbapenems and aminoglycosides). Chromosomal colistin resistance mutations have been identified in globally prevalent high-risk clonal lineages, including E. coli ST131 (n = 17) and ST1193 (n = 4). Clonally related isolates were detected in different patients, healthy individuals and livestock animals of the same site suggesting local transmission. Clonal clustering of E. coli ST10 and K. pneumoniae ST45 was identified in different sites from both countries suggesting that these clones have the potential to spread colistin resistance through the human population or were acquired by exposure to a common (food) source. In pig farms, the continuous circulation of related isolates was observed over time. Inter-host transmission between humans and livestock animals was not detected.

CONCLUSIONS

The findings of this study contribute to a broader understanding of ColR-E prevalence and the possible pathways of transmission, offering insights valuable to both academic research and public health policy development.

Assessment of the Implementation of Pakistan's National Action Plan on Antimicrobial Resistance in the Agriculture and Food Sectors

The agriculture and food (agrifood) sectors play key roles in the emergence, spread, and containment of antimicrobial resistance (AMR). Pakistan's first National Action Plan (NAP) on AMR was developed to guide One Health interventions to combat AMR through 2017-2022. To improve subsequent iterations, we assessed the implementation of Pakistan's NAP in the agrifood sectors (NAPag) in October 2022, using the Progressive Management Pathway on AMR tool developed by the Food and Agriculture Organization of the United Nations (FAO). The assessment tool addressed four crucial focus areas of the NAPag: governance, awareness, evidence, and practices. Each focus area contains multiple topics, which involve four sequential stages of activities to progressively achieve systematic management of AMR risk in the agrifood sectors. High-level representatives of the NAPag stakeholders provided information for the assessment through pre-event documentary review and workshop discussions. The assessment results showed that Pakistan's NAPag had an overall moderate coverage (59%) of the anticipated activities. Gaps were particularly notable in strengthening governance, good practices, and interventions in non-livestock sectors. Furthermore, only 12% of the evaluated activities were fully executed and documented, consistently remaining at the planning and piloting stages in the livestock sector across all the examined topics. Insufficient attention to non-livestock sectors, inadequate regulation and enforcement capacity, and resource constraints have hindered scalable and sustainable interventions under the current plan. This assessment provides valuable insights to strengthen the inclusiveness and contribution of the agrifood sectors in the next NAP iteration. In the short-to-medium term, strategic prioritization is necessary to optimize the use of limited resources and target the most critical gaps, such as improving awareness among key stakeholders and fortifying regulations for prudent antimicrobial use. In the long term, integration of AMR into the country's broader health, development, and agricultural transformation agendas will be needed to generate sustainable benefits.

The importance of meropenem resistance, rather than imipenem resistance, in defining carbapenem-resistant Enterobacterales for public health surveillance: an analysis of national population-based surveillance

BACKGROUND

In Japan, carbapenem-resistant Enterobacterales (CRE) infections were incorporated into the National Epidemiological Surveillance of Infectious Diseases (NESID) in 2014, necessitating mandatory reporting of all CRE infections cases. Subsequently, pathogen surveillance was initiated in 2017, which involved the collection and analysis of CRE isolates from reported cases to assess carbapenemase gene possession. In this surveillance, CRE is defined as (i) minimum inhibitory concentration (MIC) of meropenem ≥2 mg/L (MEPM criteria) or (ii) MIC of imipenem ≥2 mg/L and MIC of cefmetazole ≥64 mg/L (IPM criteria). This study examined whether the current definition of CRE surveillance captures cases with a clinical and public health burden.

METHODS

CRE isolates from reported cases were collected from the public health laboratories of local governments, which are responsible for pathogen surveillance. Antimicrobial susceptibility tests were conducted on these isolates to assess compliance with the NESID CRE definition. The NESID data between April 2017 and March 2018 were obtained and analyzed using antimicrobial susceptibility test results.

RESULTS

In total, 1681 CRE cases were identified during the study period, and pathogen surveillance data were available for 740 (44.0%) cases. Klebsiella aerogenes and Enterobacter cloacae complex were the dominant species, followed by Klebsiella pneumoniae and Escherichia coli. The rate of carbapenemase gene positivity was 26.5% (196/740), and 93.4% (183/196) of these isolates were of the IMP type. Meanwhile, 315 isolates were subjected to antimicrobial susceptibility testing. Among them, 169 (53.7%) fulfilled only the IPM criteria (IPM criteria-only group) which were susceptible to meropenem, while 146 (46.3%) fulfilled the MEPM criteria (MEPM criteria group). The IPM criteria-only group and MEPM criteria group significantly differed in terms of carbapenemase gene positivity (0% vs. 67.8%), multidrug resistance rates (1.2% vs. 65.8%), and mortality rates (1.8% vs 6.9%).

CONCLUSION

The identification of CRE cases based solely on imipenem resistance has had a limited impact on clinical management. Emphasizing resistance to meropenem is crucial in defining CRE, which pose both clinical and public health burden. This emphasis will enable the efficient allocation of limited health and public health resources and preservation of newly developed antimicrobials.

The erythromycin polyketide compound TMC-154 stimulates ROS generation to exert antibacterial effects against Streptococcus pyogenes

The erythromycin polyketide compound TMC-154 is a secondary metabolite that is isolated from the rhizospheric fungus Clonostachys rogersoniana associated with Panax notoginseng, which possesses antibacterial activity. However, its antibacterial mechanism has not been investigated thus far. In this study, proteomics coupled with bioinformatics approaches was used to explore the antibacterial mechanism of TMC-154. KEGG pathway enrichment analysis indicated that eight signaling pathways were associated with TMC-154, including oxidative phosphorylation, cationic antimicrobial peptide (CAMP) resistance, benzoate degradation, heme acquisition systems, glycine/serine and threonine metabolism, beta-lactam resistance, ascorbate and aldarate metabolism, and phosphotransferase system (PTS). Cell biology experiments confirmed that TMC-154 could induce reactive oxygen species (ROS) generation in Streptococcus pyogenes; moreover, TMC-154-induced antibacterial effects could be blocked by the inhibition of ROS generation with the antioxidant N-acetyl L-cysteine. In addition, TMC-154 combined with ciprofloxacin or chloramphenicol had synergistic antibacterial effects. These findings indicate the potential of TMC-154 as a promising drug to treat S. pyogenes infections. SIGNIFICANCE: Streptococcus pyogenes is a nearly ubiquitous human pathogen that causes a variety of diseases ranging from mild pharyngitis and skin infection to fatal sepsis and toxic heat shock syndrome. With the increasing incidence of known antibiotic resistance, there is an urgent need to find novel drugs with good antibacterial activity against S. pyogenes. In this study, we found that TMC-154, a secondary metabolite from the fungus Clonostachys rogersoniana, inhibited the growth of various bacteria, including Staphylococcus aureus, S. pyogenes, Streptococcus mutans, Pseudomonas aeruginosa and Vibrio parahemolyticus. Proteomic analysis combined with cell biology experiments revealed that TMC-154 stimulated ROS generation to exert antibacterial effects against S. pyogenes. This study provides potential options for the treatment of S. pyogenes infections in the future.

Global antimicrobial resistance and use surveillance system (GLASS 2022): Investigating the relationship between antimicrobial resistance and antimicrobial consumption data across the participating countries

For the first time since 2015, the World Health Organization's (WHO) global Antimicrobial Resistance and Use Surveillance (GLASS) featured both global reports for antimicrobial resistance (AMR) and antimicrobial consumption (AMC) data in its annual reports. In this study we investigated the relationship of AMR with AMC within participating countries reported in the GLASS 2022 report. Our analysis found a statistically significant correlation between beta-lactam/cephalosporin and fluoroquinolones consumption and AMR to these antimicrobials associated with bloodstream E. coli and Klebsiella pneumoniae among the participating countries (P<0.05). We observed that for every 1 unit increase in defined daily dose DDD of beta-lactam/cephalosporins and quinolone consumptions among the countries, increased the recoveries of bloodstream-associated beta-lactam/cephalosporins-resistant E. coli/Klebsiella spp. by 11-22% and quinolone-resistant E. coli/Klebsiella spp. by 31-40%. When we compared the antimicrobial consumptions between the antimicrobial ATC (Alphanumeric codes developed by WHO) groups and countries, we observed a statistically significant higher daily consumption of beta-lactam-penicillins (J01C, DDD difference range: 5.23-8.13) and cephalosporins (J01D, DDD difference range: 2.57-5.13) compared to other antimicrobial groups among the countries (adjusted for multiple comparisons using Tukey's method). Between the participating countries, we observed a statistically significant higher daily consumption of antimicrobial groups in Iran (DDD difference range: 3.63-4.84) and Uganda (DDD difference range: 3.79-5.01) compared to other participating countries (adjusted for multiple comparisons using Tukey's method). Understanding AMC and how it relates to AMR at the global scale is critical in the global AMR policy development and implementation of global antimicrobial stewardship.

Using a Stakeholder Analysis to Implement the Belgian One Health National Report for Antimicrobial Use and Resistance

(1) Background. Antimicrobial resistance (AMR) poses a substantial global health threat with profound economic implications. Acknowledging the imperative for a One Health (OH) strategy to combat this menace, Belgium introduced an annual national OH report, known as the "BELMAP report," encompassing antimicrobial use (AMU) and AMR, with the first edition completed in 2021. The integration of innovations for the healthcare system demands a meticulously planned process. (2) Methods. We introduced a three-step stakeholder analysis (SA) as a prospective framework for navigating this new report process, fostering complementary collaboration, pinpointing obstacles, suggesting approaches to overcome them, and facilitating national policy development. The SA unfolds in three steps: stakeholders identify and list their relevant activities, assess their positions regarding the BELMAP report, and complete "actor mapping" of national AMR and AMU stakeholders. (3) Results. Stakeholder identification reveals a fragmented landscape of AMR and AMU activities across Belgium. Assessment of stakeholder positions uncovers diverse expectations, collaborative challenges, and resource considerations. "Actor mapping" identifies key stakeholders, emphasizing the importance of high-interest and high-power actors. (4) Conclusions. This SA approach not only provides insights into the present stakeholder landscape in Belgium, it can also serve as a blueprint for other countries in the process of developing OH reports.

Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina

BACKGROUND

Escherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS).

MATERIALS AND METHODS

Retail chicken (breast, n = 96; giblets, n = 24), turkey (n = 96), and pork (n = 96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree was generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type.

RESULTS

Of 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as multidrug resistant (MDR: being resistant to ≥3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3'')-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2 = 2.21, p = 0.33). MDR was observed in isolates from meat products with labels indicating "no claims" (n = 29; 69%), "no antibiotics ever" (n = 9; 21.4%), and "organic" (n = 4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates.

CONCLUSIONS

E. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.

District health information system (DHIS2) as integrated antimicrobial resistance surveillance platform: An exploratory qualitative investigation of the one health stakeholders' viewpoints in Ethiopia

INTRODUCTION

There is an unmet need for One Health (OH) surveillance and reporting systems for antimicrobial resistance (AMR) in resource poor settings. District health information system, version 2 (DHIS2), is a globally recognized digital surveillance platform which has not been widely utilized for AMR data yet. Our study aimed to understand the local stakeholders' viewpoints on DHIS2 as OH-AMR surveillance platform in Jimma, Ethiopia which will aid its further context specific establishment.

METHODS

We performed an exploratory qualitative study using semi-structured key informant interviews (KIIs) in Jimma Zone at Southwest Ethiopia. We interviewed 42 OH professionals between November 2020 and February 2021. Following verbatim transcription of the audio recordings of KIIs, we conducted thematic analysis.

RESULTS

We identified five major themes which are important for understanding the trajectory of OH-AMR surveillance in DHIS2 platform. The themes were: (1) Stakeholders' current knowledge on digital surveillance platforms including DHIS2. (2) Stakeholders' perception on digital surveillance platform including DHIS2. (3) Features suggested by stakeholders to be included in the surveillance platform. (4) Comments from stakeholders on system implementation challenges. (5) Stakeholders' perceived role in the process of implementation. Despite several barriers and challenges, most of the participants perceived and suggested DHIS2 as a suitable OH-AMR surveillance platform and were willing to contribute at their current professional roles.

CONCLUSIONS

Our study demonstrates the potential of the DHIS2 as a user friendly and acceptable interoperable platform for OH-AMR surveillance if the technology designers accommodate the stakeholders' concerns. Piloting at local level and using performance appraisal tool in all OH disciplines should be the next step before proceeding to workable format.

Knowledge, attitudes, and practices regarding antibiotic use among the population of the Republic of Serbia - A cross-sectional study

BACKGROUND

Antimicrobial resistance presents one of the most significant threats to public health. This study aimed to examine antibiotic usage within the general population in the Republic of Serbia and their knowledge, attitudes, and behavior concerning this topic.

METHODS

We conducted an online cross-sectional study over two weeks in December 2022, on a sample of 1014 respondents, representative of the Republic of Serbia's population. Predictors of the Antibiotic Knowledge Score (composed of four questions) were analyzed by multivariate ordinal logistic regression.

RESULTS

In 2022, 76.8% of the participants from the Serbian population had taken antibiotics, mostly upon a medical prescription, with the most common reasons being upper respiratory tract infections. Only 31.3% of all respondents received any kind of advice about the rational use of antibiotics and half of them changed their opinions on using antibiotics after receiving this information. The average Antibiotic Knowledge Score was 2.6 out of 4, with 32.5% of respondents answering all knowledge questions correctly. The multivariate ordinal logistic regression analysis showed that female gender, higher education level, and the willingness to change opinions regarding the usage of antibiotics after receiving information about the rational use of antibiotics from any available source were significant predictors of better knowledge about antibiotics use. Respondents who were open to changing their opinion after receiving information about the rational use of antibiotics had 28% higher odds of higher antibiotic knowledge scores.

CONCLUSION

This is the first population-level study on public knowledge, attitudes, and practices about antibiotic use in Serbia and therefore the baseline for future research and measuring the impact of potential interventions. Our findings underline the importance of taking into account specific population characteristics, knowledge levels, and attitudes when designing educational and intervention strategies for antibiotic use. Policymakers can leverage these findings to target specific groups and enhance the population's knowledge and practices regarding rational antibiotic usage.

Antibiotic point prevalence survey and antimicrobial resistance in hospitalized patients across Peruvian reference hospitals

BACKGROUND

Peru reports higher levels than other countries in Latin America of resistance to antimicrobials among Gram-positive and Gram-negative bacteria, however data on antibiotic use in Peru are scarce. This study aims to estimate the prevalence and quality of antibiotic prescription in hospitalized patients and to determine the antibiotic susceptibility rates of bacteria causing key bacterial infections.

METHODS

We carried out a point prevalence survey of antibiotic prescription at ten public hospitals in nine regions of Peru. Data was collected from patients hospitalized during a 3-week period, with details about antibiotic use, patient information, and antimicrobial susceptibility.

RESULTS

1620 patient charts were reviewed; in 924 cases antibiotics were prescribed (57.0 %, range 45.9-78.9 %). Most of the antibiotics (74.2 %) were prescribed as empirical treatment, only 4.4 % as targeted treatment. For 9.5 % of cases the reason for antibiotic use was unknown. Cephalosporins were the most prescribed (30.0 %), followed by carbapenems (11.3 %). Ninety-four blood cultures were positive for bacterial growth, 48.8 % of the Staphylococcus aureus were methicillin-resistant, among Escherichia coli and Klebsiella pneumoniae, 51.7 % and 72.7 % were resistant to third-generation cephalosporins (3GC), 3.4 % and 18.2 % were resistant to carbapenems, respectively. Among bacteria isolated from urine cultures (n = 639), 43.9 % of E. coli and 49.2 % of K. pneumoniae were resistant to 3GC, and 0.9 % of E. coli and 3.2 % of K. pneumoniae were resistant to meropenem.

CONCLUSIONS

The overall proportion of hospitalized patients receiving antibiotics in hospitals from different regions in Peru was high, with only a small proportion receiving targeted treatment. Cephalosporins and carbapenems were the most frequently prescribed antibiotics, reflecting high resistance rates against 3GC and carbapenems in Enterobacterales isolated from blood and urine.

Augmented surveillance of antimicrobial resistance with high-throughput robotics detects transnational flow of fluoroquinolone-resistant Escherichia coli strain into poultry

BACKGROUND

Food animal AMR surveillance programs assess only small numbers of Escherichia coli (from 100 to 600 per animal class) nationally each year, severely limiting the evaluation of public health risk(s). Here we demonstrate an affordable approach for early detection of emerging resistance on a broad scale that can also accurately characterize spatial and temporal changes in resistance.

METHODS

Caecal samples (n = 295) obtained from 10 meat poultry were screened using high-throughput robotics. Initial screening via agar dilution (5310 plates) quantified AMR carriage (cfu/g) for each sample. Ciprofloxacin-resistant isolates (n = 91) proceeded to downstream broth microdilution susceptibility testing. A subset of 28 ciprofloxacin-resistant isolates underwent WGS and phylogenetic analysis.

RESULTS

Intra- and inter-flock carriage of resistance varied with drug class. Ampicillin and tetracycline resistance was ubiquitous to most birds in all flocks with an average carriage rate of 5.8 log10 cfu/g. Gentamicin and ciprofloxacin-resistant E. coli colonized fewer birds, and had an average carriage rate of 1.2 log10 cfu/g and 1.0 log10 cfu/g of faeces, respectively. Resistance to extended-spectrum cephalosporins was absent. ST354 was the dominant ST among the WGS isolates, but they demonstrated markedly lower resistance gene carriage than their international counterparts.

CONCLUSIONS

These data amply demonstrate the ineffectiveness of commonly relied-on approaches to AMR surveillance for achieving early detection of emergence, or for measuring spatial and temporal resistance trends. Genetic analysis suggested there has been transnational flow of a ciprofloxacin-resistant strain into Australian poultry flocks, explaining their detection in a nation that prohibits fluoroquinolone use in poultry.

Wastewater-based epidemiology for tracking bacterial diversity and antibiotic resistance in COVID-19 isolation hospitals in Qatar

BACKGROUND

Hospitals are hotspots for antimicrobial resistance genes (ARGs), and play a significant role in their emergence and spread. Large numbers of ARGs will be ejected from hospitals via wastewater systems. Wastewater-based epidemiology has been consolidated as a tool to provide real-time information, and represents a promising approach to understanding the prevalence of bacteria and ARGs at community level.

AIMS

To determine bacterial diversity and identify ARG profiles in hospital wastewater pathogens obtained from coronavirus disease 2019 (COVID-19) isolation hospitals compared with non-COVID-19 facilities during the pandemic.

METHODS

Wastewater samples were obtained from four hospitals: three assigned to patients with COVID-19 patients and one assigned to non-COVID-19 patients. A microbial DNA quantitative polymerase chain reaction was used to determine bacterial diversity and ARGs.

FINDINGS

The assay recorded 27 different bacterial species in the samples, belonging to the following phyla: Firmicutes (44.4%), Proteobacteria (33.3%), Actinobacteria (11%), Bacteroidetes (7.4%) and Verrucomicrobiota (3.7%). In addition, 61 ARGs were detected in total. The highest number of ARGs was observed for the Hazem Mebaireek General Hospital (HMGH) COVID-19 patient site (88.5%), and the lowest number of ARGs was found for the HMGH non-patient site (24.1%).

CONCLUSION

The emergence of contaminants in sewage water, such as ARGs and high pathogen levels, poses a potential risk to public health and the aquatic ecosystem.

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Effect of a national antibiotic stewardship intervention in China targeting carbapenem overuse: An interrupted time-series analysis

OBJECTIVES

To assess trends and patterns of carbapenem use and to evaluate the effects of a nationwide antibiotic stewardship policy to reduce carbapenem overuse.

METHODS

In this quasi-experimental study, using longitudinal data from the national drug procurement database and interrupted time-series analyses with carbapenems as the intervention group and possible carbapenem substitutes as the comparison group, we evaluated the effects of a national stewardship policy on carbapenem consumption and expenditures, by region and types of healthcare institutions.

RESULTS

The carbapenem procurement volume declined by -28.8% (95% CI -35.0 to -22.6) (-334.4 thousand defined daily doses [DDDs] per month), and carbapenem expenditures showed a relative reduction of -38.1% (-43.9 to -32.2). The gap between the use of carbapenems and each drug in the comparison group narrowed after the policy intervention, with an increase in tigecycline use (14.9 thousand DDDs [10.8-18.9]) and a slower decrease in use of certain third-generation cephalosporin combinations (-85.7 [-143.0 to -28.4]), penicillin combinations (-200.9 [-421.4-19.6]), and fourth-generation cephalosporins (-116.9 [-219.8 to -14.0]). Consumption was highest during the pre-policy period, and declines were largest following the intervention in the eastern region (-32.1%, -39.8 to -24.4) and among tertiary hospitals (-266.2 [-339.5 to -192.9] thousand DDDs per month).

CONCLUSION

This population-level drug utilization research represents the first comprehensive evaluation of the effectiveness of China's nationwide carbapenem stewardship. The national policy targeting carbapenem prescribing has led to a sustained reduction in carbapenem use with limited substitution. Effects varied geographically and were concentrated in tertiary and secondary hospitals.

Modelling antimicrobial resistance transmission to guide personalized antimicrobial stewardship interventions and infection control policies in healthcare setting: a pilot study

Infection control programs and antimicrobial stewardship have been proven effective in reducing the burden of diseases due to multidrug-resistant organisms, but quantifying the effect of each intervention is an open issue. For this aim, we propose a model to characterize the effect of interventions at single ward level. We adapted the Ross-Macdonald model to describe hospital cross-transmission dynamics of carbapenem resistant Klebsiella pneumoniae (CRKP), considering healthcare workers as the vectors transmitting susceptible and resistant pathogens among admitted patients. The model parameters were estimated from a literature review, further adjusted to reproduce observed clinical outcomes, and validated using real life data from a 2-year study in a university hospital. The model has been further explored through extensive sensitivity analysis, in order to assess the relevance of single interventions as well as their synergistic effects. Our model has been shown to be an effective tool to describe and predict the impact of interventions in reducing the prevalence of CRKP colonisation and infection, and can be extended to other specific hospital and pathological scenarios to produce tailored estimates of the most effective strategies.

Poor Sensitivity of the MALDI Biotyper® MBT Subtyping Module for Detection of Klebsiella pneumoniae Carbapenemase (KPC) in Klebsiella Species

Rapid detection of Klebsiella pneumoniae carbapenemase (KPC) in the Klebsiella species is desirable. The MALDI Biotyper® MBT Subtyping Module (Bruker Daltonics) uses an algorithm that detects a peak at ~11,109 m/z corresponding to a protein encoded by the p019 gene to detect KPC simultaneously with organism identification by a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-ToF MS). Here, the subtyping module was evaluated using 795 clinical Klebsiella isolates, with whole genome sequences used to assess for blaKPC and p019. For the isolates identified as KPC positive by sequencing, the overall sensitivity of the MALDI-ToF MS subtyping module was 239/574 (42%) with 100% specificity. For the isolates harboring p019, the subtyping module showed a sensitivity of 97% (239/246) and a specificity of 100%. The subtyping module had poor sensitivity for the detection of blaKPC-positive Klebsiella isolates, albeit exhibiting excellent specificity. The poor sensitivity was a result of p019 being present in only 43% of the blaKPC-positive Klebsiella isolates.

A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy

BACKGROUND

Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant microorganisms. We reported the results of a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which causes hospital-acquired infections (HAIs) and is characterized by a marked resistance profile.

METHODS

Clinical, phenotypic, and genotypic data were collected for the AMR surveillance screening program of the University Hospital of Sassari (Italy) during 2020-2021. Genomic DNA was sequenced using the Illumina Nova Seq 6000 platform. Final assemblies were manually curated and carefully verified for the detection of antimicrobial resistance genes, porin mutations, and virulence factors. A phylogenetic analysis was performed using the maximum likelihood method.

RESULTS

All 17 strains analyzed belonged to ST512, and most of them carried the blaKPC-31 variant blaOXA-48-like, an OmpK35 truncation, and an OmpK36 mutation. Phenotypic analysis showed a marked resistance profile to all antibiotic classes, including β-lactams, carbapenems, aminoglycosides, fluoroquinolone, sulphonamides, and novel β-lactam/β-lactamase inhibitors (BL/BLI).

CONCLUSION

WGS characterization revealed the presence of several antibiotic resistance determinants and porin mutations in highly resistant K. pneumoniae strains responsible for HAIs. The detection of blaKPC-31 in our hospital wards highlights the importance of genomic surveillance in hospital settings to monitor the emergence of new clones and the need to improve control and preventive strategies to efficiently contrast AMR.

Strengthening antimicrobial resistance surveillance systems: a scoping review

BACKGROUND

Antimicrobial resistance (AMR) is an emerging global public health crisis. Surveillance is a fundamental component in the monitoring and evaluation of AMR mitigation endeavours. The primary aim of the scoping review is to identify successes, barriers, and gaps in implementing AMR surveillance systems and utilising data from them.

METHODS

PubMed, Web of Science, SCOPUS, and EMBASE databases were searched systematically to identify literature pertaining to implementation, monitoring, and evaluation of AMR surveillance systems. A thematic analysis was conducted where themes within the literature were inductively grouped based on the described content.

RESULTS

The systematic search yielded 639 journal articles for screening. Following deduplication and screening, 46 articles were determined to be appropriate for inclusion. Generally, most studies focused on human AMR surveillance (n = 38, 82.6%). Regionally, there was equal focus on low- and middle-income countries (n = 7, 15.2%) and trans-national contexts (n = 7, 14.5%). All included articles (n = 46, 100.0%) discussed barriers to either implementing or utilising AMR surveillance systems. From the scoping review, 6 themes emerged: capacity for surveillance, data infrastructure, policy, representativeness, stakeholder engagement, and sustainability. Data infrastructure was most frequently discussed as problematic in evaluation of surveillance systems (n = 36, 75.0%). The most frequent success to surveillance system implementation was stakeholder engagement (n = 30, 65.2%).

CONCLUSIONS

Experiences of AMR surveillance systems are diverse across contexts. There is a distinct separation of experiences between systems with emerging surveillance systems and those with established systems. Surveillance systems require extensive refinement to become representative and meet surveillance objectives.

Prevalence and Clinical Characteristics of Bacterial Pneumonia in Neurosurgical Emergency Center Patients: A Retrospective Study Spanning 13 Years at a Tertiary Center

Patients with brain injuries are at a heightened susceptibility to bacterial pneumonia, and the timely initiation of empiric antibiotic treatment has been shown to substantially reduce mortality rates. Nevertheless, there is a need for knowledge regarding the resistance and prevalence of pulmonary bacterial infections in this patient population. To address this gap, a retrospective study was conducted at a neurosurgical emergency center, focusing on patients with brain injuries. Among the entire patient population, a total of 739 individuals (18.23%) were identified as having bacterial pneumonia, consisting of 1489 strains of Gram-negative bacteria and 205 strains of Gram-positive bacteria. The resistance of Klebsiella pneumoniae to imipenem exhibited a significant increase, rising from 21.74% in 2009 to 96.67% in 2018, and subsequently reaching 48.47% in 2021. Acinetobacter baumannii displayed resistance rates exceeding 80.0% against multiple antibiotics. The resistance profile of Pseudomonas aeruginosa was relatively low. The proportion of Staphylococcus aureus reached its peak at 18.70% in 2016, but experienced a decline to 7.83% in 2021. The abundance of Gram-negative bacteria exceeded that of Gram-positive bacteria by a factor of 5.96. Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus are prominent pathogens characterized by limited antibiotic choices and scarce treatment alternatives for the isolated strains.

The epidemiology and microbiological characteristics of infections caused by Gram-negative bacteria in Qatar: national surveillance from the Study for Monitoring of Antimicrobial Resistance Trends (SMART): 2017 to 2019

Background

The global Study of Monitoring Antimicrobial Resistance Trends (SMART) is a surveillance program for evaluation of antimicrobial resistance (AMR) in Gram-negative bacteria (GNB) from different regions including Gulf countries.

Objectives

To evaluate AMR in GNB from various clinical specimens including microbiological and genetic characteristics for existing and novel antimicrobials.

Methods

A prospective study was conducted on clinical specimens from Hamad Medical Corporation, Qatar, between 2017 and 2019 according to the SMART protocol. Consecutive GNB from different sites were evaluated including lower respiratory, urinary tract, intrabdominal and bloodstream infections.

Results

Over the 3 years study period, 748 isolates were evaluated from the specified sites comprising 37 different GNB outlining four key pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia.For the two major pathogens E. coli and K. pneumoniae, phenotypic ESBL was identified in 55.77% (116/208) compared to 39% (73/187), while meropenem resistance was 3.8% compared to 12.8% and imipenem/relebactam resistance was 2.97% compared to 11.76%, respectively. The overall ceftolozane/tazobactam resistance for E. coli was 9.6% (20/208) compared to 14.97% (28/187) for K. pneumoniae while resistance for ceftazidime/avibactam was 3.65% (5/137) and 5.98% (10/117), respectively. Genomic characteristics of 70 Enterobacterales including 48 carbapenem-resistant, revealed prevalence of β-lactamases from all classes, predominated by blaCXM-15 while carbapenem resistance revealed paucity of blaKPC and dominance of blaOXA-48 and blaNDM resistance genes.

Conclusions

Surveillance of GNB from Qatar showed prevalence of key pathogens similar to other regions but demonstrated significant resistance patterns to existing and novel antimicrobials with different underlying resistance mechanisms.

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome

Background

The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.

Methods

This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.

Results

Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.

A 7-Year Brazilian National Perspective on Plasmid-Mediated Carbapenem Resistance in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii Complex and the Impact of the Coronavirus Disease 2019 Pandemic on Their Occurrence

BACKGROUND

Carbapenemase production is a global public health threat. Antimicrobial resistance (AMR) data analysis is critical to public health policy. Here we analyzed carbapenemase detection trends using the AMR Brazilian Surveillance Network.

METHODS

Carbapenemase detection data from Brazilian hospitals included in the public laboratory information system dataset were evaluated. The detection rate (DR) was defined as carbapenemase detected by gene tested per isolate per year. The temporal trends were estimated using the Prais-Winsten regression model. The impact of COVID-19 on carbapenemase genes in Brazil was determined for the period 2015-2022. Detection pre- (October 2017 to March 2020) and post-pandemic onset (April 2020 to September 2022) was compared using the χ2 test. Analyses were performed with Stata 17.0 (StataCorp, College Station, TX).

RESULTS

83 282 blaKPC and 86 038 blaNDM were tested for all microorganisms. Enterobacterales DR for blaKPC and blaNDM was 68.6% (41 301/60 205) and 14.4% (8377/58 172), respectively. P. aeruginosa DR for blaNDM was 2.5% (313/12 528). An annual percent increase for blaNDM of 41.1% was observed, and a decrease for blaKPC of -4.0% in Enterobacterales, and an annual increase for blaNDM of 71.6% and for blaKPC of 22.2% in P. aeruginosa. From 2020 to 2022, overall increases of 65.2% for Enterobacterales, 77.7% for ABC, and 61.3% for P. aeruginosa were observed in the total isolates.

CONCLUSIONS

This study shows the strengths of the AMR Brazilian Surveillance Network with robust data related to carbapenemases in Brazil and the impact of COVID-19 with a change in carbapenemase profiles with blaNDM rising over the years.

Enhancing Insights into Australia's Gonococcal Surveillance Programme through Stochastic Modelling

Continued surveillance of antimicrobial resistance is critical as a feedback mechanism for the generation of concerted public health action. A characteristic of importance in evaluating disease surveillance systems is representativeness. Scenario tree modelling offers an approach to quantify system representativeness. This paper utilises the modelling approach to assess the Australian Gonococcal Surveillance Programme's representativeness as a case study. The model was built by identifying the sequence of events necessary for surveillance output generation through expert consultation and literature review. A scenario tree model was developed encompassing 16 dichotomous branches representing individual system sub-components. Key classifications included biological sex, clinical symptom status, and location of healthcare service access. The expected sensitivities for gonococcal detection and antibiotic status ascertainment were 0.624 (95% CI; 0.524, 0.736) and 0.144 (95% CI; 0.106, 0.189), respectively. Detection capacity of the system was observed to be high overall. The stochastic modelling approach has highlighted the need to consider differential risk factors such as sex, health-seeking behaviours, and clinical behaviour in sample generation. Actionable points generated by this study include modification of clinician behaviour and supplementary systems to achieve a greater contextual understanding of the surveillance data generation process.

Effect of substituting glutamine with lysine on structural and biological properties of antimicrobial peptide Polybia-MP1

The natural antimicrobial peptide Polybia-MP1 is a promising candidate for developing new treatment therapy for infection and cancer. It showed broad-spectrum antimicrobial and anticancer activity with high safety on healthy cells. However, previous sequence modification usually resulted in at least one of two consequences: a notable increase in hemolytic activity or a considerable decrease in activity against Gram-negative bacteria and cancer cells. Herein, a new approach was applied by replacing the amino acid Glutamine at position 12 with Lysine and generating the MP1-Q12K analog. Our preliminary data suggested an enhancement in antibacterial and antifungal activity, whereas the anticancer and hemolytic activity of the two peptides were comparable. Moreover, MP1-Q12K was found to be less self-assembly than Polybia-MP1, which further supports the enhancement of antimicrobial properties. Hence, this study provides new information regarding the structure-activity relationships of Polybia-MP1 and support for the development of potent, selective antimicrobial peptides.

Deep Domain Adaptation Enhances Amplification Curve Analysis for Single-Channel Multiplexing in Real-Time PCR

Data-driven approaches for molecular diagnostics are emerging as an alternative to perform an accurate and inexpensive multi-pathogen detection. A novel technique called Amplification Curve Analysis (ACA) has been recently developed by coupling machine learning and real-time Polymerase Chain Reaction (qPCR) to enable the simultaneous detection of multiple targets in a single reaction well. However, target classification purely relying on the amplification curve shapes faces several challenges, such as distribution discrepancies between different data sources (i.e., training vs testing). Optimisation of computational models is required to achieve higher performance of ACA classification in multiplex qPCR through the reduction of those discrepancies. Here, we proposed a novel transformer-based conditional domain adversarial network (T-CDAN) to eliminate data distribution differences between the source domain (synthetic DNA data) and the target domain (clinical isolate data). The labelled training data from the source domain and unlabelled testing data from the target domain are fed into the T-CDAN, which learns both domains' information simultaneously. After mapping the inputs into a domain-irrelevant space, T-CDAN removes the feature distribution differences and provides a clearer decision boundary for the classifier, resulting in a more accurate pathogen identification. Evaluation of 198 clinical isolates containing three types of carbapenem-resistant genes (blaNDM, blaIMP and blaOXA-48) illustrates a curve-level accuracy of 93.1% and a sample-level accuracy of 97.0% using T-CDAN, showing an accuracy improvement of 20.9% and 4.9% respectively. This research emphasises the importance of deep domain adaptation to enable high-level multiplexing in a single qPCR reaction, providing a solid approach to extend qPCR instruments' capabilities in real-world clinical applications.

Antimicrobial resistance profiles of Escherichia coli isolated from laying hens in Zambia: implications and significance on one health

Background

Antimicrobial resistance (AMR) has been deepening in the layer poultry sector in Zambia partly due to the inappropriate use of antimicrobials. Escherichia coli (E. coli), a commensal and zoonotic bacterium, can potentially be a source of AMR.

Objectives

This study assessed the phenotypic AMR profiles of E. coli isolated from the apparent health-laying hens in Lusaka and Copperbelt provinces of Zambia.

Methods

A cross-sectional study was conducted between September 2020 and April 2021 in which 365 cloacal swabs were collected from 77-layer farms based in Lusaka and Copperbelt provinces of Zambia. E. coli isolation and identification were done using cultural and biochemical properties and confirmed using the 16S rRNA gene sequencing. Antimicrobial susceptibility testing (AST) was done using the Kirby-Bauer disc-diffusion method. Data analysis was done using WHONET 2020 and Stata v.16.1.

Results

Of the 365 samples, E. coli was isolated from 92.9% (n = 339). The AMR was detected in 96.5% (n = 327) of the isolates, of which 64.6% (n = 219) were multidrug-resistant (MDR). E. coli was highly resistant to tetracycline (54.6%) and ampicillin (54%) but showed low resistance to meropenem (0.9%), ceftazidime (6.2%) and chloramphenicol (8.8%).

Conclusion

This study found a high prevalence of E. coli resistant to some commonly used antibiotics in poultry, which is a public health concern because of the potential contamination of eggs and layers of chicken meat that enter the food chain. Urgent attention is needed, including strengthening antimicrobial stewardship and surveillance programmes in layer poultry production in Zambia.

High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent

Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla _VIM, bla _IMP, bla _KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.

Early Warning Systems for Emerging Profiles of Antimicrobial Resistance in Italy: A National Survey

Antimicrobial resistance (AMR) national surveillance systems in Italy lack alert systems for timely detection of emerging profiles of AMR with potential relevance to public health. Furthermore, the existence of early warning systems (EWS) at subnational level is unclear. This study aims at mapping and characterizing EWS for microbiological threats available at regional level in Italy, focusing on emerging AMR, and at outlining potential barriers and facilitators to their development/implementation. To this end, a three-section, web-based survey was developed and administered to all Italian regional AMR representatives from June to August 2022. Twenty out of twenty-one regions and autonomous provinces (95.2%) responded to the survey. Among these, nine (45%) reported the implementation of EWS for microbiological threats at regional level, three (15%) reported that EWS are in the process of being developed, and eight (40%) reported that EWS are not currently available. EWS characteristics varied widely among the identified systems concerning both AMR profiles reported and data flow: the microorganisms most frequently included were extensively drug-resistant (XDR) Enterobacterales, with the lack of a dedicated regional IT platform reported in most cases. The results of this study depict a highly heterogeneous scenario and suggest that more efforts aimed at strengthening national AMR surveillance systems are needed.

Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes

Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.

Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century

Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.

Antibiotic resistance profiles on pathogenic bacteria in the Brazilian environments

The present study aimed to elaborate a review of multidrug-resistant (MDR) bacteria in soil, food, aquatic environments, cattle, poultry, and swine farms in Brazil. Initially, the literature database for published papers from 2012 to 2023 was Scientific Electronic Library Online (SciELO), U.S. National Library of Medicine (PubMed), and Google Scholar, through the descriptors: antimicrobial resistance, resistance profile, multidrug resistance, environmental bacteria, and pathogenic bacteria. The studies demonstrated the prevalence of pathogenic and resistant bacteria in environments that favor their rapid dissemination. Bacteria of medical importance, such as Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio spp., were present in samples from animal farms and foods, including cheese and milk, urban aquatic environments, hospital effluents, and shrimp farms. Studies suggested that important bacteria have been disseminated through different niches with easy contact with humans, animals, and food, demonstrating the danger of the emergence of increasingly difficult conditions for treating and controlling these infections. Thus, better understanding and characterizing the resistance profiles of bacteria in these regions, mainly referring to MDR bacteria, can help develop solutions to prevent the progression of this public health problem.

Better antimicrobial resistance data analysis and reporting in less time

Objectives

Insights about local antimicrobial resistance (AMR) levels and epidemiology are essential to guide decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. We aimed to compare traditional data analysis and reporting versus a new approach for reliable and reproducible AMR data analysis in a clinical setting.

Methods

Ten professionals who routinely work with AMR data were provided with blood culture test results including antimicrobial susceptibility results. Participants were asked to perform a detailed AMR data analysis in a two-round process: first using their software of choice and next using our newly developed software tool. Accuracy of the results and time spent were compared between both rounds. Finally, participants rated the usability using the System Usability Scale (SUS).

Results

The mean time spent on creating the AMR report reduced from 93.7 to 22.4 min (P < 0.001). Average task completion per round changed from 56% to 96% (P < 0.05). The proportion of correct answers in the available results increased from 37.9% in the first to 97.9% in the second round (P < 0.001). Usability of the new tools was rated with a median of 83.8 (out of 100) on the SUS.

Conclusions

This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through open-source software. Integrating these tools in clinical settings can democratize the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.

Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria

Nicotinamide adenine dinucleotide kinases (NAD kinases) are essential and ubiquitous enzymes involved in the production of NADP(H) which is an essential cofactor in many metabolic pathways. Targeting NAD kinase (NADK), a rate limiting enzyme of NADP biosynthesis pathway, represents a new promising approach to treat bacterial infections. Previously, we have produced the first NADK inhibitor active against staphylococcal infection. From this linear di-adenosine derivative, namely NKI1, we designed macrocyclic analogues. Here, we describe the synthesis and evaluation of an original series of cyclic diadenosine derivatives as NADK inhibitors of two pathogenic bacteria, Listeria monocytogenes and Staphylococcus aureus. The nature and length of the link between the two adenosine units were examined leading to sub-micromolar inhibitors of NADK1 from L. monocytogenes, including its most potent in vitro inhibitor reported so far (with a 300-fold improvement compared to NKI1).

Dissemination of Metallo-β-Lactamase-Producing Pseudomonas aeruginosa in Serbian Hospital Settings: Expansion of ST235 and ST654 Clones

This nationwide study aimed to investigate the molecular characteristics of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa in Serbia, underlying resistance mechanisms, the genetic context of detected MBL genes, and the clonal relationship between isolates harboring genes-encoding MBL. Overall, 320/5334 isolates collected from 2018 to 2021 were identified as P. aeruginosa. Carbapenem-resistant P. aeruginosa (CRPA) were screened for the presence of bla_VIM, bla_IMP, and bla_NDM, genes whereas MBL-positive isolates were tested for the presence of the bla_CTX-M-2, bla_PER, bla_TEM, bla_SHV, bla_VEB, and bla_GES. Multilocus sequence typing and phylogenomic analysis were performed for P. aeruginosa-producing MBL. The majority of the P. aeruginosa isolates were recovered from the lower respiratory tract (n = 120; 37.5%) and wound specimens (n = 108; 33.75%). CRPA isolates accounted for 43.1% (n = 138) of the tested isolates, 31 out of them being bla_NDM-1-positive (22.5%). The colistin resistance rate was 0.3%. MLST analysis revealed the occurrence of ST235 (n = 25) and ST654 (n = 6), mostly confined to Serbia. The distribution of beta-lactamase-encoding genes in these isolates suggested clonal dissemination and possible recombination: ST235/bla_NDM-1, ST235/bla_NDM-1/bla_PER-1, ST654/bla_NDM-1, ST654/bla_NDM-1/bla_PER-1, and ST654/bla_NDM-1/bla_GES-5. High-risk clones ST235 and ST654 identified for the first time in Serbia, are important vectors of acquired MBL and ESBL and their associated multidrug resistance phenotypes represent a cause for considerable concern.

Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes

Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.

Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

A review of national action plans on antimicrobial resistance: strengths and weaknesses

Background

The World Health Organization developed the Global Action Plan on Antimicrobial resistance (AMR) as a priority because of the increasing threat posed to human health, animal health and agriculture. Countries around the world have been encouraged to develop their own National Action Plans (NAPs) to help combat AMR.

The objective of this review was to assess the content of the NAPs and determine alignment with the Global Action Plan on Antimicrobial Resistance using a policy analysis approach.

Body

National Action Plans were accessed from the WHO Library and systematically analysed using a policy analysis approach for actors, process, context and content. Information was assessed using a ‘traffic light’ system to determine agreeance with the five WHO Global Action Plans objectives.

A total of 78 NAPs (70 WHO approved, eight not approved) from the five global regions were analysed. National action plans which provided more information regarding the consultative process and the current situation regarding AMR allowed greater insight to capabilities of the country. Despite the availability of guidelines to inform the development of the plans, there were many differences between plans with the content of information provided. High income countries indicated greater progression with objectives achievement while low and middle-income countries presented the need for human and financial resources.

Conclusion

The national action plans provide an overview of activities underway to combat AMR globally. This analysis reveals how disconnected the process has been and how little information is being gathered globally.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01130-x.

A matrix management of prevention and control for carbapenem-resistant Enterobacteriaceae in an urban compact medical union

PURPOSE

To understand the epidemiological characteristics of nosocomial infection of carbapenem-resistant Enterobacteriaceae (CRE) in an urban medical union includes 10 medical hospitals with different number of beds in China.

METHODS

Epidemiological data on age, department, and infection of CRE cases detected from January 2014 to December 2021 were collected via a real-time hospital-infection monitoring system or manually for subsequent characterization. A multi-departmental and multi-disciplinary matrix (MMM) management of CRE was established and implemented within a medical union.

RESULTS

A total of 1327 cases of CRE infection were detected during the 8 years, of which 352 were due to nosocomial infection, with an infection morbidity of 0.046% and a resistance rate of 10.79%. The morbidity of CRE infection showed a trend of year-to-year fluctuation. The morbidity of CRE infection was significantly higher in winter and spring than that in summer and autumn, significantly higher in men than in women (χ² ​= ​55.891, p ​< ​0.001), and 3 times higher in elderly patients ≥65 years old than in patients <65 years old (χ² ​= ​117.517, p ​< ​0.001). The morbidity of CRE infection after intervention with MMM management decreased significantly from 0.071% to 0.042% (χ² ​= ​15.628, p ​< ​0.001).

CONCLUSIONS

CRE prevention and control practice should be adapted to seasonal variations, gender and age differences. The effective prevention and control of CRE nosocomial infections can be achieved by implementing MMM management within a medical association.

A step forward in antibiotic use and resistance monitoring: a quarterly surveillance system pilot in 11 European Union/European Economic Area countries, September 2017 to May 2020

BackgroundSurveillance of antimicrobial resistance (AMR) and antimicrobial use (AMU) in Europe is currently annual.AimTo study the feasibility and scalability of a quarterly AMR/AMU surveillance system in the European Union/European Economic Area (EU/EEA).MethodsWe conducted a longitudinal study within the scope of the EU-JAMRAI project. Seventeen partners from 11 EU/EEA countries prospectively collected 41 AMU and AMR indicators quarterly from September 2017 to May 2020 for the hospital sector (HS) and primary care (PC). Descriptive statistics and coefficients of variation (CV) analysis were performed.ResultsData from 8 million hospital stays and 45 million inhabitants per quarter were collected at national (n = 4), regional (n = 6) and local (n = 7) levels. Of all partners, five were able to provide data within 3 months after each preceding quarter, and eight within 3-6 months. A high variability in AMU was found between partners. Colistin was the antibiotic that showed the highest CV in HS (1.40; p < 0.0001). Extended-spectrum beta-lactamase-producing Escherichia coli presented the highest incidence in HS (0.568 ± 0.045 cases/1,000 bed-days per quarter), whereas ciprofloxacin-resistant E. coli showed the highest incidence in PC (0.448 ± 0.027 cases/1,000 inhabitants per quarter). Barriers and needs for implementation were identified.ConclusionThis pilot study could be a first step towards the development of a quarterly surveillance system for AMU and AMR in both HS and PC in the EU/EEA. However, committed institutional support, dedicated human resources, coordination of data sources, homogeneous indicators and modern integrated IT systems are needed first to implement a sustainable quarterly surveillance system.

The Prevalence of Multidrug-Resistant Escherichia coli Producing ESBL among Male and Female Patients with Urinary Tract Infections in Riyadh Region, Saudi Arabia

The Escherichia coli that produces extended-spectrum lactamases (ESBL-E. coli) can develop resistance to many antibiotics. The control of ESBL-E. coli disorders is challenging due to their restricted therapeutic approaches, so this study aims to determine the prevalence and pattern of the antibiotic resistance of ESBL-E. coli among male and female patients with urinary tract infections in Riyadh, Saudi Arabia. During the period of 2019 to 2020 at King Fahd Medical City, Riyadh, 2250 urine samples from patients with urinary tract infections (UTIs) were collected, and microbial species were cultured and identified using standard biochemical techniques. A double-disc synergy test was used to identify ESBL-producing strains of E. coli, and an in vitro method and the clinical laboratory standard institute (CLSI) criteria were employed to determine the resistance of these strains to antimicrobial drugs. ESBL-E. coli was detected in 510 (33.49%) of the 1523 E. coli isolates, 67.27% of which were recovered from women and 33.7% of which were recovered from men. A total of 284 (55.69%) ESBL-E. coli isolates were found in patients under 50 years of age, and 226 (44.31%) were found in patients over 50 years of age. Nearly all the isolates of ESBL-E. coli were resistant to cephalosporins (ceftriaxone, cefotaxime, cefepime, cefuroxime, and cephalothin) and penicillin (ampicillin), whereas the majority of the isolates were sensitive to several carbapenems (imipenem, meropenem, and ertapenem), aminoglycosides (amikacin), and nitrofurantoins. The development of antibiotic resistance by ESBL-E. coli, the most frequent pathogen linked to urinary tract infections, plays a crucial role in determining which antibiotic therapy is appropriate.

Occurrence of Healthcare-Associated Infections (HAIs) by Escherichia coli and Klebsiella spp. Producing Extended-Spectrum β-lactamases (ESBL) and/or Carbapenemases in Portuguese Long-Term Care Facilities

Extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing bacteria are widespread in hospitals, but the extent of this problem in long-term care facilities (LTCFs) is poorly understood. We aimed to elucidate, in the Portuguese regional clinical context, the relevance of LTCFs as a reservoir of Escherichia coli and Klebsiella spp. producing ESBL- and/or carbapenemases (Ec/Kp-ESBL/CARB). Fourteen LTCFs from Portugal, corresponding to units of convalescence (UC/n = 3), medium-term internment and rehabilitation (UMDR/ n = 5), or long-term internment and maintenance (ULDM/n = 6), were analyzed (2016–2019). All patients with Ec/Kp-ESBL/CARB infections acquired during LTCF stay were included, and detailed information was collected. Prevalence of patients with healthcare-associated infections (HAIs) by Ec/Kp-ESBL/CARB did not vary significantly over time (1.48% in 2016–2017, 1.89% in 2017–2018, and 1.90% in 2018–2019), but a statistically significant association with the LTCF typology (ULDM, UMDR) was observed. HAIs were caused by K. pneumoniae (n = 51/54.3%), E. coli (n = 41/43.6%), or both (n = 2/2.1%), producing ESBL (96%) or carbapenemases (4%). Prior colonization (n = 14/16%) corresponded to seven Kp-CARB and seven Ec/Kp-ESBL. The worrying prevalence of patients acquiring HAIs by Ec/Kp-ESBL/CARB, associated with the estimated rates of those already colonized at admission, highlights a relevant role for LTCFs as a reservoir of Ec/Kp-ESBL/CARB. Epidemiological surveillance should be extended to the national level, and colonization screening at LTCF admission implemented systematically.

Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods

Introduction

Methodology

Results

Conclusion

Trends and Correlation Between Antimicrobial Resistance and Antibiotics Consumption in a Specialist Children’s Hospital from 2016 to 2021

Purpose

To explore the trends and correlation between antibiotics consumption and antimicrobial resistance in children in a specialist hospital from 2016–2021 in China.

Patients and Methods

This retrospective study investigated data on the consumption of antibiotics and antimicrobial resistance in children. Antibiotics consumption was expressed as defined daily doses (DDDs)/1000 patient-days based on the Guidelines for Anatomical Therapeutic Chemical. The trends in antibiotics consumption and antimicrobial resistance rates were analyzed by linear regression, while Spearman correlation analysis was employed to evaluate their correlations.

Results

An increasing trend in the annual consumption of carbapenems and monobactams was detected (all P<0.05). A significant upward trend was detected in the annual resistance rates of Enterococcus faecium to ciprofloxacin, Streptococcus pneumonia to ceftriaxone, Acinetobacter baumannii to carbapenems, Enterobacter cloacae to carbapenems, Pseudomonas aeruginosa to ceftazidime, and Escherichia coli to cefepime, while the annual resistance rates of Escherichia coli to carbapenems had a significant downward trend (all P<0.05). The consumption of cephalosporin/β-lactamase inhibitor (C/BLI) combinations and carbapenems had significant positive correlations with the resistance rates of Acinetobacter baumannii to carbapenems (r=0.763, P<0.001; r=0.806, P<0.001), Enterobacter cloacae to carbapenems (r=0.675, P<0.001; r=0.417, P=0.043), and Pseudomonas aeruginosa to ceftazidime (r=0.625, P=0.001; r=0.753, P<0.001), respectively. Also, increasing consumption of monobactams was related to the upward resistance rates of Acinetobacter baumannii to carbapenems (r=0.557, P=0.005) and Enterobacter cloacae to carbapenems (r=0.507, P= 0.011).

Conclusion

This study demonstrated significant positive associations between antibiotics consumption and specific antimicrobial resistance rates. The current findings pointed out some directions to pursue in controlling the prevalence of certain resistant bacterial strains in children.

Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience

Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.

Antioxidant and Antimicrobial Properties of Helichrysum italicum (Roth) G. Don Hydrosol

(1) Background: According to the emergence and spread of antibiotic resistance, there is an urge for new promising substances. The purpose of the study was to test the antioxidant, cytotoxic and antimicrobial properties of the Helichrysum italicum (Roth) G. Don essential oil (EO) and hydrosol. (2) Methods: The antioxidant potential was determined using the DPPH (2,2-diphenyl-1-picrylhydrazyl) method. The cytotoxicity for human skin and intestinal cells was tested using primary and immortalized cell line models. The minimum inhibitory concentration (MIC) of hydrosol was then determined for six bacterial strains covering four commonly reported food pathogens. Further on, the hydrosol at a concentration of 1/8 MIC was used to test the antiadhesive effect by the crystal violet (CV) staining method. (3) Results: the EO showed a 100-times higher antioxidant and 180- to 25.000-times higher cytotoxic activity, when compared to hydrosol. Nevertheless, all bacterial strains, with the exception of Staphylococcus aureus, were sensitive to hydrosol in the range of 12.5% (V/V) for Campylobacter jejuni, to MIC values of 100% (V/V) for Escherichia coli and Pseudomonas aeruginosa. The antiadhesive potential of hydrosol was also shown. (4) Conclusions: Even though hydrosols are a by-product of the EO distillation process, they possess valuable biological activities.