Antimicrobial Resistance Surveillance Program Research Articles

Antimicrobial resistance in Staphylococcus aureus and Enterococci spp. isolates from bloodstream infections in Australian children, 2013 - 2021.

Rising proportions of antimicrobial resistance (AMR) have been observed in both Staphylococcus aureus and Enterococcus spp. isolates. The Australian Group on Antimicrobial Resistance (AGAR) surveillance program captures clinical and microbiological data of isolates detected in blood cultures across Australia. EUCAST 2022 was used for MIC interpretation and the AMR package in R for data analysis. There were 2,091 BSIs with S. aureus and 534 enterococcal BSI episodes over the nine years. Three-quarters of S. aureus BSI episodes were community-onset (78.3%) whilst more than half of enterococcal BSIs were hospital-onset (56.9%). The median age for S. aureus BSIs was 6 years, whilst >50% enterococcal BSIs were in children <12 months old.Fifteen percent of S. aureus isolates were methicillin-resistant (MRSA). Overall, 85.3% of S. aureus were resistant to penicillin, 12.5% resistant to erythromycin, 10.3% to clindamycin, and 4.7% to ciprofloxacin. Resistance to penicillin decreased over time whilst clindamycin resistance increased.Resistance in Enterococcus spp. was almost entirely observed in E. faecium; only one E. faecalis isolate was ampicillin resistant, and no E. faecalis isolates were vancomycin or teicoplanin resistant. Seventy-three percent of E. faecium were resistant to ampicillin, 25.5% to vancomycin (VREfm) and 8.8% to teicoplanin. Significant shifts in the epidemiology and resistance profiles of S. aureus and Enterococcus spp. BSIs in Australian children were observed, making clear the importance of age-stratified reporting in antimicrobial resistance data.

Antimicrobial resistance in Enterobacterales, Acinetobacter spp. and Pseudomonas aeruginosa isolates from bloodstream infections in Australian children, 2013-2021.

Gram-negative bloodstream infections are associated with significant morbidity and mortality in children. Increasing antimicrobial resistance (AMR) is reported globally, yet efforts to track pediatric AMR at a national level over time are lacking. The Australian Group on Antimicrobial Resistance (AGAR) surveillance program captures clinical and microbiological data of isolates detected in blood cultures across Australia. EUCAST 2022 was used for MIC interpretation and the AMR package in R for data analysis. Over a nine-year period, there were 3,145 bloodstream infections with 3,266 gram-negative isolates reported in hospitalized children aged <18 years; 21.0% were from neonates. The median length of stay was 9 days, and 30-day all-cause mortality was 5.2%. A greater odds of death was observed in those with a multi-drug resistant organism (aOR: 2.1, 95%CI: 1.3, 3.3, p: 0.001). Escherichia coli (44.5%) and Klebsiella pneumoniae complex (12.6%) were the two most frequently reported organisms. Overall resistance in Enterobacterales to gentamicin/tobramycin was 11.6%, to ceftazidime/ceftriaxone was 12.9%, and 13.2% to ciprofloxacin. Resistance increased over time.Of 201 Pseudomonas aeruginosa isolates reported, 19.7% were resistant to piperacillin-tazobactam, 13.1% resistant to cefepime/ceftazidime and 9.8% to ciprofloxacin. Of 108 Acinetobacter spp. isolates, one was resistant to meropenem, and two were resistant to ciprofloxacin. Resistance did not increase over time. AMR in gram-negative organisms causing bloodstream infections in Australian children is increasing which should be considered when updating guidelines and empiric treatment regimens. Ongoing pediatric-specific national surveillance with pediatric reporting must remain a priority to strengthen antimicrobial stewardship and infection control programs.

Etiology and antimicrobial susceptibility patterns of bacteria causing pneumonia among adult patients with signs and symptoms of lower respiratory tract infections during the COVID-19 pandemic in Mwanza, Tanzania: a cross-sectional study

BackgroundBacterial pneumonia is among the leading causes of morbidity and mortality worldwide. The extensive misuse and overuse of antibiotics observed during the Corona Virus Disease 2019 (COVID-19) pandemic may have changed the patterns of pathogens causing bacterial pneumonia and their antibiotic susceptibility profiles. This study was designed to establish the prevalence of culture-confirmed bacterial pneumonia and describe their antimicrobial susceptibility profile in adult patients who presented with signs and symptoms of lower respiratory tract infections (LRTIs) during the COVID-19 pandemic.MethodologyThis hospital-based cross-sectional study was conducted from July 2021 to July 2022 at a zonal referral hospital and two district hospitals in Mwanza, Tanzania. Demographic and clinical data were collected using a standardized questionnaire. Sputum samples were processed by conventional culture followed by the identification of isolates and antibiotic susceptibility testing. Descriptive data analysis was performed using STATA version 15.0.ResultsA total of 286 patients with a median age of 40 (IQR 29–60) years were enrolled in the study. More than half of the patients enrolled were females (52.4%, n = 150). The overall prevalence of bacterial pneumonia was 34.3% (n = 98). The majority of the bacterial pathogens isolated were Gram-negative bacteria (GNB) (61.2%, 60/98), with a predominance of Klebsiella spp., 38.8% (38/98), followed by Streptococcus pyogenes (21.4%, 21/98). Multi drug resistant (MDR) bacteria were detected in 72/98 (73.5%) of the isolates. The proportions of GNB-resistant strains were 60.0% (36/60) for ciprofloxacin, 60% (36/60) for amoxicillin, 60% (36/60) for amoxicillin, 68.3% (41/60) for trimethoprim-sulfamethoxazole and 58.3% (35/60) for ceftriaxone.ConclusionOne-third of the patients with signs and symptoms of LRTIs had laboratory-confirmed bacterial pneumonia with a predominance of Gram negative MDR bacteria. This calls for continuous antimicrobial resistance (AMR) surveillance and antimicrobial stewardship programs in the study setting and other settings in developing countries as important strategies for tackling AMR.

Health Policy Analysis on the Containment of Antimicrobial Resistance (AMR) in India: A Mixed Methods Study of Antimicrobial Stewardship as a Pivotal Intervention in Tackling AMR

Objective: This policy report aimed at two goals, that is, to report the findings of the literature review and explore the perceptions of the key stakeholders in seeking better insight into the antimicrobial stewardship program (AMSP), and to develop antimicrobial resistance (AMR) policy recommendations for the Ministry of Health and Family Welfare (MoHFW), India, based on the findings from the rapid systematic review of the literature (both published and grey) and the views of key stakeholders. Methods: A mixed method approach using literature review and qualitative interviews has been applied. A rapid systematic literature review focusing on the antimicrobial stewardship pro-gram’s key achievements and its implementation and impact, implementation challenges, gaps and barriers, and opportunities, has been carried out, which has been followed by conducting interviews of key stakeholders and reporting the findings along with the recommendations. Results: The findings have shown significant progress towards AMSP, such as expanding to 90 secondary-level hospitals and district-level hospitals/nursing homes, and the Indian Council of Medical Research antimicrobial resistance surveillance and research network (ICMR AMRSN) program. Education, training, and microbiological testing have been found to be the current focus areas. However, there exist challenges, including a lack of leadership support, diagnostic stew-ardship, and staffing of clinical pharmacists and infectious control nurses. Key gaps and barriers identified include setting up microbiology laboratories and hiring ICN nurses and clinical phar-macists. Opportunities have also been identified. Based on these findings, we have made succinct recommendations to address the themes and issues identified. Conclusion: Without new medicines, India will struggle to manage antimicrobial resistance. This situation calls for national oversight. This study has demonstrated AMSP as crucial for fighting this silent pandemic. The Indian government and policymakers must swiftly address critical chal-lenges, gaps, and opportunities. These findings and recommendations might potentially strengthen the future antimicrobial resistance national action plan (AMR NAP).

National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches

Wastewater serves as an important reservoir of antimicrobial resistance (AMR), and its surveillance can provide insights into population-level trends in AMR to inform public health policy. This study compared two common high-throughput screening approaches, namely (i) high-throughput quantitative PCR (HT qPCR), targeting 73 antimicrobial resistance genes, and (ii) metagenomic sequencing. Weekly composite samples of wastewater influent were taken from 47 wastewater treatment plants (WWTPs) across Wales, as part of a national AMR surveillance programme, alongside 4 weeks of daily wastewater effluent samples from a large municipal hospital. Metagenomic analysis provided more comprehensive resistome coverage, detecting 545 genes compared to the targeted 73 genes by HT qPCR. It further provided contextual information critical to risk assessment (i.e. potential bacterial hosts). In contrast, HT qPCR exhibited higher sensitivity, quantifying all targeted genes including those of clinical relevance present at low abundance. When limited to the HT qPCR target genes, both methods were able to reflect the spatiotemporal dynamics of the complete metagenomic resistome, distinguishing that of the hospital and the WWTPs. Both approaches revealed correlations between resistome compositional shifts and environmental variables like ammonium wastewater concentration, though differed in their interpretation of some potential influencing factors. Overall, metagenomics provides more comprehensive resistome profiling, while qPCR permits sensitive quantification of genes significant to clinical resistance. We highlight the importance of selecting appropriate methodologies aligned to surveillance aims to guide the development of effective wastewater-based AMR monitoring programmes.

Epidemiology and antimicrobial resistance of Mycobacterium spp. in the United Arab Emirates: a retrospective analysis of 12 years of national antimicrobial resistance surveillance data.

The Eastern Mediterranean Regional Office (EMRO) region accounts for almost 8% of all global Mycobacterium tuberculosis (TB) cases, with TB incidence rates ranging from 1 per 100,000 per year in the United Arab Emirates (UAE) to 204 per 100,000 in Djibouti. The national surveillance data from the Middle East and North Africa (MENA) region on the epidemiology and antimicrobial resistance trends of TB, including MDR-TB remains scarce. A retrospective 12-year analysis of N = 8,086 non-duplicate diagnostic Mycobacterium tuberculosis complex (MTB complex) isolates from the UAE was conducted. Data were generated through routine patient care during the 2010-2021 years, collected by trained personnel and reported by participating surveillance sites to the UAE National Antimicrobial Resistance (AMR) Surveillance program. Data analysis was conducted with WHONET, a windows-based microbiology laboratory database management software developed by the World Health Organization Collaborating Center for Surveillance of Antimicrobial Resistance, Boston, United States (https://whonet.org/). A total of 8,086 MTB-complex isolates were analyzed. MTB-complex was primarily isolated from respiratory samples (sputum 80.1%, broncho-alveolar lavage 4.6%, pleural fluid 4.1%). Inpatients accounted for 63.2%, including 1.3% from ICU. Nationality was known for 84.3% of patients, including 3.8% Emiratis. Of UAE non-nationals, 80.5% were from 110 countries, most of which were Asian countries. India accounted for 20.8%, Pakistan 13.6%, Philippines 12.7%, and Bangladesh 7.8%. Rifampicin-resistant MTB-complex isolates (RR-TB) were found in 2.8% of the isolates, resistance to isoniazid, streptomycin, pyrazinamide, and ethambutol, was 8.9, 6.9, 3.4 and 0.4%, respectively. A slightly increasing trend of resistance among MTB-complex was observed for rifampicin from 2.5% (2010) to 2.8% (2021). Infections due to MTB-complex are relatively uncommon in the United Arab Emirates compared to other countries in the MENA region. Most TB patients in the UAE are of Asian origin, mainly from countries with a high prevalence of TB. Resistance to first line anti-tuberculous drugs is generally low, however increasing trends for MDR-TB mainly rifampicin linked resistance is a major concern. MDR-TB was not associated with a higher mortality, admission to ICU, or increased length of hospitalization as compared to non-MDR-TB.

Antimicrobial Resistance Profiles of Pseudomonas aeruginosa in the Arabian Gulf Region Over a 12-Year Period (2010-2021).

To evaluate literature from a 12-year period (2010-2021) on the antimicrobial resistance profile of Pseudomonas aeruginosa from the Arabian Gulf countries (Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates). An electronic literature search was conducted for articles on antimicrobial resistance in P. aeruginosa and associated phenotypes, covering the period of 1st January 2010 to 1st December 2021. Antimicrobial resistance in the Arabian Gulf was highest to meropenem (10.3-45.7%) and lowest to colistin (0.0-0.8%), among the agents tested. Annual data showed that ceftazidime resistance (Kuwait), piperacillin-tazobactam non-susceptibility (Qatar), and aztreonam, imipenem, and meropenem resistance (Saudi Arabia) increased by 12-17%. Multiple mechanisms of carbapenem resistance were identified and multiple clones were detected, including high-risk clones such as ST235. The most common carbapenemases detected were the VIM-type metallo-β-lactamases. Among P. aeruginosa in the Arabian Gulf countries, resistance to meropenem was higher than to the other agents tested, and meropenem resistance increased in Saudi Arabia during the study period. Resistance to colistin, a classic antibiotic used to treat Pseudomonas spp. infections, remained low. The VIM-type β-lactamase genes were dominant. We recommend local and regional antimicrobial resistance surveillance programs to detect the emergence of resistance genes and to monitor antimicrobial resistance trends in P. aeruginosa.

Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe.

To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Trend of distribution and antimicrobial resistance in uropathogens in China from the CHINET antimicrobial resistance surveillance program, a 7-year retrospective study

AbstractUrinary tract infections (UTIs) are common urological diseases that easily relapse and have led to an increasing economic and health burdens. The China Antimicrobial Surveillance Network (CHINET) system is one of the most influential antimicrobial resistance surveillance networks in China. This study analyzed antimicrobial resistance and distribution trends of uropathogens from 2015 to 2021 using the CHINET system. A total of 261,893 non-duplicate strains were collected; Gram-positive bacteria accounted for 23.8% while Gram-negative bacteria accounted for 76.2%. Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, and Enterococcus faecalis were the most common species. The resistance to vancomycin, linezolid, and teicoplanin in E. faecalis and E. faecium was less than 3%. The prevalence of carbapenem-resistant strains of E. coli, K. pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii was 1.7%, 18.5%, 16.4%, and 40.3%, respectively. The prevalence of carbapenem-resistant A. baumannii increased from 27.6% in 2015 to 43.4% in 2021. The prevalence of methicillin-resistant Staphylococcus aureus decreased from 40.6% in 2015 to 22.9% in 2021. The resistance rates to most β-lactam antimicrobials, aminoglycosides and fluoroquinolones in E. coli, K. pneumoniae, P. aeruginosa and A. baumannii isolated from ICU inpatients were significantly higher than in those isolated from outpatients and non-ICU inpatients. This study indicates that E. coli, Enterococcus, and K. pneumoniae were the most commonly isolated uropathogens in China. The bacterial species isolated and their antimicrobial resistance patterns differed in different patient populations. More attention must be paid uropathogen resistance surveillance to provide data for the rational use of antimicrobial agents.

Generalizability of machine learning in predicting antimicrobial resistance in E. coli: a multi-country case study in Africa.

Antimicrobial resistance (AMR) remains a significant global health threat particularly impacting low- and middle-income countries (LMICs). These regions often grapple with limited healthcare resources and access to advanced diagnostic tools. Consequently, there is a pressing need for innovative approaches that can enhance AMR surveillance and management. Machine learning (ML) though underutilized in these settings, presents a promising avenue. This study leverages ML models trained on whole-genome sequencing data from England, where such data is more readily available, to predict AMR in E. coli, targeting key antibiotics such as ciprofloxacin, ampicillin, and cefotaxime. A crucial part of our work involved the validation of these models using an independent dataset from Africa, specifically from Uganda, Nigeria, and Tanzania, to ascertain their applicability and effectiveness in LMICs. Model performance varied across antibiotics. The Support Vector Machine excelled in predicting ciprofloxacin resistance (87% accuracy, F1 Score: 0.57), Light Gradient Boosting Machine for cefotaxime (92% accuracy, F1 Score: 0.42), and Gradient Boosting for ampicillin (58% accuracy, F1 Score: 0.66). In validation with data from Africa, Logistic Regression showed high accuracy for ampicillin (94%, F1 Score: 0.97), while Random Forest and Light Gradient Boosting Machine were effective for ciprofloxacin (50% accuracy, F1 Score: 0.56) and cefotaxime (45% accuracy, F1 Score:0.54), respectively. Key mutations associated with AMR were identified for these antibiotics. As the threat of AMR continues to rise, the successful application of these models, particularly on genomic datasets from LMICs, signals a promising avenue for improving AMR prediction to support large AMR surveillance programs. This work thus not only expands our current understanding of the genetic underpinnings of AMR but also provides a robust methodological framework that can guide future research and applications in the fight against AMR.

Molecular Prevalence of MecA and MecC Genеs in Coagulasе-Positive Staphylococci Isolated From Dogs with Dermatitis and Otitis in Belgrade, Serbia: A One Year Study

Abstract The escalating global concern of antimicrobial resistance in human and veterinary medicine is exacerbated by the inappropriate prescription of antibiotics for bacterial infections in companion animals. This study aimed to determine the distribution of coagulase-positive staphylococci causing clinical skin and ear infections in dogs and to determine methicillin-resistant isolates. A total of 78 staphylococcal strains were isolated from clinical samples taken from patients at the Dermatology Clinic at the Faculty of Veterinary Medicine in Belgrade, Serbia. Multiplex PCR was used for species-specific identification, and mecA and mecC genes were used to determine methicillin resistance, in addition to phenotypic determination, MIC values and detection of PBP2a. Out of the 78 samples analyzed, 65.8% were identified as Staphylococcus pseudintermedius, 22.4% as S. aureus, 7.9% as S. coagulans, and 3.9% as S. intermedius. Four S. aureus isolates exhibited methicillin resistance confirmed by cefoxitin disk diffusion, while five were confirmed with MIC testing and latex agglutination. MecA gene was detected in 29.4% of S. aureus and 30% of S. pseudintermedius isolates. These isolates were classified as methicillin-resistant S. aureus (MRSA) and methicillin-resistant S. pseudintermedius (MRSP), respectively. No isolates carried the mecC gene. This study provides insights into the prevalence of CoPS species and methicillin resistance in isolates from dogs. Continued surveillance is essential to monitor and understand the emergence and dissemination of antimicrobial resistance in veterinary medicine and the results of this study accent the need for establishment of a continuous antimicrobial resistance surveillance program in the Republic of Serbia.

Methicillin resistant Staphylococcus aureus in the United Arab Emirates: a 12-year retrospective analysis of evolving trends.

Methicillin resistant Staphylococcus aureus (MRSA) is a major contributor to the global burden of antimicrobial resistance (AMR). As MRSA continues to evolve, the need for continued surveillance to evaluate trends remains crucial. This study was carried out to assess MRSA trends in the United Arab Emirates (UAE) based on analysis of data from the national AMR surveillance program. We carried out a 12-year (2010-2021) retrospective analysis of MRSA demographic and microbiological data collected as part of the UAE national AMR surveillance program. Participating centers from across the country routinely submit AMR surveillance data collected by trained personnel to the National AMR Surveillance Committee, where data is analyzed using a unified WHONET platform. Data on non-duplicate isolates associated with clinical infections were obtained and included in the analysis. A total of 29,414 non-duplicate MRSA isolates associated with clinical infections were reported between 2010 and 2021 (2010: n = 259; 2021: n = 4,996). MRSA represented 26.4% of all S. aureus (n = 111,623) isolates identified during the study period. In 2010, among the S. aureus isolates with reported oxacillin testing, 21.9% (n/N = 259/1,181) were identified as MRSA and this showed an increase to 33.5% (n/N = 4,996/14,925) in 2021. Although there was variation in the distribution of MRSA across the seven emirates of the country, most had an upward trend. Patient demographics reflected a male preponderance, with most being adults and from the outpatient setting. Isolates were mostly from skin and soft tissue infection specimens (72.5%; n/N = 21,335/29,414). Among the inpatients (N = 8,282), a total of 3,313 MRSA isolates were from specimens obtained ≤ 48 h after admission indicative of community acquired infection. Increasing resistance trends were observed for most antibiotics including ciprofloxacin, levofloxacin, moxifloxacin, erythromycin, gentamicin, trimethoprim-sulfamethoxazole, and quinupristin/dalfopristin. Low levels of resistance (0.0-0.8%) were sustained for linezolid except for 2015, 2016, and 2017 with 2.5, 2.6, and 2.9%, respectively. No confirmed vancomycin resistance was reported. The increasing trend of MRSA isolates associated with clinical infections in the hospital and community settings is a concern. Continued monitoring including incorporation of genomic surveillance and infection control measures are recommended to stem the dissemination.

Evolving trends among Pseudomonas aeruginosa: a 12-year retrospective study from the United Arab Emirates.

Pseudomonas is a group of ubiquitous non-fermenting Gram-negative bacteria (NFGNB). Of the several species associated with humans, Pseudomonas aeruginosa (PA) can acclimate to diverse environments. The global frequency of PA infections is rising and is complicated by this organism's high intrinsic and acquired resistance to several clinically relevant antibiotics. Data on the epidemiology, levels, and trends of antimicrobial resistance of PA in clinical settings in the MENA/GCC region is scarce. A retrospective 12-year analysis of 56,618 non-duplicate diagnostic Pseudomonas spp. from the United Arab Emirates (UAE) was conducted. Data was generated at 317 surveillance sites by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National antimicrobial resistance (AMR) Surveillance program. Data analysis was conducted with WHONET (https://whonet.org/). Among the total isolates (N = 56,618), the majority were PA (95.6%). Data on nationality revealed 44.1% were UAE nationals. Most isolates were from soft tissue (55.7%), followed by respiratory tract (26.7%). PA was more commonly found among inpatients than among outpatients, followed by ICUs. PA showed a horizontal trend for resistance to fluoroquinolones, 3rd- and 4th-generation cephalosporins, and decreasing trends of resistance for aminoglycosides and meropenem. The highest percentage of multidrug resistant (MDR) isolates was reported in 2011 at 35.6%. As an overall trend, the percentage of MDR, extensively drug-resistant (XDR), and possible pandrug-resistant (PDR) isolates generally declined over the study period. Carbapenem-resistant PA (CRPA) were associated with a higher mortality (RR: 2.7), increased admission to ICU (RR: 2.3), and increased length of stay (LOS) (12 excess inpatient days per case), as compared to carbapenem-susceptible PA (CSPA). The resistance trends in Pseudomonas species in the UAE indicated a decline in AMR and in percentages of Pseudomonas isolates with MDR and XDR profiles. The sustained Pseudomonas spp. circulation particularly in the hospital settings highlights the importance of surveillance techniques, infection control strategies, and stewardship to limit the continued dissemination. This data also shows that CRPA are associated with higher mortality, increased ICU admission rates, and a longer hospitalization, thus higher costs due to increased number of in-hospital and ICU days.

Epidemiology of vancomycin-resistant enterococci in the United Arab Emirates: a retrospective analysis of 12 years of national AMR surveillance data.

Enterococci are usually low pathogenic, but can cause invasive disease under certain circumstances, including urinary tract infections, bacteremia, endocarditis, and meningitis, and are associated with peritonitis and intra-abdominal abscesses. Increasing resistance of enterococci to glycopeptides and fluoroquinolones, and high-level resistance to aminoglycosides is a concern. National antimicrobial resistance (AMR) surveillance data for enterococci from the Middle East and North Africa (MENA) and the Gulf region is scarce. A retrospective 12-year analysis of N = 37,909 non-duplicate diagnostic Enterococcus spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET. Enterococcus faecalis was the most commonly reported species (81.5%), followed by Enterococcus faecium (8.5%), and other enterococci species (4.8%). Phenotypically vancomycin-resistant enterococci (VRE) were found in 1.8% of Enterococcus spp. isolates. Prevalence of VRE (%VRE) was highest for E. faecium (8.1%), followed by E. faecalis (0.9%). A significant level of resistance to glycopeptides (%VRE) for these two species has been observed in the majority of observed years [E. faecalis (0-2.2%), 2010: 0%, 2021: 0.6%] and E. faecium (0-14.2%, 2010: 0%, 2021: 5.8%). Resistance to fluoroquinolones was between 17 and 29% (E. faecalis) and was higher for E. faecium (between 42 and 83%). VRE were associated with higher patient mortality (RR: 2.97), admission to intensive care units (RR: 2.25), and increased length of stay (six excess inpatient days per VRE case), as compared to vancomycin-susceptible Enterococcus spp. Published data on Enterococcus infections, in particular VRE-infections, in the UAE and MENA region is scarce. Our data demonstrates that VRE-enterococci are relatively rare in the UAE, however showing an increasing resistance trend for several clinically important antibiotic classes, causing a concern for the treatment of serious infections caused by enterococci. This study also demonstrates that VRE were associated with higher mortality, increased intensive care unit admission rates, and longer hospitalization, thus poorer clinical outcome and higher associated costs in the UAE. We recommend the expansion of current surveillance techniques (e.g., local VRE screening), stricter infection prevention and control strategies, and better stewardship interventions. Further studies on the molecular epidemiology of enterococci are needed.

Surveillance of antimicrobial resistance in the United Arab Emirates: the early implementation phase.

National surveillance of antimicrobial resistance (AMR) is an important public health function. Published national AMR surveillance data from the Middle East/North Africa (MENA) region is scarce. This paper describes the early implementation phase of establishing AMR surveillance in the United Arab Emirates (UAE). Building on the existing AMR surveillance system in the Emirate of Abu Dhabi, and adopting the WHO-GLASS methodology, the UAE Ministry of Health and Prevention (MOHAP) established the national AMR Surveillance program in 2015, in collaboration with regional health authorities and healthcare providers. Main objectives of this program are to (a) set AMR surveillance standards, (b) collect and analyze AMR surveillance data for common bacterial and fungal infections, (c) report on AMR levels and trends in the UAE, (d) strengthen local and national capacity for AMR surveillance, and (e) support AMR prevention and control strategies in the UAE. AMR surveillance data is collected through a network of 317 surveillance sites (including 84 hospitals and 233 centers/clinics), and 45 microbiology labs across all seven Emirates of the UAE. Surveillance of antimicrobial resistance has been successfully established since 2010 in the UAE. A national AMR surveillance protocol has been developed, adopting the WHO GLASS protocol. Extensive capacity-building and training activities have strengthened the local and national capacity for AMR surveillance. Between 2010 and 2021, a network of 317 surveillance sites and 45 laboratories have reported a total of 1,277,080 isolates from 662,065 non-duplicate patients to the national level. AMR data is reported annually by MOHAP through a National AMR surveillance report. National AMR data is utilized for informing the development of standard treatment guidelines at national level. National surveillance of antimicrobial resistance has been successfully established in the United Arab Emirates, allowing to monitor levels and trends of antimicrobial resistance for common bacterial and fungal pathogens, and detecting emerging resistance. The availability of such national AMR surveillance data allows for the first time to inform the development of national standard treatment guidelines for empiric treatment of common bacterial and fungal infections in the UAE.

Antimicrobial resistance in Streptococcus pneumoniae: a retrospective analysis of emerging trends in the United Arab Emirates from 2010 to 2021.

Although pneumococcal conjugate vaccines (PCV) have been effective in reducing the burden of Streptococcus pneumoniae infections, there is a paucity of data on the relationship with antimicrobial resistance (AMR) trends in the Arabian Gulf region. This study was carried out to assess S. pneumoniae resistance trends in the United Arab Emirates (UAE) where PCV-13 vaccination was introduced in 2011. Retrospective analysis of S. pneumoniae demographic and microbiological data collected as part of the national AMR surveillance program from 2010 to 2021 was carried out. A survey of reporting sites and hand searching of annual reports of local health authorities was carried out to identify data on S. pneumoniae serotypes as this is not included in the AMR surveillance database. From 2010 to 2021, 11,242 non-duplicate S. pneumoniae isolates were reported, increasing from 324 in 2010 to 1,115 in 2021. Factoring in annual increment in the number of surveillance sites, the number of isolates per site showed an upward trajectory from 2015 to 2018 and declined in 2020 with the onset of the pandemic. The majority of isolates (n/N = 5,751/11,242; 51.2%) were from respiratory tract specimens with 44.5% (n/N = 2,557/5,751) being nasal colonizers. Up to 11.9% (n/N = 1,337/11,242) were invasive pneumococcal disease (IPD) isolates obtained from sterile site specimens including blood (n = 1,262), cerebrospinal (n = 52), pleural (n = 19) and joint (n = 4) fluid; and were predominantly from pediatric patients. The downward trend for amoxicillin and for penicillin G at the non-meningitis and meningitis as well as oral penicillin breakpoints was statistically significant. In contrast, increasing trends of resistance were seen for levofloxacin, moxifloxacin, trimethoprim/sulfamethoxazole and erythromycin. IPD and non-IPD isolates showed similar demographic and AMR trends. None of the surveillance sites carried out S. pneumoniae serotyping and handsearching of annual reports did not yield this information. The increasing trend of pneumococcal disease and AMR with emergence of isolates with MDR phenotype despite is of concern. In the absence of S. pneumoniae serotyping the role of non-vaccine serotypes in driving this pattern remains unknown. There is an urgent need for serotype, genomic and AMR surveillance of S. pneumoniae isolates in the UAE.

Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints

Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20–50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of >hspace{0.17em}15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.

Nocardia species distribution and antimicrobial susceptibility within Australia.

Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation. To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program. Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022. Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation. We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Antimicrobial surveillance: A 20-year history of the SMART approach to addressing global antimicrobial resistance into the future

Antimicrobial resistance (AMR) is a major global public health threat, particularly affecting patients in resource-poor settings. Comprehensive surveillance programmes are essential to reducing the high mortality and morbidity associated with AMR and are integral to informing treatment decisions and guidelines, appraising the effectiveness of intervention strategies, and directing development of new antibacterial agents. Various surveillance programmes exist worldwide, including those administered by government bodies or funded by the pharmaceutical industry. One of the largest and longest running industry-sponsored AMR surveillance programme is the Study for Monitoring Antimicrobial Resistance Trends (SMART), which recently completed its 20th year. The SMART database has grown to almost 500000 isolates from over 200 sites in more than 60 countries, encompassing all major geographic regions and including many sites in low- and middle-income countries. The SMART surveillance programme has evolved in scope over time, including additional antibacterial agents, pathogens and infection sites, in line with changing epidemiology and medical need. Surveillance data from SMART and similar programmes have been used successfully to detect emerging resistance threats and AMR patterns in specific countries and regions, thus informing national and local clinical treatment guidelines. The SMART database can be accessed readily by physicians and researchers globally, which may be especially valuable to those from countries with limited healthcare resources, where surveillance and resistance data are rarely collected. Continued participation from as many sites as possible worldwide and maintenance of adequate funding are critical factors to fully realising the potential of large-scale AMR surveillance programmes into the future.

Insight into antimicrobial resistance at a new beef cattle feedlot in western Canada.

A better understanding of how environmental reservoirs of ARGs in the feedlot relate to those found in animal pathogens will help inform and improve disease management, treatment strategies, and outcomes. Monitoring individual cattle or small groups is invasive, logistically challenging, expensive, and unlikely to gain adoption by the beef cattle industry. Wastewater surveillance has become standard in public health studies and has inspired similar work to better our understanding of AMR in feedlots. We derived our insights from sampling water bowls in a newly established feedlot: a unique opportunity to observe AMR prior to animal arrival and to monitor its development over 2 months. Importantly, the bacterial community of a single water bowl can be influenced by direct contact with hundreds of animals. Our results suggest that water bowl microbiomes are economical and pragmatic sentinels for monitoring relevant AMR mechanisms.