Resistance Surveillance Research Articles

Frequency of antimicrobial-resistant bloodstream infections in 111 hospitals in Thailand, 2022

To evaluate the frequency of antimicrobial-resistant bloodstream infections (AMR BSI) in Thailand. We analyzed data from 2022, generated by 111 public hospitals in health regions 1 to 12, using the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS), and submitted to the Ministry of Public Health, Thailand. Multilevel Poisson regression models were used. The most common cause of community-origin AMR BSI was third-generation cephalosporin-resistant Escherichia coli (3GCREC, 65.6%; 5101/7773 patients) and of hospital-origin AMR BSI was carbapenem-resistant Acinetobacter baumannii (CRAB, 51.2%, 4968/9747 patients). The percentage of patients tested for BSI was negatively associated with the frequency of community-origin 3GCREC BSI and hospital-origin CRAB BSI (per 100,000 tested patients). Hospitals in health regions 4 (lower central region) had the highest frequency of community-origin 3GCREC BSI (adjusted incidence rate ratio, 2.06; 95% confidence interval: 1.52-2.97). Health regions were not associated with the frequency of hospital-origin CRAB BSI, and between-hospital variation was high, even adjusting for hospital level and size. The high between-hospital variation of hospital-origin CRAB BSI suggests the importance of hospital-specific factors. Our approach and findings highlight health regions and hospitals where actions against AMR infection, including antimicrobial stewardship and infection control, should be prioritized.

Bacterial Genomics for National Antimicrobial Resistance Surveillance in Cambodia.

Antimicrobial resistance (AMR) surveillance in low- and middle-income countries (LMICs) often relies on poorly resourced laboratory processes. Centralized sequencing was combined with cloud-based, open-source bioinformatics solutions for national AMR surveillance in Cambodia. Blood cultures growing gram-negative bacteria were collected at six Cambodian hospitals (January 2021 - October 2022). Isolates were obtained from pure plate growth and shotgun DNA sequencing performed in-country. Using public nucleotide and protein databases, reads were aligned for pathogen identification and AMR gene characterization. Multilocus sequence typing was performed on whole genome assemblies and haplotype clusters compared against published genomes. Genes associated with acquired resistance to fluoroquinolones were identified in 59%, TMP/SMX in 45%, and aminoglycosides in 52% of 715 isolates. Extended-spectrum beta-lactamase encoding genes were identified in 34% isolates, most commonly blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55 in E. coli sequence types 131 and 1193. Carbapenemase genes were identified in 12% isolates, most commonly blaOXA-23, blaNDM-1, blaOXA-58 and blaOXA-66 in Acinetobacter species. Phylogenetic analysis revealed clonal strains of A. baumannii, representing suspected nosocomial outbreaks, and genetic clusters of quinolone-resistant typhoidal Salmonella and ESBL E. coli cases suggesting community transmission. With accessible sequencing platforms and bioinformatics solutions, bacterial genomics can supplement AMR surveillance in LMICs. Research was supported by the National Institute of Allergy and Infectious Diseases and the Bill and Melinda Gates Foundation [OPP1211806].

A Situation Analysis of the Capacity of Laboratories in Faith-Based Hospitals in Zambia to Conduct Surveillance of Antimicrobial Resistance: Opportunities to Improve Diagnostic Stewardship.

Antimicrobial resistance (AMR) is a public health problem exacerbated by the overuse and misuse of antibiotics and the inadequate capacity of laboratories to conduct AMR surveillance. This study assessed the capacity of laboratories in seven faith-based hospitals to conduct AMR testing and surveillance in Zambia. This multi-facility, cross-sectional exploratory study was conducted from February 2024 to April 2024. We collected and analysed data using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. This study found an average score of 39%, indicating a low capacity of laboratories to conduct AMR surveillance. The highest capacity score was 47%, while the lowest was 25%. Only one hospital had a full capacity (100%) to utilise a laboratory information system (LIS). Three hospitals had a satisfactory capacity to perform data management with scores of 83%, 85%, and 95%. Only one hospital had a full capacity (100%) to process specimens, and only one hospital had good safety requirements for a microbiology laboratory, with a score of 89%. This study demonstrates that all the assessed hospitals had a low capacity to conduct AMR surveillance, which could affect diagnostic stewardship. Therefore, there is an urgent need to strengthen the microbiology capacity of laboratories to enhance AMR surveillance in Zambia.

The global burden and trend of Clostridioides difficile and its association with world antibiotic consumption, 1990-2019.

To estimate the global trends and disease burden of Clostridioides difficile infection (CDI) and its correlation with worldwide antibiotic consumption. Clostridioides difficile infection and antibiotic consumption data were retrieved from the Global Burden of Disease 2019, ResistanceMap-AntibiocUse, Food and Drug Administration (FDA) Adverse Event Reporting System, and Global Antimicrobial Resistance and Use Surveillance System. Jointpoint regression and age-period-cohort model were developed to show the global trends and burden of CDI. Correlation tests were calculated to explore the relationship between CDI and antibiotics. Globally, CDI is the most significant one with a high-rocketing burden increase rate among 13 pathogens causing diarrheal deaths and disability-adjusted life years (DALYs). The age-standardised death rate (ASDR) increased from 0.19 in 1990 to 0.43 in 2019, in which the elderly and females are at higher risk. A rapid increase in ASDR in high to middle sociodemographic index (SDI) regions such as North America (average annual percentage change (AAPC) = 7.71%), Andean (AAPC = 7.82%), and Southern Latin America (AAPC = 11.08%) was identified. Antibiotic consumption has a significant positive correlation with CDI with different risk stratifications. The global burden of CDI has continuously increased for the past 30 years, especially in high to middle-SDI regions. World antibiotic consumption showed a strong positive correlation with CDI with different risk stratification. More effective prevention and control measures should be implemented in these critical regions, with a specific emphasis on vulnerable populations, to mitigate the spread of epidemics.

Investigation of Mutations in the crt-o and mdr1 Genes of Plasmodium vivax for the Molecular Surveillance of Chloroquine Resistance in Parasites from Gold Mining Areas in Roraima, Brazil.

Plasmodium vivax causes the largest malaria burden in Brazil, and chloroquine resistance poses a challenge to eliminating malaria by 2035. Illegal mining in the Roraima Yanomami Indigenous territory can lead to the introduction of resistant parasites. This study aimed to investigate mutations in the pvcrt-o and pvmdr-1 genes to determine their potential as predictors of P. vivax chloroquine-resistant phenotypes. Samples were collected in two health centers of Boa Vista. A questionnaire was completed, and blood was drawn from each patient. Then, DNA extraction, PCR, amplicon purification, and DNA sequencing were performed. After alignment with the Sal-1, the amplified fragment was analyzed. Patients infected with the mutant parasites were queried in the Surveillance Information System. Among the patients, 98% (157/164) of participants were from illegal mining areas. The pvcrt-o was sequenced in 151 samples, and the K10 insertion was identified in 13% of them. The pvmdr1 was sequenced in 80 samples, and the MYF haplotype (958M) was detected in 92% of them and the TYF was detected in 8%, while the MYL was absent. No cases of recrudescence, hospitalization, or death were found. Mutations in the pvcrt-o and pvmdr-1 genes have no potential to predict chloroquine resistance in P. vivax.

Antibiotic consumption in hospitals in humanitarian settings in Afghanistan, Bangladesh, Democratic Republic of Congo, Ethiopia and South Sudan

BackgroundAntimicrobial resistance is of great global public health concern. In order to address the paucity of antibiotic consumption data and antimicrobial resistance surveillance systems in hospitals in humanitarian settings, we estimated antibiotic consumption in six hospitals with the aim of developing recommendations for improvements in antimicrobial stewardship programs.MethodsSix hospitals supported by Médecins sans Frontières were included in the study: Boost-Afghanistan, Kutupalong-Bangladesh, Baraka and Mweso-Democratic Republic of Congo, Kule-Ethiopia, and Bentiu-South Sudan. Data for 36,984 inpatients and antibiotic consumption data were collected from 2018 to 2020. Antibiotics were categorized per World Health Organization Access Watch Reserve classification. Total antibiotic consumption was measured by Defined Daily Doses (DDDs)/1000 bed-days.ResultsAverage antibiotic consumption in all hospitals was 2745 DDDs/1000 bed-days. Boost hospital had the highest antibiotic consumption (4157 DDDs/1000 bed-days) and Bentiu the lowest (1598 DDDs/1000 bed-days). In all hospitals, Access antibiotics were mostly used (69.7%), followed by Watch antibiotics (30.1%). The most consumed antibiotics were amoxicillin (23.5%), amoxicillin and clavulanic acid (14%), and metronidazole (13.2%). Across all projects, mean annual antibiotic consumption reduced by 22.3% during the study period, mainly driven by the reduction in Boost hospital in Afghanistan.ConclusionsThis was the first study to assess antibiotic consumption by DDD metric in hospitals in humanitarian settings. Antibiotic consumption in project hospitals was higher than those reported from non-humanitarian settings. Routine systematic antibiotic consumption monitoring systems should be implemented in hospitals, accompanied by prescribing audits and point-prevalence surveys, to inform about the volume and appropriateness of antibiotic use and to support antimicrobial stewardship efforts in humanitarian settings.

Implementation of antimicrobial resistance surveillance in Ghana using the Integrated Disease Surveillance and Response strategy.

Implementation of antimicrobial resistance surveillance in Ghana using the Integrated Disease Surveillance and Response strategy.

Research note: characteristics of blaNDM and mcr-1 co-producing Escherichia coli from retail chicken meat

Carbapenems and colistin are vital antimicrobials used to treat Enterobacteriaceae-caused infections. The present study aimed to characterize the coexistence mechanism of carbapenem and colistin resistance in an Escherichia coli isolated from retail chicken meat. A total of 4 E. coli isolates co-harboring carbapenem resistance gene blaNDM (2 E. coli isolates with blaNDM-5 and 2 with blaNDM-9) and colistin resistance gene mcr-1. Antimicrobial susceptibility testing exhibited that all the 4 E. coli strains had multidrug resistance profile and consistent with the resistance genes they carried. MLST showed that 3 E. coli isolates belonged to a pathogenic E. coli lineage ST354, which is closely associated with human infections and pose a serious threat to public health. Whole genome sequencing (WGS) showed that 4 mcr-1-positive plasmids with sizes of 60.4 kb-67.4 kb all belonged to the IncI2 type. A total of 5 blaNDM-harboring plasmids ranged from 99.0 kb∼138.3 kb, among which 4 plasmids belonged to unknow type and only pCS5L-NDM belonged to IncFIA/IncFIB group of hybrid plasmids, a novel carrier for blaNDM. Comparative analysis exhibited that the mcr-1 or blaNDM-carrying plasmids of E. coli strains from chicken meat showed high identity with that from Enterobacteriaceae of human origin, which indicated the risk of mcr-1 or blaNDM dissemination from retail meat to human. The simultaneous occurrence of mcr-1 and blaNDM in E. coli emphasizes the significant of antimicrobial resistance surveillance in retail meat.

Whole-genome sequencing for antimicrobial surveillance: species-specific quality thresholds and data evaluation from the network of the European Union Reference Laboratory for Antimicrobial Resistance genomic proficiency tests of 2021 and 2022.

As antimicrobial resistance (AMR) surveillance shifts to genomics, ensuring the quality of whole-genome sequencing (WGS) data produced across laboratories is critical. Participation in genomic proficiency tests (GPTs) not only increases individual laboratories' WGS capacity but also provides a unique opportunity to improve species-specific thresholds for WGS quality control (QC) by repeated resequencing of distinct isolates. Here, we present the results of the EU Reference Laboratory for Antimicrobial Resistance (EURL-AR) network GPTs of 2021 and 2022, which included 25 EU national reference laboratories (NLRs). A total of 392 genomes from 12 AMR-bacteria were evaluated based on WGS QC metrics. Two percent (n = 9) of the data were excluded, due to contamination, and 11% (n = 41) of the remaining genomes were identified as outliers in at least one QC metric and excluded from computation of the adjusted QC thresholds (AQT). Two QC metric correlation groups were identified through linear regression. Eight percent (n = 28) of the submitted genomes, from 11 laboratories, failed one or more of the AQTs. However, only three laboratories (12%) were identified as underperformers, failing across AQTs for uncorrelated QC metrics in at least two genomes. Finally, new species-specific thresholds for "N50" and "number of contigs > 200 bp" are presented for guidance in routine laboratory QC. The continued participation of NRLs in GPTs will reveal WGS workflow flaws and improve AMR surveillance data. GPT data will continue to contribute to the development of reliable species-specific thresholds for routine WGS QC, standardizing sequencing data QC and ensure inter- and intranational laboratory comparability.IMPORTANCEIllumina next-generation sequencing is an integral part of antimicrobial resistance (AMR) surveillance and the most widely used whole-genome sequencing (WGS) platform. The high-throughput, relative low-cost, high discriminatory power, and rapid turnaround time of WGS compared to classical biochemical methods means the technology will likely remain a fundamental tool in AMR surveillance and public health. In this study, we present the current level of WGS capacity among national reference laboratories in the EU Reference Laboratory for AMR network, summarizing applied methodology and statistically evaluating the quality of the obtained sequence data. These findings provide the basis for setting new and revised thresholds for quality metrics used in routine WGS, which have previously been arbitrarily defined. In addition, underperforming participants are identified and encouraged to evaluate their workflows to produce reliable results.

Epidemiology and Impact of Anti-Pneumococcal Vaccination and COVID-19 on Resistance of Streptococcus pneumoniae Causing Invasive Disease in Piedmont, Italy.

The international surveillance of antimicrobial resistance (AMR) reports S. pneumoniae as one of leading causes of death associated with AMR. Against invasive disease, several vaccinations are available and a reduction in AMR in S. pneumoniae has been observed. Here, we evaluated the impact of anti-pneumococcal vaccination policy and the SARS-CoV2 outbreak on AMR in S. pneumoniae causing invasive disease. We collected all strains of S. pneumoniae causing invasive disease from 2008 in the Piedmont region (Italy). Each strain was typed in order to identify the serogroup and data about AMR were collected. The population under surveillance was classified as infants, children, adults, and the old population. We collected n = 2076 S. pneumoniae strains, with 21.9% and 40.3% being resistant to penicillin G and erythromycin, respectively. We reported an increased risk of infection with penicillin-resistant S. pneumoniae among all populations and evaluated whether the infection was caused by a serotype included in the vaccine formulation. A similar increase was observed after the SARS-CoV2 outbreak. In the Piedmont region, subsequently to the introduction of anti-pneumococcal vaccination, a significant increase in the risk of penicillin G-resistant invasive pneumococcal disease among infants and old population was reported. No significant impact was found for the SARS-CoV2 outbreak.

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).

Assessment of carbapenem resistance and carbapenemase genes in wastewater from cattle slaughterhouses: Implications for environmental antibiotic resistance surveillance

The objectives of the study were to determine the prevalence of carbapenem-resistant Gram-negative bacteria and assess the potential risks associated with cattle slaughterhouse wastewater. A total of 270 wastewater samples were collected from 10 different cattle slaughterhouses for microbiological analysis. Conventional culture methods were employed, followed by disc diffusion, the Modified Carbapenem Inactivation Method (mCIM), and the Modified Hodge Test (MHT) to identify carbapenem resistance. The Vitek® 2 compact system was used for species identification and antibiotic susceptibility profiling. Conventional and quantitative PCR (qPCR) were performed to detect specific carbapenemase genes (blaKPC, blaNDM, and blaOXA-48). Among the collected 72 carbapenem-resistant isolates, one Pseudomonas fluorescens, one Aeromonas hydrophila, and two Aeromonas sobria exhibited resistance to meropenem. Additionally, six P. fluorescens and two A. hydrophila isolates demonstrated intermediate resistance to meropenem. Furthermore, five carbapenem-resistant isolates were identified as Stenotrophomonas maltophilia, known to be inherently resistant to most antibiotics. Ten different antibiotics were evaluated in the antibiotic resistance panel and all Aeromonas isolates were found to be resistant to cefazolin and one A. hydrophila was detected as multi-drug resistant. The revealed data indicates that slaughterhouse wastewater can serve as a reservoir for antibiotic-resistant opportunistic pathogens. However, it may not pose a substantial risk for the distribution of carbapenemases, thereby mitigating concerns related to potential public health and environmental hazards associated with this aspect of slaughterhouse operations. This study contributes to understanding of antibiotic resistance in livestock-related environments and underscores the importance of continued monitoring and surveillance.

Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa.

We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa. We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to β-lactams. The other 43 constructs expressed transferable β-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution. Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable β-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol. Cefiderocol and new β-lactam/β-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa β-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient β-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.

Association of a rapidly selected 4.3kb transposon-containing structural variation with a P450-based resistance to pyrethroids in the African malaria vector Anopheles funestus.

Deciphering the evolutionary forces controlling insecticide resistance in malaria vectors remains a prerequisite to designing molecular tools to detect and assess resistance impact on control tools. Here, we demonstrate that a 4.3kb transposon-containing structural variation is associated with pyrethroid resistance in central/eastern African populations of the malaria vector Anopheles funestus. In this study, we analysed Pooled template sequencing data and direct sequencing to identify an insertion of 4.3kb containing a putative retro-transposon in the intergenic region of two P450s CYP6P5-CYP6P9b in mosquitoes of the malaria vector Anopheles funestus from Uganda. We then designed a PCR assay to track its spread temporally and regionally and decipher its role in insecticide resistance. The insertion originates in or near Uganda in East Africa, where it is fixed and has spread to high frequencies in the Central African nation of Cameroon but is still at low frequency in West Africa and absent in Southern Africa. A marked and rapid selection was observed with the 4.3kb-SV frequency increasing from 3% in 2014 to 98% in 2021 in Cameroon. A strong association was established between this SV and pyrethroid resistance in field populations and is reducing pyrethroid-only nets' efficacy. Genetic crosses and qRT-PCR revealed that this SV enhances the expression of CYP6P9a/b but not CYP6P5. Within this structural variant (SV), we identified putative binding sites for transcription factors associated with the regulation of detoxification genes. An inverse correlation was observed between the 4.3kb SV and malaria parasite infection, indicating that mosquitoes lacking the 4.3kb SV were more frequently infected compared to those possessing it. Our findings highlight the underexplored role and rapid spread of SVs in the evolution of insecticide resistance and provide additional tools for molecular surveillance of insecticide resistance.

HIV-1 pretreatment and acquired antiretroviral drug resistance before tenofovir/ lamivudine /dolutegravir (TLD) roll-out in Mozambique

BackgroundThe World Health Organization (WHO) recommends that HIV treatment scale-up is accompanied by a robust assessment of drug resistance emergence and transmission. The WHO HIV Drug Resistance (HIVDR) monitoring and surveillance strategy includes HIVDR testing in adults both initiating and receiving antiretroviral therapy (ART). Due to limited information about HIVDR in Mozambique, we conducted two nationally representative surveys of adults initiating and receiving first-line ART regimes to better inform the HIV program.MethodsWe carried out a cross-sectional study between March 2017 and December 2019. Adults (older than 15 years) living with HIV (PLHIV) initiating ART or receiving first-line ART for between 9-15 months at 25 health facilities across all eleven provinces in Mozambique were included. Genotypic HIVDR was assessed on dried blood spots (DBS) when viral loads were ≥ 1000 copies/ml. Genotypic resistance for non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) was determined using the Stanford HIV database algorithm 9.5 and calibrated population resistance tool 8.1.ResultsOf 828 participants -enrolled, viral load (VL) testing was performed on 408 initiators and 409 ART experienced. Unsuppressed VL was found in 68.1% 419 initiators and 18.8% (77/409) of the ART experienced. Of the 278 initiators and 70 ART experienced who underwent sequencing, 51.7% (144/278) and 75.7% (53/70) were sequenced successfully. Among the new initiators, pretreatment drug resistance (PDR) for NNRTI and PI was found in 16.0% (23/144) and 1.4% (2/144) of the participants, respectively. Acquired drug resistance (ADR) was found in 56.5% (30/53) of the ART-experienced participants of whom 24.5% (13/53) were resistant to both NRTI and NNRTI.ConclusionHigh rates of PDR and ADR for NNRTI and ADR for NRTI were observed in our study. These findings support the replacement of NNRTIs with dolutegravir (DTG) but high levels of NRTI resistance in highly treatment-experienced individuals still require attention when transitioning to new regimens. Moreover, the study underlines the need for routine VL testing and HIVDR surveillance to improve treatment management strategies.

Prevalence and characterization of quinolone resistance and integrons in clinical Gram-negative isolates from Gaza strip, Palestine.

Gram-negative bacteria with quinolone resistance and extended-spectrum beta-lactamases (ESBLs) present significant treatment challenges. This study evaluated the prevalence and characteristics of quinolone resistance in Gram-negative strains, investigating the relationship between plasmid-mediated quinolone resistance (PMQR), ESBLs, and integrons. We collected 146 Gram-negative isolates from patients in three Palestinian hospitals. For quinolone resistance isolates, the presence and characterization of PMQR, β-lactamase genes and integrons were studied by PCR and sequencing. Out of 146 clinical isolates, 64 (43.8%) were resistant to quinolones, with 62 (97%) being multidrug-resistant (MDR) and 33 (51.5%) ESBL-producers. PMQR-encoding genes were present in 45 (70.3%) isolates, including aac(6')-Ib-cr (26.6%), qnrA (18.8%), qnrS1 (20.8%), and qnrB (6.4%). BlaCTX-M genes were detected in 50% (32/64) of isolates, with blaCTX-M-15 being the most common. BlaTEM-1, blaSHV-1 and blaVIM genes were found in 13, 6, and 4 isolates, respectively. Class I integrons were found in 31/64 (48%) of isolates, with 14 containing gene cassettes conferring resistance to trimethoprim (dhfr17, dfrA12, dfrA1) and aminoglycosides resistance genes (aadA1, aadA2, aadA5, and aadA6). This study found a high rate of quinolone resistance, ESBL and integrons in clinical Gram-negative isolates from our hospitals. Urgent measures are crucial, including implementing an antimicrobial resistance surveillance system, to control and continuously monitor the development of antimicrobial resistance.

In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.

To facilitate the detection and management of potential clinical antiviral resistance, in vitro selection of drug-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) against the virus Mpro inhibitor nirmatrelvir (Paxlovid active component) was conducted. Six Mpro mutation patterns containing T304I alone or in combination with T21I, L50F, T135I, S144A, or A173V emerged, with A173V+T304I and T21I+S144A+T304I mutations showing >20-fold resistance each. Biochemical analyses indicated inhibition constant shifts aligned to antiviral results, with S144A and A173V each markedly reducing nirmatrelvir inhibition and Mpro activity. SARS-CoV-2 surveillance revealed that in vitro resistance-associated mutations from our studies and those reported in the literature were rarely detected in the Global Initiative on Sharing All Influenza Data database. In the Paxlovid Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients trial, E166V was the only emergent resistance mutation, observed in three Paxlovid-treated patients, none of whom experienced COVID-19-related hospitalization or death.

Perspectives on progression of transboundary disease, one health and ecosystem health management in the Greater Mekong Subregion and beyond

Livestock production in the Greater Mekong Subregion (GMS) reflects the inefficient smallholder ‘keeper’ system that has been slow to adapt to the rapidly expanding demand for animal protein-sourced foods in the region as urban economies have flourished and food preferences altered. The prolonged surge in demand, with only modest increases in local production, has increased the movement of animals and products into and from the GMS, accompanied by surging risks of transboundary animal disease (TAD) incursions, including the one health (OH) threats of zoonoses and antimicrobial resistance. As a consequence, the region has been subjected to epidemics of highly pathogenic avian influenza (HPAI), new strains of foot-and-mouth disease (FMD) virus, with recent incursions of African swine fever (ASF), lumpy skin disease (LSD), porcine reproductive and respiratory syndrome (PRRS) and risks of peste petits ruminants (OPR) occurring in Southeast Asia (SEA) and beyond. These incidents reflect inadequate biosecurity, a sustainability issue that was clearly of relevance in the covid-19 pandemic, reflecting ecosystem health (EH) deficits, including land-use issues and unregulated trading in wildlife-sourced and poorly processed foods through the predominant ‘wet markets’. These challenges are increasingly confounded by slow adaption to the impacts of the climate crisis, including flooding, drought, crop failures and hypothermia episodes. The increase in animal and product movements enhances disease transmission risk, yet coincides with emerging concerns of greenhouse-gas emissions (GHGe) from livestock production, especially from large ruminants, as the world attempts to find pathways in managing the climate crisis. Despite the prolonged collaborative efforts of the SEA China FMD program from 1997 to 2023, a recent review confirmed persistent deficits in biosecurity, vaccine resourcing, disease surveillance, engagement of farmers, and national emergency disease-response capacities. A major project is about to fund major improvements in livestock value chains in Cambodia, including more effective biosecurity, surveillance and emergency disease-response capacities for TADs, antimicrobial resistance (AMR) and zoonoses. Similarly, a private-sector investment in Laos has developed a more climate-resilient livestock-feeding system that decreases GHGe impacts from ruminant production. These developments are likely to extend beyond both countries and be potentially transformational for the livelihoods of many of the poorest citizens in the region.

Comparative Analysis of Methicillin-Resistant Staphylococcus pseudintermedius Prevalence and Resistance Patterns in Canine and Feline Clinical Samples: Insights from a Three-Year Study in Germany.

The emergence of methicillin-resistant Staphylococcus pseudintermedius (MRSP) presents a significant public health concern globally, particularly within veterinary medicine. MRSP's resistance to multiple antibiotics is limiting treatment options and potentially leading to severe infections in companion animals. This study aimed to understand antimicrobial resistance in dogs and cats, focusing on MRSP resistance patterns and its prevalence in Germany. We analyzed results of bacterial diagnostic samples from canines and felines, sourced from a German veterinary diagnostic microbiology laboratory between 2019 and 2021. This dataset included samples from 3491 veterinary practices, covering 33.1% of veterinary practices and clinics in Germany. MRSP rates were detailed by host species, sample types and co-resistance patterns. Analysis of 175,171 bacterial examination results revealed S. pseudintermedius in 44,880 samples, yielding a 25.6% isolation rate. S. pseudintermedius was more prevalent in dogs (35.0%) than cats (3.6%). Methicillin resistance was found in 7.5% of all S. pseudintermedius isolates. MRSP prevalence was higher in feline samples (16.1%, 95% CI 14.4-17.8) compared to canine samples (7.1%, 95% CI 6.8-7.0). S. pseudintermedius showed high resistance rates to ampicillin (cats: 48.6%, dogs: 67.6%) and clindamycin (cats: 37.2%, dogs: 32.7%), while MRSP exhibited high co-resistance to clindamycin (cats: 82.8%, dogs: 85.4%) and sulfamethoxazole + trimethoprim (cats: 66.4%, dogs: 66.2%). Our study revealed distinct resistance patterns of MRSP in cats compared to dogs, highlighting the need for tailored treatment approaches and the importance of antimicrobial resistance surveillance.

Antimicrobial Resistance Surveillance: Data Harmonisation and Data Selection within Secondary Data Use.

Resistance to last-resort antibiotics is a global threat to public health. Therefore, surveillance and monitoring systems for antimicrobial resistance should be established on a national and international scale. For the development of a One Health surveillance system, we collected exemplary data on carbapenem and colistin-resistant bacterial isolates from human, animal, food, and environmental sources. We pooled secondary data from routine screenings, hospital outbreak investigations, and studies on antimicrobial resistance. For a joint One Health evaluation, this study incorporates epidemiological metadata with phenotypic resistance information and molecular data on the isolate level. To harmonise the heterogeneous original information for the intended use, we developed a generic strategy. By defining and categorising variables, followed by plausibility checks, we created a catalogue for prospective data collections and applied it to our dataset, enabling us to perform preliminary descriptive statistical analyses. This study shows the complexity of data management using heterogeneous secondary data pools and gives an insight into the early stages of the development of an AMR surveillance programme using secondary data.