Resistant Genotypes Research Articles

Comparison of Molecularly Identified Resistant and Susceptible Johnsongrass (Sorghum halepense L.) Populations at ALS Gene, in the Absence and Presence of Field Crops

Background/Objectives: Johnsongrass (Sorghum halepense) is an erect tetraploid, perennial, C4 grass weed species categorized among the world’s most noxious weeds due to its high competitive ability against crops and the increased number of field-evolved herbicide-resistant populations. The aim of the present study was to assess the growth rate and performance of resistant (R) johnsongrass genotypes hosting Trp574Leu target-site cross-resistance at ALS gene, inhibiting various herbicides, compared to susceptible (S) conspecific weeds, in the absence and presence of corn or sunflower antagonism. Methods: The aboveground biomass, tiller, and rhizome production ability of one S and one R johnsongrass population with a Trp574-Leu substitution conferring cross-resistance to ALS-inhibiting herbicides were compared under non-competitive conditions. Furthermore, the competitive ability of these two johnsongrass populations against corn or sunflower was determined in a target-neighborhood design. Results: The S and R johnsongrass populations displayed similar growth rates concerning aboveground biomass and tiller number, whereas the R population displayed a slightly greater growth rate for rhizome production compared to the S population. Both populations grown with corn produced more aboveground biomass than the ones grown with sunflowers. The aboveground biomass of corn was reduced to a greater extent than sunflower by the presence of both johnsongrass populations, while both crops were affected more by the S than by the R population. Conclusions: Although the inheritance and the genetic background of plant materls were not addressed, the findings of this study indicate clearly that the growth rate and competitive ability of the ALS-resistant johnsongrass population are not associated with the resistance mechanism involved.

A Sensitivity and Consistency Comparison Between Next-Generation Sequencing and Sanger Sequencing in HIV-1 Pretreatment Drug Resistance Testing

Next-generation sequencing (NGS) for HIV drug resistance (DR) testing has an increasing number of applications for the detection of low-abundance drug-resistant variants (LA-DRVs) in regard to its features as a quasi-species. However, there is less information on its detection performance in DR detection with NGS. To determine the feasibility of using NGS technology in LA-DRV detection for HIV-1 pretreatment drug resistance, 80 HIV-infected individuals who had never undergone antiretroviral therapy were subjected to both NGS and Sanger sequencing (SS) in HIV-1 drug resistance testing. The results reported in this study show that NGS exhibits higher sensitivity for drug resistance identification than SS at a 5% detection threshold. NGS showed a better consistency compared with that of SS for both protease inhibitors (PIs) and integrase inhibitors (INSTIs), with a figure amounting to more than 90%, but worse consistency in nucleotide reverse transcriptase inhibitors (NRTIs), with a consistency ranging from only 61.25% to 87.50%. The consistency of non-nucleotide reverse transcriptase inhibitors (NNRTIs) between NGS and SS was around 85%. NGS showed the highest sensitivity of 87.0% at a 5% threshold. The application of NGS technology in HIV-1 genotype resistance detection in different populations infected with HIV requires further documentation and validation.

Genome-wide analysis of calmodulin binding Protein60 candidates in the important crop plants.

Efficient management of environmental stresses is essential for sustainable crop production. Calcium (Ca²⁺) signaling plays a crucial role in regulating responses to both biotic and abiotic stresses, particularly during host-pathogen interactions. In Arabidopsis thaliana, calmodulin-binding protein 60 (CBP60) family members, such as AtCBP60g, AtCBP60a, and AtSARD1, have been well characterized for their involvement in immune regulation. However, a comprehensive understanding of CBP60 genes in major crops remains limited. In this study, we utilized the Phytozome v12.1 database to identify and analyze CBP60 genes in agriculturally important crops. Expression patterns of a Oryza sativa (rice) CBP60 gene, OsCBP60bcd-1, were assessed in resistant and susceptible rice genotypes in response to infection by the bacterial pathogen Xanthomonas oryzae. Localization of CBP60 proteins was analyzed to predict their functional roles, and computational promoter analysis was performed to identify stress-responsive cis-regulatory elements. Phylogenetic analysis revealed that most CBP60 genes in crops belong to the immune-related clade. Expression analysis showed that OsCBP60bcd-1 was significantly upregulated in the resistant rice genotype upon pathogen infection. Subcellular localization studies suggested that the majority of CBP60 proteins are nuclear-localized, indicating a potential role as transcription factors. Promoter analysis identified diverse stress-responsive cis-regulatory elements in the promoters of CBP60 genes, highlighting their regulatory potential under stress conditions. The upregulation of OsCBP60bcd-1 in response to Xanthomonas oryzae and the presence of stress-responsive elements in its promoter underscore the importance of CBP60 genes in pathogen defense. These findings provide a basis for further investigation into the functional roles of CBP60 genes in crop disease resistance, with implications for enhancing stress resilience in agricultural species.

Archived HIV-1 Drug Resistance Mutations: Role of Proviral HIV-1 DNA Genotype for the Management of Virological Responder People Living with HIV

Despite its effectiveness in controlling plasma viremia, antiretroviral therapy (ART) cannot target proviral DNA, which remains an obstacle to HIV-1 eradication. When treatment is interrupted, the reservoirs can act as a source of viral rebound, highlighting the value of proviral DNA as an additional source of information on an individual’s overall resistance burden. In cases where the viral load is too low for successful HIV-1 RNA genotyping, HIV-1 DNA can help identify resistance mutations in treated individuals. The absence of treatment history, the need to adjust ART despite undetectable viremia, or the presence of LLV further support the use of genotypic resistance tests (GRTs) on HIV-1 DNA. Conventionally, GRTs have been achieved through Sanger sequencing, but the advances in NGS are leading to an increase in its use, allowing the detection of minority variants present in less than 20% of the viral population. The clinical significance of these mutations remains under debate, with interpretations varying based on context. Additionally, proviral DNA is subject to APOBEC3-induced hypermutation, which can lead to defective, nonviable viral genomes, a factor that must be considered when performing GRTs on HIV-1 DNA.

Multi-component resistance responses of melon to zucchini yellow mosaic virus.

A major resistance gene of the melon accession PI414723 to zucchini yellow mosaic virus (ZYMV) is located at the Zym-1 locus on chromosome 2, but the underlying defense mechanisms are poorly understood. The physiological responses and expression of selected genes at Zym-1 were assessed in PI414723 and in the susceptible genotype Védrantais. Viral titers and the expression of genes related to systemic acquired resistance (SAR) were evaluated in inoculated (Inoc) and non-inoculated (Non-Inoc) portions of the cotyledons at 3, 7 and 10 days after inoculation (dai) and in apical leaves at 10 dai. ZYMV was detected in both portions of the cotyledons but not in the apical leaves of PI414723 plants. Also, ZYMV was recovered in a susceptible zucchini only from Inoc portions at 3 dai. By contrast, in Védrantais ZYMV was detected and recovered from all tissues at high concentrations. Starchy local lesions and accumulation of transcripts of the SAR marker genes PR1 and PR4 were also detected in the resistant genotype. Plus, transcripts of one candidate resistance gene analog previously located at Zym-1 and of two melon homologs of restricted tobacco etch virus movement 2 (RTM2) genes located close to Zym-1, accumulated only in PI414723. It is proposed that resistance results from the combined action of the R gene, involved in restricting ZYMV replication after a supposed recognition event and of the RTM genes which impact viral systemic movement to distal apical tissues.

Calcium-Binding Protein and Polymorphism in Musa spp. Somaclones Resistant to Fusarium oxysporum

The fresh fruits of ‘Grande Naine’ (Cavendish AAA—Musa spp.) dominate the world market, especially in countries with a population in a situation of social vulnerability. However, Fusarium wilt, caused by the fungus Fusarium oxysporum f.sp. cubense race 4 Subtropical (Foc ST4), emerges as a serious threat to banana production, requiring the development of resistant cultivars based on biotechnological strategies, such as the induction of mutation in tissue culture. This study aimed to identify and characterize genetic variation in somaclones resistant to Fusarium oxysporum f.sp. cubense subtropical race 4 (Foc ST4), derived from ‘Grand Naine’ bananas, by molecular markers based on retrotransposons IRAP (Inter-retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Nine combinations of IRAP and six combinations of REMAP primers were used. The low number of polymorphic bands did not allow for genetic diversity studies; however, ten polymorphic bands between the somaclones and control were sequenced. Of these, three presented good base calling and were aligned, namely, 1AF, 2AF, and 3AF bands. Only the 1AF band presented function related to stress response with homology to a calcium-binding protein. These proteins act early in plant infection as secondary messengers activated by pathogen-associated molecular patterns (PAMPs), initiating the cascade of plant defense signals. The fact that this band is present in all somaclones reinforces previous assessments of their resistance to Foc ST4. The use of markers IRAP and REMAP produced polymorphic bands that can, through future primer design and field validations, accelerate the identification of resistant banana genotypes for use in banana genetic breeding programs.

The V410L kdr allele in the VGSC confers higher levels of field resistance to permethrin in urban mosquito populations of Aedes aegypti (L.).

Females of Aedes aegypti transmit emerging arboviruses including Zika, dengue, yellow fever, and chikungunya. Control of these adult mosquitoes heavily relies on synthetic insecticides, including pyrethroids. However, insecticide resistance development in populations poses a significant challenge to vector control, particularly from knockdown resistance (kdr) mutations in the voltage-gated sodium channel (VGSC), the target of pyrethroids. This study investigated the field efficacy of Permanone, a pyrethroid-based insecticide, against Ae. aegypti by assessing the impact of three common kdr mutations (V410L, V1016I, F1534C) on mosquito survival under a real operational mosquito control scenario, by quantifying the pesticide delivered in the field. Field cage tests (FCTs) were conducted while conducting a realistic mosquito control application. Female mosquitoes from six operational areas from Harris County, TX, USA were exposed to Permanone delivered with a handheld sprayer. Permanone deposited near the cages was estimated from aluminum boats placed in the field during FCTs using gas chromatography-mass spectrometry (GC-MS). Mortality rates were recorded, and individual mosquitoes were genotyped for kdr mutations. A probit regression model was used to analyze the factors influencing mosquito survivorship. As the distance from the application source route increased, the amount of Permanone deposited decreased, resulting in higher survivorship frequency of Ae. aegypti females with the triple-resistant kdr genotype (LL/II/CC). The L allele at the 410-site significantly contributed to an increased resistance level when co-occurring with other kdr mutations. This study linked the survival probabilities of mosquitoes with different kdr genotypes, and the amount of pesticide they received in the field. Pesticide quantification, control efficacy results and genotyping allowed us to empirically determine the impact of genotypic resistance on vector control in the field. © 2024 Society of Chemical Industry.

Time-Course Transcriptome Analysis Reveals Distinct Transcriptional Regulatory Networks in Resistant and Susceptible Grapevine Genotypes in Response to White Rot.

Grapevine (Vitis vinifera L.) is a globally significant economic crop. However, its widely cultivated varieties are highly susceptible to white rot disease. To elucidate the mechanisms of resistance in grapevine against this disease, we utilized time-ordered gene co-expression network (TO-GCN) analysis to investigate the molecular responses in the grapevine varieties 'Guifeimeigui' (GF) and 'Red Globe' (RG). An assessment of their resistance demonstrated that GF is highly resistant to white rot, whereas RG is highly susceptible. We conducted transcriptome sequencing and a TO-GCN analysis on leaf samples from GF and RG at seven time points post-infection. Although a significant portion of the differentially expressed genes related to disease resistance were shared between GF and RG, the GF variety rapidly activated its defense mechanisms through the regulation of transcription factors during the early stages of infection. Notably, the gene VvLOX3, which is a key enzyme in the jasmonic acid biosynthetic pathway, was significantly upregulated in GF. Its upstream regulator, Vitvi08g01752, encoding a HD-ZIP family transcription factor, was identified through TO-GCN and yeast one-hybrid analyses. This study provides new molecular insights into the mechanisms of grapevine disease resistance and offers a foundation for breeding strategies aimed at enhancing resistance.

Response of host Indian Musa germplasm against artificially induced root lesion nematodes (Pratylenchus coffeae)

Under greenhouse condition, the host response of fifty-nine banana genotypes (Musa spp.) from the Eumusa section to the root-lesion nematode (Pratylenchus coffeae) was assessed. In a factorial completely randomized design (FCRD) with five replications, healthy banana suckers of the diploid and triploid accessions were planted in cement pots. Uninoculated controls were included in the experiment as comparison to study the sensitivity of the genotypes. Two varieties (Pisang Lilin and Nendran) with known reaction to lesion nematode were also included as reference clones because of their resistance and susceptibility to P. coffeae. Banana accessions maintained in the pots were inoculated with infective juveniles of root-lesion nematode, P. coffeae at 45 days after planting at the rate of 400 nematodes/pot. Ninety days after inoculation, the plants were harvested to observe the response of the different banana genotypes to P. coffeae. Data were recorded on plant growth (plant height, girth at the base, number of standing leaves, number of roots and weight of the root system), root damage assessment (percentage of infected roots and percentage necrosis) and nematode reproduction. When inoculated with nematodes, the reduction in plant growth attributes was relatively higher in genotypes that were susceptible. The reduction in growth characters viz., plants height, number of roots and root fresh weight were maximum in the diploid genotypes Manguthamng (26.80, 27.2, 33.0 %) and Manohar (25.70, 29.2, 35.2 %) and in the triploid genotypes Kaali, Rajthali, Digjowa, Saapkal, Cheenichampa, Dasaman, Borchampa, Jahaji, Manjahaji, Barjahaji and Sabri when inoculated with Pratylenchus coffeae. Even after nematode inoculation, root investigations showed that resistant and tolerant genotypes had greater numbers of roots as well as high fresh and dry weight of roots. Root and soil population of nematodes assessed at 90 days after inoculation indicated very high population buildup of Pratylenchus coffeae (>28) in diploids Manguthamng and Nendrapadathi and in triploids Jahaji, Manjahaji, Saapkal, Borchampa, Therahaw-1163 and 1164, Ankur-I and Bersain. The rate was the lowest (<9) in the diploid genotypes Kanai Bansi, Kechulepa, M.balbisiana, Athiakol, Bhimkol and Aittakola and in the triploids Karthobiumtham and Ankur-II. The results of the experiment showed that the diploids Musa balbisiana (BB), Aittakola (BB), Bhimkol (BB), Kechulepa (BB), Kanai Bansi (AA) and Athiakol (BB) and the triploid genotypes Kachkel (ABB), Karthobiumtham (ABB) and Ankur-II (ABB) were resistant to Pratylenchus coffeae.

Optimising Paediatric HIV Treatment: Recent Developments and Future Directions.

Treatment options for children living with HIV have historically been less effective, less practical and more difficult to implement compared with those for adults, as the research and development of new drugs for children has lagged behind. Significant progress has been achieved in response to the paediatric HIV epidemic over the last decade. Several optimised paediatric antiretroviral formulations are currently available or in development, including fixed-dose combination tablets containing a complete World Health Organization-recommended regimen. Despite these advancements, virological suppression rates in children are generally lower than in adults. Even when oral fixed-dose combinations with the optimal target profiles are developed, for some children virological suppression is not achievable for reasons such as adherence challenges, intolerance, toxicity and genotypic resistance. New safe, effective, well-tolerated antiretroviral agents from existing and novel classes, as well as innovative administration strategies are essential. To achieve the UNAIDS target of virological suppression in 95% of children receiving antiretroviral therapy, concerted efforts are required. This includes identifying priority drugs in line with latest developments, focusing drug development studies on these priorities, ensuring a timely technical knowledge transfer between originator and generic companies, accelerating regulatory approvals and facilitating procurement and implementation in countries. Success in these efforts depends on collaboration among all stakeholders, including communities, researchers, pharmaceutical companies, guideline and policymakers, governments, funders, regulators and healthcare providers. This review outlines which paediatric antiretroviral therapies are currently available, those which are under development and the future directions of paediatric HIV treatment.

Antimicrobial Resistance and Pathotypes of Escherichia coli Isolates from Yellow-Legged Seagulls (Larus michahellis) in Central Italy.

Seagulls are synanthropic wild birds that can contaminate, through their droppings, beaches, urban and peri-urban environments. This concern is more serious when seagulls eliminate antimicrobial-resistant pathogenic bacteria. This study analyzed the fecal samples from 137 yellow-legged seagulls (Larus michahellis) from Central Italy. A total of 218 Escherichia coli strains were isolated and analyzed for phenotypic and genotypic antimicrobial resistance and to identify the virulence genes characterizing different pathotypes. The disk diffusion method on all isolates found relevant resistance rates to ampicillin (38.99%), tetracycline (23.85%), and enrofloxacin (21.10%). On the basis of all results obtained with this test, 62 (28.44%) isolates were classified as multidrug-resistant (MDR) and 6 (2.75%) as extensive drug-resistant (XDR). Molecular analyses conducted on the strains phenotypically resistant to carbapenems, cephalosporins, and penicillins found 9/37 (24.32%) strains positive for blaOXA-48, 52/103 (50.49%) for blaTEM, 12/103 (11.65%) for blaCMY2, 3/103 (2.91%) for blaCTX, and 1/103 (0.97%,) for blaSHV. PCR to detect virulence genes characterizing different pathotypes found that 40 (18.35%) isolates had the astA gene, indicative of the enteroaggregative (EAEC) pathotype, 2 (0.92%) had cnf1, 2 (0.92%) had cnf2, and 1 (0.46%) had cdt-IV. All five (2.29%) strains were reportable as necrotoxigenic (NTEC), while 4 (1.83%) had both eaeA and escV, reportable as enteropathogenic (EPEC). Measures to limit seagulls' access where humans and other animals reside are pivotal to reduce the risk of infection with antimicrobial-resistant and pathogenetic E. coli strains.

Emergent resistance-associated mutations at first- or second-line HIV-1 virologic failure with second-generation InSTIs in two- and three-drug regimens: the Virostar-1 study.

Second-generation integrase strand transfer inhibitors (InSTIs) have a high barrier to resistance and potent antiretroviral activity. They are recommended as first- or second-line (FL and SL) options in two- and three-drug regimens (2DR and 3DR) in international treatment guidelines. However, there are limited real-world data on emerging resistance at the time of virological failure (VF) with these regimens. The Virostar-1 study objective is to analyse the emergence of resistance-associated mutations (RAMs) over 3 years with DTG-based 2DRs and DTG- or bictegravir (BIC)-based 3DRs in people living with HIV (PLWH) experiencing a VF (FL or SL). Retrospective analysis of genotypic resistance detected at the time of a FL or SL VF with BIC/FTC/TAF, DTG/ABC/3TC, DTG/3TC and DTG/RPV between 2019 and 2022 was conducted from a French multicentre database. VF was defined as two consecutive HIV-1 plasma viral loads > 50 c/mL. Sanger assays were performed at VF within standard clinical care. Resistance mutations were reported using the ANRS algorithm. Selection biases prevent group comparisons. During the period, N = 5986 PLWH were followed either in FL or SL. The VF rate was overall low: BIC/FTC/TAF, 6.8%; DTG/ABC/3TC, 7.5%; DTG/3TC, 5.1%; and DTG/RPV, 2.1%. Some emergent InSTI or NRTI RAMs were detected with BIC/FTC/TAF 4%, DTG/ABC/3TC 8.5%, DTG/3TC 18% and 39% emergent NNRTI RAMs with DTG/RPV. However, a complete absence of dual resistance against NRTIs and InSTIs was observed. We detected rare emergent InSTI RAMs and few emergent NRTI RAMs in PLWH failing DTG- or BIC-based regimens in FL or SL. The observed rates of emergent RAMs at VF were 4% with BIC/FTC/TAF, 8.5% with DTG/ABC/3TC, 18% with DTG/3TC and 39% with DTG/RPV.

Assessing the spread of sulfachloropyridazine in poultry environment and its impact on Escherichia coli resistance

Sulfachloropyridazine (SCP) is an antimicrobial (AM) commonly used in the poultry industry. This drug is excreted as the original compound, which may accumulate in litter. This work was done to assess whether SCP residues from droppings of broiler chickens that were treated with therapeutic doses of this drug spread into the production environment and to determine if these events were associated with the selection of resistant bacteria. To this end, broiler chickens were raised under controlled conditions, and their droppings and litter were processed to detect and identify SCP residues using an HPLC-MS/MS technique. This study selected Escherichia coli as an indicator bacterium for AM resistance. Its phenotypic resistance was determined using the Kirby-Bauer disk diffusion method, and its genotypic resistance was determined by performing a conventional PCR test. Our results showed that SCP residues did spread from the treated group to untreated sentinel groups because SCP residues in the litter reached levels up to 43.05 µg·kg−1 in a group placed immediately adjoining to the treated group, while another group placed 30 cm away showed a concentration of 29.79 µg·kg−1. Meanwhile, only trace concentrations were detected in droppings collected from sentinel groups. Of 239 strains of E. coli isolated from droppings, 12.13 % were resistant to sulfonamides, whereas 23.91 % of 92 E. coli isolated from broiler litter were resistant. The most prevalent resistance gene was the sul2 gene, both in droppings and litter, followed by the sul1 gene. The SCP concentrations were associated with the probability of E. coli being resistant to sulfonamides (p-value = 0.01). A Multiple Correspondence Analysis (MCA) also showed that phenotypic and genotypic resistances were associated and that both genes sul1 and sul2 would determine phenotypic resistance to sulfonamides in E. coli. The results presented in this study show that inedible by-products of the poultry industry are potentially a source of drug resistance that can spread from the animal production line to the environment, so awareness of the correct use of antimicrobials is essential to combat antimicrobial resistance.

Molecular Patterns and Antimicrobial Resistance Characterization of Salmonella enterica Non-Typhoidal from Human, Food, and Environment Samples Isolated in Luanda, Angola

The aim of this study was to characterize the antimicrobial resistance phenotype and genotype of non-typhoidal Salmonella spp. isolated in Luanda, Angola. Between 2013 and 2015, human clinical samples, food, and environmental samples (n = 290) were collected at different regions of Luanda city and screened for the presence of Salmonella spp. Bacterial isolates were preliminarily identified using the API 20E Kit, and their identification was confirmed using PCR and serotyping. All Salmonella spp. isolates were tested by minimum inhibitory concentration against 19 antimicrobials. The isolates were also screened using PCR for the presence of resistance genes (blaOXA-1, blaSHV, blaTEM, sul1, sul2, sul3, qnrA, qnrB, qnrS, qnrC, qnrD, aac(6′)-Ib, dfrIa [targeting dfrA1, dfrA5, dfrA15, dfrA15b, dfrA16, dfrA16b] and dfrA12, cmlA, and floR) and typed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Salmonella enterica non-typhoidal was detected in 21.3% of the clinical samples (n = 32/150), 11.1% of the food samples (n = 10/90), and 26% of the environmental samples (n = 13/50). Serotyping revealed that the monophasic variant of Salmonella Typhimurium (Salmonella enterica serovar 4,[5],12:i:-) was detected in 38.1% of the samples. Moreover, serovar Salmonella Enteritidis was the second most frequent. Only 7.3% of the isolates were resistant to at least one antimicrobial. Furthermore, isolates from different origins (clinical, environmental, and food) were associated with the same lineages, Salmonella Enteritidis ST11 and S. enterica ser. Typhimurium ST313. The detection of S. enterica serovar 4,[5],12:i:- in different settings reinforces the need for a One Health approach to control this zoonosis in Angola.

Comparison of genotypic features between two groups of antibiotic resistant Klebsiella pneumoniae clinical isolates obtained before and after the COVID-19 pandemic from Egypt

Klebsiella pneumoniae is a common pathogen capable of causing a wide range of infections. Antibiotic resistance complicates treatment of these infections significantly. We are comparing resistance levels and genotypes among two collections of K. pneumoniae clinical isolates from Alexandria Main University Hospital (AMUH). We used disc diffusion and Minimum Inhibitory Concentration (MIC) by microbroth dilution to assess resistance levels and performed whole genome sequencing (WGS) to describe multilocus sequence types (MLST) and resistance gene presence. Among a collection of 56 K. pneumoniae clinical isolates (19 from 2019 to 37 from 2021), multidrug resistance (MDR) was 33% and 10%, extended drug resistance (XDR) was 24% and 46% and pan-drug resistance (PDR) was 43% and 43%, respectively. We identified 15 MLST STs including two novel types (ST-6118 and ST-6119 ). ST-101 and ST-383 were common between the two collections; ST-101 was the most common genotype in 2019 (28.6%) and ST-147 was most common in 2021 (25%). Ampicillin/sulbactam, amikacin, cefepime, ceftriaxone and ertapenem MICs were significantly higher in 2021. Prevalence of aph(3’) – Ia, aph(3’)-VI, mphA was significantly higher in 2021. The increasing resistance levels and the persistence of some MDR/XDR genotypes is concerning. Understanding mechanisms of resistance will inform infection control and antimicrobial stewardship plans to prevent evolution and spread of XDR and PDR strains.

Patterns of HIV-1 Drug Resistance Observed Through Geospatial Analysis of Routine Diagnostic Testing in KwaZulu-Natal, South Africa.

HIV-1 drug resistance (HIVDR) impedes treatment and control of HIV-1, especially in high-prevalence settings such as KwaZulu-Natal (KZN) province, South Africa. This study merged routine HIV-1 genotypic resistance test (GRT) data with Geographic Information Systems coordinates to assess patterns and geographic distribution of HIVDR in KZN, among ART-experienced adults with virological failure. We curated 3133 GRT records generated between 1 January 2018 and 30 June 2022, which includes the early phase of dolutegravir (DTG) rollout, of which 2735 (87.30%) had HIVDR. Of the 2735, major protease, nucleoside, and non-nucleoside reverse transcriptase inhibitor mutations were detected in 41.24%, 84.97% and 88.08% of GRTs, respectively. Additional genotyping of HIV-1 integrase for 41/3133 (1.31%) GRTs showed that 17/41 (41.46%) had integrase strand transfer inhibitor resistance. Notably, of 26 patients on DTG with integrase genotyping, 9 (34.62%) had DTG-associated resistance mutations. Dual- or triple-class resistance was observed in four of every five GRTs. The odds of HIVDR increased significantly with age, with ≥60 years having 5 times higher odds of HIVDR compared to 18-29 years (p = 0.001). We identified geospatial differences in the burden of HIVDR, providing proof of concept that this could be used for data-driven public health decision making. Ongoing real-time HIVDR surveillance is essential for evaluating the outcomes of the updated South African HIV treatment programme.

Quinolone and Tetracycline-Resistant Biofilm-Forming Escherichia coli Isolates from Slovak Broiler Chicken Farms and Chicken Meat

Escherichia coli isolates from intensive poultry production are associated with antimicrobial resistance and worldwide health problems. The aim of the study was to detect and evaluate the phenotypic and genotypic antimicrobial resistance, biofilm formation, phylogenetic typing, and virulence factors in E. coli isolates from the rectal swabs of chickens from two farms and swabs of chicken meat purchased from Slovakian food markets. Interpretative readings of minimal inhibitory concentration (MIC) revealed dominant resistance to ampicillin (>50%) in both groups. We also detected higher resistance to ciprofloxacin (45%), tetracycline, ampicillin + sulbactam, and trimethoprim + sulfonamide (each >30%). Here, 28.57% of the strains studied were multidrug-resistant (MDR). The formation of weak biofilms was confirmed in 8.8% of E. coli, while one of the strains obtained from chicken cloacal swabs was classified as a strong biofilm producer. The most frequently confirmed phylogenetic groups in E. coli were B1 and A1 in all groups. PCR detection revealed the presence of genes encoding tetracycline resistance (tetAB) and plasmid-mediated quinolone resistance (qnrABS), and Int1 (52.9%), Tn3 (76.5%), kpsMT II (8.8%), fimA (97.1%), cvaC (38.2%), and iutA (76.5%) genes in the strains studied. Our results demonstrate that chickens and chicken meat were the source of antibiotic-resistant, biofilm-forming, and virulent E. coli, representing a potential risk from the point of view of the One Health concept.

Identification of Soybean Mosaic Virus Resistant Soybean Genotypes using Gene-Linked Markers

Soybean is widely consumed legumes both in the form of food and feed. In the present scenario, the quality and quantity of soybean production is largely affected by different biotic factors, Soybean Mosaic Virus being one of the major biotic stress. Plant host resistance is an effective major to develop durable resistance from viral diseases, therefore understanding the molecular mechanism and identifying the resistant genotypes can contribute to resistance breeding in soybean. In 2020, ninety genotypes collected from Grain Legume Research Program, local collection and National Agricultural Genetic Resource Center were screened for the presence of resistant genes using gene linked molecular markers. Among them, three genotypes were identified with Soybean Mosaic Virus resistant loci, Rsv1 amplified by linked marker Satt114, four genotypes were identified with resistant loci, Rsv3 with linked marker Sat_424, and eight genotypes were identified with resistant loci, Rsv4 amplified by linked marker Satt558. Thus, showing expression of dominant resistance to some SMV strains. Interestingly, two genotypes (Co 175 and TGx1990-55) possessed both Rsv1 and Rsv3 loci thus showing potential of resisting broad spectrum SMV resistance to all SMV strains. Therefore, this study has identified potential genotypes that can be used as parental materials for resistant gene pyramiding in soybean breeding for SMV resistance

Detection of carbapenem-resistant gram-negative bacilli in Japan using the fully automated bacterial testing device RAISUS S4

ObjectiveWe investigated a rapid detection method for carbapenemase-producing gram-negative bacilli (CP-GNR) using meropenem (MEPM) to assess the efficiency of the antimicrobial susceptibility testing. MethodsWe used the function that can monitor the growth curve with the resistant bacteria monitoring function (RAISUS S4). Rapid detection of CP-GNR was performed using RAISUS S4 in two types of antimicrobial susceptibility testing, the RAISUS 18-hour method (18-h method) and RAISUS rapid method (rapid method) for Enterobacterales (F-GNR) and non-fermenting Gram-negative bacilli (NF-GNR). ResultsWhen F-GNR were based on MEPM MIC ≥ 0.25 μg/mL, CP-GNR were detected with a sensitivity of 100% (58/58) for the 18-h method and 98.3% (57/58) for the rapid method; the shortest detection times were 5.3 and 4.0 h, respectively. When NF-GNR were based on MEPM MIC > 8 μg/mL, it was possible to detect CP-GNR with 100% sensitivity (58/58) in both methods. Furthermore, in the analysis using the 18-h method for monitoring resistant bacteria, when ≥ 2 µg/mL was used as the screening concentration for F-GNR, approximately 50% of the resistant genotypes, NDM, GES, and KPC, were detected in approximately 7 h. However, detecting the IMP and VIM took 11–12 h. ConclusionsThe 18-h and rapid methods with RAISUS S4 were highly correlated with the results of the microdilution method of CLSI, and CP-GNR detection was rapid using a function that can monitor the growth curve with RAISUS S4.

Management of low-level HIV viremia during antiretroviral therapy: Delphi consensus statement and appraisal of the evidence

ObjectiveWhile antiretroviral therapy (ART) is highly effective, detection of low levels of HIV-1 RNA in plasma is common in treated individuals. Given the uncertainties on the topic, we convened a...