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At least 19 recordsLinked to original sources
PubMed2026

Patterns of Drug Resistance, Drug Resistance Conferring Mutations and Genomic DNA Methylation Revealed in Mycobacterium tuberculosis From South Africa.

Tuberculosis remains a major public health threat globally, with drug-resistant strains undermining treatment efficacy. We analyzed 126 Mycobacterium tuberculosis (M. tuberculosis) isolates with diverse drug resistance spectra and selected 35 for whole genome sequencing (WGS) using Illumina NextSeq, SMRT PacBio Onso and SMRT PacBio Revio sequencing platforms. The study aimed to characterize drug resistance profiles, compare short- and long-read sequencing performance, identify lineages among South African isolates, detect known drug resistance mutations and their lineage-specific patterns, and utilize long-read SMRT platforms for epigenetic profiling. Multiple drug resistance mutations were identified, some lineage-specific, and notably, East-African-Indian (EAI) Lineage 1 isolates often considered less pathogenic, showed significant potential for multidrug-resistance development, including higher fluoroquinolone resistance as compared to other lineages. Three DNA motifs with methylated adenines, namely CACGCaG, CtCCaG and GaTNNNNRtAC, were detected, with methylation patterns varying by lineage and strain due to mutations in the corresponding methyltransferases (MTases). A particularly notable finding was the stable maintenance of a genetic heterogeneity in the mamB MTase, performing methylation at CACGCaG motifs. These results highlight the combined role of genetic and epigenetic variation in M. tuberculosis adaptive evolution and underscore the value of integrating long-read sequencing into TB surveillance and research.

Mycobacterium tuberculosis↗
PubMed1979

Ara-C metabolism: implications for drug resistance and drug interactions.

Clinical studies of resistance to cytosine arabinoside have not produced agreement as to the specific biochemical lesions responsible for altered sensitivity, although experimental and clinical work supports the concept that a decreased ability to generate ara-CTP must be the ultimate effect of this lesion. 3-deazauridine, an inhibitor of CTP synthetase, was found to enhance ara-CTP production in murine tumor cells, and in the present study, was shown to inhibit deamination of ara-C at both the nucleoside and nucleotide level. Enhanced ara-CTP formation was observed in cells lacking cytidine deaminase (L1 210 and HL60), indicating that 3-deazauridine inhibition of deoxycytidylate deaminase may be important in this drug interaction.

3-Deazauridine↗
PubMed1979

Primary drug resistance in children. Drug susceptibility of strains of Mycobacterium tuberculosis isolated from children during the years 1973 through 1977 at the Kings County Hospital Center of Brooklyn.

A continuing study of the frequency of primary drug resistance among children treated at the Kings County Hospital Center of Brooklyn during the years 1973 through 1977 showed a high incidence of primary drug resistance to isoniazid (8.8 per cent) and to streptomycin (12.3 per cent). In contrast, there were no strains resistant to cycloserine, viomycin, ethambutol, or rifampin, and only one of 57 strains (1.8 per cent) was resistant to ethionamide, and one (1.8 per cent) was resistant to para-aminosalicylic acid. Comparison with previous studies begun in 1961 showed no significant increase in resistance to isoniazid during 3 prior periods of study and no increase in resistance to streptomycin during the last 2 periods of study. It must be emphasized that these findings relate only to the children of a local community, and do not reflect the prevalence of primary drug resistance elsewhere in this country or among different age groups.

Adolescent↗
PubMed1977

Drug resistance and plasmid mediated transfer of drug resistance in Escherichia coli isolated from various districts of the human organism. A possible relationship with the antimicrobial drug concentrations during therapy.

The study of the prevalence of drug resistances and of the frequency of R factors among resistant strains, in E. coli isolated respectively from the respiratory, intestinal and urinary tracts of patients, during 1976, has shown that the frequency of drug resistances is highest among E. coli strains isolated from the respiratory tract and lowest among the E. coli strains isolated from urines. The frequency of R factors, among resistant strains, follows an exactly opposite distribution. This behaviour could be related to the gradient of antimicrobial drug concentrations achieved in the various compartments during ordinary antimicrobial therapy.

Anti-Bacterial Agents↗
PubMed2025

Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta.

The parasitic nematode Teladorsagia circumcincta is one of the most important pathogens of sheep and goats in temperate climates worldwide and can rapidly evolve resistance to drugs used to control it. To understand the genetics of drug resistance, we have generated a highly contiguous genome assembly for the UK T. circumcincta isolate, MTci2. Assembly using PacBio long-reads and Hi-C long-molecule scaffolding together with manual curation resulted in a 573 Mb assembly (N50 = 84 Mb, total scaffolds = 1,286) with five autosomal and one sex-linked chromosomal-scale scaffolds consistent with its karyotype. The genome resource was further improved via annotation of 22,948 genes, with manual curation of over 3,200 of these, resulting in a robust and near complete resource (96.3% complete protein BUSCOs) to support basic and applied research on this important veterinary pathogen. Genome-wide analyses of drug resistance, combining evidence from three distinct experiments, identified selection around known candidate genes for benzimidazole, levamisole and ivermectin resistance, as well as novel regions associated with ivermectin and moxidectin resistance. These insights into contemporary and historic genetic selection further emphasise the importance of contiguous genome assemblies in interpreting genome-wide genetic variation associated with drug resistance and identifying key loci to prioritise in developing diagnostic markers of anthelmintic resistance to support parasite control.

Animals↗
PubMed2025

Transfer learning with multiomics integration and deep neural networks reveals drug resistance mechanisms in cancer.

Drug resistance remains one of the primary challenges in effective cancer therapy. In this study, we employed a deep neural network (DNN)-based transfer learning (TL) approach to predict drug response and uncover drug resistance mechanisms. We integrated gene expression, somatic mutation, and copy number aberration (CNA) data with drug response profiles using multi-omics integration (MI). We used the Genomics of Drug Sensitivity in Cancer (GDSC) data for training and incorporated drugs with same pathways into the training models. We then evaluated drug response predictions on independent in-vivo PDX Encyclopedia (PDX) and ex-vivo the Cancer Genome Atlas (TCGA) datasets. In addition, we conducted pathway enrichment analyses to elucidate the mechanisms underlying drug resistance for paclitaxel, 5-fluorouracil (5-FU), gemcitabine, and cetuximab. We also applied Fisher's exact test (FET) to assess potential associations between drug resistance and the presence of mutations or CNAs. Our pan-drug models outperformed other methods based on the area under the precision-recall curve (AUCPR). Our pathway enrichment analyses revealed LDHB-mediated pyruvate metabolism and FYN-mediated focal adhesion might have pivotal roles in paclitaxel resistance, while PINK1-mediated mitophagy might be critical in 5-FU resistance. In addition to transcriptional activation, FET suggested that CNAs in LDHB and PINK1 may also be associated with resistance to paclitaxel and 5-FU, respectively. Furthermore, enrichment results for paclitaxel and cetuximab indicated shared resistance mechanisms between the two drugs. Importantly, our findings are consistent with prior experimental studies, providing literature-based validation of our results. Overall, our DNN-based TL approach achieved strong predictive performance across PDX & TCGA datasets and enrichment analyses provided valuable biological insights into drug resistance mechanisms.

Humans↗
PubMed2026

Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.

While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.

Animals↗
PubMed2025

Evolutionary engineering and molecular characterization of an antimycin A-resistant Saccharomyces cerevisiae strain: the key role of pleiotropic drug resistance (PDR1).

Antimycin A, an antifungal agent that inhibits mitochondrial respiration, provides a useful model for studying resistance mechanisms. Antifungal resistance is an escalating clinical concern with limited treatment options available. To understand the molecular mechanisms of antimycin A resistance, a genetically stable, antimycin A-resistant Saccharomyces cerevisiae strain was successfully developed for the first time through an evolutionary engineering strategy, based on long-term systematic application of gradually increasing antimycin A stress in repetitive batch cultures without prior chemical mutagenesis. Comparative whole genome resequencing analysis of the evolved strain ant905-9 revealed two missense mutations in PDR1 and PRP8 genes involved in pleiotropic drug resistance and RNA splicing, respectively. Using CRISPR/Cas9 genome editing tools, the identified mutations were introduced individually and together into the reference strain, and it was confirmed that the Pdr1p.M732R mutation alone confers antimycin A-resistance in S. cerevisiae. Comparative transcriptomic analysis of the reverse-engineered Pdr1p.M732R strain showed alterations in PDR (pleiotropic drug resistance), transmembrane transport, vesicular trafficking, and autophagy pathways. Our results highlight the potential key role of PDR1 in antifungal drug resistance. This study provides new insights into mitochondrial drug resistance and the adaptive potential of yeast under respiratory stress.

Saccharomyces cerevisiae↗
PubMed1978

[Transmissible drug resistance in E. coli isolated from calves].

The study of 30 strains of Escherichia coli, isolated from calves on various farms of the district of Haskovo, revealed that 70.0% of them manifested resistance to drugs. The capacity of calf E. coli organisms of being donors of resistance factors pointed to the episomal nature of their polyresistance. The comparatively readily effected transmission of drug resistance from E. coli isolated from calves was shown to be potential clinical and epizootic hazard. Such animals proved to be carriers and a source of R+ Escherichia coli organisms. It was found that the transmission of drug resistance was not coupled with the transmission of chromosomal inheritance. A high frequency of the drug-resistance transmission phenomenon was established.

Animals↗
PubMed2025

Whole genome sequencing-based detection of extensively drug-resistant tuberculosis from Ethiopia.

BACKGROUND: Rapid and accurate detection of extensively drug-resistant tuberculosis is crucial for effective intervention. Next-generation sequencing technologies have been recommended to rapidly and accurately detect resistance to second-line anti-TB drugs. We deployed whole-genome sequencing to detect mutations associated with drug resistance in pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis strains in Ethiopia. METHODS: This report is part of the routine laboratory-based drug-resistance surveillance in Ethiopia. Among 15 pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis isolates identified during the study period, eleven isolates were retrieved by Whole-genome sequencing. Illumina NextSeq 550 instruments were used to generate genomic data. Lineage and drug-resistance prediction were performed with Tuberculosis Profiler, while phylogeny was conducted by IQ-tree. RESULTS: Of the genotyped isolates, whole-genome sequencing identifies five extensively drug-resistant tuberculosis and four pre-extensively drug-resistant tuberculosis strains. It detects fluoroquinolone resistance mutations gyrA (Ala90Val, Asp94Tyr, Asp94Gly). Bedaquiline resistance mutations are found in atpE (Glu61Asp) and Rv0678 (139dupG, 141 and 142dupTC). Cross-resistance is identified between bedaquiline and clofazimine (n = 4) and delamanid and pretomanid (n = 1). Concordance result is observed between phenotypic drug-susceptibility testing and whole-genome sequencing for eight cases, while three cases are discordant (fluoroquinolones, delamanid, and pretomanid). Phylogenetic analysis reveals three major lineages: Lineage 4 (Euro-American, n = 6 isolates), Lineage 3 (East African-Indian, n = 3 isolates), and Lineage 1 (Indo-Oceanic, n = 2 isolates). CONCLUSIONS: Whole-genome sequencing identifies dominant mutations in genes such as gyrA, atpE, and Rv067 that are associated with resistance to second-line anti-tuberculosis drugs. Significant cross-resistance is observed between key second-line drugs, bedaquiline and clofazimine, as well as delamanid and pretomanid. This finding highlights the need for routine genomic surveillance to detect drug resistance early, improve treatment outcomes, and prevent transmission.

Journal Article↗
PubMed1978

Low molecular weight RNA species encoded by a multiple drug resistance plasmid.

Multiple drug resistance plasmid NR1 is shown to code for at least 10 low molecular weight RNAs. These species, ranging in size from 60 to 120 nucleotides, have been purified from minicells by two-dimensional gel electrophoresis and characterized by RNase T1 fingerprinting. Hybridization of purified RNAs to restriction endonuclease digests of NR1 DNA indicates that most are derived from the resistance transfer factor region of the plasmid genome. One RNA was found to be coded by the transposable tetracycline resistance element Tn10, and several are associated with DNA fragments that contain origins of replication.

Escherichia coli↗
PubMed1977

Changing patterns of plasmid-mediated drug resistance during tetracycline therapy.

The patterns of drug resistance and the frequency of conjugative R plasmids in intestinal Escherichia coli from 88 patients treated for a skin disease (acne vulgaris) with low oral doses of tetracycline are reported. The proportion of patients with resistant bacteria was progressively greater in patients who received tetracycline for 1 week, 4 weeks, or longer (from 50 to 88%). No multiply drug-resistant bacteria were detected before treatment or after 1 week of treatment. After more than 4 weeks of treatment, multiply drug-resistant E. coli were isolated from about 50% of the patients. The origin and selection of R plasmid-determined multiple drug resistance are discussed.

Acne Vulgaris↗
PubMed1978

Primary antituberculous drug resistance in Hawaii, 1957 to 1977.

A study of primary antituberculous drug resistance in Hawaii was conducted from 1957 to 1977 to determine the incidence of primary resistance with respect to time. A total of 1,869 initial cultures of Mycobacterium tuberculosis submitted to Leahi Hospital in Honolulu were screened to identify drug resistance. Of 256 patients who excreted resistant bacilli, only 55 had no history of previous antituberculous chemotherapy. The frequencies of primary drug resistance from July 1957 to July 1977 were as follows: streptomycin, 0.86 per cent; isoniazid, 1.2 per cent; para-aminosalicylic acid, 1.5 per cent. No strains were resistant to ethambutol or rifampin. A slight decrease in the incidence of drug resistance during a 20-year period was observed. This was especially significant because Hawaii's tuberculosis problem is principally confined to its foreighn-born population. Although no serious primary drug resistance problem was discovered, Hawaii possesses both the highest immigration rate and the highest incidence of tuberculosis in the United states. Therefore, there is a need for continued periodic monitoring of drug resistance in Hawaii.

Aminosalicylic Acid↗
PubMed2024

Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows.

BACKGROUND: Drug-resistant tuberculosis remains a major obstacle in ending the global tuberculosis epidemic. Deployment of molecular tools for comprehensive drug resistance profiling is imperative for successful detection and characterisation of tuberculosis drug resistance. We aimed to assess the diagnostic accuracy of a new class of molecular diagnostics for drug-resistant tuberculosis. METHODS: We conducted a prospective, cross-sectional, multicentre clinical evaluation of the performance of two targeted next-generation sequencing (tNGS) assays for drug-resistant tuberculosis at reference laboratories in three countries (Georgia, India, and South Africa) to assess diagnostic accuracy and index test failure rates. Eligible participants were aged 18 years or older, with molecularly confirmed pulmonary tuberculosis, and at risk for rifampicin-resistant tuberculosis. Sensitivity and specificity for both tNGS index tests (GenoScreen Deeplex Myc-TB and Oxford Nanopore Technologies [ONT] Tuberculosis Drug Resistance Test) were calculated for rifampicin, isoniazid, fluoroquinolones (moxifloxacin, levofloxacin), second line-injectables (amikacin, kanamycin, capreomycin), pyrazinamide, bedaquiline, linezolid, clofazimine, ethambutol, and streptomycin against a composite reference standard of phenotypic drug susceptibility testing and whole-genome sequencing. FINDINGS: Between April 1, 2021, and June 30, 2022, 832 individuals were invited to participate in the study, of whom 720 were included in the final analysis (212, 376, and 132 participants in Georgia, India, and South Africa, respectively). Of 720 clinical sediment samples evaluated, 658 (91%) and 684 (95%) produced complete or partial results on the GenoScreen and ONT tNGS workflows, respectively, with 593 (96%) and 603 (98%) of 616 smear-positive samples producing tNGS sequence data. Both workflows had sensitivities and specificities of more than 95% for rifampicin and isoniazid, and high accuracy for fluoroquinolones (sensitivity approximately ≥94%) and second line-injectables (sensitivity 80%) compared with the composite reference standard. Importantly, these assays also detected mutations associated with resistance to critical new and repurposed drugs (bedaquiline, linezolid) not currently detectable by any other WHO-recommended rapid diagnostics on the market. We note that the current format of assays have low sensitivity (≤50%) for linezolid and more work on mutations associated with drug resistance is needed. INTERPRETATION: This multicentre evaluation demonstrates that culture-free tNGS can provide accurate sequencing results for detection and characterisation of drug resistance from Mycobacterium tuberculosis clinical sediment samples for timely, comprehensive profiling of drug-resistant tuberculosis. FUNDING: Unitaid.

Humans↗
PubMed1976

Sulfamethoxazole-trimethoprim-polymyxin therapy of serious multiply drug-resistant Serratia infections.

Nonpigmented multiply drug-resistant Serratia marcescens caused an extensive outbreak of infection at the Nashville Veterans Administration Hospital. Isolates were of one serotype resistant to all currently available antimicrobial agents for therapy of systemic infections except for occasional susceptibility to chloramphenicol and kanamycin. Frequently strains were susceptible to nalidixic acid, and all were susceptible to amikacin (BB-K8). Drug-resistant strains caused 130 infections, 12 bacteremias, and 7 infection-associated deaths. Combinations of antimicrobial agents were evaluated for synergism against Serratia strains from infected patients. "Checkerboard" isobolograms indicated in vitro static synergism between sulfamethoxazole, trimethoprim, and polymyxin (STP). Killing curves using clinically achievable concentrations of STP verified the bactericidal effect of STP against these strains. In a daily dosage of 1,600 mg of sulfamethoxazole and 320 mg of trimethoprim orally in combination with 100 to 300 mg of colistimethate parenterally, serum cidal levels at 1:8 or greater were achieved in five of six patients. Clinical improvement or microbiological cure was effected in four of six patients. STP may be potentially useful for selected Serratia infections for which single agents are unavailable or ineffective.

Clinical Trials as Topic↗
PubMed1979

Drug-resistant and atypical mycobacterial disease. Bacteriology and treatment.

The treatment of drug-resistant mycobacterial disease requires excellent laboratory technology combined with an effective means of monitoring patients for drug toxicity and assuring patient compliance in treatment. Most tuberculosis is readily treated with easily administered, well-tolerated antituberculous combination medications such as isoniazid-ethambutol hydrochloride or isoniazid-rifampin. Primary drug-resistant tuberculosis is prevalent in many developing countries; drug resistance in the United States is generally acquired through inadequate or irregular drug ingestion. Drug-resistant tuberculosis and many "atypical" mycobacterioses required carefully designed drug regimens based on accurate drug susceptibility studies. Occasionally, patients with certain types of infection will have isolated pulmonary involvement for which surgical extirpation is beneficial. Despite the continued decline in the incidence of tuberculosis, atypical mycobacterial disease has remained constant and may eventually become the most prevalent mycobacteriosis in the United States.

Antitubercular Agents↗
PubMed2026

Whole-genome profiling of antimicrobial resistance and virulence determinants in extensively-drug resistant Pseudomonas aeruginosa isolates causing ventilator associated pneumonia in Egypt.

Among critically ill ICU patients under prolonged mechanical ventilation, Pseudomonas aeruginosa is one of the most common cause of ventilator-associated pneumonia (VAP), with antimicrobial pressure leading to emergence of multidrug, extensively drug and pandrug-resistant (PDR) strains. In Egypt, very little genomic data exist on P. aeruginosa associated with VAP. This study aimed at characterizing the antimicrobial resistance (AMR) determinants, virulence repertoire, MGEs, and sequence types of two highly drug-resistant Pseudomonas aeruginosa isolates, including one pandrug-resistant colistin-resistant isolate and one extensively drug-resistant colistin-susceptible isolate from respiratory tract of Egyptian ICU patients suffering from VAP. The two isolates were identified conventionally and confirmed to the species level using MALDI-TOF MS. Antibiotic susceptibility was assessed using the VITEK-2 Compact system and the broth microdilution method. Genome analysis was performed using PATRIC, ResFinder, CARD, and Mobile Element Finder. For both isolates, resistance was found to all antibiotics routinely tested, however, one isolate had high-level colistin resistance (MIC > 64 µg/mL), while the other isolate was still colistin susceptible. Whole-genome sequencing identified two rare sequence types, ST2023 and ST2685, both 6.5-7.6 Mb in size with a 66% GC content. The presence of 21 MGEs in the SRR36105565 genome shows that it has high genomic flexibility, including a broader resistome than other strains, such as blaVIM-2 and OXA variants, aminoglycoside-modifying enzymes, crpP, and disinfectant-resistance markers. Both isolates retained large virulence determinants including Type III and Type VI secretion systems, alginate regulation genes, quorum-sensing networks, and siderophore biosynthesis clusters. It also represents one of the first genomic studies of VAP associated PDR P. aeruginosa from Egypt. The combination of widespread AMR with intact virulence supports the potential value of future genomic surveillance efforts and improved antimicrobial stewardship in local ICUs.

Pneumonia, Ventilator-Associated↗