Biology subjects

Goodman, R. N.

Publications and source records attributed to Goodman, R. N..

9 recordsLinked to original sources

bioRxiv2026

Effects of different concentrations and combinations of antibiotics on the dynamics of intracellular transposition in Escherichia coli

The use of antimicrobial compounds in humans, animals and in agriculture leads to environmental antimicrobial contamination through domestic, industrial and agricultural wastewater. Efforts have been made to perform environmental risk assessments based on the potential of these compounds to select for antimicrobial resistance (AMR) at certain concentrations in bacteria. This has resulted in predicted no effect concentrations (PNEC) which determine the minimum thresholds required to select for resistance. However, the effects of these compounds on intracellular transposition within bacterial isolates, a major driver of AMR, have not been previously assessed. Here, we assess the effect of differing sub-inhibitory concentrations of the third-generation cephalosporin, ceftriaxone, on the rate of intracellular transposition in combination with colistin and kanamycin. Two triple replicons systems (RS1 and RS2) were developed to assess this, each containing a chromosome, plasmid and entrapment vector. We show that sub-inhibitory concentrations of ceftriaxone exert hormetic effects on the intracellular transposition rate in RS1 and a steady linear increase in RS2. This defines a predicted no effect concentration for transposition (PNECT) for ceftriaxone as 320 ng/L in RS1 and 3200 ng/L in RS2. This provides a minimum threshold for the environmental impact of ceftriaxone on biological systems at the sub-cellular scale, which is applicable to industrial standards of waste management, where consideration of ecological impact is central.

microbiology↗

bioRxiv2026

Population bottlenecks shape laboratory evolution of piperacillin-tazobactam resistance in Klebsiella grimontii and reveal a shared within-patient evolutionary trajectory

Laboratory-based experimental evolution is widely used to investigate how antimicrobial resistance (AMR) emerges and to identify resistance-associated trade-offs that could inform treatment strategies. However, there is limited understanding of how in vitro AMR evolution reflects the complexity of resistance evolution within the human host, where selective pressures, and therefore evolutionary pathways, are more variable. Here, we investigated the effect of population bottleneck size and growth environment on the evolution of piperacillin-tazobactam (TZP) resistance in Klebsiella grimontii and compared this to resistance evolution observed during a recurrent bloodstream infection. Three clonal K. grimontii isolates cultured from one patient over four months included a TZP-susceptible ancestor and a within-patient evolved TZP-resistant isolate. The susceptible ancestor was evolved under TZP selection using either a small 0.1% bottleneck or a larger 5% bottleneck, and under a second environment, LB supplemented with 5% sheep blood, using a 0.1% bottleneck. Evolved isolates were assessed for TZP susceptibility, {beta}-lactamase activity, fitness, and genomic changes. A single nucleotide polymorphism (SNP) in the promoter region of the chromosomally located {beta}-lactamase gene blaOXY-6-4 was identified in the within-patient evolved isolate and was replicated in all 0.1% bottleneck lineages across both environments. In contrast, the larger 5% bottleneck lineages exhibited greater phenotypic variation and genetic diversity, including multiple blaOXY-6-4 promoter variants and variable TZP MICs. These findings show that laboratory evolution can reproduce key within-patient resistance mechanisms, but that bottleneck size strongly shapes the resistance phenotypes and mutational landscapes observed in vitro. ImportanceAdaptive laboratory evolution is increasingly used to predict how antimicrobial resistance emerges and to identify trade-offs associated with resistance acquisition that could inform future treatment strategies. Here, we directly compared piperacillin-tazobactam resistance evolution in the laboratory with resistance that emerged within a patient during a recurrent bloodstream infection. We show that a small population bottleneck reproducibly selected the same blaOXY-6-4 promoter mutation observed in the patient, whereas a larger bottleneck produced more diverse evolutionary outcomes. These findings build on previous work showing that experimental conditions shape laboratory evolution outcomes and highlight population bottleneck size as an important experimental parameter when designing laboratory evolution studies that intend to model clinically relevant resistance evolution.

evolutionary biology↗

bioRxiv2026

Antimicrobial activity of polymyxin A, and characterisation of the cognate biosynthetic gene cluster within the genome of the producing Paenibacillus polymyxa.

We report the isolation and identification of a Paenibacillus polymyxa strain from the citizen science project; Swab and Send. Through whole genome sequencing we are able to describe the biosynthetic gene cluster of polymyxin A produced by P. polymyxa 1G (NCBI accession no. JBVPZV000000000), compare the pmxA, pmxB and pmxE genes to five other polymyxin genes encoding known polymyxin variants, and provide mass spectrometry data that supports the production of polymyxin A1 (1157 m/z) and A2 (1143 m/z). Polymyxins are ranked in the highest priority critically important antimicrobials classification by the WHO and are of particular importance for treating gram-negative multidrug resistant pathogens. Due to the discovery of polymyxins occurring in the 1940s, there is little genetic research around polymyxins, and the literature focusses primarily on clinically used polymyxin E (colistin) and polymyxin B. Previous literature suggests that polymyxin A1 has similar/lower toxicity to clinically used polymyxins E and B. To test if polymyxin A was able to overcome current resistance mechanisms to clinically used polymyxins, the cell free supernatant from P. polymyxa 1G was tested against a panel of clinical isolates with various resistance genes. We found that resistance genes mcr-1 and mcr-4 confer resistance to polymyxin A produced by our isolate meaning that, while polymyxin A has good antimicrobial activity, clinical resistance mechanisms already confer resistance to this variant of polymyxin.

microbiology↗

bioRxiv2026

AMRgen: an R package for antimicrobial resistance genotype-phenotype analysis

Microbial whole-genome sequence data is now generated at scale, including to support antimicrobial resistance (AMR) surveillance and understand resistance mechanisms, yet analytical infrastructure for systematically linking AMR genotypes to measured phenotypes remains fragmented. Here we present AMRgen, an R package to support systematic AMR genotype-phenotype analysis. AMRgen imports and harmonises genotypic data from common bioinformatics tools, alongside phenotypic data from automated antimicrobial susceptibility testing instruments and public repositories. It supports common analyses linking data to reference distributions, modelling associations, quantifying concordance, and producing publication-ready visualisations including UpSet plots that jointly display genotypic marker combination frequencies and associated phenotypic distributions. We demonstrate AMRgens utility using publicly available surveillance data for World Health Organization priority AMR pathogens, Neisseria gonorrhoeae, Klebsiella pneumoniae, Escherichia coli and Salmonella enterica. AMRgen, available free and open-source at https://AMRgen.org, provides a reproducible end-to-end foundation for genotype-phenotype research in AMR genomics, clinical microbiology, and public health surveillance.

microbiology↗

bioRxiv2026

Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts

Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa (SSA). Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. We investigated the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023-24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8-41.0) to 54.2% (95% CI: 46.0-62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in [≥]3 households that were typically separated by short geographic distances (<400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by [≤]10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.

microbiology↗

bioRxiv2025

From Colonisation to Invasion: Genomic and Phenotypic Comparison of Faecal and Bloodstream Isolates from the same patients

Gram-negative bloodstream infections (GNBSI) carry a significant global health burden. Escherichia coli and Klebsiella pneumoniae are the two most common causes of healthcare-associated GNBSI, which may arise from gastrointestinal tract (GIT) colonisation. Understanding genomic and phenotypic adaptations that underpin transition from GIT colonisation to invasive bloodstream infection could improve understanding of pathogenesis. This study identified linked faecal and blood isolates from children with healthcare-associated GNBSI caused by E. coli and K. pneumoniae. Linked pairs were compared for antimicrobial resistance, biofilm formation, and underwent comparative genomic analysis via whole-genome sequencing, comparative average nucleotide identity (ANI) and core genome single nucleotide polymorphism (SNP) analysis. Five isolate pairs (three E. coli, two K. pneumoniae) showed high relatedness, supporting GIT origin of bloodstream infection. Isolates within pairs had identical virulence genes whereas phenotypic assays revealed changes in antimicrobial susceptibility, with one pair undergoing changes in resistance gene profiles, and increased biofilm formation in 4/5 isolates. This study provides insight into within-host evolution from gastrointestinal colonisation to bloodstream invasion in Gram-negative pathogens. Convergence on metabolic adaptation and biofilm formation suggests these traits may be advantageous in healthcare-associated GNBSI. Further studies involving larger cohorts alongside functional validation of mutations are needed to better understand GNBSI pathogenesis.

microbiology↗

bioRxiv2025

Shotgun metagenomic analysis of the oral microbiomes of children with noma reveals a novel disease-associated organism

Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome-assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from global healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but rare in controls. This study identifies Treponema--particularly Treponema sp. A--as a strong candidate organism associated with noma pathogenesis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly {beta}-lactams and metronidazole, especially among Prevotella species. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.

pathology↗

bioRxiv2025

Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania

Blood stream infections (BSIs) are a major cause of hospitalisation and death for children under the age of five in sub-Saharan Africa with members of the Gram-negative bacteria Enterobacterales such as Klebsiella pneumoniae and Escherichia coli among the most common causative agents. These bacteria usually colonise the human gastrointestinal (GI) tract which has been identified as a reservoir for invasive infections into extra-intestinal environments such as the urinary tract and bloodstream. In this study we used comparative genomics to compare hybrid genome assemblies of blood and faecal isolates taken from the same patients (all neonates under 19 days old) to determine if the BSI associated bacterial isolates originated in their GI tract. We show that both E. coli and K. pneumoniae likely translocated from the GI tract to the blood in multiple cases of BSI. We also highlight key virulence genes and acquired mutations that are indicative of pathogenic strains capable of BSI. These findings expand our understanding of BSI pathogenesis and could help guide targeted interventions to prevent future BSI infections in neonates.

genomics↗

bioRxiv2023

Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales

Infections with Enterobacterales (E) are increasingly difficult to treat due to antimicrobial resistance. After ceftriaxone replaced chloramphenicol (CHL) as empiric therapy for suspected sepsis in Malawi in 2004, ESBL-E rapidly emerged. Concurrently, resistance to CHL in Escherichia coli and Klebsiella spp. decreased, raising the possibility of CHL re-introduction. However, many phenotypically susceptible isolates still carry CHL acetyltransferase (CAT) genes. We used a combination of genomics, phenotypic susceptibility assays, experimental evolution and functional assays for CAT activity to understand the molecular mechanisms and stability of this re-emerging CHL susceptibility. Of 840 Malawian isolates, 31% had discordant CHL susceptibility genotype-phenotype, and we selected 42 isolates for in-depth analysis. Stable degradation of cat genes by insertion sequences led to re-emergence of CHL susceptibility. Our study suggests CHL could be reintroduced as reserve agent for critically ill patients with ESBL-E infections in Malawi and similar settings and highlights the ongoing challenges in inferring antimicrobial resistance from sequence data.

microbiology↗