Frontiers in microbiology · 2026
Nanopore sequencing in suitcase lab enables improved detection of β-lactamase genes in food-borne E. coli.
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Ghosh Prakash, Binsker Ulrike, Kobialka Rea Maja, Ceruti Arianna, Asaduzzaman Muhammad, Joardar Siddhartha Narayan, Asad Asaduzzaman, Savareh Behrouz Alizadeh, Frimpong Michael, Taneja Bhupesh, Siegel Martin, Dieye Yakhya, Truyen Uwe, El Wahed Ahmed Abd
Аннотация
BACKGROUND: The application of next-generation sequencing (NGS) is rapidly expanding for antimicrobial resistance (AMR) surveillance and clinical decision-making. However, despite a high AMR burden, many low- and middle-income countries lack the infrastructure and technical capacity required to implement sequencing-based approaches. To address this gap and demonstrate the practical application of the technology, we compared the performance of nanopore sequencing combined with real-time analysis using the EPI2ME platform in a mobile laboratory with that of a hybrid sequencing approach integrating Illumina short reads and nanopore long reads.
METHODS: In this exploratory diagnostic evaluation study, 25 Escherichia coli isolates obtained through the German annual national AMR monitoring program were included. Isolates resistant to at least one β-lactam antibiotic were considered as resistant isolate. Genomic DNA was subjected to both Illumina and nanopore sequencing. Following the sequencing, the EPI2ME whole genome sequencing pipeline was used to detect and identify β-lactamase genes in E. coli isolates. As the comparator, both long and short read-based hybrid assemblies were used to detect and identify the β-lactamase genes. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the sequencing approaches were calculated against the phenotypic classification of E. coli isolates, treating the presence or absence of β-lactamase-encoding genes as the genotypic predictor of β-lactam resistance.
RESULTS: A total of 36 β-lactamase-encoding genes, predominantly from the bla CTX-M, bla SHV, and bla TEM families, were detected. Both analytical approaches achieved a promising accuracy towards predicting β-lactam resistance. Moderate agreement was observed between methods, with an overall concordance of 68.9%. A distinct distribution pattern of β-lactamase genes was observed across the MIC ranges of the isolates for third-generation cephalosporins and the carbapenems.
DISCUSSION: These findings support the feasibility of deploying nanopore sequencing in mobile suitcase laboratories to strengthen AMR surveillance in food production systems. Given its portability, rapid turnaround time, and minimal infrastructure requirements, the approach may also have broader applications for One Health based AMR surveillance, clinical decision-making, and outbreak investigations in resource-limited settings.
METHODS: In this exploratory diagnostic evaluation study, 25 Escherichia coli isolates obtained through the German annual national AMR monitoring program were included. Isolates resistant to at least one β-lactam antibiotic were considered as resistant isolate. Genomic DNA was subjected to both Illumina and nanopore sequencing. Following the sequencing, the EPI2ME whole genome sequencing pipeline was used to detect and identify β-lactamase genes in E. coli isolates. As the comparator, both long and short read-based hybrid assemblies were used to detect and identify the β-lactamase genes. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the sequencing approaches were calculated against the phenotypic classification of E. coli isolates, treating the presence or absence of β-lactamase-encoding genes as the genotypic predictor of β-lactam resistance.
RESULTS: A total of 36 β-lactamase-encoding genes, predominantly from the bla CTX-M, bla SHV, and bla TEM families, were detected. Both analytical approaches achieved a promising accuracy towards predicting β-lactam resistance. Moderate agreement was observed between methods, with an overall concordance of 68.9%. A distinct distribution pattern of β-lactamase genes was observed across the MIC ranges of the isolates for third-generation cephalosporins and the carbapenems.
DISCUSSION: These findings support the feasibility of deploying nanopore sequencing in mobile suitcase laboratories to strengthen AMR surveillance in food production systems. Given its portability, rapid turnaround time, and minimal infrastructure requirements, the approach may also have broader applications for One Health based AMR surveillance, clinical decision-making, and outbreak investigations in resource-limited settings.