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PubMed2025

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017-20: a prospective national surveillance study.

BACKGROUND: Surveillance of the invasive disease burden caused by Streptococcus pneumoniae in England is performed by the UK Health Security Agency (UKHSA). In 2017, UKHSA switched from phenotypic methods to whole-genome sequencing (WGS) approaches for pneumococcal surveillance. Here, we present the first results of national WGS surveillance, up to the start of the COVID-19 pandemic, with the aim of describing the population genomics of this important pathogen. METHODS: We examined prospective national surveillance data from England, using bacterial isolates from cases of invasive pneumococcal disease (IPD) submitted to the national reference laboratory at UKHSA. A bioinformatic pipeline was developed to quality control WGS data and routinely report species and serotype. We assembled isolate data, assigned global pneumococcal sequencing clusters (GPSCs), and predicted antimicrobial resistance (AMR) profiles for isolates that passed further quality control. We collected additional data on patient outcomes and characteristics using enhanced surveillance questionnaires completed by patients' general practitioners. We used logistic regression analysis to assess the effects of various genomic and patient characteristics on the outcomes of IPD. FINDINGS: In England, between July 1, 2017, and Feb 29, 2020, there were 15 400 cases of IPD. From these cases, 13 749 (89·3%) isolates were sequenced, passed quality control, and were included in analyses. Serotype diversity was high during the study period, with 2751 (20%) isolates serotyped as 13-valent pneumococcal conjugate vaccine (PCV13) types, whereas serotype 8 was the most prevalent serotype (n=3074 [22·4%]) overall. There were 157 GPSCs within the collection, with GSPC3 the most common, encompassing 98·7% (3033 of 3074) of serotype 8 isolates. Most isolates (n=10 198 [74·2%]) did not contain AMR-associated genes. Resistance to co-trimoxazole was the most frequently predicted resistance (n=2331 [17%]), followed by resistance to tetracycline (n=1199 [8·7%]) and β-lactams (n=1149 [8·4%]). Logistic regression analysis found the presence of AMR-associated genes significantly increased the odds of patient death (odds ratio 1·18, 95% CI 1·01-1·38). Some GPSCs were also associated with a significant increase in the odds of patient death, such as GPSC12 (1·88, 1·48-2·38). Isolates from 2018 were associated with a significant increase in the odds of patient death (1·12, 1·00-1·25), whereas younger patient age was significantly associated with a reduction in the odds of patient death compared with being aged 85 years or older. INTERPRETATION: WGS-based surveillance has allowed us to interrogate country-wide population dynamics driving changes in pneumococcal serotype frequency. Here, we observe a stable but diverse population before the COVID-19 pandemic restrictions were enforced in England, with low rates of AMR. These findings will provide the baseline for pandemic and post-pandemic data, to collectively inform implementation and development of the vaccination programme within the country. FUNDING: None.

Streptococcus pneumoniae↗
PubMed2026

Mapping Sub-National Respiratory Virus Circulation in Cambodia Using Metatranscriptomic Sequencing: A Multi-Center Hospital-Based Surveillance Study.

BACKGROUND: Genomic surveillance can guide early detection of and response to emerging epidemics. Metatranscriptomic sequencing was used to investigate sub-national respiratory virus circulation in Cambodia from 2020 to 2023. METHODS: Nasopharyngeal swabs were collected from individuals aged 2 months to 65 years with influenza-like illness in four Cambodian hospitals. Metatranscriptomic data were generated by short-read RNA sequencing. Bernoulli space-time scan statistics were used to identify temporal virus clusters. Bayesian inference of phylogenetic trees was used to compute divergence times for temporally clustered, highly represented viruses (influenza A/H3N2 and B, Betacoronavirus 1, respiratory syncytial virus [RSV] A and B), and publicly available global influenza virus genomes. RESULTS: Of 1093 individuals, 499 (45.7%) had detectable respiratory viruses belonging to 68 distinct species. Moderate (N > 20) discrete time-clusters were noted of RSV-A (37 cases), Betacoronavirus 1 (21 cases), RSV-B (22 cases), and A/H3N2 (30 cases). The posterior median of time to most recent common ancestor ranged from 0.71 years (95% HPD 0.38-1.10) for Betacoronavirus 1 and 1.31 years (95% HPD 0.60-3.20) for A/H3N2, to 2.75 years (1.82-4.26) for RSV-A and 4.79 years (2.39-7.74) for RSV-B. A/H3N2 and influenza B virus genomes mapped to clades 3C.2a1b.2a.2a and Victoria 1A.3a.2, respectively, and inter-mixed with concurrent global strains. CONCLUSIONS: Multiple respiratory viruses circulated at a sub-national level in Cambodia from 2020 to 2023 despite pandemic disruptions. Influenza virus population diversity decreased during the height of lockdown but recovered in mid-2022. Re-emerging influenza strains were distinct from historically circulating strains and clustered with contemporaneous global variants, suggesting multiple external introductions.

Humans↗
PubMed2026

Triazole resistance in clinical Aspergillus fumigatus isolates in India, a multicenter surveillance study.

BACKGROUND: Triazole resistance in Aspergillus fumigatus is a global public health concern associated with treatment failure, notably in invasive aspergillosis. However, population-level data on triazole resistance from India remain limited, with most reports originating from single-center studies. METHODS: We conducted a multicenter surveillance study to assess the prevalence of triazole resistance among clinical A. fumigatus isolates across India. Antifungal susceptibility testing was performed using the CLSI broth microdilution method (M38-Ed3), and molecular characterization was conducted on resistant isolates. A total of 518 isolates were analyzed: 115 prospectively collected from 13 tertiary-care hospitals from 2015-2020, and 403 archived isolates obtained from the National Culture Collection of Pathogenic Fungi (1994-2020). RESULTS: The overall pooled prevalence of non-wildtype isolates was 4.1% for itraconazole (95% CI: 2.54-6.17%), 3.9% for posaconazole (95% CI: 2.39-5.94%), while 1.4% were resistant to voriconazole (95% CI: 0.55-2.77%). One multi-azole-resistant isolate from an immunocompromised, mold-active triazole-na&#xef;ve patient carried the TR34/L98H mutation, suggesting environmental acquisition. Prevalence of resistance did not differ significantly across geographic regions or between public and private sector hospitals. Linear regression analysis revealed a significant temporal increase in median MICs of all three licensed triazoles between 1994 and 2020. Approximately 29% of isolates exhibited amphotericin B MICs exceeding the epidemiological cutoff value; however, the clinical significance of this finding remains uncertain. CONCLUSIONS: Azole resistance among clinical A. fumigatus isolates in India remains uncommon (<5%), supporting the continued use of triazoles as first-line therapy. However, the observed temporal increase in triazole MICs underscores the need for sustained national surveillance to detect emerging resistance trends.

Aspergillus fumigatus↗
PubMed2025

SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.

BACKGROUND: Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of persistent infections in the general population. We aimed to characterise the within-host evolution of SARS-CoV-2 during persistent infections identified through a large community surveillance study. METHODS: We used data from the Office for National Statistics COVID-19 Infection Survey (ONS-CIS), a large-scale, longitudinal, population-based surveillance study conducted in the UK from April, 2020, to March, 2023. For this analysis, we focused on infections with high viral load (cycle threshold &#x2264;30) and available genome sequences, from seven major SARS-CoV-2 lineages (alpha, delta, BA.1, BA.2, BA.4, BA.5, and XBB). ONS-CIS participants were randomly selected from the general population and tested regularly by RT-PCR, regardless of symptoms. We defined persistent infections as those with sustained or rebounding high viral RNA titres for 26 days or longer. We examined associated host characteristics and used raw sequence data to identify de novo mutations and estimate within-host synonymous and non-synonymous evolutionary rates across the SARS-CoV-2 genome. FINDINGS: Between Nov 2, 2020, and March 21, 2023, we identified 576 persistent infections with at least two sequences, including 11 alpha, 106 delta, 102 BA.1, 204 BA.2, 16 BA.4, 133 BA.5, and 4 XBB. Persistent infections were more common in males than females (p<0&#xb7;0001) and individuals older than 60 years (p=0&#xb7;0027). The median within-host genome-wide evolutionary rate was 7&#xb7;9&#x2009;&#xd7;&#x2009;10-4 substitutions per site per year (IQR 7&#xb7;0-9&#xb7;0&#x2009;&#xd7;&#x2009;10-4), with high inter-individual variability driven largely by non-synonymous mutations, particularly in the N-terminal and receptor-binding domains of the spike protein. Longer infection duration was associated with higher evolutionary rates, while no associations were found with age, sex, vaccination status, previous infection, or virus lineage. We found no clear evidence of transmission beyond the first month of infection in any of the 84 persistent infections lasting 56 days or longer. In total, we identified 379 recurrent mutations, including many with known or predicted negative fitness effects and low prevalence at the population level, as well as de novo reversions to the Wuhan-Hu-1 reference sequence, which were likely under positive selection within those individuals. INTERPRETATION: This study highlights the heterogeneous nature of within-host SARS-CoV-2 evolution in individuals with persistent infection in the community. Notably, a small subset of persistent infections with high viral loads underwent accelerated viral evolution or recurrently acquired hallmark mutations found in novel variants. In addition, onward transmission from a persistent infection during the later stages of infection is likely to be rare. These insights have important implications for prioritising genomic surveillance and managing patients with persistent infections. FUNDING: Department of Health and Social Care.

Humans↗
PubMed2026

Clinical and genomic characterization of Influenza A co-infection with SARS-CoV-2 and Influenza B: a respiratory surveillance study in Assam, India.

Influenza and SARS-CoV-2 are the primary contributors to seasonal respiratory infections and frequently co-circulate, creating significant health challenges. The present respiratory surveillance study was conducted in Dibrugarh, Assam, India from January 2025&#xa0;to August 2025 to investigate the genomic characteristics of circulating viruses and identify potential co-infections. Overall, 4,948 respiratory samples were screened using multiplex real-time PCR, followed by subtyping of Influenza A and Influenza B. Next-generation sequencing (NGS) was performed in selected positives of SARS-CoV-2 and Influenza A. Genomic analysis included mutational profiling, phylogenetic analysis and N-glycosylation site prediction using bioinformatics tools. Two co-infection cases were detected: one involving Influenza A (H3N2) with SARS-CoV-2 (Omicron XFG lineage) and another involving Influenza A (H3N2) with Influenza B (Victoria lineage). Both patients experienced mild illness without hospitalisation. NGS revealed that the Influenza A (H3N2) viruses belonged to clade 3C.2a1b.2a.2a.3a.1 while SARS-CoV-2 sequence was classified under the Omicron XFG lineage. Mutational analysis of the HA gene showed several amino acid differences compared to the reference vaccine strain A/Darwin/6/2021. N-glycosylation analysis predicted conserved sites at positions 79, 181, 262, and 301 in all strains along with an additional predicted site at position 110 in both co-infection cases. Although the co-infection cases presented with mild clinical manifestations, the observed genomic variations indicate a potential role of co-infecting viruses in shaping viral evolution. Given the limited genomic data available from Northeast India, the study underscores the need for sustained large scale follow up and genomic surveillance to monitor emerging mutations and target future vaccine strategies.

Humans↗
PubMed2026

Cefiderocol susceptibility rates in carbapenem-resistant Gram-negative bacteria in a comparative, multicenter surveillance study in China.

BACKGROUND: Cefiderocol is a siderophore cephalosporin with potent, broad spectrum of activity against carbapenem-resistant (CR) Gram-negative bacteria. The objective of this surveillance study was to assess cefiderocol susceptibility in molecularly characterized CR Gram-negative pathogens collected from hospitalized patients across China. METHODS: Susceptibility testing was performed by the broth microdilution method according to Clinical and Laboratory Standards Institute guidelines, using pre-prepared frozen 96-well microtiter Thermo Fisher plates. Susceptibilities to cefiderocol and most comparators were determined by Clinical and Laboratory Standards Institute breakpoints, to tigecycline by US Food and Drug Administration breakpoints, and to colistin by European Committee on Antimicrobial Susceptibility Testing criteria. Carbapenemases were identified by whole-genome sequencing and polymerase chain reaction. RESULTS: Of 149 CR Klebsiella pneumoniae, 95.3% were susceptible to cefiderocol (OXA-48-positive 100% [n = 15]; IMP-positive 100% [n = 9]; KPC-positive 95.4% [n = 108]; NDM-positive 88.2% [n = 17]) and against 103 NDM-positive CR Escherichia coli, cefiderocol susceptibility was 45.6%. Among comparator antibiotics, ceftazidime-avibactam was only active against K. pneumoniae carbapenemase-positive and OXA-48-positive K. pneumoniae isolates. Susceptibilities to tigecycline and colistin were between 22.2% and 97.1% and between 88.2% and 100% across CR Enterobacterales with different carbapenemases, respectively. High cefiderocol susceptibility rates were found for CR Pseudomonas aeruginosa (98.4%), CR Acinetobacter baumannii (99.6%), and Stenotrophomonas maltophilia (99.6%). Among comparator antibiotics, only colistin showed high activity against CR P. aeruginosa (99.2%) and CR A. baumannii (99.2%). CONCLUSIONS: Cefiderocol susceptibility rates were &#x2265;88% against a collection of carbapenemase-positive CR Gram-negative isolates, except for lower susceptibility in NDM-positive CR E. coli isolates. Continuous monitoring of cefiderocol susceptibility is warranted.

Cefiderocol↗
PubMed2025

First surveillance study of avian orthoavulavirus type 1 in wild birds in Morocco: Insights and implications for future monitoring.

BACKGROUND: Wild birds, particularly migratory species, can act as natural reservoirs and vectors of avian orthoavulavirus type 1 (AOAV-1) or Newcastle disease virus (NDV), contributing to its spread across regions and potentially threatening domestic poultry populations. AOAV-1, also known as NDV, is a major pathogen affecting avian species and poses a global threat to poultry production. It belongs to the Paramyxoviridae family and is an RNA virus encoding six key proteins, including the fusion (F) protein, which determines pathogenicity. AOAV-1 is classified into three pathotypes based on virulence: velogenic (highly pathogenic), mesogenic (moderately pathogenic), and lentogenic (mild or asymptomatic). In Morocco, AOAV-1 is endemic in poultry production systems, as evidenced by recent studies reporting a 52.1% seroprevalence and active viral RNA detection in backyard chickens in the Khemisset and Skhirat-Temara provinces; however, effective vaccination strategies have contributed to controlling the clinical signs and widespread dissemination of the virus. AIM: The main objective of this study was to investigate the presence of AOAV-1 in wild bird populations across Morocco, providing insights into possible transmission of infection affecting domestic poultry. METHODS: From November 2016 to April 2022, a total of 1984 samples were collected from 840 individual birds, encompassing 79 species, 25 families, and 12 orders. The majority of the samples belonged to Charadriiformes, Anseriformes, Pelecaniformes, and Passeriformes. Sampling was conducted at 17 wetlands and six additional locations throughout Morocco. Viral detection was performed using real-time reverse transcriptase PCR (RT-qPCR) targeting Matrix (M) and RNA polymerase (L) genes to confirm the presence of AOAV-1. RESULTS: Although the study spanned 6 years and included a large number of samples from bird orders considered primary AOAV-1 reservoirs, all samples tested negative for NDV RNA using both M and L gene targets. CONCLUSION: This study represents the first effort in Morocco to monitor wild birds for AOAV-1. The samples analyzed were initially collected for avian influenza surveillance, which shares epidemiological similarities with Newcastle's disease. However, to improve future surveillance efforts, sample collection should be optimized to target scenarios with the highest probability of virus detection.

Animals↗
PubMed2026

Emergence of carbapenemase-producing Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

BACKGROUND: The emergence of carbapenem resistance in Escherichia coli is of major concern due to the high propensity of spread of this species and scarce treatment options. Herein, we examined the occurrence and spread of carbapenem-resistant E coli based on the carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE) survey performed across European countries in 2019. METHODS: We analysed epidemiological, microbiological, and whole-genome sequencing data of 548 E coli isolates from individual patients from 156 hospitals in 32 European countries over 6 months in 2019. These hospitals collected the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) Klebsiella pneumoniae species complex or E coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species. Antimicrobial susceptibility testing was performed for 19 antimicrobial agents. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: Of the 548 E coli isolates, 211 (38&#xb7;5%) were carbapenem-resistant or susceptible, increased exposure (carbapenem-R/I), and 337 (61&#xb7;5%) were carbapenem-susceptible (carbapenem-S). Five sequence types (STs) accounted for 96 (45&#xb7;5%) of 211 carbapenem-R/I isolates: ST131 (27), ST410 (20), ST38 (19), ST167 (16), and ST648 (14). Carbapenemase genes were identified in 182 (86&#xb7;3%) carbapenem-R/I isolates, a pronounced increase from the 2013-14 EuSCAPE study (36 of 99, 36&#xb7;4%). The most common genes were blaNDM-5 (62 of 182, 34&#xb7;1%) and blaOXA-48 (40 of 182, 22&#xb7;0%). blaNDM-5 carriage increased substantially compared with that in EuSCAPE (two of 99, 2&#xb7;02%). Phylogenetic analysis showed substantial clonal spread of globally disseminated blaNDM-5-harbouring lineages, with numerous introductions into Europe but minimal onward transmission. INTERPRETATION: High-risk STs of E coli carrying carbapenemase genes are rapidly spreading globally, although our results indicate that, in 2019, most cases in Europe were sporadic. We urge vigilant monitoring, including genomic surveillance, and strengthening of control efforts, to reduce mortality and morbidity associated with the impending rise in carbapenem-R/I E coli cases. FUNDING: European Centre for Disease Prevention and Control and the Centre for Genomic Pathogen Surveillance.

Humans↗
PubMed2026

Temporal shifts in K-locus composition and expansion of dual-carbapenemase-producing ST11-KL62 Klebsiella pneumoniae: a retrospective genomic surveillance study.

OBJECTIVES: To characterize longitudinal changes in carbapenem-resistant Klebsiella pneumoniae (CRKP) and investigate the recent increase in dual-carbapenemase-producing ST11-KL62 isolates. METHODS: We retrospectively analysed 1,239 non-duplicate CRKP isolates recovered at a tertiary hospital in China during 2018-2025. Antimicrobial susceptibility testing, whole-genome sequencing, K-locus and resistance/virulence gene profiling, core-genome single-nucleotide polymorphism analysis, reference-guided plasmid comparison, conjugation and stability assays, and a murine lethality model were used. RESULTS: ST11 accounted for 936/1,239 isolates (75.5%). KL47 declined from 39/151 (25.8%) in 2018-2019 to 45/755 (6.0%) in 2024-2025, whereas KL62 increased from 3/151 (2.0%) to 147/755 (19.5%). Among 148 ST11-KL62 isolates, 13/148 (8.8%) co-harboured blaKPC-2 and blaNDM-1, of which 12/13 (92.3%) met the study's molecular definition of hypervirulent CRKP. Pairwise single-nucleotide polymorphism distances among local ST11-KL62 isolates ranged from 0 to 43 (median, 14), suggesting that clonal expansion may have contributed to their increase. Complete genome analysis of ZD872 located blaKPC-2, blaNDM-1, and major virulence-associated genes on distinct plasmids; related plasmid backbones were predicted in other isolates using short-read comparisons. ZD872 exhibited a hypervirulent phenotype in the murine model. CONCLUSIONS: The ST11 CRKP population underwent temporal shifts in K-locus composition, including expansion of a closely related ST11-KL62 subset carrying dual carbapenemases and hypervirulence-associated markers. These findings support integrating longitudinal genomic surveillance with local transmission analysis.

Carbapenem-resistant Klebsiella pneumoniae↗
PubMed2026

Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

BACKGROUND: Carbapenem-resistant Enterobacterales pose a substantial threat to patients and health-care systems. We conducted a survey of carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE survey) in 37 European countries to describe their occurrence, geographical distribution, and population dynamics and inform control policies. We report the results of Klebsiella pneumoniae species complex isolates in this study. METHODS: In this cross-sectional, epidemiological, microbiological, and genomic study conducted in all EU, European Economic Area and EU candidate countries as of 2019, hospital microbiology laboratories were selected on the basis of population coverage. Participating laboratories collected, from patient samples, the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) K pneumoniae species complex or Escherichia coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species, accompanied by patient epidemiological and clinical information. Isolate collection started in 2019, with three possible starting dates-ie, March 1, April 1, or May 1, 2019, and ended after collection of ten carbapenem-R/I and carbapenem-S isolates or a maximum period of 6 months. Isolates were tested for phenotypic susceptibility to 16 antimicrobial agents of relevance to K pneumoniae species complex. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: 1566 carbapenem-R/I and 1407 carbapenem-S K pneumoniae species complex isolates collected from patients in 302 hospitals in 36 countries (one country did not send isolates) were analysed in this study. The high-risk lineages identified during a previous similar survey in 2013-14 (EuSCAPE) were found to continue to circulate across European hospitals in 2019 (ST11, ST15, ST101, and ST258/512). Moreover, concerning shifts in the pathogen population were observed. First, a higher proportion of carbapenem-R/I isolates was found to carry a carbapenemase gene in the CCRE survey (1398 [89&#xb7;3%] of 1566) than in EuSCAPE (657 [69&#xb7;6%] of 944), mainly related to increased acquisition of carbapenemase genes by high-risk lineages. Of note, among ST307 isolates from all hospitals, the proportion of carbapenem-R/I isolates carrying a carbapenemase gene increased from 14 (60&#xb7;9%) of 23 in EuSCAPE to 164 (91&#xb7;1%) of 180 in the CCRE survey. Second, an expansion of emerging multidrug-resistant lineages (ST147, ST307, and ST39) was also noted: Among 113 hospitals that contributed K pneumoniae species complex isolates to both EuSCAPE and the CCRE survey, the proportion of ST147 increased from 16 (3&#xb7;4%) of 476 in EuSCAPE to 49 (7&#xb7;4%) of 662 carbapenem-R/I isolates in the CCRE survey, that of ST307 increased from 15 (3&#xb7;2%) of 476 to 88 (13&#xb7;3%) of 662, and that of ST39 increased from 3 (0&#xb7;6%) of 476 to 10 (1&#xb7;5%) of 662. Third, there was an increased spread of isolates harbouring acquired virulence loci: isolates with the highest Kleborate virulence score of five increased from 7 (0&#xb7;4%) of 1717 in EuSCAPE to 40 (1&#xb7;3%) of 2973 in the CCRE survey. Notably, the increase was mainly observed in the carbapenem-S-group. INTERPRETATION: The survey findings portray an escalating epidemiological situation and suggest that control measures have not been able to interrupt transmission of high-risk lineages of carbapenemase-producing K pneumoniae in European hospitals. The heterogeneous and evolving situation with regards to circulating lineages and dominant carbapenemase genes requires strengthening and continuous adaptation of diagnostic, treatment, and control measures guided by genomic surveillance. FUNDING: European Centre for Disease Prevention and Control and Centre for Genomic Pathogen Surveillance.

Humans↗
PubMed2026

Genomic epidemiology and antimicrobial resistance profile of Shigella isolated from diarrhoea diseases in under-five children in Blantyre, Malawi.

Antimicrobial resistance (AMR) in Shigella is rising globally, complicating shigellosis management. Whole-genome sequence analysis (WGSA) has advanced our understanding of AMR and transmission dynamics, yet contemporary whole-genome sequencing data from Shigella in sub-Saharan Africa remain scarce. In this study, we applied WGSA to 27 Shigella isolates collected from children presenting with diarrhoea at Ndirande Health Centre in Malawi (2022-2023), as part of the Enterics for Global Health Shigella surveillance study. Serotyping, AMR profiling and phylogenetic analysis revealed Shigella sonnei as the dominant serogroup, with distinct genetic clustering relative to global reference strains among S. sonnei, Shigella flexneri and Shigella boydii. We identified 16 AMR genes linked to ten antimicrobial classes with qnrS1 and qnrB19 genes conferring resistance to fluoroquinolone, alongside IncFIB(K) and IncFII plasmid replicon markers. Importantly, no azithromycin resistance determinants were detected both genotypically and phenotypically, providing baseline evidence that warrants continued surveillance of current first-line treatment. However, the detection of fluoroquinolone resistance genes with plasmid replicon markers in the absence of phenotypic resistance might indicate a silent reservoir with epidemic potential. This is the first contemporary Shigella data from a large-scale diarrhoea disease surveillance study in Malawi, providing essential baseline information for guiding antibiotic treatment and future vaccine development efforts, contributing to the efforts to combat shigellosis in Malawi and other similar regions.

Humans↗
PubMed2024

Genotypic and phenotypic characterisation of respiratory syncytial virus after nirsevimab breakthrough infections: a large, multicentre, observational, real-world study.

BACKGROUND: Nirsevimab, a long-acting monoclonal antibody, has been approved for the prevention of respiratory syncytial virus (RSV) infection in infants. In France, more than 210&#x2009;000 single doses were administered in infants younger than 1 year during the 2023-24 season. In this context, the selection and spread of escape variants might be a concern. Here, we aimed to characterise RSV associated with breakthrough infection. METHODS: We did a multicentre, national, observational study in France during the 2023-24 RSV season in RSV-infected infants (aged <1 year) who either received or did not receive a dose of nirsevimab before their first RSV season. We excluded infants with insufficient information about nirsevimab treatment or without parental consent. We used respiratory samples collected in each laboratory for full-length RSV RNA sequencing to analyse changes in the nirsevimab binding site &#xd8;. We tested clinical RSV isolates for neutralisation by nirsevimab. We analysed F candidate substitutions by fusion-inhibition assay. FINDINGS: Of the 695 RSV infected infants, we analysed 545 (78%) full-length RSV genome sequences: 260 (48%) from nirsevimab-treated breakthrough infections (236 [91%] RSV-A and 24 [9%] RSV-B) and 285 (52%) from untreated RSV-infected infants (236 [83%] RSV-A and 49 [17%] RSV-B). Analysis of RSV-A did not reveal any substitution in site &#xd8; known to be associated with resistance to nirsevimab. Two (8%) of 24 RSV-B breakthrough infections had resistance-associated substitutions: F:N208D (dominant resistance-associated substitution) and a newly described F:I64M plus F:K65R combination (minority resistance-associated substitution), both of which induced high levels of resistance in the fusion-inhibition assay. INTERPRETATION: This study is, to the best of our knowledge, the largest genotypic and phenotypic surveillance study of nirsevimab breakthrough infections to date. Nirsevimab breakthrough variants remain very rare despite the drug's widespread use. The detection of resistance-associated substitutions in the RSV-B F protein highlights the importance of active molecular surveillance. FUNDING: ANRS Maladies Infectieuses Emergentes and the French Ministry of Health and Prevention.

Humans↗
PubMed2025

Characterization of ertapenem-resistant Enterobacterales in Canadian hospitals: 17 years of the CANWARD study (2007-23).

OBJECTIVES: To review phenotypic and genotypic characteristics of ertapenem-resistant Enterobacterales isolates identified by the CANWARD study from 2007 to 2023. METHODS: Bacterial isolates were collected as part of the CANWARD surveillance study from 2007 to 2023. CLSI M7 broth microdilution antimicrobial susceptibility testing (12th edition, 2024) was performed. MICs were interpreted by CLSI M100 breakpoints (34th edition, 2024). WGS was performed to identify antimicrobial resistance markers. RESULTS: Only 134 (0.7%) of the 19&#x200a;642 Enterobacterales were ertapenem-resistant. Carbapenemase producing Enterobacterales (CPE) accounted for 17.9% (n&#x200a;=&#x200a;24) of ertapenem-resistant isolates and were predominantly Klebsiella pneumoniae (54.2%) and Escherichia coli (20.8%). KPC was the most common carbapenemase identified (62.5%). K. pneumoniae ST834, ST16 and ST258, and E. coli ST131 were the most frequent STs detected. CPE percent resistant values ranged from 20.8% to 25.0% for ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam. Most non-CPE ertapenem-resistant isolates were Enterobacter spp. (51.8%), E. coli (15.5%) and K. pneumoniae (10.9%). Non-CPE STs were most commonly E. cloacae ST108, ST50 and ST133, and E. coli ST131. Non-CPE percent resistant values ranged from 2.7% to 4.5% for ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam. At least one of an AmpC, an ESBL or porin alternations were observed in most non-CPE isolates. CONCLUSIONS: In Canada, ertapenem-resistant Enterobacterales remain uncommon (0.7%). CPE isolates demonstrated higher percent resistant values for multiple antimicrobial classes and harboured more antimicrobial resistance genes than non-CPE isolates. Continued monitoring for ertapenem-resistant Enterobacterales, particularly CPE, is important given their associated multidrug resistance to both established and newer agents.

Ertapenem↗
PubMed2026

Mobilome-driven antimicrobial resistance in a one health context: evidence and lessons from Africa.

Antimicrobial resistance (AMR) is one of the most urgent global health threats and is increasingly recognized as a One Health challenge driven by interactions among human, animal, and environmental reservoirs. Central to the emergence and dissemination of AMR across these interfaces are mobile genetic elements (MGEs), which form an interconnected mobilome capable of transferring resistance genes across bacterial taxa and ecological niches. These elements facilitate the accumulation and spread of multidrug resistance determinants and are shaped by co-selective pressures operating at the animal-environment-human interface. Despite their critical role, genomic surveillance of MGEs remains limited, particularly in high-burden regions such as Africa. This narrative review synthesizes evidence from published genomic surveillance studies, primarily whole-genome sequencing-based analyses, to examine the distribution and dynamics of AMR genes and MGEs across One Health interfaces. We highlight animal-environmental systems as major hotspots for mobilome-driven resistance dissemination and also evaluate key advances, methodological approaches, and persistent surveillance challenges and gaps specific across Africa. By integrating findings from diverse genomic studies, and highlighting key lessons and implementation gaps from One Health studies across Africa, this review underscores the need for coordinated One Health surveillance strategies to better capture mobilome dynamics and inform sustainable AMR control efforts.

Africa↗
PubMed2026

Wastewater-based sequencing of respiratory syncytial virus to investigate lineage dynamics and antigenic site mutations: a retrospective genomic epidemiology study.

BACKGROUND: Respiratory syncytial virus (RSV) infections pose a substantial health burden, particularly for clinically vulnerable populations such as infants and older adults. Although novel immunoprophylactic interventions show promise in providing protection, many countries may not have robust surveillance systems to monitor circulating RSV lineages and detect mutations that might reduce the effectiveness of these new interventions. We aimed to assess the diversity and temporal dynamics of circulating RSV lineages in urban populations through amplicon-based sequencing and analysis of wastewater extracts. METHODS: In this prospective observational wastewater-based genomic surveillance study, 32 raw influent 24-h composite samples were collected during the 2022-23 and 2023-24 RSV seasons from both Zurich and Geneva, Switzerland. We applied an RSV subtype-specific amplicon-based sequencing approach to obtain RSV-A and RSV-B sequences from all 64 samples. Mutations relative to reference genomes were identified at positions with read depth above 30. Relative abundances of RSV lineages were estimated from frequencies of lineage-signature mutations, present in greater than 90% of publicly available sequences of that lineage. FINDINGS: Relative abundances of RSV-B (2022-23) and RSV-A (2023-24) lineages were estimated over the two RSV seasons. During the 2022-23 season, the RSV-B B.D.E.1 lineage prevailed in both cities. In the 2023-24 season, multiple RSV-A lineages cocirculated, including A.D.1, A.D.3, A.D.5, and their sub-lineages. Identification and frequency estimation of mutations showed low-frequency, non-synonymous mutations in antigenic sites on the fusion gene of both RSV-A and RSV-B, some of which have not been reported in clinical sequences. The primary outcome was identification and relative abundance of RSV lineages in wastewater samples. INTERPRETATION: These findings show the potential of wastewater-based genomic surveillance to identify and track circulating RSV lineages and clinically relevant mutations. As novel RSV immunoprophylaxis measures are introduced in upcoming RSV seasons, wastewater-derived genomic RSV data provide a valuable baseline for understanding RSV diversity and future viral evolution under increased immunological pressure. FUNDING: This study was funded by the Swiss National Science Foundation and in part by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health. Funding for sample collection and processing was provided by the Swiss Federal Office of Public Health.

Humans↗
PubMed2026

Recent Advances in Surveillance Strategies for Nasopharyngeal Carcinoma.

PURPOSE OF REVIEW: Nasopharyngeal carcinoma (NPC) is a malignant tumor characterized by a distinct geographical distribution. Effective surveillance is crucial for the early detection of recurrence or metastasis and for improving patient prognosis.This review systematically examines current NPC follow-up protocols and recent developments to inform individualized precision surveillance. RECENT FINDINGS: This review focuses on two main aspects. 1) We compare and analyze current major NPC follow-up guidelines, with key discussions covering follow-up frequency, imaging modalities (including magnetic resonance imaging [MRI] and positron emission tomography [PET]), plasma Epstein-Barr virus DNA (EBV-DNA) monitoring, and functional assessments. 2)We elaborate on the application prospects and research progress of genomics, radiomics, and artificial intelligence in NPC surveillance. Studies suggest that risk-stratified, individualized follow-up strategies, such as those based on conditional survival models, can enhance the cost-effectiveness of surveillance. Additionally, emerging technologies, including radiomics and artificial intelligence, show promise for improving recurrence risk assessment, prognostic stratification, and individualized surveillance in NPC. Concurrently, advances in genomics and radiomics offer new opportunities for predicting complications and guiding treatment adjustments. Future efforts should focus on integrating multidisciplinary expertise to develop dynamic monitoring systems that enable precise follow-up and ultimately improve patient survival outcomes.

Humans↗
PubMed2026

Multidimensional prophage profiling of carbapenem-resistant Enterobacteriaceae in Thailand: a nationwide, multicentre, genomic study.

BACKGROUND: Prophages influence bacterial fitness, resistance, and evolution, yet their epidemiology remains poorly understood in carbapenem-resistant Enterobacteriaceae (CRE). In this nationwide study in Thailand, we aimed to describe prophage repertoires in clinical CRE isolates and to explore their potential relevance for molecular epidemiology. METHODS: We performed a nationwide, retrospective, genomic analysis of all CRE clinical isolates collected through our previous national surveillance study involving 11 hospitals in 11 provinces in Thailand between March 25, 2012, and Jul 21, 2017. Whole-genome sequencing data from 747 CRE isolates were analysed. Intact prophages were identified using PHAge Search Tool Enhanced Release (PHASTER) and clustered by nucleotide sequence similarity. Prophage profiles were compared across multilocus sequence types, carbapenemase genotypes, specimens, geography, and patient demographics (age and sex). FINDINGS: Of the included 747 CRE isolates, 170 (23%) were Escherichia coli and 577 (77%) were Klebsiella pneumoniae. 220 (29%) of 747 strains had been isolated from female patients and 264 (35%) from male patients; metadata on patient sex were missing for 263 (35%) isolates. The median patient age was 63 years (IQR 50-72). 71 (10%) of isolates were from blood, 283 (38%) from sputum, 284 (38%) from urine, and 109 (15%) from other specimens. 374 distinct prophage clusters were identified, with significantly more prophages per genome in K pneumoniae (mean 3&#xb7;01 [SD 1&#xb7;55]) than in E coli (1&#xb7;64 [1&#xb7;46]; p<0&#xb7;0001). Prophage repertoires largely mirrored bacterial multilocus sequence types. However, even within the highly clonal K pneumoniae sequence type 16 lineage, discrete prophage variation was identified, with common profiles observed in geographically dispersed patients. Respiratory K pneumoniae frequently carried a mosaic prophage with environmental signatures and a type VI secretion system, whereas blood-derived E coli harboured a prophage with immune-modulating genes. Distinct prophage clusters were observed across clinical specimens, age groups, carbapenemase genotype, and geographical region. Strains coharbouring blaNDM-1 plus blaOXA-232 (114 [15%] of 747) had the highest prophage loads. INTERPRETATION: The prophage content was shaped by the bacterial lineage, ecological niche, and temporal dynamics, providing an additional layer of epidemiological resolution beyond conventional genome typing. Integrating prophage profiling into molecular surveillance frameworks could help to identify transmission events, improve infectious source attribution, and enhance infection control strategies. FUNDING: Japan Agency for Medical Research and Development.

Female↗
PubMed2026

Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024.

BACKGROUND: Human metapneumovirus (hMPV) is a major contributor of acute respiratory infections (ARI) in childhood and vulnerable adults. It comprises two antigenically distinct lineages (A and B), with multiple sub-lineages. Genomic analyses of hMPV strains enable monitoring of viral evolution and transmission to inform future interventions but remain underutilized in Africa. METHODS: We generated 52 near-complete hMPV genomes from respiratory samples collected in Kilifi, Coastal Kenya, using a tiled-amplicon approach and Oxford Nanopore Technologies sequencing. These samples had been identified as hMPV positive by quantitative PCR during (a) a multi-facility outpatient ARI surveillance in nine health facilities in Kilifi between 2016 and 2017, and 2021 to 2023 and (b) a community-based respiratory infection cohort surveillance study between 2023-2024 that sampled enrolled participants irrespective of symptom status. RESULTS: Of the 192 positive samples analyzed from the two studies, children under 5 years accounted for most hMPV cases (134/186, 72%). 52 samples were sequenced (>70% genome coverage), and hMPV-A (27/52, 53.8%) and hMPV-B (25/52, 46.2%) lineages were identified. The recovered sequences mapped into sub-lineages A2c (27/52, 53.8%), B1 (12/52, 21.2%), and B2b (13/52, 25%). A shift in the predominant sub-lineage was observed from B2b (2016) to B1 (2021), and finally to A2c-wild type (2023). In February 2021, for the first time, we detected a single A2c strain with a 111-nucleotide duplication in the G gene among Kenyan samples. CONCLUSION: Our study expands the global nucleotide sequence database for hMPV by adding new whole-genome sequences from Kenya collected over the last decade. It highlights the ongoing replacement of locally predominant hMPV lineages and the importation and local transmission of globally circulating strains. These findings underscore the importance of sustained hMPV genomic surveillance to detect emerging variants and monitor lineage circulation patterns that may impact viral transmission, molecular detection, and future control measures.

A2c-111nt-dup↗