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PubMed2026

Dynamics and virulence of Enterobacteriaceae reservoirs harboring blaCTX-M group 1 in community wastewater.

UNLABELLED: Extended-spectrum beta-lactamase (ESBL)-producing bacteria are ubiquitous and can cause serious infections. Here, we examined untreated community wastewater influent as a reservoir for blaCTX-M group 1 organisms and their virulence potential. Raw influent samples (n = 268) were collected from four wastewater treatment plants (WWTPs) representing dense urban populations. We observed that blaCTX-M group 1 levels were high at all WWTPs and only ~1-2 log10 lower and not correlated to common human-specific microbiome fecal markers, Lachno3 and HF183, indicating a lack of connection to human fecal inputs. Concentrations of blaCTX-M group 1 genes and markers for presumptive host organisms Escherichia coli and Klebsiella pneumoniae were influenced by travel time and season. Amplicon sequencing revealed high diversity of blaCTX-M group 1-9 genes, with 63% belonging to group 1. Selective culture and 16S rRNA gene sequencing showed blaCTX-M group 1 isolates were 26% E. coli, 26% K. pneumoniae, 40% other Enterobacteriaceae, and 8% Aeromonas. Overall, E. coli averaged 3.6E7 cells/L, with 3% of all E. coli found to contain blaCTX-M group 1. Whole-genome sequencing of blaCTX-M group 1 E. coli from wastewater revealed resistance and virulence gene profiles similar to clinical isolates and distinct from other wastewater ESBL-resistant and non-resistant E. coli. Interpretation of wastewater data needs to consider both the existence of environmental reservoirs that contain potentially pathogenic organisms and the strong influence the dynamics of the conveyance system can have on final concentrations measured at the WWTP. IMPORTANCE: The CTX-M enzyme family is highly abundant in nosocomial, community, and environmental settings and is leading to treatment of infections with carbapenem antibiotics, a last-line therapeutic option. The progressive increase of the clinically relevant blaCTX-M group 1 resistance genes in the human population warrants investigation, particularly to understand the establishment and dynamics of environmental reservoirs. This study utilized molecular and culture methods to gain insight into the possible origin, abundance, and dynamics of blaCTX-M group 1 genes in untreated wastewater influent samples. We found extremely high levels of these genes, with Escherichia coli as a major host organism that closely resembled clinical strains, suggesting they are seeded and propagate in sewer pipe systems. The significance of our research is in developing approaches to monitor antimicrobial resistance reservoirs in community wastewater, which could shed light on global burdens and potential transmission cycles and indicate increasing inputs of clinically relevant strains originating from human populations.

E. coli↗
PubMed2024

Non-replicative phage particles delivering CRISPR-Cas9 to target major blaCTX-M variants.

Cluster regularly interspaced short palindromic repeats and CRISPR associated protein 9 (CRISPR-Cas9) is a promising tool for antimicrobial re-sensitization by inactivating antimicrobial resistance (AMR) genes of bacteria. Here, we programmed CRISPR-Cas9 with common spacers to target predominant blaCTX-M variants in group 1 and group 9 and their promoter in an Escherichia coli model. The CRISPR-Cas9 was delivered by non-replicative phagemid particles from a two-step process, including insertion of spacer in CRISPR and construction of phagemid vector. Spacers targeting blaCTX-M promoters and internal sequences of blaCTX-M group 1 (blaCTX-M-15 and -55) and group 9 (blaCTX-M-14, -27, -65, and -90) were cloned into pCRISPR and phagemid pRC319 for spacer evaluation and phagemid particle production. Re-sensitization and plasmid clearance were mediated by the spacers targeting internal sequences of each group, resulting in 3 log10 to 4 log10 reduction of the ratio of resistant cells, but not by those targeting the promoters. The CRISPR-Cas9 delivered by modified ΦRC319 particles were capable of re-sensitizing E. coli K-12 carrying either blaCTX-M group 1 or group 9 in a dose-dependent manner from 0.1 to 100 multiplicity of infection (MOI). In conclusion, CRISPR-Cas9 system programmed with well-designed spacers targeting multiple variants of AMR gene along with a phage-based delivery system could eliminate the widespread blaCTX-M genes for efficacy restoration of available third-generation cephalosporins by reversal of resistance in bacteria.

CRISPR-Cas Systems↗
PubMed2026

Transferable IncHI2-Associated blaLAP-2 and blaCTX-M-55 Resistance Platforms in Foodborne Salmonella.

Extended-spectrum β-lactamase genes in foodborne Salmonella enterica can disseminate through mobile multidrug-resistance platforms. IncHI2 plasmids are important resistance vehicles capable of carrying complex resistance regions and facilitating their horizontal transfer across diverse bacterial backgrounds, but the transfer and genomic organization of IncHI2 elements co-carrying blaLAP-2 and blaCTX-M-55 remain insufficiently characterized. This study investigated two multidrug-resistant foodborne isolates recovered in Shanghai in 2022: Salmonella Agona ST13 isolate Sal22C150 and Salmonella Havana ST1527 isolate Sal22P208. Antimicrobial susceptibility testing, whole-genome sequencing, conjugation, plasmid-retention analysis, comparative genomics, as well as strain- and plasmid-level phylogenetic analyses were performed. Both isolates exhibited broad antimicrobial resistance, including resistance to extended-spectrum cephalosporins. In both isolates, blaLAP-2 and blaCTX-M-55 co-transferred with the IncHI2 replicon to Escherichia coli J53 at frequencies of (4.95 ± 0.41) × 10-5 and (4.46 ± 0.42) × 10-6 transconjugants per donor cell, respectively. All tested plasmid markers remained detectable through 20 passages without antimicrobial selection. Complete assembly of Sal22P208 confirmed the location of the three β-lactamase genes on the 275,096 bp IncHI2 plasmid pSal22P208. The plasmid contained a conserved conjugative backbone and mosaic accessory regions carrying 15 antimicrobial-resistance determinants together with mercury- and tellurium-resistance loci. SNP-based analysis placed pSal22P208 within a closely related cluster containing six reference IncHI2 plasmids differing by fewer than 30 SNPs and recovered from Salmonella and E. coli of animal, food, and human origin, suggesting a broad distribution of this plasmid lineage across diverse bacterial and ecological backgrounds. Sal22P208 additionally contained a Tn3-associated chromosomal multidrug-resistance region between rpmJ and rpmE that shared extensive structural similarity with a region in Citrobacter braakii LBA3. These findings highlight the role of transferable IncHI2 resistance platforms in the horizontal dissemination and short-term post-transfer maintenance of linked resistance determinants, while chromosomally integrated resistance regions may provide an additional route for the accumulation and inheritance of multidrug resistance in foodborne Salmonella.

IncHI2 plasmid↗
PubMed2026

Transferable IncX3-blaKPC-2 plasmid and chromosomal blaCTX-M-27 in a commensal Escherichia coli ST7854 isolated from a healthy companion dog.

OBJECTIVES: Carbapenemase-producing Enterobacterales have disseminated globally, largely via highly transmissible plasmids. Their emergence in companion animals is of particular concern, indicating that clinically important carbapenem-resistance determinants have spread beyond healthcare settings. This study characterized a multidrug-resistant Escherichia coli isolate from a healthy dog in South Korea. METHODS: Antimicrobial susceptibility was determined by standardized reference methods. Hybrid whole-genome assembly resolved chromosomal and plasmid architectures, and plasmid transferability was assessed by conjugation assays. Comparative genomic analysis based on nucleotide identity and alignment coverage evaluated relatedness to publicly available blaKPC-carrying IncX3 plasmids. RESULTS: The E. coli ST7854 isolate was resistant to carbapenems (imipenem MIC = 8 µg/mL), third-generation cephalosporins, fluoroquinolones, tetracycline, gentamicin, phenicols, and trimethoprim-sulfamethoxazole, but susceptible to amikacin and colistin. Assembly resolved a 4.77 Mb circular chromosome and seven plasmids. The ESBL gene blaCTX-M-27 was chromosomally integrated, whereas carbapenem resistance was conferred by blaKPC-2 on a 54,805 bp IncX3 plasmid. This IncX3-blaKPC-2 plasmid was transferred to E. coli J53 at a frequency of 5.91 × 10⁻⁴, whereas the large IncFIB multidrug resistance plasmid was not co-transferred. Comparative analysis revealed extensive structural similarity with Korean clinical IncX3 plasmids, whereas most representative international plasmids shared only the conserved IncX3 backbone. CONCLUSIONS: A commensal E. coli ST7854 isolate from a healthy companion dog carried a conjugative IncX3-blaKPC-2 plasmid and chromosomally integrated blaCTX-M-27. Similarity to Korean clinical plasmids suggests potential human-animal dissemination, and this asymptomatic carriage of mobile carbapenem-resistance determinants supports continued genomic surveillance of antimicrobial resistance in companion animals within a One Health framework.

Bla(CTX-M-27)↗
PubMed2026

Complete genome sequence of a multidrug-resistant Proteus mirabilis clinical isolate harboring 22 antimicrobial resistance genes including blaCTX-M-15.

Proteus mirabilis causes urinary tract infections and wound infections and frequently exhibits multidrug resistance, complicating patient treatment. Here, we describe the complete genome sequence of a multidrug-resistant P. mirabilis wound isolate from 2025, providing insight into the repertoire of antimicrobial resistance genes in a recent P. mirabilis clinical isolate.

Proteus mirabilis↗
PubMed2026

Frequency and characteristics of extended-spectrum beta-lactamase-producing Escherichia coli in wastewater in Dakar, Senegal.

OBJECTIVE: This study aimed to investigate the occurrence, antimicrobial resistance profiles, and genetic characteristics of extended-spectrum beta-lactamase (ESBL)-producing E. coli in wastewater collected in Dakar, Senegal. RESULTS DESCRIPTION: All samples (n = 48) carried ESBL-producing isolates. The concentrations of ESBL-producing E. coli ranged from 1.4 × 10⁴ to 3.3 × 10⁵ CFU/100 mL, whereas the ratio of ESBL-producing E. coli among the total E. coli population varied between 0.2% and 16.3%. All the 107 isolated ESBL-producing E. coli isolates were multidrug resistant (MDR), with 100% resistance to beta-lactams (ampicillin, cefalotin, cefotaxime, ceftazidime, cefepime, aztreonam) and high resistance rates to non-beta-lactam antibiotics, including ciprofloxacin (77.6%). No resistance was observed to imipenem. CTX-M-type genes were present in all isolates, with blaCTX-M-1 group (89.7%) and blaCTX-M-8 group (88.8%) being the most prevalent. The blaCTX-M-15 variant, a subgroup of blaCTX-M- group1, was detected in 96.9% of blaCTX-M-1 positive isolates. Additionally, blaTEM (31.8%) and blaOXA-1 (34.6%) were detected, while blaSHV and blaCTX-M-25 group were absent. Phylogenetic analysis of 107 isolates revealed a diverse distribution across four phylogroups: A (37.4%), D (22.4%), B1 (14.0%), and B2 (5.7%). The predominance of phylogroup A, mainly associated with intestinal commensal carriage, suggests fecal contamination as a primary source.

Senegal↗
PubMed2026

Prevalence, genomic characterization, and biofilm-forming capacity of extended-spectrum β-lactamase-producing Escherichia coli from faecal samples of broiler chickens in Jinan City, China.

The emergence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in food animals threatens both veterinary and human medicine by compromising critically important antimicrobials. This study characterized the prevalence, antimicrobial resistance profiles, molecular epidemiology, and virulence attributes of ESBL-producing E. coli isolated from broiler farms in Jinan City, China. From 600 faecal samples, 537 E. coli isolates were recovered (89.5 % isolation rate), with 71 (13.2 %) identified as ESBL producers. Antimicrobial susceptibility testing revealed markedly more severe resistance among ESBL-producing isolates, with complete ampicillin resistance (100 %) and high-level resistance to sulfamethoxazole/trimethoprim (94.37 %), streptomycin (87.32 %), chloramphenicol (78.87 %), and tetracycline (70.42 %). Resistance to extended-spectrum cephalosporins cefuroxime and ceftriaxone reached 43.66 % and 36.62 %, respectively, while amoxicillin/clavulanic acid susceptibility declined to 61.97 %. Whole-genome sequencing identified blaCTX-M-55 (29.58 %) as the predominant ESBL genotype, followed by blaCTX-M-64 (23.94 %), blaCTX-M-15 (19.71 %), blaCTX-M-14 (12.68 %), and blaCTX-M-65 (9.86 %). The plasmid-mediated colistin resistance gene mcr-1 was detected in 25.35 % of ESBL-producing isolates, indicating a substantial reservoir of last-resort antibiotic resistance determinants, though physical linkage between mcr-1 and ESBL-encoding genes remains undetermined due to short-read sequencing limitations. Multilocus sequence typing revealed ST117 (18.3 %) as the predominant sequence type, associated mainly with serogroup O78 (25.4 %). Virulence gene profiling demonstrated high prevalence of the serum survival gene iss (85.9 %), commonly associated with avian pathogenic E. coli, though avian pathogenicity was not experimentally confirmed. Notably, 90.14 % of ESBL-producing isolates demonstrated biofilm-forming capacity, with 16.90 % classified as strong biofilm producers forming mature, mushroom-shaped microcolonies. These findings demonstrate that broiler chickens in the sampled Jinan farms constitute a significant reservoir of multidrug-resistant, biofilm-forming ESBL-producing E. coli harboring clinically relevant genotypes, including mcr-1. The predominance of ST117, reported in both poultry and human clinical settings, along with extensive co-resistance profiles, underscores the value of integrated surveillance and antimicrobial stewardship in poultry production, though direct zoonotic transmission evidence requires further comparative genomic and epidemiological investigation.

Antimicrobial resistance↗
PubMed2026

Escalation of CTX-M-producing extensively drug-resistant Shigella spp. in Kolkata, India, following the COVID-19 pandemic.

Shigella spp. is recognized by the World Health Organization as a high-priority pathogen due to its global prevalence, unique pathogenic mechanisms, and growing antimicrobial resistance (AMR). Nearly half of all Shigella strains worldwide are now multidrug-resistant (MDR), and the emergence of extensively drug-resistant (XDR) variants-resistant to ciprofloxacin, ceftriaxone, and azithromycin-has severely limited effective treatment options. The present study is based on prospective laboratory surveillance involving 323 Shigella isolates collected during 2021-2023, with pre-COVID-19 pandemic data included from a previously published study solely for historical comparison. The presence of antibiotic resistance genes (ARGs) was investigated, and whole-genome sequencing (WGS) was performed on representative isolates to assess phylogenetic relatedness with global isolates. Approximately 10% of isolates exhibited resistance to third-generation cephalosporins. While only 3% of Shigella isolates carried the blaCTX-M-15 gene from 2013 to 2019, its prevalence increased to 26% by 2022-2023. Among 38 ceftriaxone-resistant S. sonnei isolates, 33 were also resistant to azithromycin, categorizing them as XDR. These isolates showed 48% clonal similarity and high phylogenetic resemblance to the isolates reported from England. Hybrid genome assembly revealed a plasmid harboring both the blaCTX-M-15 and mphA ARGs. Conjugation experiments and plasmid profiling confirmed the plasmid's transferability. We report a rising trend in third-generation cephalosporin resistance among Shigella spp., primarily driven by the spread of extended-spectrum β-lactamase-producing S. flexneri and the emergence of XDR S. sonnei. These findings underscore the urgent need for strengthened national AMR containment strategies and enhanced international surveillance of cephalosporin-resistant Shigella to mitigate this growing public health threat.IMPORTANCEShigella is a leading cause of diarrheal disease globally and has been prioritized by the World Health Organization due to its rapid acquisition of antimicrobial resistance. Our prospective surveillance in Kolkata, India, reveals a worrisome escalation of third-generation cephalosporin resistance over the past decade, primarily associated with the spread of blaCTX-M-15 and the emergence of extensively drug-resistant (XDR) S. sonnei. The detection of plasmids carrying both blaCTX-M-15 and mphA, coupled with evidence of their transferability, highlights the potential for accelerated dissemination of multidrug resistance. When compared with a global data set of international genomes, the Kolkata XDR isolates were found to cluster closely with isolates reported from England. By linking local surveillance with global genomic context, our findings provide critical insights for treatment guidelines, antimicrobial stewardship, and the design of international containment strategies aimed at curbing the rise of cephalosporin- and azithromycin-resistant Shigella.

India↗
PubMed2026

Characteristics of an NDM-1-producing Klebsiella pneumoniae strain belonging to ST105.

Uncommon multilocus sequence types (MLSTs) of NDM-producing Klebsiella pneumoniae may pose a significant threat to patients, although they are often overlooked in surveillance studies. Characterizing these isolates is therefore important for infection control. In this study, the antimicrobial susceptibility and pathogenicity of K. pneumoniae strain KP_WXD, pertaining to the atypical sequence type ST105, were evaluated, including capsular polysaccharide (CPS) production, biofilm formation, and resistance to serum killing. Whole-genome sequencing (WGS) was performed to analyze its genomic features. K. pneumoniae KP_WXD strain was resistant to all tested β-lactam agents. Its virulence was lower than that of K. pneumoniae strains ST11-KL64 and NTUH-k2044 used as references, while its biofilm formation ability was stronger than that of both strains. WGS analysis revealed carriage of IncF and IncN plasmids carrying multiple antibiotic resistance genes, alongside blaNDM-1 and blaCTX-M, integrated into well-characterized mobile genetic elements. Moreover, both blaNDM-1 and blaCTX-M-harboring plasmids were transferable to E. coli J53 by conjugation without significant fitness cost on the recipient strain.

Klebsiella pneumoniae↗
PubMed2025

Molecular characterization of antimicrobial resistance in Escherichia coli from dairy farm environment.

The present study was carried out to study the prevalence and genetic mechanisms of antimicrobial resistance in E. coli strains from dairy farms. A total of 60 E. coli strains were initially isolated from 192 dairy farm samples using a selective antibiotic approach and confirmed as E. coli by PCR. Among these, 48 E. coli isolates predominantly from fecal samples were further studied. These isolates were majorly classified in phylogroup A (43.75 %) and B1 (16.66 %) and showed predominant resistance against ampicillin (60.41 %) followed by piperacillin (56.25 %), tetracycline (54.16 %), and other β-lactams such as cefotaxime (47.91 %) and cefuroxime (43.75 %). A significant portion (22.9 %) of the E. coli isolates were multidrug-resistant (MDR) and 50 % were ESBL-positive. Multiple antibiotic resistance (MAR) index ≥0.4 was exhibited by three isolates. Genotypic analysis identified resistance genes associated with β-lactams (blaCTX-M-1, 64.58 %; blaTEM, 35.41 %; blaCTX-M-9, 4.16 %), tetracycline (tetA,37.58 %; tetB, 47.91 %), trimethoprim (dfrA17, 16.66 %), aminoglycosides [aac(6')-Ib-cr, 2.08 %] and fluoroquinolones [qnrB, 25 %; qnrS, 16.66 %; gyrB (S492N), 45.83 %; gyrA (S83L), 45.83 %; gyrA(S87L), 39.58 %; parC (S80I), 14.58 %]. E. coli isolates also showed a high frequency of mobile genetic elements (MGEs) such as IS26 (56.25 %), IncFIB plasmids (52.08 %), and Tn3 transposons (56.25 %). Class 1 integrons harbouring 200 and 800 bp gene cassettes were also detected in 5 E. coli isolates (10.4 %). Overall, this study highlights the high prevalence of diverse AMR genes in cattle-derived E. coli and their strong association with various MGEs. These findings emphasize the need for continuous genomic surveillance to mitigate resistance spread, particularly within and from dairy environments.

Escherichia coli↗
PubMed2025

Municipal sewage as a pathway for multidrug-resistant KPC-producing Klebsiella pneumoniae from hospital effluent to urban stream: challenges for wastewater management.

Carbapenemase-producing Klebsiella pneumoniae is among the mainly reasons for death from bacterial infection associated with antibiotic resistance. Its widespread dissemination, especially due to KPC enzyme, is one of the main challenges in One Health perspective. Here, we studied 42 KPC-producing K. pneumoniae isolates from hospital wastewater, municipal wastewater from wastewater treatment plant (WWTP), and urban stream which receives treated municipal effluent. The isolates presented broad resistance to β-lactams antibiotics, as well as to fluoroquinolones, and show antibiotic resistance profile very similar, even those from out-of-hospital settings. Along to blaKPC gene, blaCTX-M-1 (33,3 %, n = 14), blaCTX-M-8 (19 %, n = 8), qnrB (52,3 %, n = 22), qnrS (2,38 %, n = 1), and rmtB (19 %, n = 8) were detected. There was a predominance of gene that confers tolerance to silver and copper metals, as well as to virulence factor related to enterobactin and colibactin production. Macrorestriction genomic analysis by XbaI enzyme demonstrated several pulsotype, but some ones are related. Isolates from hospital wastewater were detected after 4 months at the same sampling point, as well as similar to those detected in WWTP and urban stream demonstrating the effluents role as spreaders of antibiotic resistance. This study provides data on the characterization of KPC-producing K. pneumoniae, which contributes to the epidemiological characterization of human pathogens transmitted by aquatic matrices. In view of the universal sanitation and control of antimicrobial resistance in the One Health perspective, greater investment in effluent treatment is necessary to avoid contamination and environmental dissemination of antibiotic-resistant bacteria.

Klebsiella pneumoniae↗
PubMed2026

Genomic characterization of novel human-associated CTX-M-15-producing Serratia nevei ST625 lineage infecting a vulnerable loggerhead sea turtle.

BACKGROUND: Serratia nevei is a newly classified and opportunistic bacterial species belonging to the Serratia marcescens complex (SMC). Genomic data from this species is highly relevant for public health and epidemiological tracking. OBJECTIVE: To report the first identification and genomic characterization of extended-spectrum β-lactamase (CTX-M-15)-producing S. nevei sequence type (ST) ST625 lineage infecting a vulnerable loggerhead sea turtle. METHODS: Strain BP02 was recovered from the coelomic cavity of a loggerhead sea turtle (Caretta caretta) admitted to a rehabilitation center in southeastern Brazil. MALDI-TOF MS was initially used for species identification and was further confirmed by whole-genome sequencing on the Illumina HiSeq platform, followed by ANI, dDDH, multilocus sequence typing, resistome, plasmidome, virulome, and SNP-based phylogenomic analyses. RESULTS: Strain BP02 exhibited a multidrug-resistant profile, including resistance to third- and fourth-generation cephalosporins. Genomic analyses identified BP02 as S. nevei ST625 carrying blaCTX-M-15 within the ISEcp1-blaCTX-M-15-wbuC-ΔTn2 genetic environment, in addition to multiple AMR determinants and the IncC plasmid replicon. Phylogenomic analysis demonstrated close relatedness between BP02 and human clinical ST625 strains, previously reported in São Paulo, Brazil, including a urine-derived strain isolated in 2019, differing by only 27 SNPs. Notably, all publicly available ST625 genomes were associated with human clinical sources and displayed multidrug resistance genotypes. CONCLUSION: This study expands the current knowledge regarding the ecology and genomic features of S. nevei, demonstrating the emergence of a human multidrug-resistant clone in marine wildlife. Our findings reinforce the importance of monitoring clinically relevant SMC members across distinct ecological niches within a One Health perspective.

ESBL↗
PubMed2025

Transmission of extended spectrum β-lactamase-producing Escherichia coli and antimicrobial resistance gene flow across One Health compartments in eastern Africa: a whole-genome sequence analysis from a prospective cohort study.

BACKGROUND: The One Health paradigm considers interdependence of human, animal, and environmental health. However, there is little evidence from high-income countries to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, understanding how the close interactions of humans with animals and the environment in low-income settings affect the spread of AMR is important. We aimed to investigate diversity and transmission of extended spectrum β-lactamase (ESBL)-producing Escherichia coli across household-linked One Health compartments using genomic data. METHODS: We sequenced whole genomes of ESBL-producing E coli isolates from humans, animals, and the environment from a prospective, longitudinal cohort study conducted in Malawi (April 29, 2019, to Dec 3, 2020) and Uganda (July 16, 2020, to Aug 6, 2021). In the cohort study, 259 households were enrolled at baseline in Malawi and 92 in Uganda from a mix of urban, peri-urban, and rural areas. Households were followed up at months 1, 3, and 6 in Malawi and at months 1, 2, and 4 in Uganda. Samples collected at each visit included human and animal stool, environmental samples from hand-contact areas, food, and water, and broader environmental samples such as river water. Samples were cultured in buffered peptone water and then ESBL chromogenic agar to isolate ESBL-producing E coli. ESBL-producing E coli isolates underwent whole-genome sequencing. We performed phylogenetic analyses, and in-silico multi-locus sequence typing, characterised AMR determinants and linked genotypes with sample location, ecological source, and other covariates. We performed fine-scale single nucleotide polymorphism (SNP) and network analysis to infer strain and plasmid transmission across ecological compartments. The primary outcome was colonisation with ESBL-producing E coli. Secondary outcomes were genomic clusters and ESBL genomic determinants within and between One Health compartments. FINDINGS: We found high diversity of ESBL-producing E coli, with 170 sequence types and 166 genomic clusters identified from 2344 genomes, including 1814 genomes from Malawi (907 human, 221 animal, and 686 environmental) and 530 genomes from Uganda (380 human, 147 animal, and three environmental). Sequence type (ST)131 dominated in Malawi (209 [11·5%] of 1814 genomes), and ST10 dominated in Uganda (45 [8·5%] of 530 genomes). Common ESBL genes blaCTX-M-15 (1604 [68·4%] of 2344 genomes) and blaCTX-M-27 (336 [14·3%] of 2344 genomes) were carried on a complex network of 55 and 30 different plasmids. This diversity of plasmids presented multiple pathways for dissemination and revealed high force of selection. Phylogenetic analyses revealed common intermixing of isolates between humans, animals, and the environment. SNP transmission analysis revealed ecologically overlapping clusters, suggesting ESBL-producing E coli co-circulation both within and between compartments with frequent spillover events. Applying a five-SNP threshold, we inferred 463 human-environment transmission events, 146 human-animal events, and 142 animal-environment events. INTERPRETATION: Our work suggests that a One Health approach is crucial to addressing AMR in eastern Africa. Improving water, sanitation, and hygiene systems will create a safer environment, reduce spillovers of AMR bacteria between compartments, and eventually reduce AMR reservoirs in the environment and in animals. FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

Humans↗
PubMed2026

Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli across humans, poultry and wastewater sectors in Douala, Cameroon.

BACKGROUND: The global health threat of antimicrobial resistance involves the human, animal and environmental sectors. Data from Cameroon are scarce. OBJECTIVES: This study aimed to define extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) rates and associated risk factors across the three sectors in Douala, Cameroon, and to define molecular characteristics of isolates. METHODS: From June 2022 to May 2023, we collected blood cultures from hospitalized patients, rectal swabs from healthy pregnant women, caeca from broiler chickens and environmental wastewater. Samples were screened for ESBL-Ec using CHROMAgar™ ESBL and cefotaxime-supplemented Tryptone Bile X-glucuronide agar. Antimicrobial susceptibility testing was performed by disk diffusion following EUCAST guidelines. Whole-genome sequencing was carried out using Illumina technology. RESULTS: Of 628 samples, 374 yielded ESBL-Ec. Prevalence was 54.6% (131/240) in pregnant women, 70.4% (169/240) in chickens and 93.1% (67/72) in wastewater. The proportion of ESBL-Ec among E. coli-positive-blood cultures was 9.2% (7/76). Multi-family household living was independently associated with ESBL-Ec carriage among pregnant women (adjusted odds ratio = 1.7, 95% CI 1.0-3.1, P = 0.03). High co-resistance (>70%) was observed for tetracycline, ciprofloxacin and trimethoprim/sulfamethoxazole. Sequencing of 32 isolates revealed 45 distinct resistance genes, including blaCTX-M-15 (n = 13, 40.6%), blaCTX-M-55 (n = 11, 34.4%) and last-resort antibiotic resistance genes mcr-1 and bla OXA-181. High-risk sequence types included ST131 (pregnant women) and ST10 (chickens). Notably, ST48 was shared between pregnant women and chickens, and ST155 between pregnant women and wastewater. CONCLUSION: Cross-sectoral ESBL-Ec in Douala exhibits high genomic diversity and alarming resistance. The occurrence of last-resort genes requires immediate One Health surveillance and coordinated interventions.

Journal Article↗
PubMed2026

Molecular determinants of antimicrobial resistance in Klebsiella pneumoniae isolates among geriatric patients in Chattogram, Bangladesh: a cross-sectional study.

Klebsiella pneumoniae (KPN) infections pose heightened risks in the geriatric population due to weakened immunity, prevalent comorbidities, potential exposure in long-term care settings, and increased likelihood of antibiotic resistance (ABR). The study focused on the prevalence and antibiotic resistance of KPN infections, the presence of ABR genes in KPN, and the genomic characterization of KPN obtained from geriatric patients in Chattogram. A total of 543 specimens were collected from four hospitals in Chattogram, along with demographic data from hospital records. Genomic DNA was extracted from multi-drug-resistant (MDR) KPN, and the presence of ABR genes, blaTEM-1, sul-1, aadB, blaNDM-1, blaSHV-11, and phoE was identified. To characterize the KPN genomes, two MDR KPN isolates were subjected to whole-genome sequencing (WGS), and the data were analyzed using bioinformatics tools to identify genomic determinants of ABR. KPN exhibited high resistance to ceftazidime (96%), cefuroxime (92%), and cefixime (83%), but sensitivity to colistin (79%) and amikacin (75%). MDR KPN was mostly detected in sputum (36%) and urine (27%) specimens, where the prevalence of ABR genes, blaTEM-1, sul1, aadB, blaNDM-1, and blaSHV-11 were 28.2%, 17%, 6.17%, 56%, and 48% of these strains, respectively. These genomes exhibited distinct profiles for sequence types, ST420 and ST277 in Kpn007 and Kpn016, respectively, and ABR genes (qnrS1, blaCTX-M-15, and blaSHV-27), virulence factors (ybt, iuc1, iro1), and contained both K (K20, K46) and O antigens (O1, O3b). MDR KPN in the geriatric population poses a serious health concern due to their increased vulnerability to infections and limited treatment options, requiring careful management.IMPORTANCEMultidrug resistance (MDR) and the hypervirulence nature of Klebsiella pneumoniae (KPN) in geriatric patients pose a critical health concern in nosocomial infections worldwide and result in high clinical complexity and mortality. The study investigated the factors for KPN infections and analyzed antimicrobial resistance profiles. More than 60% of Klebsiella pneumoniae isolates from geriatric patients were resistant to third- and fourth-generation cephalosporins, and most isolates carried blaNDM-1 and blaSHV-11 genes. Analyzing whole genomes of two KPNs, Kpn007 (ST277) was identified as a hypervirulent strain with aerobactin and yersinia siderophores, contributing to virulence, and Kpn016 (ST420) carried fluoroquinolone (qnrS1), ESBL (blaCTX-M-15 and blaSHV-27) resistance. Both genomes contained K antigens (K20 and K46) and O antigens (O1 and O3b).

Humans↗
PubMed2024

Antibiotic resistance genotype, phenotype, and clinical outcomes in patients with Gram-negative infections at Rabin Medical Center in Israel.

UNLABELLED: Antibiotic resistance is a major cause of morbidity and mortality. However, a better understanding of the relationship between bacterial genetic markers, phenotypic resistance, and clinical outcomes is needed. We performed whole-genome sequencing on five medically important pathogens (Acinetobacter baumannii, Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) to investigate how resistance genes impact patient outcomes. A total of 168 isolates from 162 patients with Gram-negative infections admitted to Beilinson Hospital at Rabin Medical Center in Israel were included for final analysis. Genomes were analyzed for resistance determinants and correlated with microbiologic and clinical data. Thirty-day mortality from time of culture was 26.5% (43/162). Twenty-nine patients had carbapenem-resistant isolates (29/168, 17.2%), while 63 patients had multidrug-resistant isolates (63/168, 37.5%). Albumin levels were inversely associated with mortality and length of stay, while arrival from a healthcare facility and cancer chemotherapy predicted having a multidrug-resistant isolate. Sequencing revealed possible patient-to-patient transmission events. blaCTX-M-15 was associated with multidrug-resistance in E. coli (OR = 3.888, P = 0.023) on multivariate analysis. Increased blaOXA-72 copy number was associated with carbapenem-resistance in A. baumannii (P = 0.003) and meropenem minimum inhibitory concentration (P = 0.005), yet carbapenem-resistant isolates retained sensitivity to cefiderocol and sulbactam-durlobactam. RJX84154 was associated with multidrug-resistance across all pathogens (P = 0.0018) and in E. coli (P = 0.0024). Low albumin levels were associated with mortality and length of stay in this sample population. blaCTX-M-15 was correlated with multidrug-resistance in E. coli, and blaOXA-72 depth predicted meropenem minimum inhibitory concentration in A. baumannii. RJX84154 may play a role in multidrug-resistance. IMPORTANCE: While there have been several studies that attempt to find clinical predictors of outcomes in patients hospitalized with bacterial infections, less has been done to combine clinical data with genomic mechanisms of antibiotic resistance. This study focused on a hospitalized patient population in Israel with infections due to medically important bacterial pathogens as a way to build a framework that would unite clinical data with both bacterial antibiotic susceptibility and genomic data. Merging both clinical and genomic data allowed us to find both bacterial and clinical factors that impact certain clinical outcomes. As genome sequencing of bacteria becomes both rapid and commonplace, near real-time monitoring of resistance determinants could help to optimize clinical care and potentially improve outcomes in these patients.

Humans↗
PubMed2026

Genomic analysis of community-associated multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae and the identification of the ST2059-KL1 clone in the U.S.

UNLABELLED: Klebsiella quasipneumoniae subsp. similipneumoniae is an important member of the K. pneumoniae species complex (KpSC) and is increasingly reported as multidrug-resistant (MDR) in healthcare- and community-associated infections. Since clinical laboratories do not routinely distinguish K. quasipneumoniae subsp. similipneumoniae from K. pneumoniae, national prevalence estimates, particularly for MDR, are lacking. In this study, a total of 2,006 community-associated MDR KpSC isolates were collected from 42 U.S. states, with 30 K. quasipneumoniae subsp. similipneumoniae isolates originating from 12 states identified using whole genome sequencing. All isolates were resistant to ceftriaxone and exhibited high rates of resistance to other antimicrobial agents, including ampicillin-sulbactam (56.7%, 17/30), levofloxacin (75.9%, 22/29), and trimethoprim-sulfamethoxazole (53.3%, 16/30). Notably, five isolates were also carbapenem-resistant. Genomic analysis resolved 10 sequence types (STs), with ST2059 (n = 13) and ST414 (n = 9) predominating. Ceftriaxone resistance in most isolates (90%, 27/30) was conferred by an extended-spectrum β-lactamase gene, predominantly blaCTX-M-15 (73.3%, 22/30); the remaining isolates carried either a carbapenemase (blaKPC-3) or an AmpC β-lactamase (blaCMY-2). Nanopore sequencing identified blaCTX-M-15 harbored on two types of IncFIB(Kpn3) antimicrobial resistance (AMR) plasmids, either with or without the conjugative tra gene cluster. Interestingly, the KL1 locus, associated with canonical hypervirulent K. pneumoniae strains, was detected in all ST2059 isolates. Further analysis of public genomic data showed that the KL1 locus is widely distributed across KpSC. KL1 phylogenetic analyses indicated frequent intrasubspecies recombination but limited intersubspecies exchange of KL1. The identification of the dominant MDR K. quasipneumoniae subsp. similipneumoniae KL1-ST2059 clone in the U.S. underscores the importance of ongoing genomic surveillance. IMPORTANCE: Klebsiella quasipneumoniae subsp. similipneumoniae is an underrecognized member of the Klebsiella pneumoniae species complex that is frequently misidentified in clinical laboratories, leading to an incomplete understanding of its role in antimicrobial resistance. In this study, we used large-scale genomic surveillance of community-associated multidrug-resistant isolates across the U.S. to identify this subspecies as a reservoir of clinically relevant resistance plasmids. Notably, we detected a widely distributed ST2059 lineage carrying the K1 capsular locus, a feature traditionally associated with hypervirulent K. pneumoniae. These findings highlight the convergence of resistance and virulence-associated traits in an overlooked species and underscore the need for genomic surveillance to monitor emerging high-risk lineages in community settings.

Drug Resistance, Multiple, Bacterial↗
PubMed2025

Molecular characterization of drug-resistance genes and dynamics of multidrug-resistant Salmonella spp. in waterfowl: a pre- and post-antibiotic ban surveillance in Guangdong, China from 2013 to 2023.

BACKGROUND: Multidrug-Resistant Organism (MDRO) refers to bacteria that are Resistant to three or more types of antibiotics in clinical use. The global health threat posed by multidrug-resistant (MDR) bacterial pathogens and their cross-species transmission necessitates rigorous Surveillance. This urgency is amplified in China where antibiotic growth promoters were widely used in animal husbandry until the 2020 implementation of Announcement No. 194 launched by Ministry of Agriculture and Rural Affairs (Announcement 194), banning non-therapeutic antibiotics in feed. This study conducted a decade long investigation on the correlation between antimicrobial resistance (AMR) phenotypes and genetic determinants in 314 Salmonella isolates collected from waterfowl across Guangdong Province, China, utilizing disk diffusion (Kirby-Bauer method) and PCR-based detection of antibiotic resistance genes (ARGs). The study period covered the antibiotic policy transition in China, specifically encompassing the pre-ban (2013-2019) and post-ban (2020-2023) phases of the nationwide prohibition on growth-promoting antimicrobials in animal feed. METHODS: Antimicrobial Susceptibility profiles against 16 agents were determined via Kirby-Bauer testing, while PCR amplification targeted 20 ARGs. Statistical analyses evaluated phenotype-genotype correlations using Pearson`s chi-square test. RESULTS: Surveillance revealed escalating resistance rates annually. Highest resistance prevalence was observed against &#x3b2;-lactams and amphenicols (92.25%), whereas amikacin exhibited the lowest resistance rate (9.55%). MDR prevalence reached 87.23%, with the AMP-CAZ-GEN-FFC-TET resistance profile predominating (51.6% of isolates). Genetic analysis identified 3 to 16 ARGs per isolate was harboring, with blaTEM demonstrating the highest detection frequency (90.76%). Significant phenotype-genotype correlations (p&#x2009;<&#x2009;0.05) were observed for 13 genes: blaCTX-M, blaTEM, blaOXA, aacC2, aph(3')-I, aac(3)-IV, aadA1, qnrS, qnrA, clmA, floR, sulII, tetA. Notably, significant declines in resistance to aminoglycosides (e.g., gentamicin from 71.7 to 3.5%) and florfenicol (from 81.1 to 9.6%) were observed after China's 2019 antibiotic ban policy (p&#x2009;<&#x2009;0.001), underscoring the impact of targeted antimicrobial stewardship in avian husbandry. CONCLUSIONS: Analysis of 314 waterfowl Salmonella strains revealed severe multidrug resistance (MDR) and diverse resistance genes (DRGs), with 13 DRGs linked to resistance. China's antibiotic ban reduced targeted resistance, but MDR persists alarmingly via acquired DRGs and adaptation. Continued enforcement may lower aminoglycoside/phenicol resistance, but &#x3b2;-lactam resistance will likely endure, worsened by transcontinental blaCTX-M spread. Critically, plasmid co-selection threatens to amplify MDR, demanding genomic surveillance. Mitigation requires boosting policy compliance, developing non-antibiotic therapies, mapping mutations, establishing cross-species barriers, and prioritizing One Health interventions to block resistance spread.

China↗