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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↗

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

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

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↗

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

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

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↗

PubMed2026

Regional genomic analysis of lineage distribution and transferable multidrug resistance among chicken-associated Salmonella Kentucky isolates in China.

Salmonella enterica serovar Kentucky is an important multidrug-resistant foodborne pathogen in the poultry meat supply chain. Although recent broader genomic studies have elucidated the population structure and epidemiological significance of major lineages in China (e.g., ST198 and ST314), the regional dynamics within local poultry supply chains remain insufficiently characterized. In this study, 31 chicken meat-derived isolates from Shanghai and 39 publicly available genomes from China were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, phylogenetic analysis, conjugation experiments, and complete sequencing of representative plasmids. This enabled a systematic characterization of the molecular epidemiological features of the population and the mechanisms underlying resistance dissemination. Population genomic analysis revealed a lineage composition markedly different from the global epidemiological pattern: ST314 was the predominant sequence type among the Shanghai chicken-derived isolates (74.2%), whereas the internationally recognized high-risk clone ST198 accounted for only 25.8% of the local isolates. However, risk stratification analysis indicated that although ST198 was detected less frequently, it carried a significantly greater burden of acquired resistance genes and therefore represented a higher-risk resistant lineage. Functional and structural validation further elucidated the molecular basis of resistance dissemination within this high-risk lineage. Conjugation experiments confirmed the co-transfer of a multidrug resistance module carrying blaTEM-1 and blaCTX-M-267 to the recipient strain Escherichia coli J53. Complete plasmid analysis revealed that these two β-lactam resistance genes were co-localized on a 242-kb transferable plasmid flanked by Tn1331, Tn3, and multiple transposase-associated elements, thereby providing a structural basis for their horizontal transfer. This study provides important molecular epidemiological evidence for lineage-specific surveillance and risk-stratified control of resistant Salmonella in the poultry meat supply chain and further underscores the need for continuous monitoring of mobile genetic elements within a One Health framework.

Animals↗

PubMed2025

Influence of antimicrobial consumption (AMC) on the detection of antimicrobial resistance genes (ARGs) in urban wastewater.

BACKGROUND: Antimicrobial resistance (AMR) is a global health threat, causing over 1.27 million deaths annually and linked to an additional 4.95 million. AMR transmission occurs beyond clinical settings, with wastewater serving as a sentinel of community-level spread. This study investigated how temporal changes in antimicrobial consumption (AMC) correlate with the prevalence of antimicrobial resistance genes (ARGs) in wastewater, using wastewater surveillance (WS) to monitor resistance trends in Quebec, Canada. METHODOLOGY: AMC data (January 2019-May 2023) were obtained from the Institut National de Santé Publique du Québec (INSPQ) under a license from IQVIA Solutions Canada Inc. Wastewater samples (September 2020-September 2022) were obtained from three WWTPs and screened for 11 ARGs, including blaTEM, blaSHV, blaCTX-M, blaNDM, blaOXA-1/30, qnrA, qnrB, mphE, and mefA. Analyses assessed temporal and spatial associations between AMC and ARGs. RESULTS: Total prescriptions declined from 537 to 392 per 1000 inhabitants between 2019 and 2020 (-27 %), likely due to the impact of the COVID-19 pandemic. This shift created a contrast that allowed us to better capture the signal of AMC through the noise in wastewater composition. β-lactams, macrolides, and fluoroquinolones were the most prescribed classes. ARGs were consistently detected in all 41 samples, with macrolide resistance genes being the most abundant. Strong correlations were observed between AMC and ARG prevalence in wastewater, particularly for β-lactams and fluoroquinolones (Spearman R = 0.80 and 0.81, p < 0.05). Spatial patterns showed uniform AMC but variable ARG levels. CONCLUSIONS: Our study highlights the correlation between AMC and ARG. WS shows promise for real-time AMR monitoring.

Wastewater↗

PubMed2026

From regionalization to homogenization: Nationwide metagenomic assessment of priority pathogens and the resistome in Polish hospital wastewater.

Hospital wastewater (HWW) is a critical hotspot for the dissemination of antibiotic resistance genes (ARGs) and pathogens. This study provides the first comprehensive metagenomic characterization of HWW across Poland, analyzing 64 medical facilities across two seasons via Nanopore long-read sequencing (total of 128 HWW samples). The HWW microbiome was mostly dominated by Proteobacteria, Bacteroidota, and Firmicutes. Multivariate analysis confirmed a significant seasonal shift in the resistome. Winter samples exhibited geographic regionalization, with localized hotspots of specific ARGs, including vancomycin resistance (operon van) and carbapenemase genes (blaOXA, blaNDM). Conversely, summer samples showed a significant trend toward nationwide homogenization, characterized by a uniform distribution of ESBL genes (blaTEM, blaCTX-M) and multidrug resistance (MDR) determinants, alongside the persistence of localized clinical hotspots. Klebsiella pneumoniae emerged as a central network hub, particularly in summer, showing strong correlations with ESBLs. Quantitative genomic co-occurrence analysis revealed a functional division within dominant taxa: while environmental species like Acinetobacter johnsonii comprised the general background microbiome, clinical pathogens such as Acinetobacter baumannii served as primary vectors, showing frequent associations with high-risk ARGs. Environmental and opportunistic bacteria, such as Aeromonas spp. and Citrobacter spp., were identified as putative 'bridge hosts' associated with mobile resistance determinants and potentially contributing to HGT. The findings indicate that seasonal factors, such as increased temperature and sub-inhibitory antibiotic concentrations, may contribute to the transition from regionalized to homogenized resistance profiles, demonstrating that background resistome convergence can coexist with point-source clinical outbreaks. This seasonal "blurring" of regional boundaries positions HWW as an active vector for large-scale antimicrobial resistance (AMR) dissemination. These results underscore the urgent need for nationwide metagenomic surveillance and advanced wastewater treatment strategies within the "One Health" framework to mitigate the environmental spread of WHO priority pathogens.

Acinetobacter baumannii↗

PubMed2026

Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.

Antimicrobial resistance in commensal Escherichia coli provides a useful indicator for overall antimicrobial resistance burden. We applied this approach to assess antimicrobial resistance within and between commercial pig herds across Australia. A high-throughput robotic workflow was used to isolate 2730 E. coli colonies from rectal contents collected in 2022 from healthy slaughter pigs (n = 300) representing 30 herds (∼70% of national production). Up to 94 isolates per herd underwent antimicrobial susceptibility testing using the Robotic Antimicrobial Susceptibility Platform. Isolate- and herd-level antimicrobial resistance indices were calculated, weighting antimicrobials by their human health importance. Resistance to first-line agents was widespread: ampicillin 77% and tetracycline 79%. By contrast, resistance to critically important antimicrobials was rare (ciprofloxacin 0.11%; extended-spectrum cephalosporins 0.04%), and no clinical resistance to carbapenems or colistin was detected. Overall, 56.9% of isolates were multi-class resistant. Herd-level antimicrobial resistance within indices ranged from 1.51 to 5.76, revealing substantial between-herd heterogeneity. Three herds carried critically important antimicrobials-resistant isolates that would likely have been missed using conventional, lower-density sampling approaches. Whole-genome sequencing identified fluoroquinolone-resistant isolates belonging to ST10 and ST69 (both qnrS1), and ST744 (Quinolone Resistance Determining Region mutations plus blaCTX-M-27). By testing approximately tenfold more isolates than conventional surveys, we uncovered considerable antimicrobial resistance with heterogeneity within and between animals and herds, including farm-specific variability. This expanded sampling also enabled detection of critically important antimicrobial resistance at very low prevalence. In conclusion, high-throughput, high-density testing offers a practical early-warning system and herd-level benchmark to inform surveillance and targeted interventions.

Animals↗

PubMed2026

Molecular characterization and antimicrobial resistance profiles of Shigella flexneri isolates from pediatric clinical cases in Ahvaz, Iran.

Shigella is a highly invasive pathogen that causes dysentery and is associated with significant morbidity and mortality in children under five years of age. This agent is a major public health problem in developing countries. Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a reliable, cost-effective typing method with high discriminatory power and reproducible results. The rise of drug resistance in Shigella strains is a growing global health threat. Despite the significance of Shigella in Iran, there is limited knowledge about genetic diversity and drug resistance profiles of local strains. Therefore, the purpose of this study was to characterize the genetic diversity and drug resistance profiles of Shigella strains isolated in Ahvaz, Iran. A total of 49 Shigella flexneri isolates were recovered from 500 stool samples of pediatric patients. Routine biochemical tests were used to identify all isolates. Antimicrobial susceptibility testing was performed, and resistance genes were detected by polymerase chain reaction (PCR). Extended-spectrum β-lactamases (ESBL), carbapenemase, and Metallo-β-lactamase (MBL) production were detected phenotypically using combination disk assays and confirmed by the CLSI-recommended modified Carbapenem inactivation method (mCIM) and EDTA-modified carbapenem inactivation method (eCIM). MLVA based on seven VNTR loci was performed to characterize the genetic diversity of the isolates. All 49 isolates were resistant to ceftazidime, trimethoprim/sulfamethoxazole, ampicillin, and ceftriaxone (100% each). High resistance rates were also observed for imipenem 36/49 (73.5%), meropenem 36/49 (73.5%), azithromycin 21/49 (42.9%), and ciprofloxacin 16/49 (32.7%). Furthermore, phenotypic testing revealed ESBL production in 46/49 (93.9%) isolates and carbapenemase activity in 36/49 (73.5%), of which 22/49 (44.9%) were MBL. PCR analysis identified blaCTX-M 38/49 (77.6%) and blaSHV 35/49 (71.4%) as the most prevalent ESBL genes, whereas blaNDM 14/49 (28.6%), and blaOXA-48 14/49 (28.6%) were the most common carbapenemase genes. MLVA typing divided the isolates into 22 different MLVA types, including 10 clusters and 12 singletons, and locus ms21 showed the highest discriminatory power. The isolates exhibited high genetic diversity with a non-clonal distribution of resistance, which indicates dissemination through horizontal gene transfer. Our results demonstrated that mCIM/eCIM and MLVA are viable methods for investigating Shigella species as they are cost-effective, provide quick results, and allow for easy sharing of numerical data between laboratories.

Humans↗

PubMed2025

Molecular insights into carbapenemase-producing Enterobacterales from Senegal.

BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are an urgent global health threat, especially in resource-limited countries. Here we determined the prevalence and the molecular characteristics of CPE isolated from infections in Dakar, Senegal. METHOD: From January 2019 to December 2020, Enterobacterales with reduced susceptibility to ertapenem (diameter < 25 mm) from infections were collected at the Pasteur Institute of Dakar. Carbapenemases were detected using biochemical and immunochromatographical assays. WGS was used to determine resistome, MLST, plasmids, virulence genes and genetic relatedness. RESULTS: Of the 1045 Enterobacterales collected during the study period, 86 had a diameter around ertapenem of <25 mm (8%) and 19 were confirmed as CPE (2%). These included Escherichia coli (n = 6) [ST410 (n = 3), ST405 (n = 2) and ST2083], Enterobacter spp. (n = 6) [ST231 (n = 3), ST245, ST760 and ST960] and Klebsiella spp. (n = 5) (ST22, ST25, ST231, ST1535, ST4843), Citrobacter freundii ST22 (n = 1) and Citrobacter koseri with unknown ST (n = 1). blaOXA-48 (n = 7; 35%), blaOXA-181 (n = 7; 35%) and blaNDM-5 (n = 6; 30%) genes were identified. C. freundii ST22 harboured blaNDM-5, blaOXA-48 and blaCTX-M-15 genes. Some E. coli isolates belonging to the high-risk clone ST410 were closely related (<20 SNPs) to isolates recovered in France from patients returning from Senegal, suggesting transnational spread. In addition, 5/6 carbapenemase-producing E. coli isolates possessed a four amino acid insertion in PBP3, conferring reduced susceptibility to aztreonam/avibactam and cefiderocol. CONCLUSIONS: This study highlights the spread of NDM-5 and OXA-181 in Senegal, and reports the first co-occurrence of NDM-5 and OXA-48 in sub-Saharan Africa. The spread of CPE, especially in high-risk clones, underscores the urgent need for continued surveillance and targeted interventions.

Senegal↗

PubMed2026

Global Diffusion of IncC Plasmid Harboring blaNDM-1in the High-Risk Escherichia coli ST131 Clone.

AIMS: The global expansion of quinolone-resistant Escherichia coli (QR-EC) is increasingly associated with β-lactam resistance and mobile genetic elements that facilitate resistance dissemination. This study investigated the molecular mechanisms underlying fluoroquinolone and β-lactam resistance in clinical QR-EC isolates and explored the plasmid type associated. METHODS AND RESULTS: A total of 123 non-duplicate QR-EC clinical isolates responsible mainly for gastrointestinal colonization were collected between 2019 and 2021. Plasmid-mediated quinolone resistance (PMQR), extended-spectrum β-lactamase (ESBL), and carbapenemase genes were screened by PCR. Mutations in the quinolone resistance-determining regions (QRDR) of gyrA and parC were analyzed using sequencing and mismatch amplification mutation assay PCR (MAMA-PCR). Selected isolates underwent multilocus sequence typing (MLST). Whole-genome sequencing (WGS) of a representative extensively drug-resistant strain carrying multiple quinolone resistance determinants, ESBL genes, and carbapenemase genes, was performed. PMQR genes were prevalent among QR-EC, dominated by aac(6')-Ib-cr (60.9% of isolates). ESBL genes were identified in 93.5% of isolates, predominantly blaCTX-M (95.7%). Among ertapenem-resistant isolates (QCR-EC) (n=18), blaNDM-1 and blaOXA-48 were detected in 13 and 11 isolates, respectively. QRDR mutations were highly frequent, particularly gyrA83 (98.4%) and parC80 (30.9%). Major QCR-EC genotypes belonged to sequence types ST167 (n=2), ST1196, ST469, and ST410. High-risk E. coli ST131 clone harboring IncC plasmid encoding blaNDM-1 was described for the first time in Africa, following its emergence, in two continents, Asia and America. Despite the very rare description of these strains worldwide, their description in three continents sign their global diffusion. CONCLUSIONS: This finding highlights the ongoing spread of carbapenem resistance and underscores the urgent need for strengthened genomic surveillance.

Escherichia coli↗

PubMed2025

A systematic review and meta-analysis on antibiotic resistance genes in Ghana.

BACKGROUND: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources. METHODS: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis. RESULTS: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was blaCTX-M, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by blaTEM (19.5% [95% CI: 9.7-29.3]), and blaSHV (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for blaNDM to 10.3% (95% CI: 1.9-18.7) for blaOXA. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources. CONCLUSION: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.

Ghana↗

PubMed2026

Phylogrouping and genotyping of mcr-1 postives avian pathogenic Escherichia coli isolates in Algerian poultry farms.

Colibacillosis is a highly prevalent bacterial disease in poultry, resulting in the widespread use of antibiotics for both curative and preventive purposes. Consequently, avian pathogenic Escherichia coli (APEC) continues to act as a reservoir for antibiotic resistance genes, including the mcr-1 gene, which codes for resistance to colistin, a crucial antibiotic in human medicine. The aim of this study was to evaluate the antibiotic resistance pattern of APEC and to investigate the genotyping, phylogrouping, and virulence of mcr-1-positive isolates. A total of 113 APEC were isolated, of which 92% were multidrug resistant (MDR). The mcr-1 gene was detected in 41 isolates originating from turkeys and broilers. Two isolates carried blaTEM, one of which also harboured blaCTX-M encoding beta-lactamases. The Clermont phylogrouping revealed that 76% of the isolates belonged to phylogroup B1. Concerning the detection of the virulence-associated genes, 88% of isolates carried at least 3 genes. The ERIC-PCR classified our isolates into 6 different clusters. Our study highlights the emergence of colistin resistance and MDR, which pose a real threat to poultry production and public health. Control of antibiotic use in the poultry sector is urgent and mandatory.

Animals↗

PubMed2024

Extended-spectrum beta-lactamase-producing Enterobacterales in human health: Experience from the tricycle project, Ghana.

BACKGROUND: Vulnerable groups, such as pregnant women, are at increased risk of potentially life-threatening infections with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) for both mother and newborn. However, data regarding ESBL-E carriage and associated risk factors in Ghanaian pregnant women remain scarce. OBJECTIVE: This study aimed to determine the prevalence of ESBL-E carriage and its associated risk factors among pregnant women attending the antenatal clinic at the Korle Bu Teaching Hospital. METHODS: A systematic sample of 700 pregnant women with gestational age ≥ 34 weeks attending the antenatal clinic at Korle Bu Teaching Hospital was included in the study. After administering a structured questionnaire to assess potential risk factors associated with ESBL-E carriage, patients were given a sterile stool container to submit at least 1 g of stool specimen. Recovered isolates from faecal specimens were identified using MALDI-TOF-MS technology. These isolates were then subjected to susceptibility testing and ESBL identification. A random subset of 24 ESBL-producing Escherichia coli isolates was whole-genome sequenced on the MiSeq Illumina platform. Risk factors associated with ESBL-E carriage were determined using multivariable logistic regression analysis. RESULTS: Among the 700 pregnant women, 42% (294) carried ESBL-E. The predominant ESBL-producing Enterobacterales were Escherichia coli (95%). Fifty percent (50%) of ESBL-E were multidrug resistant isolates (MDRs). Whole-genome sequencing of 24 ESBL-producing E. coli isolates revealed that blaCTX-M-15 (96%) was the most prevalent ESBL gene type. Notably, most isolates belonged to commensal phylogenetic groups (A, B1, and C; 88%). Having a primary level of education (aOR 1.45, 95% CI 1.05-1.96) and consuming legumes as the main source of protein (aOR 0.17, 0.40-0.83) were significantly associated with intestinal carriage of ESBL-E. CONCLUSION: This study identified a high prevalence of ESBL-E and MDR-ESBL-E carriage among pregnant women. Our findings underscore the urgent need for public health interventions to control the spread of AMR.

Humans↗