In silico characterization of Edwardsiella tarda strain ET-1 isolated from aquarium water reveals zoonotic and pathogenic potential

Antimicrobial resistance, biofilm formation, and molecular detection of efflux pump and biofilm genes among Klebsiella pneumoniae clinical isolates from Northern Jordan

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, whole-genome sequencing (WGS) was used to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement among susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50–60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring blaCMY- and blaCTX–M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.

Shiga toxin-producing Escherichia coli (STEC) O157:H7 are zoonotic pathogens and transmission to humans occurs via contaminated food or contact with infected animals. The aim of this study was to describe the frequency, and distribution across the phylogeny, of antimicrobial resistance (AMR) determinants in STEC O157:H7 isolated from human cases in England. Short-read whole-genome sequencing data from 1473 isolates of STEC O157:H7 from all seven sub-lineages (Ia-Ic, IIa-IIc and I/II) were mapped to genes known to confer phenotypic resistance to 10 different classes of antibiotic. Long-read sequencing was used to determine the location and genomic architecture of the AMR determinants within phylogenetic clusters exhibiting multidrug resistance. Overall, 216/1473 (14.7%) isolates had at least one AMR determinant, although the proportion of isolates exhibiting AMR varied by sub-lineage. The highest proportion of AMR determinants were detected in sub-lineages Ib (28/64, 43.7%), I/II (18/51, 35.3%) and IIc (122/440, 27.7%). In all sub-lineages, the most commonly detected AMR determinants conferred resistance to the aminoglycosides, tetracyclines and sulphonamides, while AMR determinants conferring resistance to fluroquinolones, macrolides and third-generation cephalosporins were rarely detected. Long-read sequencing analysis showed that the AMR determinants were co-located on the chromosome in sub-lineages Ib and lineage I/II, whereas those associated with sub-lineage IIc were encoded on the chromosome and/or large plasmids. AMR genes were unevenly distributed across the different sub-lineages of STEC O157:H7 and between different clades within the same sub-lineage. Long-read sequencing facilitates tracking the transmission of AMR at the pathogen and mobile genetic element level.

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

"Challenges with antimicrobial susceptibility testing for Neisseria gonorrhoeae in the era of extensively drug-resistant gonorrhoea — molecular antimicrobial resistance testing crucial." Pathogens and Global Health, 108(5), pp. 214–215

The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farm environment after manure application on land. Manure and soil samples were collected on day 0 before and after manure application on six farms in North Carolina, and sequential soil samples were recollected on days 7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella, and their plasmid contents were further characterized. A total of 14 isolates including Salmonella enterica serotypes Johannesburg (n = 2), Ohio (n = 2), Rissen (n = 1), Typhimurium var5- (n = 5), Worthington (n = 3), and 4,12:i:- (n = 1), representing different farms, were selected for plasmid analysis. Antimicrobial susceptibility testing was done by broth microdilution against a panel of 14 antimicrobials on the 14 confirmed transconjugants after conjugation assays. The plasmids were isolated by modified alkaline lysis, and PCRs were performed on purified plasmid DNA to identify the AMR determinants and the plasmid replicon types. The plasmids were sequenced for further analysis and to compare profiles and create phylogenetic trees. A class 1 integron with an ANT(2″)-Ia-aadA2 cassette was detected in the 50-kb IncN plasmids identified in S Worthington isolates. We identified 100-kb and 90-kb IncI1 plasmids in S Johannesburg and S Rissen isolates carrying the blaCMY-2 and tet(A) genes, respectively. An identical 95-kb IncF plasmid was widely disseminated among the different serotypes and across different farms. Our study provides evidence on the importance of horizontal dissemination of resistance determinants through plasmids of multiple Salmonella serotypes distributed across commercial swine farms after manure application.IMPORTANCE The horizontal gene transfer of antimicrobial resistance (AMR) determinants located on plasmids is considered to be the main reason for the rapid proliferation and spread of drug resistance. The deposition of manure generated in swine production systems into the environment is identified as a potential source of AMR dissemination. In this study, AMR gene-carrying plasmids were detected in multiple Salmonella serotypes across different commercial swine farms in North Carolina. The plasmid profiles were characterized based on Salmonella serotype donors and incompatibility (Inc) groups. We found that different Inc plasmids showed evidence of AMR gene transfer in multiple Salmonella serotypes. We detected an identical 95-kb plasmid that was widely distributed across swine farms in North Carolina. These conjugable resistance plasmids were able to persist on land after swine manure application. Our study provides strong evidence of AMR determinant dissemination present in plasmids of multiple Salmonella serotypes in the environment after manure application.

Antimicrobial resistance (AMR) is a serious concern globally in human and animal health sectors and the menace is percolating to the aquaculture too. Since the aquaculture sector is at the receiving end of the terrestrial run-off, the AMR detection strategy would vary. Hence, AMR determination in the aquaculture sector strategy needs triangular approaches viz. pathogens of aquatic animals, commensal bacteria of the aquaculture ponds and food safety pathogens in harvested food fish. Farmed aquatic animals are being transported as food material to distant places of intra, inter-countries and continents. In this context, robust surveillance of AMR in microflora associated with farmed aquatic animals remains an essential tool for identification and control of its spread. Despite numerous reviews that have been published for determining resistance in pathogens of clinical importance, literature is scant on aquaculture and seafood safety. The present review is oriented to illustrate the different approaches possible for the identification of AMR especially in the aquatic animal pathogen, commensal bacteria and seafood pathogens along with the molecular approach. The need of the hour is rapid identification of resistance in the surveillance platforms, thereby limiting the spread of the resistance and improving food security.

BackgroundSurveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.MethodsFor this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.ResultsForty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n = 23 in 2020–2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.ConclusionThis systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.Clinical trial numberNot applicable.

Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections. In the present study, we aimed to investigate the presence of virulence associated genes (VAGs) and antimicrobial resistance (AMR) among two groups of APEC and avian fecal E. coli (AFEC) strains from apparently healthy birds and identify any associations among VAGs, AMR, phylogenetic groups. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC), plus E. coli strains from the feces of healthy birds (AFEC) were compared by their content of VAGs, antimicrobial susceptibility patterns, and assignment to phylogenetic groups. In addition, isolates were fingerprinted using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). All strains were susceptible to fosfomycin, ceftriaxone, and cefixime, while resistance rate to other tested antimicrobials was more than 50% except for gentamicin and furazolidone. All strains (except two) harbored at least three or more VAGs. tonB, csg, and iutA were the genes most commonly identified occurring with a prevalence of 99, 96, and 83% respectively. All phylogenetic groups were found in isolates from YSI, colisepticemia and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings further revealed that AMRs and VAGs were common among E. coli isolated from poultry in Iran; however, the association between VAG and AMR was not direct in most instances that may reflect different evolutionary pathways conferring resistance and virulence. Exceptionally, strains related to phylogenetic group C had higher virulence and AMR compared to other groups that indicates the importance of this phylogroup. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, and other traits; therefore, it may prove useful in primary classification of APEC strains.

<p>Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.</p>

Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections. In the present study, we aimed to investigate the presence of virulence associated genes (VAGs) and antimicrobial resistance (AMR) among two groups of APEC and avian fecal E. coli (AFEC) strains from apparently healthy birds and identify any associations among VAGs, AMR, phylogenetic groups. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC), plus E. coli strains from the feces of healthy birds (AFEC) were compared by their content of VAGs, antimicrobial susceptibility patterns, and assignment to phylogenetic groups. In addition, isolates were fingerprinted using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). All strains were susceptible to fosfomycin, ceftriaxone, and cefixime, while resistance rate to other tested antimicrobials was more than 50% except for gentamicin and furazolidone. All strains (except two) harbored at least three or more VAGs. tonB, csg, and iutA were the genes most commonly identified occurring with a prevalence of 99, 96, and 83% respectively. All phylogenetic groups were found in isolates from YSI, colisepticemia and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings further revealed that AMRs and VAGs were common among E. coli isolated from poultry in Iran; however, the association between VAG and AMR was not direct in most instances that may reflect different evolutionary pathways conferring resistance and virulence. Exceptionally, strains related to phylogenetic group C had higher virulence and AMR compared to other groups that indicates the importance of this phylogroup. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, and other traits; therefore, it may prove useful in primary classification of APEC strains.

<p>Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.</p>

Patients with cardiac disease are highly susceptible to hospital-acquired urinary tract infections (HA-UTI) due to immunosuppression, invasive procedures, and prolonged hospitalization. Although Enterobacteriaceae are frequent pathogens, the contribution of vancomycin-resistant Staphylococcus aureus (VRSA) remains unexplored. Among 11 known glycopeptide resistance genes (vanA, vanB, vanD, vanF, vanI, vanM, vanC, vanE, vanG, vanL, and vanN), vanA and vanB are most commonly reported. However, the diversity of other van genes and their interplay with antimicrobial resistance (AMR) and virulence determinants are poorly characterized. Between March 2020 and April 2022, 189 cardiac ward patients were screened for VRSA-associated HA-UTI. The presence of van genes, efflux pump genes (norA, norB, sepA, mepA, mdeA), and virulence genes (hla, sea, icaA, fnbA) was determined using singleplex PCR, correlation analysis, and qRT-PCR for expression profiling. Antimicrobial susceptibility was assessed via disk diffusion, minimum inhibitory concentration (MIC), hierarchical clustering, and multiple antibiotic resistance indexing. 55% of VRSA isolates harboured limited van gene diversity, with vanA predominant. These isolates exhibited extensive AMR, high vancomycin MICs (> 256µg/mL), and multidrug resistance. Co-occurrence of efflux pump genes (norA + norB, norB + norC, sepA + norB) and virulence genes (hla + sea, icaA + fnbA) showed significant positive correlations. All isolates were susceptible to linezolid and chloramphenicol. vanA-mediated resistance in VRSA from HA-UTI is strongly associated with efflux pump activity and virulence gene expression. Integrative genomic and transcriptomic approaches are essential for deciphering these networks, guiding precision therapeutics, and strengthening infection control measures.

Occurrence and fate of antibiotics, antimicrobial resistance determinants and potential human pathogens in a wastewater treatment plant and their effects on receiving waters in Nanjing, China

Genomic and phylogenetic analysis of a multidrug-resistant Burkholderia contaminans strain isolated from a patient with ocular infection