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306500.9748Species diversity, virulence, and antimicrobial resistance of the nasal staphylococcal and mammaliicoccal biota of reindeer. BACKGROUND: Staphylococcus (S.) spp. and Mammaliicoccus (M.) spp., in addition to their established role as components of the human and animal microbiota, can also cause opportunistic infections. This study aimed to characterize bacteria recovered from nasal cavities of healthy adult reindeer from two farms located in Poland (15 reindeer) and Germany (15 reindeer). The research include bacteria isolation, species identification, detection of selected superantigen (SAg) genes, assessment of biofilm-forming capability in vitro, and evaluation of antimicrobial resistance. RESULTS: Seventy-four staphylococci and mammaliicocci from 14 different species were isolated from 30 nasal swabs, with one to four strains obtained from each reindeer. The most frequently identified species was S. equorum, followed by S. succinus, M. sciuri, S. xylosus, M. lentus, S. chromogenes, S. devriesei, M. vitulinus, S. auricularis, S. agnetis, S. edaphicus, S. petrasii, S. simulans, and S. warneri. A greater species diversity was observed among the reindeer from Poland compared to those from Germany. All isolated bacteria were coagulase negative and clumping factor negative and did not carry any of the 21 analyzed SAg genes. M. sciuri demonstrated the highest antimicrobial resistance (100%), followed by S. succinus (91%) and S. equorum (78%). Resistance to rifampicin was the most common (30% strains). Sixteen strains (22%) exhibited biofilm production at least 10% greater than the strong biofilm-forming S. aureus ATCC 6538. CONCLUSIONS: This study reveals a significant knowledge gap regarding the nasal microbiota of reindeer. It contributes to our understanding of staphylococcal and mammaliicoccal biota of reindeer and underscores the necessity for monitoring of microbial populations to assess their health implications for both animals and humans, particularly concerning the zoonotic transmission of bacteria.202540452044
236410.9731Association of multilocus sequencing types and antimicrobial resistance profiles of methicillin-resistant Mammaliicoccus sciuri in animals in Southern Thailand. BACKGROUND AND AIM: Mammaliicoccus sciuri, formerly known as Staphylococcus sciuri, is an opportunistic pathogen in the environment, human and animal mucosa, and skin. Although this pathogen is becoming more resistant to drugs and harmful to animals and humans, basic knowledge of this pathogen remains limited. This study aimed to investigate a new multilocus sequencing type (MLST) related to the antibiotic resistance pattern of M. sciuri from animals in southern Thailand. MATERIALS AND METHODS: We used 11 methicillin-resistant M. sciuri (MRMS) isolates in this study which were obtained from six horses, four cows, and one chicken of the previous study. Antimicrobial resistance (AMR) was re-evaluated based on the minimum inhibitory concentration using the VITEK(®) 2 automated system. Three AMR genes were examined, namely mecA, mecC, and blaZ. Staphylococcal chromosomal cassette mec (SCCmec) gene detection was performed through the multiplex polymerase chain reaction (PCR). Internal segments of the seven housekeeping genes, ack, aroE, ftsZ, glpK, gmk, pta1, and tpiA, were used for multilocus sequence typing. The population of resistant bacteria and the types of multidrug-resistant, extensively drug-resistant, and pandemic drug-resistant bacteria were classified through descriptive analysis. RESULTS: mecA and blaZ genes were detected in all isolates; however, the mecC gene was not observed in any isolate based on the PCR results. All MRMS isolates revealed a non-typable SCCmec. Seven MLSTs (71, 81, 120, 121, 122, 199, and 200) were identified in this study. CONCLUSION: The characteristics of MRMS in Southern Thailand were variable, particularly in cattle and horses. The antibiogram and SCCmec types of this pathogen remain concerns with regard to antibiotic-resistant gene transmission among Staphylococcus and Mammaliicoccus species. All MLSTs in Thailand revealed the distribution among clones in Asia, including the virulence of a zoonotic clone in Southern Thailand.202337041994
519120.9731Draft genome sequences data of Mammaliicoccus lentus isolated from horse farm soil. Mammallicoccus lentus is a member of the commensal microflora of the Staphylococcaceae family, which colonizes the skin of several species of farm animals, including poultry and dairy animals (Huber et al., 2011; Zhang et al., 2009). The study of the members of the Staphylococcaceae family, such as the Mammaliicoccus genus, isolated from various sources is of great importance for agriculture and public health as contributes to the accumulation of knowledge and understanding of the mechanisms of antibiotic resistance gene transmission among bacterial pathogens. This thesis is supported by recent studies showing that some members of the Mammallicoccus genus serve as a reservoir of virulence and antibiotic resistance genes and may also be a source of horizontal gene transfer (Saraiva et al., 2021). Here, we present a draft genome sequence of Mammallicoccus lentus strain PVZ.22 from a horse farm soil sample. The sequencing was performed on the Illumina MiSeq platform. The genome was assembled using the Geneious software package. The genome contains 2,802,282 bp with a total of 2805 genes, 8 perfect and 12 strict AMR genes and 58 tRNAs genes.202338075610
523730.9727Phenotypic and genomic analysis of Enterococcus avium MC09 pathogenicity isolated from Scylla spp. (mud crab) in a Thai market. Enterococcus avium is a Gram-positive pathogenic bacterium classified under the Enterococcaceae family. E. avium has been isolated from diverse environmental sources, raising concerns about its potential role in the spread of antibiotic resistance. E. avium MC09, isolated from a mud crab in a Thai market, was analyzed for its antibiotic resistance and pathogenic potential in this study. The isolation of E. avium from mud crab is significant as it highlights the potential role of seafood as a reservoir for antibiotic-resistant bacteria, which may pose risks to public health throughout the food chain. Antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method revealed that E. avium MC09 is resistant to clindamycin, erythromycin, streptomycin, and tetracycline, and exhibits alpha hemolysis on blood agar, indicating its potential virulence. Genomic DNA was extracted and sequenced using the Oxford Nanopore Technologies (ONT) platform, revealing the presence of resistance genes for macrolides (ermB) and tetracyclines (tetL and tetM). Furthermore, several virulence-associated genes were detected, such as srtC, ecbA, efaA, dltA, cpsA/uppS, cpsB/cdsA, cylR2, icps4I, cpsY, epsE, vctC, mgtB, ndk, lisR, and lgt suggesting a pathogenic potential. Additionally, the study identified several insertion sequences (ISs), including (IS1216, IS1216E, IS1216V, IS6770, ISEfa7, ISEfa8, and ISS1W which are commonly found in pathogenic Enterococcus strains. The presence of these IS elements further emphasizes the strain's potential for virulence and genetic adaptability. This study provides comprehensive insights into both the phenotypic and genotypic characteristics of E. avium MC09, highlighting its antimicrobial resistance and pathogenic mechanisms, and underlines the importance of monitoring antibiotic resistance in seafood-associated bacteria.202540015576
306740.9727An Insight into the Presence of Antimicrobial Resistance Genes in Opportunistic Pathogenic Bacteria Isolated from Farm-Reared Crickets. To support the role of insects as sustainable feed and food ingredients, evaluating their potential microbiological risk and safety is crucial. In this study, we investigated the presence of antimicrobial resistance (AMR) genes in selected live opportunistic pathogenic bacteria isolated during the rearing process from clinically healthy farm-reared crickets. Molecular analysis was performed by wholegenome sequencing of a total of 14 of these bacterial strains, 7 from house crickets (Acheta domesticus) and 7 from banded crickets (Gryllodes sigillatus), belonging to Enterobacteriaceae, Staphylococcaceae, Enterococcaceae, and Bacillaceae families. The β-lactam AMR genes (bla(OXY2-6), bla(ACT-16), and bla(SHV) variants) were the most predominant genes identified, mainly in Enterobacteriaceae strains and in association with fosfomycin (fosA) and oqxAB efflux pump complexes. In addition, blaZ and mecA genes were detected in Bacillus cereus and Mammaliicoccus sciuri strains isolated from both insect species. Genetic mobile elements including IncFIA, IncFIB, IncHI1A, IncHI1B, rep13, and Col3M-like plasmids were detected in Klebsiella pneumoniae, Enterobacter hormaechei, Staphylococcus arlettae, and B. cereus, respectively. The results indicate that, not only in the final product but also during the insect-rearing process, microbial safety control, regarding the presence of pathogenic bacteria and AMR genes, is essential for effectively decreasing the microbiological risk between cricket batches within their environment and in terms of the related feed and food chain.202540005757
518550.9726Genomic characterisation of nasal isolates of coagulase-negative Staphylococci from healthy medical students reveals novel Staphylococcal cassette chromosome mec elements. Coagulase-negative staphylococci (CoNS) are a diverse group of Gram-positive bacteria that are part of the normal human microbiota. Once thought to be non-pathogenic, CoNS has emerged in recent years as opportunistic pathogens of concern particularly in healthcare settings. In this study, the genomes of four methicillin-resistant CoNS isolates obtained from the nasal swabs of healthy university medical students in Malaysia were sequenced using the Illumina short-read platform. Genome sequencing enabled the identification of the four isolates as Staphylococcus warneri UTAR-CoNS1, Staphylococcus cohnii subsp. cohnii UTAR-CoNS6, Staphylococcus capitis subsp. urealyticus UTAR-CoNS20, and Staphylococcus haemolyticus UTAR-CoNS26. The genome of S. cohnnii UTAR-CoNS6 harboured the mecA methicillin-resistance gene on a Staphylococcal cassette chromosome mec (SCCmec) element similar to SCCmec type XIV (5 A) but the SCCmec cassettes identified in the other three CoNS genomes were novel and untypeable. Some of these SCCmec elements also encoded heavy metal resistance genes while the SCCmec type XIV (5 A) variant in S. cohnii UTAR-CoNS6 harboured the complete ica operon, a known virulence factor that functions in biofilm formation. In S. cohnii UTAR-CoNS6, the macrolide resistance genes msrA and mphC along with copper and cadmium resistance genes were located on a 26,630 bp plasmid, pUCNS6. This study showcased the diversity of CoNS in the nasal microbiota of medical students but the discovery of novel SCCmec elements, various antimicrobial and heavy metal resistance along with virulence genes in these isolates is of concern and warrants vigilance due to the likelihood of spread, especially to hospitalised patients.202540595841
272060.9726Phenotypic and genotypic characterization of antimicrobial resistance in Enterococcus spp. Isolated from the skin microbiota of channel catfish (Ictalurus punctatus) in Southeastern United States. BACKGROUND: Aquaculture systems may contribute to the emergence and persistence of antimicrobial-resistant (AMR) bacteria, posing risks to animal, environmental, and human health. This study characterized the phenotypic and genotypic antimicrobial resistance profiles of Enterococcus spp. isolated from the skin microbiota of 125 channel catfish (Ictalurus punctatus) harvested from two earthen ponds in Alabama, USA. METHODS: Skin swabs from the body of channel catfish were enriched in Enterococcosel broth and cultured on Enterococcosel agar at 28 °C for 24 h. Isolates were confirmed using Biolog Gen III and VITEK(®)2, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Thirty-five randomly sampled isolates underwent whole-genome sequencing for genotypic characterization. RESULTS: 36% of isolates exhibited multidrug resistance (resistance to ≥ 3 antimicrobial classes), with the highest resistance rates observed for ampicillin (44.8%), rifampicin (42.4%), and tetracycline (38.4%). The most prevalent resistance genes were aac(6')-Iid (65.7%), aac(6')-Ii (22.9%), efmA, and msr(C) (20.0% each). Plasmid replicons rep1 and repUS15 frequently co-occurred with resistance genes. Biofilm-associated genes, including efaA, fsrA, fsrB, sprE, ebpABC, ace, and scm, were commonly detected. Multivariate analyses (PERMANOVA, PCA) revealed no significant species-level differences in resistance burden or biofilm gene carriage, indicating similar resistance and virulence gene carriage across species in this dataset. CONCLUSIONS: The skin microbiota of pond-raised catfish harbors antimicrobial-resistant Enterococcus spp. with mobile resistance elements and biofilm-associated virulence factors, suggesting a potential role in AMR persistence within aquaculture settings. These findings support the need for targeted AMR surveillance in fish-associated microbiota as part of integrated One Health strategies.202540760424
237470.9726Phenotypic and genetic antimicrobial resistance of the intestinal microbiota isolated from two alpacas (Vicugna pacos) post mortem. INTRODUCTION: In Poland, alpacas are commonly companion animals and producers of wool. Human-alpaca-environment interactions raise One Health concerns about antimicrobial resistance (AMR). No medications are licensed in Poland for camelids, and so all are prescribed under the cascade; they include β-lactams, cephalosporin, florfenicol, enrofloxacin, marbofloxacin, gentamicin, tetracycline and trimethoprim/sulfamethoxazole. Human and animal bacterial AMR is a matter of global concern. Consequently, the aim of the present study was to determine the prevalence of phenotypic and genotypic AMR among bacteria isolated from alpaca intestines. MATERIAL AND METHODS: Fifty-four strains were identified using matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry and biochemical methods. Antibacterial susceptibility was assessed by determining minimum inhibitory concentrations and by the Kirby-Bauer method. RESULTS: Citrobacter spp., Enterobacter spp. and Serratia spp. exhibited resistance to β-lactams, first-generation cephalosporins and tetracyclines, with Serratia spp. also resistant to colistin, polymyxin B and florfenicol. Enterococcus spp. were resistant to penicillin G, benzylpenicillin and erythromycin, but not to vancomycin, while Staphylococcus spp. showed resistance to amoxicillin and penicillins, but not to methicillin. Bacillus spp. and Corynebacterium spp. were resistant to some penicillins, tetracyclines and trimethoprim-sulfamethoxazole. Enterobacteriaceae isolates carried resistance genes (aadA, dfrA1, tetA, sul1, sul2, strA/strB and floR); therefore, the tested alpacas' microbiomes harboured AMR determinants. CONCLUSION: Alpacas should be monitored over an extended period to know the risk of transmission of AMR genes from components of their microbiome.202541064399
306880.9724Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes. Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.202540833454
545390.9723Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals. Antibiotic resistance in pathogens is often associated with mobile genetic elements, such as genomic islands (GI) including integrative and conjugative elements (ICEs). These can transfer resistance genes within and between bacteria from humans and/or animals. The aim of this study was to investigate whether Tn5801-like GIs carrying the tetracycline resistance gene, tet(M), are common in Staphylococcus pseudintermedius from pets, and to do an overall sequences-based characterization of Tn5801-like GIs detected in Gram-positive bacteria from humans and animals. A total of 27 tetracycline-resistant S. pseudintermedius isolates from Danish pets (1998-2005) were screened for tet(M) by PCR. Selected isolates (13) were screened for GI- or ICE-specific genes (int Tn5801 or xis Tn916 ) and their tet(M) gene was sequenced (Sanger-method). Long-range PCR mappings and whole-genome-sequencing (Illumina) were performed for selected S. pseudintermedius-isolates (seven and three isolates, respectively) as well as for human S. aureus isolates (seven and one isolates, respectively) and one porcine Enterococcus faecium isolate known to carry Tn5801-like GIs. All 27 S. pseudintermedius were positive for tet(M). Out of 13 selected isolates, seven contained Tn5801-like GIs and six contained Tn916-like ICEs. Two different Tn5801-like GI types were detected among S. pseudintermedius (Tn5801 and GI6287) - both showed high similarity compared to GenBank sequences from human pathogens. Two distinct Tn5801-like GI types were detected among the porcine E. faecium and human S. aureus isolates (Tn6014 and GI6288). Tn5801-like GIs were detected in GenBank-sequences from Gram-positive bacteria of human, animal or food origin worldwide. Known Tn5801-like GIs were divided into seven types. The results showed that Tn5801-like GIs appear to be relatively common in tetracycline-resistant S. pseudintermedius in Denmark. Almost identical Tn5801-like GIs were identified in different Gram-positive species of pet and human origin, suggesting that horizontal transfer of these elements has occurred between S. pseudintermedius from pets and human pathogens, including S. aureus.201627199912
2483100.9722Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. Proteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the relationship between Proteus spp. and tree shrews. In this study, the complete genome sequencing method was used to analyse the characteristics of Proteus spp. isolated from tree shrews, and comparative genomic analysis was performed to reveal their relationships. The results showed that 36 Proteus spp. bacteria were isolated, including 34 Proteus mirabilis strains and two Proteus vulgaris strains. The effective rate of sequencing was 93.53%±2.73%, with an average GC content of 39.94%±0.25%. Briefly, 3682.89±90.37, 2771.36±36.01 and 2832.06±42.49 genes were annotated in the NCBI non-redundant nucleotide database (NR), SwissProt database and KEGG database, respectively. The high proportions of macrolide-, vancomycin-, bacitracin-, and tetracycline-resistance profiles of the strains were annotated in the Antibiotic Resistance Genes Database (ARDB). Flagella, lipooligosaccharides, type 1 fimbriae and P fimbriae were the most abundantly annotated virulence factors in the Virulence Factor Database (VFDB). SNP variants indicated high proportions of base transitions (Ts), homozygous mutations (Hom) and non-synonymous mutations (Non-Syn) in Proteus spp. (P<0.05). Phylogenetic analysis of Proteus spp. and other references revealed high genetic diversity for strains isolated from tree shrews, and host specificity of Proteus spp. bacteria was not found. Overall, this study provided important information on characteristics of genome for Proteus spp. isolated from tree shrews.202032084183
5623110.9720Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.202337583512
5385120.9717Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements. Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.201931670141
5236130.9716Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits (Physalis peruviana L.). INTRODUCTION: Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question. METHODS: This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes. RESULTS: The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood). CONCLUSION: Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.202439104589
1386140.9715ESBL/pAmpC-producing Enterobacterales in common leopard geckos (Eublepharis macularius) and central bearded dragons (Pogona vitticeps) from Portugal. Common leopard geckos (Eublepharis macularius) and central bearded dragon (Pogona vitticeps) are widely kept as pets but can harbor pathogenic bacteria, including antimicrobial-resistant (AMR) bacteria. This study aimed to research the frequency of β-lactamase-producing Enterobacterales in these two reptile species. A total of 132 samples were collected from the oral and cloacal cavities of healthy common leopard geckos and central bearded dragons in the Lisbon area, Portugal. Antimicrobial resistance was assessed for third-generation cephalosporin (3GC)-resistant Enterobacterales. The results revealed that 3GC-resistant Enterobacterales were observed in 17.9% (n = 14/78) of the reptiles. The most commonly identified species were: Citrobacter freundii and Klebsiella aerogenes. Furthermore, some isolates produced extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases (AmpC) encoding genes such as bla (CMY-2), bla (CTX-M-15,) and bla (TEM-1). These findings emphasize the potential role of these reptiles in the spread of AMR bacteria, particularly in urban settings where human- animal interactions are frequent. Given the zoonotic risks, this study emphasizes the importance of continued surveillance and responsible antimicrobial use in both veterinary and human medicine to mitigate the spread of AMR bacteria.202540370835
1992150.9714Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.201931057528
1211160.9714Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia. Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::bla(CTX-M-2)) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.202234982979
2093170.9714Are Enterobacteriaceae and Enterococcus Isolated from Powdered Infant Formula a Hazard for Infants? A Genomic Analysis. Powdered infant formulas (PIF) are the most used dietary substitutes that are used in order to supplement breastfeeding. However, PIF are not sterile and can be contaminated with different microorganisms. The objective of this study was to genomically characterize Enterobacteriaceae (ENT) and Enterococcus strains that were isolated from PIF. Strains were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS). Genomic typing, detection of virulence, and resistance profiles and genes were performed with the Ridom SeqSphere+ software; the comprehensive antibiotic resistance database (CARD) platform; ResFinder and PlasmidFinder tools; and by the disk diffusion method. Nineteen isolates from PIF were analyzed, including ENT such as Kosakonia cowanii, Enterobacter hormaechei, Franconibacter helveticus, Mixta calida, and lactic acid bacteria such as Enterococcus faecium. The strains exhibited resistance to beta-lactams, cephalosporins, and macrolides. Resistance genes such as AcrAB-TolC, marA, msbA, knpEF, oqxAB, fosA, bla(ACT-)(7), bla(ACT-)(14,)qacJ, oqxAB(,)aac(6')-Ii, and msr(C); and virulence genes such as astA, cheB, cheR, ompA ompX, terC, ironA, acm, and efaAfm, adem were also detected. All the analyzed strains possessed genes that produced heat-shock proteins, such as IbpA and ClpL. In PIF, the presence of ENT and Enterococcus that are multiresistant to antibiotics-together with resistance and virulence genes-pose a health risk for infants consuming these food products.202236429148
1351180.9714Characteristics of High-Level Ciprofloxacin-Resistant Enterococcus faecalis and Enterococcus faecium from Retail Chicken Meat in Korea. Genes encoding ciprofloxacin resistance in enterococci in animals may be transferred to bacteria in the animal gut and to zoonotic bacteria where they could pose a human health hazard. The objective of this study was to characterize antimicrobial resistance in high-level ciprofloxacin-resistant (HLCR) Enterococcus faecalis and Enterococcus faecium isolated from retail chicken meat. A total of 345 enterococci (335 E. faecalis and 10 E. faecium) were isolated from 200 chicken meat samples. Of these, 85 E. faecalis isolates and 1 E. faecium isolate were confirmed as HLCR enterococci. All 86 HLCR enterococci displayed gyrA- parC point mutations consisting of S83I-S80I (94.2%, 81 isolates), S83F-S80I (2.3%, 2 isolates), S83Y-S80I (2.3%, 2 isolates), and S83Y-S80F (1.2%, 1 isolate). Sixty-one (72.9%) of the 86 HLCR enterococci showed multidrug resistance to three to six classes of antimicrobial agents. Multilocus sequence typing revealed that E. faecalis had 17 different sequence types (ST) and E. faecium had 1 different ST, with ST256 observed most often (44 isolates, 51.8%). Although these results cannot exclude the possibility that pathotypes of enterococci isolated from chicken might represent transmission to or from humans, the foodborne HLCR E. faecalis indicated that the food chain is a potential route of enterococcal infection in humans.201830015506
1194190.9714Presence of Broad-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Zoo Mammals. Broad-spectrum beta-lactamase (BSBL)-producing Enterobacteriaceae impose public health threats. With increased popularity of zoos, exotic animals are brought in close proximity of humans, making them important BSBL reservoirs. However, not much is known on the presence of BSBLs in zoos in Western Europe. Fecal carriage of BSBL-producing Enterobacteriaceae was investigated in 38 zoo mammals from two Belgian zoos. Presence of bla-genes was investigated using PCR, followed by whole-genome sequencing and Fourier-transform infrared spectroscopy to cluster acquired resistance encoding genes and clonality of BSBL-producing isolates. Thirty-five putatively ceftiofur-resistant isolates were obtained from 52.6% of the zoo mammals. Most isolates were identified as E. coli (25/35), of which 64.0% showed multidrug resistance (MDR). Most frequently detected bla-genes were CTX-M-1 (17/25) and TEM-1 (4/25). Phylogenetic trees confirmed clustering of almost all E. coli isolates obtained from the same animal species. Clustering of five isolates from an Amur tiger, an Amur leopard, and a spectacled bear was observed in Zoo 1, as well as for five isolates from a spotted hyena and an African lion in Zoo 2. This might indicate clonal expansion of an E. coli strain in both zoos. In conclusion, MDR BSBL-producing bacteria were shown to be present in the fecal microbiota of zoo mammals in two zoos in Belgium. Further research is necessary to investigate if these bacteria pose zoonotic and health risks.202133919869