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Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case.

Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.

Animals↗

Nucleotide sequence-based typing of bacteria and the impact of automation.

DNA-based typing methods are increasingly important for the characterisation of bacteria. They are used to monitor the epidemiology of pathogens with public health significance and also to help understand the evolution and population biology of bacteria. However, these methods require accuracy and reproducibility and are often of a high-throughput nature. Laboratory automation is therefore the key to the successful implementation of such methods. This review describes the impact of automation on DNA-based typing methods, particularly multi-locus sequence typing (MLST), and the method components that can be automated.

Automation↗

Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces.

The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.

Animals↗

Cloning of the full-length coding sequence of rat liver-specific organic anion transporter-1 (rlst-1) and a splice variant and partial characterization of the rat lst-1 gene.

The full-length coding sequence of rat liver-specific organic anion transporter-1 (lst-1) and its splice variant have been cloned. The full-length rat lst-1 (designated rlst-1a) encodes a protein containing 687 amino acids and has 12-putative transmembrane domains, multiple potential N-glycosylation and phosphorylation sites. Therefore, rat lst-1a has 35 additional amino acid residues compared to the previously reported rat lst-1. A splice variant (designated rlst-1c) reported in this communication encodes a protein containing 654 amino acids and has 10-putative transmembrane domains. PCR analysis suggests that rlst-1a is the most abundant form in liver. Phylogenetic analysis reveals that rat lst-1a is an ortholog of human LST-1 (hLST-1) and mouse lst-1 (mlst-1). The rlst-1 gene is composed of 15 exons and 14 introns. Analysis of exon-intron boundary reveals that the splice variant rlst-1c lacks the entire exon 7, while the previously reported rat lst-1 (designated herein as rlst-1b) lacks approximately half of exon 10, and the splicing has occurred through alternative usage of a splice donor site within exon 10.

Alternative Splicing↗

Isolation and Molecular Characterization of Three Staphylococcus pseudintermedius Strains from Dogs and Humans in Egypt.

Staphylococcus pseudintermedius is an opportunistic pathogen that is largely associated with canine hosts but is becoming more widely recognized as a zoonotic pathogen. Understanding its genetic and phenotypic properties, such as virulence factors and antimicrobial resistance (AMR) profiles, is critical for infection control and vaccine development. In this study, we isolated and molecularly characterized three S. pseudintermedius isolates from dogs (hereafter referred to as S. pseudintermedius D8) and humans (hereafter referred to as S. pseudintermedius H10 and S. pseudintermedius H11) in Egypt. All three isolates showed 100% sequence identity with the nuc gene of the S. pseudintermedius SP_11304-3A reference genome. Multilocus sequence typing (MLST) revealed novel sequence types (STs) in the three isolates. The AMR determinants varied substantially among the isolates. While the mecA gene was absent, blaZ was detected in the canine isolate, indicating beta-lactamase-mediated penicillin resistance. Additionally, tetK and tetM genes were found conferring tetracycline resistance in different isolates. Resistance genes for aminoglycosides, chloramphenicol, fusidic acid, macrolides, streptothricin, and trimethoprim were also identified. All isolates were positive for key virulence genes, including immune evasion (AdsA), coagulase (coa), immunoglobulin-binding protein (sbi/spsK), exfoliative toxin (speta), enterotoxins (se-int and siet), fibrinogen binding protein gene (fnbB), and two-component pore-forming leukocidin genes (lukF and lukS). The S. pseudintermedius H11 isolate uniquely harbored the neuraminidase gene (nanB), while none of the isolates contained the gene coding for immunoglobulin G binding protein (spsQ). These findings highlight the differences in virulence and antimicrobial resistance genes among these S. pseudintermedius isolates, underlining the need for global surveillance and molecular characterization of this pathogen.

Dogs↗

Heterogeneity of methicillin-resistant Staphylococcus aureus strains at a German university hospital during a 1-year period.

Heterogeneous methicillin-resistant Staphylococcus aureus (MRSA) strains, including community-acquired MRSA strains, have been observed in Central Europe. The purpose of this study was to characterize by molecular methods MRSA isolated during the period 2002-2003 at the Otto-von-Guericke University Hospital in Magdeburg, Germany, and at a nearby chronic care facility. Strains were analyzed for their resistance phenotype. Selected isolates were typed by multilocus sequence typing (MLST), by a multiplex polymerase chain reaction (PCR) for the staphylococcal cassette chromosome mec (SCCmec), by an allele-specific PCR for the staphylococcal accessory gene regulator (agr), and by PCR for the presence of toxin genes (sea-sej, tsst-1, hlgA, C, and B, lukE/D, and luk-pvl). Of the 2,731 S. aureus isolates studied, 199 (7.3%) were MRSA, with a prevalence of 21.6%, 19.6%, and 12% in the department of dermatology, the chronic care facility, and the intensive care units. Six different sequence types (ST247, ST228, ST22, ST22a, ST225, and ST45) were observed. Of these, ST22, ST22a, and ST45 dominated (>50%) in the department of dermatology and the chronic care facility. Strains with these sequence types were usually not resistant to gentamicin and were associated with agr group I, the SCCmec type IV element, and the presence of the sec and sed toxin genes. ST228 strains were found mainly in the intensive care units and had a broader resistance phenotype and were associated with agr group II and the SCCmec type I element. All luk-pvl-positive MRSA isolates (n=8) belonged to agr group I and were typed as ST22 or ST45 and contained the SCCmec type I (n=1), type III (n=1), or type IV (n=6) element. The main observations of this study are in concordance with previously reported findings showing dissemination of MRSA in Central Europe. Through the multitude of applied methods, the data from this study contribute to a more precise knowledge about the heterogeneity of MRSA in a clinical setting. Rapid dissemination of MRSA clones at a university hospital was demonstrated, indicating that dissemination may depend on the environmental conditions within the individual departments.

Bacterial Proteins↗

Epidemiological typing of MRSA isolates from blood cultures taken in Irish hospitals participating in the European Antimicrobial Resistance Surveillance System (1999-2003).

Between 1999 and 2003, meticillin-resistant Staphylococcus aureus (MRSA) isolates recovered from blood cultures in Irish hospitals that participate in the European Antimicrobial Resistance Surveillance System were investigated by epidemiological typing using antibiogram-resistogram (AR) typing, biotyping, and DNA macrorestriction digestion using SmaI followed by pulsed-field gel electrophoresis (PFGE). PFGE patterns were assigned five-digit pulsed-field type (PFT) numbers, and PFTs of apparently related patterns were abbreviated to two-digit PFT groups (PFGs). AR and PFGE typing results were combined to produce AR-PFG types. Representative isolates of each AR-PFG type recovered in 2002 were typed by multilocus sequence typing and staphylococcal cassette chromosome (SCC) mec analysis. Isolates from 1999 and 2000 were also typed by phage typing. The extent to which epidemiological types of MRSA from blood cultures could be extrapolated to the total MRSA population was investigated by comparing results obtained with isolates from the total MRSA population versus those obtained with blood cultures during three study periods. Over the 5 years from 1999 to 2003, 1,580 blood culture isolates from 1,495 patients were analysed. Typeability and discriminatory indices were as follows: AR typing, 1 and 0.97; phage typing, 0.29 and 0.89; PFGE, 0.99 and 0.95; AR-PFG typing, 1 and 0.95. The most frequently occurring AR-PFG types were 06-01, 07-02, 13-00, and 14-00 and were exhibited by 57, 7, 14, and 12% of isolates, respectively. During the study period, the distribution of AR-PFG type changed markedly, with the prevalence of one type (AR-PFG 06-01) increasing by 880%, from 22% (39/181) in 1999 to 80% (343/430) in 2003. Investigation of whether epidemiological types among blood culture isolates of MRSA were representative of the total MRSA population showed that there was no significant difference in most instances. MLST and SCCmec typing showed that AR-PFG types 06-01, 07-02, 13-00, and 14-00 were ST22-MRSA-IV, ST36-MRSA-II, ST8-MRSA-IID, and ST8-MRSA-IIE, respectively.

Animals↗

Combination of staphylococcal chromosome cassette SCCmec type V and Panton-Valentine leukocidin genes in a methicillin-resistant Staphylococcus aureus that caused necrotizing pneumonia in Greece.

We describe a case of necrotizing pneumonia in Greece caused by a community-acquired methicillin-resistant Staphylococcus aureus (MRSA) producing Panton-Valentine leukocidin (PVL) carrying the staphylococcal chromosome cassette mec (SCCmec) type V. The pulse field gel electrophoresis (PFGE) pattern of this strain differed significantly from the PVL-positive multi-locus sequence typing (MLST)-80 clone of MRSA, which predominates in Greece and in Europe. Further analysis of this strain revealed that it belonged to the agr1 allele type, and its resistance to tobramycin, gentamicin, and kanamycin was associated to the presence of aac-(6')-Ie+aph(2') gene. This is the 1st report that documents the emergence of CA-MRSA with PVL genes in combination with the SCCmec type V in Europe.

Adult↗

Tn125-borne blaNDM-1 is decoupled from clonal background in a transcontinental Acinetobacter baumannii ST126/KL14 lineage.

BACKGROUND/OBJECTIVES: Carbapenem-resistant A. baumannii (CRAB) is a WHO Critical Priority pathogen. The blaNDM-1-carrying ST126/KL14 lineage has been independently reported from Vietnam (2015), Malaysia (2016), the USA (2023-2026), and Costa Rica (2024). Whether these geographically distinct reports represent a single transcontinental clone and through what mechanism blaNDM-1 disseminates has not been formally tested. METHODS: We performed comprehensive whole-genome reanalysis of the Vietnamese sentinel isolate DMS06669_L1 using three nested panels (n = 19, n = 138, and n = 609 Vietnamese A. baumannii genomes) and surveyed 429 plasmids extracted from 99 NDM-1 A. baumannii genomes retrieved from NCBI Pathogen Detection. RESULTS: Four ST126/KL14 isolates share high inter-regional average nucleotide identity (ANI; 99.77-99.92%) but wide intra-clade core-SNP distances (41-731 SNPs, well above the ∼20-40-SNP range typical of single-outbreak transmission clusters) and lack a significant molecular clock, consistent with a related transcontinental lineage rather than a single recent clone. NDM-1 plasmid evolution is statistically uncorrelated with chromosomal sequence type (Spearman ρ = 0.131, P = 0.573). At 609-strain population scale, under a fragmentation-aware detection criterion, all 41 blaNDM-1-carrying Vietnamese strains also carry ISAba125, with none carrying blaNDM-1 without it (Fisher exact test; Haldane-Anscombe-corrected OR ≈2.0 × 10³, 95% CI 1.2 × 10² to 3.4 × 10⁴; P = 4.74×10⁻⁴⁸; φ = 0.79). CONCLUSIONS: The blaNDM-1 dissemination pattern in this ST126/KL14 lineage is primarily consistent with Tn125 transposition acting alongside plasmid-borne spread. Standard MLST-based surveillance is insufficient; multi-level genomic monitoring - including chromosomal and plasmid-level detection of the Tn125/ISAba125 unit - is required to track this resistance threat.

A. baumannii↗

Multilocus sequence typing reveals that Bacillus cereus strains isolated from clinical infections have distinct phylogenetic origins.

Eight strains of Bacillus cereus isolated from bacteremia and soft tissue infections were assigned to seven sequence types (STs) by multilocus sequence typing (MLST). Two strains from different locations had identical STs. The concatenated sequences of the seven STs were aligned with 65 concatenated sequences from reference STs and a neighbor-joining tree was constructed. Two strains were distantly related to all reference STs. Three strains were recovered in a clade that included Bacillus anthracis, B. cereus and rare Bacillus thuringiensis strains while the other three strains were assigned to two STs that were more closely affiliated to most of the B. thuringiensis STs. We conclude that invasive B. cereus strains do not form a single clone or clonal complex of highly virulent strains.

Aged↗

Nosocomial infections by Staphylococcus epidermidis: how a commensal bacterium turns into a pathogen.

Staphylococcus epidermidis is a commensal bacterium of the human skin. However, S. epidermidis and other coagulase-negative staphylococci (CNS) emerge also as common nosocomial pathogens infecting immunocompromized patients carrying medical devices. Antibiotic resistance and the ability of many nosocomial S. epidermidis isolates to form biofilms on inert surfaces make these infections hard to treat. Epidemiological analyses using multilocus sequence typing (MLST) and genetic studies suggest that S. epidermidis isolates in the hospital environment differ from those obtained outside of medical facilities with respect to biofilm formation, antibiotic resistance, and the presence of mobile DNA elements. Since S. epidermidis isolates exhibit high genome flexibility, they are now regarded as reservoirs for the evolution and spread of resistance traits within nosocomial bacterial communities.

Biofilms↗

Staphylococcus aureus strain designation by agr and cap polymorphism typing and delineation of agr diversification by sequence analysis.

The allelic variations of the regulatory operon agr (groups I-IV) and the cap polymorphism (capsular types 5 and 8) were used as a typing scheme for rapid strain designation in Staphylococcus aureus. In combining 10 agr subgroups resolved by restriction fragment length polymorphism (RFLP) analysis with the two cap polymorphisms 12 types could be defined. To assess whether this type designation is informative for the population structure of the species S. aureus, agr and cap types were determined in clonal lineages defined by pulsed-field gel electrophoresis (PFGE) of a collection of 219 isolates. agr groups and cap types were both linked to certain clone complexes. However, little correlation was found between the two polymorphic loci. By PFGE cluster analysis 11 prevalent and 52 sporadic clones were defined. Most of the prevalent clones (9/11) could be discriminated by agr/cap typing. Thus, this technique allows a first subdivision of isolates and an inter-center comparable designation of S. aureus clones preceding a more detailed clonal analysis by PFGE or multi-locus sequence typing (MLST). To get insight into agr diversification, sequence analysis of the variable and conserved part of agr from selected S. aureus clones was performed. Strains of agr-I displayed the highest sequence divergence on the nucleotide and amino acid level, suggesting an early diversification of this group. When analyzing the relationship between the four agr interference groups we could show: (i) one intermediate between agr-I and agr-IV alleles; (ii) agr-IV sequences seem to bridge the agr-I and -III groups and (iii) two cases of horizontal transfer of the variable gene cassette from an agr-I strain to an agr-II strain. Thus, stepwise evolutionary progression and rare events of recombination were evident in the diversification of the agr locus.

Alleles↗

Community-associated meticillin-resistant Staphylococcus aureus: nosocomial transmission in a neonatal unit.

Community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging pathogen, increasingly reported worldwide to cause infections in individuals without classical risk factors for acquiring healthcare-associated MRSA (HA-MRSA). This report describes the first documented transmission of CA-MRSA in a healthcare setting in the UK, involving four babies and a member of staff in a neonatal unit. Detailed microbiological characterization of the isolates revealed that they represented a single clone with the following characteristics: multi-locus sequence type (MLST) 1; staphylococcal cassette chromosome mec (SCCmec) type IVa; protein A (spa) type t127; agr group 3, and encoding enterotoxins A and H. The Panton-Valentine leukocidin genes were not detected. The CA-MRSA strain appeared to be circulating alongside several subtypes of epidemic MRSA-15, the most prevalent HA-MRSA in the UK. A combination of infection control measures contained the outbreak. This report highlights the changing epidemiology of MRSA in the UK, and emphasizes the need for healthcare personnel to be alert to the fact that CA-MRSA can occur not only in the community but also in the healthcare setting.

Community-Acquired Infections↗

Real time PCR using TaqMan and SYBR Green for detection of Enterobacter sakazakii in infant formula.

Enterobacter sakazakii is an emerging pathogen that causes meningitis, bacteremia, sepsis, and necrotizing enterocolitis in neonates and children. Powdered milk-based infant formulas have been associated with the E. sakazakii-related outbreaks in premature or other immunocompromised infants. In this study, we developed two real time PCR assays using TaqMan and SYBR Green to identify the pathogen after selective enrichment in mLST and BHI. The accuracy of two detections was tested by 35 strains of E. sakazakii and 88 non-E. sakazakii bacterial strains. The results showed that all of these E. sakazakii strains were positive reaction to the detections and all of the non-E. sakazakii strains were negative. The newly developed assays enable us to detect 1.1 CFU/100 g infant formula. And both of the assays can be accomplished within 2 business days. Compared to the traditional detection, the real time PCR procedures are quicker and simpler. In this study, we also developed a new method to design the primers, which can support multiple real time PCR with one pair of primers in SYBR Green detection. The detection methods are more sensitive and effective based on Two-Tm-Value of PCR.

Animals↗

Rapid pulsed-field gel electrophoresis protocol for subtyping of Streptococcus suis serotype 2.

A rapid pulsed-field gel electrophoresis (PFGE) protocol for subtyping of Streptococcus suis serotype 2 was developed and evaluated using 27 clinical isolates from 22 epidemiologically unrelated patients. Results were matched against antibiogram, virulence genotyping and multi locus sequence typing (MLST). PFGE appeared to be the most discriminatory with numerical index of discrimination (D) equal to 0.87.

Animals↗

Salmonella Pullorum strain SPullorum-YN-07 from dead embryos of Yanjin black-bone chickens: Complete genome with IncFII(S) and Col(pVC) plasmids and pathogenicity.

Salmonella Pullorum is a host-adapted pathogen that causes Pullorum disease in chickens and can be vertically transmitted via eggs, leading to embryonic mortality. The susceptibility and vertical transmission of S. Pullorum may vary among chicken breeds, yet genomic characterization of strains from dead embryos of indigenous breeds remains limited. This study isolated and characterized a Gram-negative short rod, designated Salmonella Pullorum strain SPullorum-YN-07, from dead embryos of Yanjin black-bone chickens, a native breed in Yunnan, China. The strain formed colorless colonies on MacConkey agar and red, non-H2S colonies on XLD agar, with biochemical reactions consistent with the genus Salmonella. Whole-genome sequencing using Illumina and PacBio platforms generated a complete genome consisting of one circular chromosome and four circular plasmids; plasmid replicon types IncFII(S) and Col(pVC) were identified in two of the plasmids. On the chromosome, a total of 340 virulence-associated genes were detected, including those involved in secretion systems, adhesion, motility, and immune modulation. Resistance gene analysis identified the acquired aminoglycoside resistance gene aac(6')-Iaa, alongside multiple intrinsic resistance determinants related to efflux pumps and target alteration. Multilocus sequence typing (MLST) assigned the strain to sequence type ST92, and core-genome phylogenetic analysis confirmed its clustering within the Salmonella Pullorum lineage. In a chick infection model, the strain induced depression, white diarrhea, and growth retardation, with clinical scores peaking at 10 days post-infection and a mortality rate of 10%. Bacterial colonization was highest in the cecum, and histopathological lesions were observed in the liver, spleen, and cecum. This study provides the first complete genomic characterization and pathogenicity assessment of an S. Pullorum strain isolated from dead embryos of Yanjin black-bone chickens, offering a foundation for understanding host-pathogen interactions in indigenous breeds and assessing cross-transmission risks to commercial poultry populations.

Complete genome↗

Population structure and antibiotic resistance of Salmonella isolates from diseased poultry in Jiangxi Province, China.

Salmonella poses a significant threat to human and animal health. However, the relationship among population diversity, antibiotic resistance, and infection risk remains largely unexplored. In this study, 69 Salmonella strains were isolated from diseased poultry in Jiangxi Province from 2021 to 2024. Using whole-genome sequencing, serotype prediction, MLST, virulence and resistance gene analysis, antibiotic susceptibility testing, and mobile genetic element annotation, we characterized the diversity, resistance profiles, and transmission mechanisms of these strains. The results showed high diversity, with Salmonella enterica subsp. enterica serovar Typhimurium (>60%) and ST19 (62.31%) as the dominant serovar and sequence type, respectively. Several avian isolates were genomically similar to human isolates, indicating potential zoonotic risk. All strains harbored conserved core virulence modules, whereas accessory modules (e.g., cdtB, astA, pefA) varied and may affect pathogenicity. The multidrug resistance rate was 97.1%, with 100% resistance to erythromycin, tilmicosin and tiamulin, and resistance rates of 91.3%, 84.1%, and 71.0% to sulfonamides, enrofloxacin, and ceftiofur, respectively. Sixty-eight resistance genes were identified. Highly conserved antimicrobial resistance gene (ARG) modules (e.g., sul2-aph(3″)-Ib-aph(6')-Id-tet(A)) were shared between chromosomes and plasmids and were flanked by mobile elements such as Tn3 and IS3. Genomic islands (GIs) and plasmids in some strains carried resistance gene clusters highly homologous to those in pathogens from humans, pigs, and chickens, suggesting active horizontal transfer of resistance genes across hosts. This study revealed high diversity, prevalent multidrug resistance, and active horizontal transfer of resistance genes in avian-derived Salmonella from Jiangxi Province, emphasizing the need for cross-host resistance monitoring and antibiotic management within the 'One Health' framework.

Horizontal gene transfer↗

Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia.

A collection of 57 isolates of Vibrio nigripulchritudo from either diseased or healthy shrimp and from shrimp farms environment was studied in order to gain a better understanding of the epidemiology of this pathogen, notably isolated from two distinct shrimp disease complexes. Molecular typing using two different techniques, arbitrarily primed PCR (AP-PCR) and multi-locus sequence typing (MLST), studied together with experimental pathology data allowed a relevant epidemiological insight into this possibly emerging pathogen. Additionally, results obtained with the two molecular typing techniques were congruent and allowed discriminating the strains associated with the "Summer Syndrome" from strains isolated from other contexts, especially the other shrimp vibriosis "Syndrome 93". These results highlight that the "Summer Syndrome" is most probably caused by an emergent clonal pathogen that therefore deserves surveillance and that AP-PCR can satisfactorily be used for that purpose.

Animals↗