Search Results (44)

In hospital environments, pathogenic bacteria spread easily and acquire virulence and antibiotic resistance genes. The aim of the study was an evaluation of the genetic diversity of 109 K. pneumoniae isolates recovered from patients of a district hospital in central Poland. The frequencies of genes coding for β-lactamases, efflux pumps, and virulence factors were determined. Genotyping of the isolates was performed with ERIC (Enterobacterial Repetitive Intergenic Consensus) and REP (Repetitive Element Sequence Based) PCR techniques, with 21 and 19 genotypes being identified, respectively. The bla_SHV-1 (92.7%), bla_CTX-M group 1 (83.5%), bla_TEM-1 (28.4%), bla_NDM-1 (16.5%), bla_VEB-1 (11.0%), bla_CTX-M group 9 (3.7%), bla_KPC (1.8%), bla_IMP, bla_OXA-48, bla_CTX-M group 2, bla_CTX-M groups 8, and 25/26 (0% each) and efflux pumps: AcrAB (100%), tolC (93.6%), and mdtk (60.5%), and virulence genes coding: urease subunit ureA (94.5%) endotoxins wabG (92.7%) and uge (64.2%), and siderophore iucB (3.7%) were detected. The bla_SHV-1, bla_CTX-M group 1, mdtk, tolC, AcrAB (16.5%); bla_SHV-1, bla_CTX-M group 1, tolC, AcrAB (15.6%), and bla_SHV-1, bla_CTX-M group 1, bla_NDM-1, mdtk, tolC, AcrAB (11.9%) were the most common resistance patterns. The distribution of resistance and virulence genes varied more between hospital wards than between different clinical materials. Hospital’s antibiotic-resistant and virulent K. pneumoniae, able to spread among humans, animals, and in the environment, pose a significant threat to public health. Full article

Avian pathogenic Escherichia coli (APEC) causes avian colibacillosis, leading to significant economic losses and concerns for food safety in the poultry industry. This study focused on examining the virulence gene profile, antibiotic resistance prevalence, and resistance patterns of APEC isolates. A total of 250 bacterial strains were collected from birds affected by colibacillosis. Serogrouping revealed diverse serotypes, with O2 being the most common (16%), followed by O1, O8, and O76. All isolates tested positive for at minimum one virulence gene, with 7.2% carrying all five targeted genes, particularly in serogroups O1, O8, O45, and O88. The most detected gene was iss, present in 79.6% of isolates, followed by tsh, iucC, sitA, and papC. The antibiotic resistance analysis showed that all isolates exhibited multidrug resistance, although they remained susceptible to gentamicin, amikacin, ciprofloxacin, and chloramphenicol. Moreover, specific antibiotic resistance genes were known in the isolates, with tetA detected in 54.8%, tetB in 51.7%, sul1 in 50%, and aadA1 in 29.2%. These findings highlight the widespread antibiotic resistance in chicken carcasses, which poses a hazard to human health in terms of transfer of resistance to humans, reduced effectiveness of antibiotics and impaired ability to contain infectious diseases. Therefore, it is crucial to implement strict monitoring programs to regulate antibiotic usage in poultry production. Full article

Escherichia coli contamination in poultry is a significant concern due to its potential to cause foodborne illness. The presence of extraintestinal pathogenic E. coli (ExPEC) strains in chicken carcasses can lead to severe human infections. This study investigates the prevalence, virulence, and antibiotic resistance of E. coli isolates from chicken carcasses processed in both wet market and industrial environments, with a focus on the detection capabilities of MALDI-TOF MS. A total of 119 E. coli isolates were obtained. Only a small proportion (5/119) carried enteropathogenic virulence genes. In contrast, 71.42% (85/119) of the isolates harbored multiple extraintestinal virulence genes. Among these, iucC and sitA, which are associated with systemic infections, were present in 68.24% (58/85) and 43.53% (37/85) of the isolates, respectively. Furthermore, 47.06% (56/119) of the isolates carrying at least two extraintestinal virulence genes were classified as ExPEC. Additionally, 94.6% (54/56) of ExPEC isolates were multidrug resistant (MDR), showing resistance to over three antibiotic classes, raising concerns about the spread of antibiotic resistance. MALDI-TOF MS profiling revealed significant heterogeneity among the ExPEC isolates, with no distinct clustering patterns based on processing environment or sampling site. These findings underscore the public health risks posed by ExPEC in poultry and emphasize the need for improved surveillance, stringent hygiene practices, and responsible antibiotic use in poultry production. Full article

This study was undertaken to determine the effect of bird age and administering either Lactococcus lactis ssp. lactis 1 (LL) or Limosilactobacillus fermentum 1 (LF) in the drinking water on the prevalence of antimicrobial resistance by phenotypic test, multilocus sequence typing (MLST) and virulence genes of Escherichia coli (E. coli) isolated from broiler caeca by whole-genome sequencing (WGS) analysis. Male (Ross 308) day-old chicks (240) were reared for 28 days. Water was provided either untreated (CON) or with LL (10⁷/mL) or LF (10⁷/mL) via a nipple drinker on three days each week during the starter phase (days 1, 3, 5, 7, 9 and 11 d) in eight replicate pens per treatment, with initially ten chicks per pen. One chick from each pen was sacrificed when LL or LF was added to the water, and again on d 14 and 28. There was no evidence that LL and LF had any effect on the prevalence of antimicrobial resistance and virulence genes in E. coli isolates. The population density of Lactobacillus sp. and coliforms decreased with age (p < 0.001). The high resistance of E. coli to ampicillin and tetracycline was maintained throughout the life of the broilers. The prevalence of virulence genes was greatest during the starter phase but declined when birds were 28 days of age (p < 0.05). In birds < 14 d of age, E. coli MLST 457, 1640, 1485 and 155 were dominant, and these carried iucD, irp2, astA, iutA and iroN genes. When birds were 28 d of age, MLST 1286, 1112 and 973 predominated, and these carried few virulence genes. This suggests that young birds were more susceptible to putative pathogenic E. coli than older birds. Supporting the development of a healthy microbiome that might control the proliferation of potentially pathogenic E. coli is an area of future research. Full article

Despite the increased reporting of Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) in Egypt, there is a paucity of information regarding the molecular characteristics of such strains. Herein, we present the genome sequence of two CR-hvKp strains, K22 and K45, which were isolated from VAP (ventilator-associated-pneumonia) patients admitted to pediatric ICU at Assiut University Children’s Hospital, Egypt. K22 and K45 isolates were subjected to antimicrobial susceptibility testing and whole-genome sequencing. Genomic analysis was performed to characterize each strain, determining their plasmids, antimicrobial resistance (AMR) genes, and virulence determinants. K22 possessed an extensive drug resistance phenotype (XDR), whilst K45 exhibited a multidrug resistance phenotype (MDR), with genome sequencing revealing the presence of a diverse array of AMR genes. Both strains were resistant to the carbapenem antibiotic imipenem, carrying the OXA-48 carbapenemase, with K22 additionally possessing an NDM-1 carbapenemase. Each strain was considered high-risk, with K22 and K45 respectively belonging to sequence types ST383 and ST14 and possessing virulence genes implicated in hypervirulence (e.g., iucABCD-iutA and rmpA). Importantly, both strains carried multiple plasmid replicons, including an AMR/virulence IncHI1B/FIB hybrid plasmid and MDR IncL/M plasmids. This report highlights the critical role of plasmids in the evolution of virulent K. pneumoniae strains and suggests the circulation of an IncHI1B/FIB hybrid plasmid, simultaneously disseminating AMR and hypervirulence, amongst K. pneumoniae strains within Assiut University Children’s Hospital. Full article

Avian Pathogenic Escherichia coli (APEC) constitutes a major etiological agent of avian colibacillosis, which significantly hinders the development of the poultry industry. Conducting molecular epidemiological studies of APEC plays a crucial role in its prevention and control. This study aims to elucidate the molecular epidemiological characteristics of Avian Pathogenic Escherichia coli in Shanxi Province. In this study, 135 APEC strains were isolated and identified from 150 liver samples of diseased and deceased chickens exhibiting clinical symptoms, which were collected from farms in Shanxi Province between 2021 and 2023. The isolates were then analyzed for phylogenetic clustering, drug resistance, resistance genes, virulence genes, and biofilm formation capabilities. The results revealed that the proportions of the A, B1, B2, and D evolutionary subgroups were 26.67%, 32.59%, 17.78%, and 15.56%, respectively. The drug resistance testing results indicated that 92% of the isolates exhibited resistance to cotrimoxazole, kanamycin, chloramphenicol, amoxicillin, tetracycline, and other antibiotics. In contrast, 95% of the strains were sensitive to ofloxacin, amikacin, and ceftazidime. The most prevalent resistance genes included tetracycline-related (tetA) at 88.15%, followed by beta-lactam-related (bla-TEM) at 85.19%, and peptide-related (mcr1) at 12.59%. The virulence gene analysis revealed that ibeB, ompA, iucD, and mat were present in more than 90% of the isolates. The results revealed that 110 strains were biofilm-positive, corresponding to a detection rate of 81.48%. No significant correlation was found between the drug resistance genes, virulence genes, and the drug resistance phenotype. A moderate negative correlation was observed between the adhesion-related gene tsh and biofilm formation ability (r = −0.38). This study provides valuable insights into the prevention and control of avian colibacillosis in Shanxi Province. Full article

Escherichia coli (E. coli) has the ability to induce clinical and subclinical mastitis in dairy cows, causing a huge loss for the dairy industry. In this study, 51 subclinical mastitis isolates and 36 clinical mastitis isolates from eight provinces of China between 2019 and 2021 were used to investigate the differences in their biological characteristics. The results showed that B1 (52.9%) and A (39.1%) were the predominant phylogroups; R1 (50.6%) was the predominant lipopolysaccharide (LPS) core type; and 44 STs (ST10 and ST58 were the most sequence-prevalent STs) and 2 new STs (ST14828 and ST14829) were identified; however, no significant difference was observed between the clinical and subclinical group strains. To compare the virulence gene differences between the clinical and subclinical mastitis-related isolates, 18 common virulence genes (including afaE, eaeA, papC, saa, sfa, ompA, aer, irp2, iucD, escV, sepD, east1, estB, stx2e, CNF1, cba, hlyA and traT) were determined using the PCR method. The results showed that the detection rates of traT, irp2 and iucD in clinical mastitis isolates were significantly higher than those in subclinical mastitis isolates (p ˂ 0.05). Meanwhile, subclinical-group E. coli had stronger biofilm formation abilities than the clinical group (p < 0.05) in 78 (89.7%) mastitis-related E. coli that could form biofilms. Furthermore, 87 mastitis-related E. coli showed severe resistance against tetracycline (37.9%), ampicillin (36.8%), streptomycin (34.5%) and cotrimoxazole (28.7%); their most prevalent resistance genes were blaCTX-M (33.3%), tetA (27.6%), sul2 (18.4%) and strB (28.7%). It was noteworthy that the clinical-group strains had a higher resistance against ampicillin and possessed higher amounts of the resistance gene blaCTX-M (p < 0.05) compared to the subclinical group. This study aims to provide references for preventing the E. coli isolates from inducing different types of mastitis. Full article

Hypervirulent Klebsiella pneumoniae is a highly pathogenic variant of Klebsiella pneumonae, which represents a global public health issue because it is very virulent and spreads easily. The objectives of this study were to assess the predominance of hvKp among health care-associated infections in intensive care units of Tanta University Hospital and to compare hvKp with classical K. pneumoniae (cKp) in terms of antibiotic resistance, virulence, and molecular features. The study included 300 patients suffering from HAIs from different ICUs of Tanta University Hospitals. K. pneumoniae isolates were identified and subjected to string testing and antibiotic susceptibility testing, and the tissue culture assay for biofilm formation and polymerase chain reaction (PCR) tests were performed for the identification of capsular genes (K1, K2, K57) and virulence genes (rmpA, rmpA2, iuc A). Fifty-seven K. pneumonaie isolates were isolated. A total of 21 (36.8%) of them were hvKp and 36 (63.15%) were cKp. Significantly higher antibiotic resistance was detected in the cKp group. There was a significant difference between biofilm formation between cKp and hvKp isolates (p < 0.004*). iucA, rmpA2, and K1 genes were significantly associated with hvKp. The string test shows 100% sensitivity and negative predictive value for the detection of hvKp. Consequently, using the string test alone for the screening of hvKp is required. However, combining aerobactin-positive with hypermucoviscous isolates while screening for hvKp is crucial. Full article

Background/Objectives: Antimicrobial resistance represents a challenge to public health systems because of the array of resistance and virulence mechanisms that lead to treatment failure and increased mortality rates. Although for years the main driver of carbapenem resistance in Italy has been the Klebsiella pneumoniae KPC carbapenemase, recent years have seen an increase in VIM and NDM metallo-beta-lactamases (MBLs). We conducted a five-year survey of New Delhi Metallo-beta-Lactamase (NDM)-producing Klebsiella pneumoniae (NDM-Kpn) clinical isolates from the Lazio region, Italy; the study aimed to elucidate the molecular mechanisms underpinning their resistant and virulent phenotype. Methods: Antimicrobial susceptibility was evaluated by automated systems and broth microdilution. In silico analysis of acquired resistance and virulence genes was performed using whole-genome sequencing (WGS), molecular typing through MLST, and core genome multi-locus sequence typing (cgMLST). Conclusions: A total of 126 clinical NDM-Kpn isolates were collected from 19 distinct hospitals in the Lazio region. Molecular analysis highlighted the existence of NDM-1 (108/126) and NDM-5 (18/126) variants, 18 Sequence Types (STs), and 15 Cluster Types (CTs). Notably, 31/126 isolates displayed a virulence score of 4, carrying ybt, ICEKp, iuc, and rmp genes. This study identified a variety of NDM-Kpn STs, mainly carrying the bla_NDM-1 gene, with a significant number linked to high-risk clones. Of these isolates, 24.6% showed high-level resistance and virulence, emphasizing the risk of the spread of strains that combine multi-drug-resistance (MDR) and virulence. Proactive surveillance and international collaborations are needed to prevent the spread of high-risk clones, as well as further research into new antimicrobial agents to fight antibiotic resistance. Full article

The present study shows the genomic characterization of three pathogenic Escherichia coli hybrid strains. All strains were previously characterized as diarrheagenic pathotypes (DEC), obtained from feces. The three sequenced strains have genes that encode adhesins (fimH and iha) and iron uptake systems (iucC and iutA). Antibiotic resistance genes were also found for fluoroquinolone and aminoglycoside families in the three strains. The presence of genomic islands (GIs) in the sequenced study strains presented 100% identity (Ec-25.2) and 99% identity (Ec-36.1) with previously reported Extraintestinal Pathogenic E. coli (ExPEC) strains. The Ec-36.4 strain shared a 99% identity with GI from the Enterotoxigenic E. coli (ETEC) pathotype of the diarrheagenic E. coli strain. Ec-25.2 belongs to ST69 and harbors a FimH27 variant, while Ec-36.1 and Ec-36.4 belong to ST4238 and share a FimH54 variant. Four incompatibility groups associated with conjugative plasmids were identified (IncFIB, IncF11, IncI1, and IncB/O/K/Z), as well as Insertion Sequences and MITEs elements. Full article

A 42-year-old man was admitted to the emergency room complaining of fever and headache. His cerebrospinal fluid showed a cloudy appearance, and his white blood cell count was elevated at 2460/mm³, with a predominance of neutrophils (81%), and abnormal protein and glucose levels (510.7 mg/dL and 5 mg/dL, respectively). A lobulated lesion with rim enhancement, suggestive of abscess, was detected through magnetic resonance imaging. Klebsiella pneumoniae was detected in nasopharyngeal swab and blood cultures. The capsular serotype of K. pneumoniae was K2 and the sequence type determined by multilocus sequence typing was 23. The hypervirulent phenotype was associated with multiple virulent genes, including rmpA, rmpA2, entB, ybtS, kfu, iucA, iutA, iroB mrkD, allS, peg-344, peg-589, and peg-1631. After six weeks of receiving appropriate antibiotics and exhibiting clinical resolution of the brain abscesses, the patient was discharged. We present the first reported case of a healthy community-dwelling adult with solitary brain abscesses, and no other invasive abscesses, related to hypervirulent K. pneumoniae. Full article

Purulent vulvar discharge is a clinical sign of genitourinary tract infections, which are a significant concern in swine facilities, leading to sow culling and mortality. Escherichia coli is one of the main agents involved in these diseases. This study aimed to characterize the virulence and antimicrobial resistance profiles as well as the phylotype of Escherichia coli strains isolated from sows with purulent vulvar discharge. The results showed that at least 2 of the 29 tested virulence genes related to extraintestinal pathogenic E. coli were present in all strains tested. The most frequent gene was iutA, present in all strains, followed by the genes iucD, csgA, iss2, and irp2. Associations between iron uptake genes, genes related to adhesion, attachment, and serum resistance, as well as genes related to toxin release and bacteriocin, were frequent. The most prevalent phylotype was B1 (40.0%), followed by A (18.5%), D (11.9%), C (9.6%), B2 (7.4%), E (4.4%), F (1.5%), and Clade I (0.7%), with B2 being related to highly virulent traits. The strains presented elevated resistance to antimicrobials such as ciprofloxacin, streptomycin, cephalexin, florfenicol, and ampicillin. More than 90% of the strains were identified as multidrug-resistant, indicating the selection that is induced by the high use of antimicrobials in swine farming. Full article

Background: The emergence and global spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) are of great concern to health services worldwide. These β-lactamases hydrolyze almost all β-lactams, are plasmid-encoded, and are easily transferable among bacterial species. They are mostly of the KPC types in CR-hvKp. OXA-48-producing hvKP strains have been rarely reported in the literature. Methods: OXA-48-producing hvKP strains were collected from clinical specimens at the First Affiliated Hospital of Hainan Medical University from January 2022 to March 2023. Hypervirulent strains were tested for virulence in a mouse lethality study and underwent whole genome sequencing to identify genomic features. Results: A total of 42 unique OXA-48-bearing K. pneumoniae strains were identified, including three CR-hvKP strains (KP2683-1, NCRE61, and KP2185), which were isolated from bacteremia, pulmonary abscess, and liver abscess separately. The three CR-hvKP strains belonged to two different clones of ST11 KL64 (KP2185 and NCRE61) and ST23 K1 (KP2683-1). The KP2683-1 strain had the highest virulence. Whole genome sequencing analysis indicated that NCRE61 and KP2185 acquired IncFIB-type plasmids with a set of virulence genes (iroBCDN, iucABCD, iutA, rmpA, and rmpA2), while KP2683-1 acquired an IncL-type bla_OXA-48-harboring plasmid. Consecutive cultures showed that the bla_OXA-48-harboring plasmids were highly stable in the three hvKP strains and could be transmitted to Escherichia coli J53 by conjugation. The drug susceptibility testing results show that Ceftazidime/avibactam is sensitive for OXA-48-producing hvKP. Conclusions: Our study highlighted the two evolutionary pathways of OXA-48-producing hvKP strains and confirmed their virulence through in vivo testing. Ceftazidime/avibactam may be a viable option for treating OXA-48-producing hvKP strains. Full article

The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms. Results indicated that both susceptible and resistant E. coli isolates recovered from animals on commercial dairy operations were highly diverse and encoded a large pool of virulence factors. In total, 838 transferrable antimicrobial resistance genes (ARGs) were detected, with genes conferring resistance to aminoglycosides being the most common. Multiple sequence types (STs) associated with mild to severe human gastrointestinal and extraintestinal infections were identified. A Fisher’s Exact Test identified 619 genes (ARGs and non-ARGs) that were significantly enriched in MDR isolates and 147 genes that were significantly enriched in susceptible isolates. Significantly enriched genes in MDR isolates included the iron scavenging aerobactin synthesis and receptor genes (iucABCD-iutA) and the sitABCD system, as well as the P fimbriae pap genes, myo-inositol catabolism (iolABCDEG-iatA), and ascorbate transport genes (ulaABC). The results of this study demonstrate a highly diverse population of E. coli in commercial dairy operations, some of which encode virulence genes responsible for severe human infections and resistance to antibiotics of human health significance. Further, the enriched accessory genes in MDR isolates (aerobactin, sit, P fimbriae, and myo-inositol catabolism and ascorbate transport genes) represent potential targets for reducing colonization of antimicrobial-resistant bacteria in the calf gut. Full article

Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard, Pedobacter spp. have recently gained attention, not only for their role as plant growth promoters but also for their potential in producing antimicrobials. This study focuses on the genomic analysis of Pedobacter spp. to unveil the diversity of the SMs encoded in their genomes. Among the 41 genomes analyzed, a total of 233 biosynthetic gene clusters (BGCs) were identified, revealing the potential for the production of diverse SMs, including RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Overall, BGC distribution did not correlate with phylogenetic lineage and most of the BGCs showed no significant hits in the MIBiG database, emphasizing the uniqueness of the compounds that Pedobacter spp. can produce. Of all the species examined, P. cryoconitis and P. lusitanus stood out for having the highest number and diversity of BGCs. Focusing on their applicability and ecological functions, we investigated in greater detail the BGCs responsible for siderophore and terpenoid production in these species and their relatives. Our findings suggest that P. cryoconitis and P. lusitanus have the potential to produce novel mixtures of siderophores, involving bifunctional IucAC/AcD NIS synthetases, as well as carotenoids and squalene. This study highlights the biotechnological potential of Pedobacter spp. in medicine, agriculture and other industries, emphasizing the need for a continued exploration of its SMs and their applications. Full article