Search Results (265)

Background/Objectives: Staphylococcus aureus and Staphylococcus pseudintermedius are major opportunistic pathogens in both humans and dogs. In pets, the dissemination of methicillin-resistant isolates (MRSA or MRSP) is problematic for the treatment of animals and is a public health issue due to their zoonotic potential. MRSA and MRSP may also harbor virulent genes that increase their dangerousness. This study aimed to assess the prevalence of (MR)SA and (MR)SP in healthy dogs and their owners in Algeria. Methods: Swabs were collected from various body sites of healthy dogs (n = 88) and from the nose of their owners (n = 38). Antimicrobial susceptibility testing was performed by antibiograms according to the disc diffusion method, and clonality was assessed using Pulsed-Field Gel Electrophoresis (PFGE). All methicillin-resistant isolates were short-read whole-genome sequenced using the Illumina technology. Results: 26 S. aureus and 17 S. pseudintermedius isolates were respectively collected from 13 dogs (13/88, 14.8%). No MRSP isolate was detected, while MRSA was found in six dogs (6.8%). Isolates belonged to ST1 (n = 3), ST 80 (n = 1), and ST 22 (n = 2, including the single-locus variant ST7118). All MRSA displayed the immune evasion cluster (IEC) type E. The ST80 isolate presented the Panton–Valentine toxin, and the ST22/ST7118 isolates carried the tst gene coding for the toxic shock syndrome toxin. Conclusions: The epidemiology of MRSA in healthy Algerian dogs mirrors the one in Algerian people. This poses a zoonotic and public health concern due to the virulence and resistance genes displayed by these isolates. Our results indicate the need for developing One Health strategies to avoid a large-scale dissemination of MRSA in Algerian dogs. Full article

The aim of this study was to characterize the antimicrobial resistance phenotype and genotype of non-typhoidal Salmonella spp. isolated in Luanda, Angola. Between 2013 and 2015, human clinical samples, food, and environmental samples (n = 290) were collected at different regions of Luanda city and screened for the presence of Salmonella spp. Bacterial isolates were preliminarily identified using the API 20E Kit, and their identification was confirmed using PCR and serotyping. All Salmonella spp. isolates were tested by minimum inhibitory concentration against 19 antimicrobials. The isolates were also screened using PCR for the presence of resistance genes (bla_OXA-1, bla_SHV, bla_TEM, sul1, sul2, sul3, qnrA, qnrB, qnrS, qnrC, qnrD, aac(6′)-Ib, dfrIa [targeting dfrA1, dfrA5, dfrA15, dfrA15b, dfrA16, dfrA16b] and dfrA12, cmlA, and floR) and typed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Salmonella enterica non-typhoidal was detected in 21.3% of the clinical samples (n = 32/150), 11.1% of the food samples (n = 10/90), and 26% of the environmental samples (n = 13/50). Serotyping revealed that the monophasic variant of Salmonella Typhimurium (Salmonella enterica serovar 4,[5],12:i:-) was detected in 38.1% of the samples. Moreover, serovar Salmonella Enteritidis was the second most frequent. Only 7.3% of the isolates were resistant to at least one antimicrobial. Furthermore, isolates from different origins (clinical, environmental, and food) were associated with the same lineages, Salmonella Enteritidis ST11 and S. enterica ser. Typhimurium ST313. The detection of S. enterica serovar 4,[5],12:i:- in different settings reinforces the need for a One Health approach to control this zoonosis in Angola. Full article

Escherichia coli is a Gram-negative bacterium and part of the intestinal microbiota. However, it can cause various diarrhoeal illnesses, i.e., traveller’s diarrhoea, dysentery, and extraintestinal infections when the bacteria are translocated from the intestine to other organs, such as urinary tract infections, abdominal and pelvic infections, pneumonia, bacteraemia, and meningitis. It is also an important pathogen in intensive care units where cross-infection may cause intrahospital spread with serious consequences. Within this study, four E. coli isolates from the tracheal aspirates of a tracheotomised paediatric patient on chronic respiratory support were analysed and compared for antibiotic resistance and virulence potential. Genomes of all four isolates (5381a, 5381b, 5681, 5848) were sequenced using Oxford Nanopore Technology. According to PFGE analysis, the clones of isolates 5681 and 5848 were highly similar, and differ from 5381a and 5381b which were isolated first chronologically. All four E. coli isolates belonged to an unknown sequence type, related to the E. coli ST131, a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. All four E. coli isolates in this study exhibited a multidrug-resistant phenotype as, according to MIC data, they were resistant to ceftriaxone, ciprofloxacin, doxycycline, minocycline, and tetracycline. In addition, principal component analyses revealed that isolates 5681 and 5848, which were recovered later than 5381a and 5381b (two weeks and three weeks, respectively) possessed more complex antibiotic resistance genes and virulence profiles, which is concerning considering the short time period during which the strains were isolated. Full article

Leptospirosis is a widespread zoonosis caused by spirochaetes belonging to the pathogenic species of Leptospira, which are classified into more than 25 serogroups and 250 serovars. Vaccination can prevent the disease in dogs but offers incomplete efficacy because of a lack of cross-protection between serogroups. The aim of this study was to validate a robust recruitment and sampling process, with the objectives of isolating and typing circulating Leptospira pathogenic strains and then selecting those of proven virulence and pathogenicity for vaccine development. Blood and urine samples from dogs with clinical syndromes compatible with acute leptospirosis were sterilely collected and transported to a reference laboratory for a micro-agglutination test (MAT), PCR, and bacterial isolation. Isolated strains underwent molecular typing using RNA16S, variable-number tandem repeat (VNTR), and pulsed-field gel electrophoresis (PFGE). Subtyping was performed using core genome multilocus sequence typing (CgMLST). Among 64 included dogs, 41 had MAT and/or PCR results compatible with Leptospira infection, and 14 Leptospira strains were isolated. Based on molecular typing, 11 isolates were classified as L. interrogans serogroup Australis, serovar Bratislava, and 3 as serogroup Icterohaemorrhagiae, serovar Icterohaemorrhagiae. CgMLST subtyping revealed a diversity of clonal groups (CGs) distributed in several regional clusters. Besides validating a robust recruitment and sampling process, this study outlines the value of combining PCR and serological testing when suspecting leptospirosis and the usefulness of implementing molecular typing methods to identify circulating field strains. It also confirms the epidemiological importance of the Australis serogroup and allows for the collection of different highly pathogenic strains for vaccine development. Full article

A total of 265 Salmonella Enteritidis isolates collected from retail markets and children’s hospitals in Shanghai were used to investigate the prevalence and molecular epidemiology of plasmid-mediated fosfomycin resistance genes. Nine of the isolates—7 from the 146 (4.79%) retail chicken-related samples and 2 from the 119 (1.68%) samples from clinical children—were fosfomycin-resistant (Fos^R). The fosA3 gene was detected in all of the nine Fos^R isolates, which were located on Inc F-type (8/9, 88.9%) and unknown-type (1/9, 11.1%) transferable plasmids. In total, five plasmid types, namely Inc HI2 (1/9, 11.1%), Inc I1 (3/9, 33.3%), Inc X (8/9, 88.9%), Inc FIIs (9/9, 100%), and Inc FIB (9/9, 100%), were detected in these Fos^R isolates, which possessed five S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) profiles. The extended-spectrum β-lactamase determinant bla_CTX-M-14 subtype was identified in one Fos^R S. Enteritidis isolate, which was located in a transferable unknown-type plasmid co-carrying fosA3 and tetR genes. Sequence homology analysis showed that this plasmid possessed high sequence similarity to previously reported bla_CTX-M-14- and fosA3-positive plasmids from E. coli strains, implying that plasmids carrying the fosA3 gene might be disseminated among Enterobacterales. These findings highlight further challenges in the prevention and treatment of Enterobacteriaceae infections caused by plasmids containing fosA3. Full article

Understanding the epidemiology of mecA-positive Staphylococcus pseudintermedius strains, including those that are oxacillin-susceptible but potentially inducible to resistance, is crucial for developing effective treatment strategies and mitigating public health risks. This study characterized 87 mecA-positive S. pseudintermedius isolates obtained from skin lesions and nasal orifices of 46 dogs with pyoderma enrolled at a referral hospital in Thailand between 2019 and 2020. All isolates underwent antibiogram profiling, SCCmec typing, and pulsed-field gel electrophoresis (PFGE) for phenotypic and genetic analysis. Among the 87 isolates, 33 isolates (37.9%) recovered from 15 dogs were oxacillin-resistant (OR-MRSP), while 54 isolates (62.1%) from 31 dogs were oxacillin-susceptible (OS-MRSP). All OR-MRSP isolates exhibited multidrug resistance (MDR), and 44% of the OS-MRSP isolates also showed MDR. SCCmec typing revealed type V as predominant among OR-MRSP isolates (69.7%), while many oxacillin-susceptible isolates (70.4%) were non-typeable. The OR-MRSP isolates from the same dog showed consistent antibiogram and SCCmec types, while OS-MRSP isolates displayed both identical and diverse patterns. No dominant pulsotypes were observed among the OR-MRSP or OS-MRSP strains. Genetic diversity was also noted among the isolates within the same dogs and among the others, highlighting the complexity of S. pseudintermedius colonization and infection dynamics in pyoderma-affected dogs. Full article

Listeriosis is one of the most serious foodborne diseases under surveillance, with an overall mortality rate in the EU currently being high at 18.1%. Therefore, this study aims to investigate Listeria monocytogenes strains isolated from clinical and food samples for susceptibility to antimicrobials, presence of virulence factors, and genetic diversity. Species were identified using the MALDI-TOF, resistance to 11 antibiotics was determined according to EUCAST guidelines, and multiplex PCR was used for serotyping and detecting virulence genes. Strains were genotyped using the PFGE method. Clinical strains showed full sensitivity to all tested antibiotics. In total, 33.3% of strains from food products were found to be resistant to ciprofloxacin and 4.2% to tetracycline. Most of the tested isolates (79.2%) belonged to serotype 1/2a-3a, and the rest (20.8%) belonged to serotype 4ab-4b,4d-4e. Five virulence genes (prfA, hlyA, plcB, inlA, and lmo2672) were detected in all strains studied. The llsX gene was the least common, in 37.5% of clinical strains and 18.75% of strains isolated from food products. Among the analyzed strains, 13 strains displayed unique PFGE profiles. The other 11 strains belong to 3 clusters of pulsotypes: cluster 1 (2 strains), cluster 2 (6 strains), and cluster 3 (2 strains). The percentage of hospitalizations and deaths of Polish patients with listeriosis indicates the seriousness of this disease, especially in an aging society, while the molecular testing of clinical strains has been rarely performed, which makes it difficult to determine the source of infection. Full article

This study aimed to identify contamination sources in raw milk and cheese on small farms in Brazil by isolating Escherichia coli at various stages of milk production and cheese manufacturing. The study targeted EAEC, EIEC, ETEC, EPEC, STEC, and ExPEC pathotypes, characterizing isolates for the presence of virulence genes, phylogroups, antimicrobial susceptibility, and phylogenetic relationships using PFGE and MLST. The presence of antimicrobial resistance genes and serogroups was also determined. Three categories of E. coli were identified: pathogenic, commensal, and ceftriaxone-resistant (ESBL) strains. Pathogenic EPEC, STEC, and ExPEC isolates were detected in milk and cheese samples. Most isolates belonged to phylogroups A and B1 and were resistant to antimicrobials such as nalidixic acid, ampicillin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Genetic analysis revealed that E. coli with identical virulence genes were present at different stages within the same farm. The most frequently identified serogroup was O18, and MLST identified ST131 associated with pathogenic isolates. The study concluded that E. coli was present at multiple points in milk collection and cheese production, with significant phylogroups and high antimicrobial resistance. These findings highlight the public health risk posed by contamination in raw milk and fresh cheese, emphasizing the need to adopt hygienic practices to control these microorganisms. Full article

Staphylococcus aureus, being one of the most common human pathogens, is responsible for infections in both hospital and community settings. Its virulence is attributed to its ability to evade the immune system by producing immune evasion (IE) proteins. The aim of this study was to detect the frequency of selected IE genes (spin, sbi, sea, sak, chp, scin, sep, ecb), belonging to the immune evasion cluster (IEC), and IEC types in 86 methicillin-susceptible S. aureus (MSSA) strains isolated from unrelated outpatients. In order to determine the diversity of analyzed strains, the phylogenetic relatedness was also determined. All strains were examined for the presence of IE genes using polymerase chain reaction assay. To analyze the clonal relatedness of S. aureus, pulsed-field gel electrophoresis (PFGE) was performed. All analyzed strains harbored the scn gene, followed by sbi (95.4%), ecb (91.7%), spin (89.5%), sak (83.7%), chp (67.4%), sep (67.4%) and sea (5.8%). Seventy-three (84.9%) S. aureus strains were classified into IEC types, of which, IEC type F was most commonly observed. IEC type A was not detected. PFGE results showed no association between clonal relatedness and the presence of IE genes/IEC types. In conclusion, the abundant and so diverse repertoire of genes determining invasion in analyzed strains may prove the fact that these strains are highly advanced and adapted to evade the host immune response. Full article

Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly uses biochemical methods, such as the API 20NE or Vitek-2. The typing studies of O. anthropi have mainly utilized PFGE, rep-PCR, AFLP, 16s rDNA sequencing, RecA-PCR RFLP, and MALDI-TOF MS. This study aims to evaluate the polymorphisms of variable-number tandem-repeats (VNTRs) within genomic DNA of O. anthropi strains. The tandem repeats (TRs) in genomic DNA are discovered using Tandem Repeat Finder software (version 4.09). Twelve different VNTRs are designated and assigned to the nomenclature. The primers for PCR of 12 loci are designed. The PCR product size is converted to the number of tandem repeats in every locus. The relatedness of 65 O. anthropi strains from geographically different countries are analyzed by means of 12-variable-number tandem-repeat analysis(MLVA-12). A total of 51 different genotypes are found in 65 O. anthropi strains. These strains, which were collected from the same environmental samples, hospitals, and countries, are clustered within the same or closely genotypes. The MLVA-12 assay has a good discriminatory power for species determination, typing of O. anthropi, and inferring the origin of bacteria. Full article

Background: Assessing the risk of multidrug-resistant colonization and infections is pivotal for optimizing empirical therapy in hematopoietic stem cell transplants (HSCTs). Limited data exist on extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) colonization in this population. This study aimed to assess whether ESBL-E colonization constitutes a risk factor for ESBL-E bloodstream infection (BSI) and to evaluate ESBL-E colonization in HSCT recipients. Methods: A retrospective analysis of ESBL-E colonization and BSI in HSCT patients was conducted from August 2019 to June 2022. Weekly swabs were collected and cultured on chromogenic selective media, with PCR identifying the β-lactamase genes. Pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) assessed the colonizing strains’ similarities. Results: Of 222 evaluated HSCT patients, 59.45% were colonized by ESBL-E, with 48.4% at admission. The predominant β-lactamase genes were bla_TEM (52%) and bla_SHV (20%). PFGE analysis did not reveal predominant clusters in 26 E. coli and 15 K. pneumoniae strains. WGS identified ST16 and ST11 as the predominant sequence types among K. pneumoniae. Thirty-three patients developed thirty-five Enterobacterales-BSIs, with nine being third-generation cephalosporin-resistant. No association was found between ESBL-E colonization and ESBL-BSI (p = 0.087). Conclusions: Although the patients presented a high colonization rate of ESBL-E upon admission, no association between colonization and infection were found. Thus, it seems that ESBL screening is not a useful strategy to assess risk factors and guide therapy for ESBL-BSI in HSCT-patients. Full article

Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information. Full article

In the case of a food poisoning outbreak, it is essential to understand the relationship between cooking workers and food poisoning. Many biological diagnostic methods have recently been developed to detect food poisoning pathogens. Among these diagnostic tools, this study presents PCR-based pulsed-field gel electrophoresis and nucleotide sequencing diagnostic analysis results for diagnosing food poisoning outbreaks associated with cooking employees in Chungcheongnam-do, Republic of Korea. Pulsed-field gel electrophoresis was useful in identifying the food poisoning outbreaks caused by Staphylococcus aureus and Enteropathogenic Escherichia coli. In the case of Norovirus, nucleotide sequencing was used to identify the relationship between cooking workers and the food poisoning outbreak. However, it is difficult to determine whether cooking employees directly caused the food poisoning outbreaks based on these molecular biological diagnostic results alone. A system is needed to integrate epidemiological and diagnostic information to identify a direct correlation between the food poisoning outbreak and cooking employees. Full article

AmpC beta-lactamases cause resistance to third-generation cephalosporins, including beta-lactamase inhibitors. In Escherichia coli from the German food production chain, the majority of AmpC beta-lactamase activity can be attributed to plasmid-mediated CMY-2 or overproduction of chromosomal AmpC beta-lactamase, but occasionally other enzymes like DHA-1 are involved. This study investigated the prevalence of the AmpC beta-lactamase DHA-1 in ESBL/AmpC-producing E. coli (n = 4706) collected between 2016 and 2021 as part of a German antimicrobial resistance monitoring program along the food chain. Eight isolates (prevalence < 0.2%) were detected and further characterized by PFGE, transformation and conjugation experiments as well as short-read and long-read sequencing. All eight strains harbored bla_DHA-1 together with qnrB4, sul1 and mph(A) resistance genes on an IS26 composite transposon on self-transferable IncFII or IncFIA/FIB/II plasmids. During laboratory experiments, activation of the translocatable unit of IS26-bound structures was observed. This was shown by the variability of plasmid sizes in original isolates, transconjugants or transferred plasmids, and correspondingly, duplications of resistance fragments were found in long-read sequencing. This activation could be artificial due to laboratory handling or naturally occurring. Nevertheless, DHA-1 is a rare AmpC beta-lactamase in livestock and food in Germany, and its dissemination will be monitored in the future. Full article

Pseudomonas aeruginosa is a leading cause of hospital-acquired infections worldwide. Biofilm production, antibiotic resistance, and a wide range of virulence factors contribute to their persistence in nosocomial environments. We describe an outbreak caused by a multidrug-resistant P. aeruginosa strain in an ICU. Antibiotic susceptibility was determined and bla_PER-1 and qnrVC were amplified via PCR. Clonality was determined using PFGE and biofilm formation was studied with a static model. A combination of antibiotics was assessed on both planktonic cells and biofilms. WGS was performed on five isolates. All isolates were clonally related, resistant to ceftazidime, cefepime, amikacin, and ceftolozane-tazobactam, and harbored bla_PER-1; 11/19 possessed qnrVC. Meropenem and ciprofloxacin reduced the biofilm biomass; however, the response to antibiotic combinations with rifampicin was different between planktonic cells and biofilms. WGS revealed that the isolates belonged to ST309 and serotype O11. bla_PER-1 and qnrVC6 were associated with a tandem of ISCR1 as part of a complex class one integron, with aac(6′)-Il and ltrA as gene cassettes. The structure was associated upstream and downstream with Tn4662 and flanked by direct repeats, suggesting its horizontal mobilization capability as a composite transposon. ST309 is considered an emerging high-risk clone that should be monitored in the Americas. Full article