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Mycobacteria is a diverse genus that includes both innocuous environmental species and serious pathogens like Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium ulcerans, the causative agents of tuberculosis, leprosy, and Buruli ulcer, respectively. This study focuses on Mycobacterium marinum, a closely related species known for its larger genome and ability to infect ectothermic species and cooler human extremities. Utilizing whole-genome sequencing, we conducted a comprehensive pan-genome analysis of 100 M. marinum strains, exploring genetic diversity and its impact on pathogenesis and host specificity. Our findings highlight significant genomic diversity, with clear distinctions in core, dispensable, and unique genes among the isolates. Phylogenetic analysis revealed a broad distribution of genetic lineages, challenging previous classifications into distinct clusters. Additionally, we examined the synteny and diversity of the virulence factor CpnT, noting a wide range of C-terminal domain variations across strains, which points to potential adaptations in pathogenic mechanisms. This study enhances our understanding of M. marinum's genomic architecture and its evolutionary relationship with other mycobacterial pathogens, providing insights that could inform disease control strategies for M. tuberculosis and other mycobacteria. [ABSTRACT FROM AUTHOR]

Tuberculosis, a disease caused by Mycobacterium tuberculosis (Mtb), is a significant health problem worldwide. Here, we developed a method to detect large insertions and deletions (indels), which have been generally understudied. Leveraging this framework, we performed a comprehensive analysis of single nucleotide variants and small and large indels across 1,960 Mtb clinical isolates. Comparing the distribution of variants demonstrated that gene disruptive variants are underrepresented in genes essential for bacterial survival. An evolutionary analysis revealed that Mtb genomes are enriched in partially deleterious mutations. Genome-wide association studies identified small and large deletions in eccB2 significantly associated with patient prognosis. Additionally, we unveil significant associations with antibiotic resistance in 23 non-canonical genes. Among these, large indels are primarily found in genetic regions of Rv1216c , Rv1217c , fadD11 , and ctpD. This study provides a comprehensive catalog of genetic variations and highlights their potential impact for the future treatment and risk prediction of tuberculosis. [Display omitted] • A comprehensive variant analysis across 1,960 Mtb clinical isolates was performed • Mtb genomes are enriched with partially deleterious mutations • GWAS analysis identified eccB2 as being significantly associated with patient prognosis • GWAS analysis of antibiotic resistance associations identified 23 non-canonical genes Accumulation of genetic variations including large-sized mutations in Mycobacterium tuberculosis 's genes associated with tuberculosis patient outcomes and bacterial antibiotic resistance ability. [ABSTRACT FROM AUTHOR]

Background: Coagulase-negative staphylococci (CoNS) have been linked to severe conditions such as bloodstream infection, with biofilm formation regarded as the major virulence mechanism. This study determined virulence genes (VGs) (icaA, icaB, icaC, and icaD) responsible for biofilm formation and antibiotic resistance genes (ARGs) (blaZ, mecA, and aac(6')-Ie-aph(2")-Ia) in CoNS isolated from blood samples of 70 neonates with sepsis in Dar es Salaam, Tanzania. We used VITEK®MS (BioMérieux, France) for speciation and phenotypically detected biofilm production using the Congo red agar. Polymerase chain reaction was performed for ARGs and VGs detection; principal component analysis was used to ascertain their relationship. Results: Out of 70 CoNS, Staphylococcus epidermidis, 27 (36.8%) was the most commonly isolate, subsequently to Staphylococcus haemolyticus, 24 (34.3%). The intercellular adhesion genes (ica) were detected in all isolates, with IcaD found in 70 (100.0%), followed by icaB 69 (98.6%), icaC 69 (98.6%), and icaA 65 (92.9%). Four virulence gene combinations (icaADBC, icaBCD, icaACD, and icaABD) were detected, predominantly icaADBC 63 (90.0%). Sixty-one (87.1%) isolates harbored three ARGs, mostly the mecA gene 69 (98.6%), followed by blaZ 67 (95.7%) and aac (6')-Ie-aph (2")-Ia, 65 (92.7%). We observed a moderate positive correlation between mecA and icaA genes (r = 0.4341). Sixty-five (97.0%) isolates resistant to penicillin harbored blaZ genes, and all 62 (100%) resistant to oxacillin harbored mecA genes. Of the 66 isolates resistant to gentamycin, 62 (93.9%) harbored the aac (6')-Ie-aph (2")-Ia gene. The mecA gene contributed most of the resistance, followed by aac(6')-Ie-aph(2")-Ia genes. However, the icaA and icaD genes significantly influenced the virulence of CoNS. Conclusions: Most CoNS isolated from blood samples of neonates with sepsis harbor a variety of clinically relevant virulence and resistance genes, indicating their ability to cause severe infections that are difficult to treat. Significantly, 59 (84.3%) isolates were phenotypically penicillin, gentamycin, and oxacillin resistant; the antibiotics recommended in the national guidelines for empiric treatment of neonatal sepsis. [ABSTRACT FROM AUTHOR]

Background: The investigation on natural antimicrobial compounds against zoonotic pathogens has gained more attention due to the public health concerns regarding the emergence of antimicrobial resistance. Objectives: The current study aimed to assess the effects of thyme essential oil at sub‐minimal inhibitory concentrations (sub‐MICs) on bacterial growth and expression of some virulence genes in Salmonella enteritidis. Methods: The bacterial growth rate and the expression of four virulence genes in S. enteritidis during 18–72 h of exposure to the essential oil at 25%–75% MIC were evaluated via colony counting and real‐time polymerase chain reaction (PCR), respectively. Results: Sub‐inhibitory concentrations of thyme essential oil significantly reduced the growth rate compared to the control. Expression of all tested virulence genes was also reduced by the essential oil in a significant dose‐ and time‐dependent manner. As an example, decreased down‐regulation of hilA, spv, sefA and invA as 1.7‐, 4.14‐, 2.92‐ and 1.04‐fold in 25% MIC and 6.42‐, 7.81‐, 4.4‐ and 3.75‐fold in 75% MIC was observed, respectively, after 24 h of incubation. Likewise, levels of transcription for hilA, spv, sefA and invA were reduced 4.75‐, 6.95‐, 3.75‐ and 2.98‐fold after 18 h and 9.54‐, 8.81‐, 5.65‐ and 4.77‐fold, respectively, after 72 h in 75% MIC compared to the control. Conclusions: According to our data, aside from the growth inhibitory effect of thyme essential oil, the results of current study highlight the potential of thyme for reducing the transcriptional level of virulence genes and therefore the pathogenicity of S. enteritidis. [ABSTRACT FROM AUTHOR]

Salmonella enterica, a prominent foodborne pathogen, contributes significantly to global foodborne illnesses annually. This species exhibits significant genetic diversity, potentially impacting its infectivity, disease severity, and antimicrobial resistance. Whole genome sequencing (WGS) offers comprehensive genetic insights that can be utilized for virulence assessment. However, existing bioinformatic tools for studying Salmonella virulence have notable limitations. To address this gap, a Salmonella Virulence Database with a non-redundant, comprehensive list of putative virulence factors was constructed. Two bioinformatic analysis tools, Virulence Factor Profile Assessment and Virulence Factor Profile Comparison tools, were developed. The former provides data on similarity to the reference genes, e-value, and bite score, while the latter assesses the presence/absence of virulence genes in Salmonella isolates and facilitates comparison of virulence profiles across multiple sequences. To validate the database and associated bioinformatic tools, WGS data from 43,853 Salmonella isolates spanning 14 serovars was extracted from GenBank, and WGS data previously generated in our lab was used. Overall, the Salmonella Virulence database and our bioinformatic tools effectively facilitated virulence assessment, enhancing our understanding of virulence profiles among Salmonella isolates and serovars. The public availability of these resources will empower researchers to assess Salmonella virulence comprehensively, which could inform strategies for pathogen control and risk evaluations associated with human illnesses. [ABSTRACT FROM AUTHOR]

Background: Daycare centres play a critical role in early childhood development but are high-risk environments for infectious disease transmission due to close physical contact, shared toys, inadequate hygiene, and poor ventilation. These risks are especially concerning in low- and middle-income countries (LMICs) like Nigeria, where resources for infection control may be limited. This study aimed to identify and characterise virulence genes in bacterial isolates from daycare centres in Ile-Ife, Nigeria, to assess infection risks. Methods: Between November 2017 and July 2019, 233 samples were collected from 76 children, 33 daycare workers, and 124 fomites in 17 daycare centres. The bacterial isolates were analysed using conventional PCR and RAPD analysis to detect the presence of virulence genes. The frequency of crucial virulence genes and the prevalence of each bacterial species were recorded. Results: Key virulence genes were detected, including fimH in Klebsiella species (22.73% of Gram-negative isolates), algD in Pseudomonas aeruginosa (50%), and icaA and cna in Staphylococcus aureus (16.67%). Staphylococcus aureus was the most prevalent species (35%), followed by Klebsiella (28%) and Pseudomonas aeruginosa (20%). Conclusion: This study highlights the presence of virulent bacterial pathogens in daycare environments, posing a severe infection risk to children. To mitigate these risks, it is essential to implement enhanced infection control measures, such as regular microbial screening, improved hand hygiene practices, and disinfection protocols for fomites. Training programs for daycare workers on hygiene practices and routine monitoring could also significantly reduce infection transmission. These interventions are vital for safeguarding the health of daycare children in Nigeria and similar settings globally. [ABSTRACT FROM AUTHOR]

Background: Clostridioides difficile has been recognized as an emerging pathogen in both humans and animals. In this context, antimicrobial resistance plays a major role in driving the spread of this disease, often leading to therapeutic failure. Moreover, recent increases in community-acquired C. difficile infections have led to greater numbers of investigations into the animal origin of the disease. The aim of this study was to evaluate the genetic similarities between 23 environmental and animal isolates by using whole-genome sequencing and to determine antimicrobial resistance and virulence factor genes in toxigenic C. difficile strains to provide important data for the development of diagnostic methods or treatment guidelines. Results: The most common sequence type was ST11 (87%), followed by ST2 (9%) and ST19 (4%). In addition, 86.95% of the strains exhibited multidrug resistance, with antimicrobial resistance to mainly aminoglycosides, fluoroquinolones, tetracycline and B-lactams; nevertheless, one strain also carried other resistance genes that conferred resistance to lincosamide, macrolides, streptogramin a, streptogramin b, pleuromutilin, oxazolidinone and amphenicol. In addition, a wide range of virulence factor genes, such as those encoding adherence factors, exoenzymes and toxins, were found. However, we observed variations between toxinotypes, ribotypes and sequence types. Conclusions: The results of this study demonstrated significant genetic similarity between ST11 strains isolated from environmental sampling and from animal origin; these strains may represent a reservoir for community-acquired C. difficile infection, which is becoming a growing public health threat due to the development of multridug resistant (MDR) bacteria and the number of virulence factors detected. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic bacterium that is widely distributed in aquatic environments and causes major economic losses in fish and public health hazards.This study aimed to identify the occurrence of P. aeruginosa in samples collected from fish and fish handlers, and to investigate the antimicrobial susceptibility, virulence determinants, and biofilm genes of P. aeruginosa isolates. A total of 276 samples were cross-sectionally collected from Nile tilapia (53), Golden grey mullet (52), Mediterranean horse mackerel (50), Striped red mullet (71), and fish handlers (50) at five different retail fish markets in Damietta Governorate, Egypt. Pseudomonas species (spp.) were biochemically identified in 57.9% of the total examined samples. Peudomonas aeruginosa were the most prevalent species isolated from the fish and human samples via PCR technique. Peudomonas aeruginosa isolates exhibited full resistance (100%) to tobramycin (TOB), gentamicin (CN), and colistin (CL), with a high level of susceptibility (88.5%) to imipenem (IPM) using the disk diffusion method. Most P. aeruginosa isolates (84.6%) exhibited drug resistance, with 61.5% were multidrug resistance (MDR) and 23.1% were extensive drug resistance (XDR). Most isolates had at least four virulence-associated genes (lasB, toxA, exoU, and oprL) and three biofilm genes (psIA, peIA, and lasR) by using uniplex PCR. The lasI, and rhlR Quorum Sensing (QS) genes were identified in 84.6% and 61.5% in the examined P. aeruginosa isolates, respectively. The highest mortality rate in Nile tilapia experimentally infected with P. aeruginosa isolate encoding most of virulent genes. Multivariate analyses revealed high heterogeneity among the examined isolates. This study revealed the emergence of virulent and drug resistant P. aeruginosa isolates in fish, poses high risks to consumers and food. Thus, strict hygienic measures should be considered when catching, handling, and storing fish, in addition to the routine application of antimicrobial susceptibility testing. [ABSTRACT FROM AUTHOR]

Simple Summary: Trueperella pyogenes is a significant opportunistic pathogen that can infect a wide range of animals and humans. Understanding its virulence factors and antibiotic resistance mechanisms is essential for the prevention and control of infections. Presently, research predominantly concentrates on Trueperella pyogenes in dairy cows and pigs, with limited investigations into its prevalence in small ruminants like sheep and goats, despite their importance as food sources. In light of the rapid expansion of China's sheep and goat industry, this study focused on the isolation rate of Trueperella pyogenes from clinical samples obtained from various farms in western China. The objectives were to identify virulence genes and assess drug resistance characteristics in the isolated strains. Furthermore, the genetic relationships and virulence gene profiles, including antibiotic resistance gene carriage, were evaluated in selected isolates. The study underscored the threat posed by Trueperella pyogenes to sheep and goats and highlighted the high levels of antibiotic resistance observed. These findings provide crucial insights for the prevention and treatment strategies on farms and advocate for the prudent use of antibiotics to mitigate the transmission of drug-resistant bacteria through the food chain, thereby protecting human health. Trueperella pyogenes is a significant opportunistic pathogen that causes substantial economic losses in animal agriculture due to its ability to infect various animal tissues and organs. Limited research has been conducted on the prevalence and biological characteristics of T. pyogenes isolated from sheep and goats. This study aimed to isolate T. pyogenes from clinical samples of sheep and goats in western China, examining genetic evolutionary relationships, antibiotic resistance, and virulence genes. Between 2021 and 2023, standard bacteriological methods were used to isolate and identify T. pyogenes from 316 samples (209 from goats and 107 from sheep) collected from 39 farms. Susceptibility to 14 antibiotics was tested using broth microdilution per CLSI guidelines, and PCR detected eight virulence genes. Whole-genome sequencing analyzed genetic relationships and gene carriage status in 39 isolates. The results indicated that 86 strains of T. pyogenes were isolated from 316 samples, yielding an isolation rate of 27.2% (goats n = 47, 22.5%; sheep n = 39, 36.4%). The virulence genes plo, cbpA, nanH, nanP, fimA, fimC, and fimE were present in 100%, 66.7%, 64.1%, 71.8%, 69.2%, 59.0%, and 82.1% of isolates, respectively, with none carrying the fimG gene. The dominant virulence genotype was plo/nanH/nanP/fimA/fimC/fimE. The isolates exhibited resistance to erythromycin (44.2%, 38/86), gentamicin (38.4%, 33/86), sulfamethoxazole/trimethoprim (37.2%, 32/86), tetracycline (32.6%, 28/86), and streptomycin (32.6%, 28/86), and low resistance to chloramphenicol (14.0%, 12/86), ciprofloxacin (7.0%, 6/86), penicillin (5.8%, 5/86), and clindamycin (4.7%, 4/86). All isolates were susceptible to cefotaxime, vancomycin, and linezolid. Among the 86 isolates, 37 (43.0%) displayed multidrug resistance (MDR) characteristics. The whole genome sequencing of 39 isolates identified eight types of resistance genes, including ant(2″)-Ia, ant(3″)-Ia, cmlA1, cmx, erm(X), lnu(A), sul1, and tet(W). Except for tet(W), erm(X), and sul1, the other resistance genes were reported for the first time in T. pyogenes isolated in China. The drug susceptibility test results and resistance gene detection for the isolated strains were consistent for tetracycline, erythromycin, gentamicin, and sulfisoxazole. Similar allelic profiles and genetic evolutionary relationships were found among isolates from different farms. This study highlights the antibiotic resistance status and virulence gene-carrying rate of Trueperella pyogenes, providing a basis for clinical medication. [ABSTRACT FROM AUTHOR]

Yersinia is an important genus comprising foodborne, zoonotic and pathogenic bacteria. On the other hand, species of the so-called group Yersinia enterocolitica-like are understudied and mostly characterized as non-pathogenic, despite of some reports of human infections. The present study aimed to provide genomic insights of Yersinia frederiksenii (YF), Yersinia intermedia (YI) and Yersinia kristensenii (YK) isolated worldwide. A total of 22 YF, 20 YI and 14 YK genomes were searched for antimicrobial resistance genes, plasmids, prophages, and virulence factors. Their phylogenomic relatedness was analyzed by Gegenees and core-genome multi-locus sequence typing. Beta-lactam resistance gene blaTEM-116 and five plasmids replicons (pYE854, ColRNAI, ColE10, Col(pHAD28) and IncN3) were detected in less than five genomes. A total of 59 prophages, 106 virulence markers of the Yersinia genus, associated to adherence, antiphagocytosis, exoenzymes, invasion, iron uptake, proteases, secretion systems and the O-antigen, and virulence factors associated to other 20 bacterial genera were detected. Phylogenomic analysis revealed high inter-species distinction and four highly diverse YF clusters. In conclusion, the results obtained through the analyses of YF, YI and YK genomes suggest the virulence potential of these strains due to the broad diversity and high frequency of prophages and virulence factors found. Phylogenetic analyses were able to correctly distinguish these closely related species and show the presence of different genetic subgroups. These data contributed for a better understanding of YF, YI and YK virulence-associated features and global genetic diversity, and reinforced the need for better characterization of these Y. enterocolitica-like species considered non-pathogenic. [ABSTRACT FROM AUTHOR]

Campylobacter is one of the most frequent bacterial foodborne pathogens worldwide. Poultry is the disease's most clinically significant host species. Despite their importance to public health, the virulence factors and mechanisms that drive C. jejuni pathogenicity are poorly understood, and the relationships between these genes and strain origins remain unclear. In this study, we intended to examine the prevalence, virulence and biofilm formation genes, and antibiotic resistance of C. jejuni isolated from cloacal swab samples of commercial chicken in Aswan Governorate, Egypt. Random samples of fresh chickens (n = 103) were collected from different retail markets. To identify the virulence genes (flaA, cdtB, and cadF genes), polymerase chain reaction was employed in conjunction with the 23S rRNA and mapA genes unique to Campylobacter and C. jejuni, respectively. 17 (16.5%) of the 103 samples had positive Campylobacter spp. tests. C. jejuni was present in nine (8.7%) of the positive isolates. In 77%, 100%, and 88.8% of C. jejuni strains, the genes flaA, cdtB, and cadF were detected, respectively. The antibiotic resistance of the C. jejuni isolates was determined via the disc diffusion method and was observed most frequently to ceftazidime (88.9%), ceftriaxone (77.8%), cephalexin (77.8%), erythromycin (66.6%), while low resistance to levofloxacin (11.1%), and chloramphenicol (11.1%) was detected. These findings highlight the high prevalence of Campylobacter in fresh chickens, which is thought to be the main risk factor for domestically obtained campylobacteriosis in Aswan Governorate, Egypt. [ABSTRACT FROM AUTHOR]

This study was designed to find out the prevalence of Listeria monocytogenes in raw milk and some dairy products and the molecular identification of their virulence genes. One hundred and twenty samples in all, including milk, Kareish cheese, and yogurt (40 of each), were gathered randomly from various sources for this study and examined for the presence of Listeria monocytogenes. Eight distinct strains of L. monocytogenes were identified and molecularly examined for 16 srRNA-specific genes for Listeria monocytogenes, as well as the identification of many pathogenicity genes (inlA, inlB, hlyA, and prfA genes). All eight isolates harbored 16srRNA-specific genes for Listeria monocytogenes; seven isolates harbored both inlA and inlB; six isolates harbored hlyA; and five isolates harbored the prfA gene. The results of antimicrobial susceptibility testing showed high sensitivity to Ciprofloxacin (CP), Gentamycin (CN), Vancomycin (VA), Doxycycline (DO), and Trimethoprim-sulfamethoxazole (SXT) with 100, 87.5, 87.5, 78.5, and 62.5%, respectively, while showing high resistance to Ampicillin (AM), Amoxicillin (AX), Oxicillin (OX), Erythromycin (E), Lincomycin (L), and Ceftriaxone (CRO) with 100, 100, 100, 100, and 75%, respectively. All eight Listeria monocytogenes isolates were multidrug-resistant, holding a variety of antibiotic resistance indexes (MARI) in the range of 0.417-0.833. In conclusion, the study's findings highlight the necessity of implementing more stringent sanitary control procedures, particularly while processing, storing, and marketing dairy products. The pasteurization temperatures must not be less than 85 °C, where only 85% of the bacteria are destroyed by pasteurization at 71-75 °C for 15 seconds. [ABSTRACT FROM AUTHOR]

Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci. [ABSTRACT FROM AUTHOR]

Introduction: Diarrhea is a very important disorder in calves, especially in the first days after birth, due to mortality and economic losses. Among infectious agents, pathogenic strains of Escherichia coli (E. coli) have been known as the most important causes of diarrhea in calves. Therefore, phenotypic and genotypic studies on E. coli strains that cause diarrhea in calves can be helpful for understanding their prevelance control methods. Material and method: In this study, rectal swabs were collected from 1 to 30-day-old calves with diarrhea during 2021. The antibiotic-resistant pattern of the isolates was determined by the KirbyBauer disk diffusion susceptibility test. The prevalence of the pathogenic genes (bundle-forming pilus (bfp) and enteropathogenic attachment epithelial cells (eae) for enteropathogenic E. coli (EPEC) strains and verotoxigenic E. coli (VTEC), Shiga toxin (stx1 and stx2) strains was investigated using PCR. Results and discussion: Out of 105 samples, 81 isolates (85.05%) of E. coli were identified. The resistance of the isolates was observed for penicillin (56.84%), tetracycline (38.3%), sulfamethoxazole-trimethoprim (38.3%), gentamicin (29.6%), ceftazidime (29.2%), colistin (25.9%), imipenem (23.5%), ceftriaxone (22.21%), nalidixic acid (22.2%), ciprofloxacin (14.8%) and ofloxacin (9.9%) were detected in the isolates. Furtheremore, 16% of the isolates had the eae gene and (24.7%) had both the stx1 and stx2 genes. In the present study, the infection rate of calves with diarrhea with VTEC strains was higher than EPEC strains. According to the results of the present study, the presence of antibiotic resistance in E. coli isolates indicates the high importance of this bacterium in terms of epidemiology and public health. [ABSTRACT FROM AUTHOR]

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Simple Summary: The increase in respiratory infections, particularly acute pneumonia, in puppies poses a significant health risk due to the disease's rapid severity. This study successfully identified four multidrug-resistant strains of extraintestinal pathogenic Escherichia coli from puppies with acute pneumonia, which contained various virulence genes and were classified using sequence typing. This study emphasizes the need to understand the molecular traits of Escherichia coli strains causing canine pneumonia. Such an understanding facilitates the formulation of targeted intervention strategies and the exploration of novel therapeutic approaches for the effective treatment of acute pneumonia in puppies. To determine the etiological agents responsible for acute pneumonia in puppies in China, this study utilized bronchoalveolar lavage (BAL) fluid extraction to enable the isolation, culture, biochemical identification, and 16S rRNA PCR amplification of the pathogens. Following preliminary identification, the pathogens underwent analysis for antibiotic resistance phenotypes and resistance genes. Additionally, the study examined the presence of virulence genes, conducted multilocus sequence typing (MLST), and performed whole-genome sequencing (WGS). The findings revealed that all four isolated pathogens were characterized as extraintestinal pathogenic Escherichia coli (ExPEC). The examined ExPEC strains demonstrated resistance to cephalosporins, tetracyclines, and penicillins, while remaining susceptible to aminoglycosides, beta-lactamase inhibitors, carbapenems, chloramphenicols, and sulfonamides. An analysis of virulence genes identified the presence of eight genes, namely CNF-I, fyuA, fimC, papC, ompA, fimH, irp2, and iroN, which are implicated in their invasiveness and potential to inflict tissue damage. The MLST analysis revealed that all ExPEC strains were classified under either sequence type ST131 (Achtman database) or ST43 (Pasteur database). The study further determined that these strains were absent in the kennel's drinking water source, thereby ruling out water contamination as a potential factor in the emergence of ST131-type ExPEC. This study offers a theoretical framework and empirical evidence for elucidating the potential pathogenic mechanisms and clinical therapeutic strategies of ExPEC in the etiology of acute pneumonia in puppies. [ABSTRACT FROM AUTHOR]

This study was important to improve proper biosecurity measures and controlling the spread of Aeromonas to prevent future outbreaks. This research sought to determine whether virulent Aeromans species were present in morbid rainbow trout, their resistance and their genetic relatedness. A total number of 542 tissue lesion specimens were collected from gill, liver, heart and kidneys in morbid domesticated fish in Duhok province, Iraq. The gyrB DNA sequence analysis was used to determine the species classification. Drug susceptibility testing was conducted for all isolated strains using disc diffusion technique. The genotyping analysis was carried out using enterobacterial repetitive intergenic consensus-polymerase chain reaction. Thirty-four isolates were found and they were classified into three species (Aeromonas veronii, Aeromonas sorbia, and Aeromonas allosaccharophila), where A. veronii stand as one of the most prevalent species. The most frequently affected organ by Aeromonas was the gills among four different organs. The detection frequencies of the virulence genes aerolysin, outer membrane protein, glycerophospholipid-cholesterol acyltransferase, elastase, flagella, serine protease, cytotonic heat-labile, and hemolysin were 100%, 100%, 79.41%, 64.70%, 76.47%, 67.64%, 70.58%, and 41.17, respectively. None of the strains possessed all of the virulence markers. All isolates were completely resistant to ceftazidime, amoxicillin and doxycycline. All isolates were found to be multi-drug-resistant. Regardless of the nearest geographic source area of samples and the same Aeromonas species, there was a high genetic diversity. The results of this study could help farmers and researchers make informed decisions about measures of biosecurity and proper therapeutic drugs to apply to prevent current outbreaks and prevent them from recurring again. [ABSTRACT FROM AUTHOR]

The increase in the number of hospital strains of hypervirulent and multidrug resistant (MDR) Pseudomonas aeruginosa is a major health problem that reduces medical treatment options and increases mortality. The molecular profiles of virulence and multidrug resistance of P. aeruginosa-associated hospital and community infections in Mexico have been poorly studied. In this study, we analyzed the different molecular profiles associated with the virulence genotypes related to multidrug resistance and the genotypes of multidrug efflux pumps (mex) in P. aeruginosa causing clinically critical infections isolated from Mexican patients with community- and hospital-acquired infections. Susceptibility to 12 antibiotics was determined using the Kirby–Bauer method. The identification of P. aeruginosa and the detection of virulence and efflux pump system genes were performed using conventional PCR. All strains isolated from patients with hospital-acquired (n = 67) and community-acquired infections (n = 57) were multidrug resistant, mainly to beta-lactams (ampicillin [96.7%], carbenicillin [98.3%], cefalotin [97.5%], and cefotaxime [87%]), quinolones (norfloxacin [78.2%]), phenicols (chloramphenicol [91.9%]), nitrofurans (nitrofurantoin [70.9%]), aminoglycosides (gentamicin [75%]), and sulfonamide/trimethoprim (96.7%). Most strains (95.5%) isolated from patients with hospital- and community-acquired infections carried the adhesion (pilA) and biofilm formation (ndvB) genes. Outer membrane proteins (oprI and oprL) were present in 100% of cases, elastases (lasA and lasB) in 100% and 98.3%, respectively, alkaline protease (apr) and alginate (algD) in 99.1% and 97.5%, respectively, and chaperone (groEL) and epoxide hydrolase (cif) in 100% and 97.5%, respectively. Overall, 99.1% of the strains isolated from patients with hospital- and community-acquired infections carried the efflux pump system genes mexB and mexY, while 98.3% of the strains carried mexF and mexZ. These findings show a wide distribution of the virulome related to the genotypic and phenotypic profiles of antibiotic resistance and the origin of the strains isolated from patients with hospital- and community-acquired infections, demonstrating that these molecular mechanisms may play an important role in high-pathogenicity infections caused by P. aeruginosa. [ABSTRACT FROM AUTHOR]

Background: This study investigated Bacillus cereus and Bacillus subtilis from food vendors in Ondo State, Nigeria. Methods: A comprehensive whole-genome sequencing (WGS) analysis of Bacillus genomes, including genome assembly, plasmid prediction, species identification, antimicrobial resistance (AMR) gene identification, virulence gene identification, and multilocus sequencing typing, was conducted. Results: The genome assembly revealed a B. cereus genome with 87 contigs, a length of 5,798,917 base pairs, and a GC content of 34.79%, whereas B. subtilis had a genome length of 4,238,143 bp and was composed of 253 contigs with a contig L50 of 24, a contig N50 of 55,053, and a GC content of 43.14904%. Plasmid prediction revealed the absence of prominent plasmids in the assembled B. cereus genome, whereas the repUS12 plasmid was recognized with an identity of less than 95.63% for the B. subtilis genome. Species identification via the average nucleotide identity (ANI) calculation confirmed that Bacillus cereus had a 98.97% ANI value, whereas a 98.39% ANI value was confirmed for B. subtilis WAUSV36. AMR genes were identified, with virulence genes such as the alo, cytK, and hbl genes also detected in B. cereus, whereas clpX, codY, purA, and purB genes were detected in B. subtilis. Multiple-locus sequence typing (MLST) revealed that B. cereus belongs to sequence type 73 with 100% identity, identifying housekeeping gene alleles, including glp_13, gmk_8, and ilv_9, whereas B. subtilis belongs to sequence type 130, with the ilvD gene showing a perfect match and the highest allele length of 471 for the housekeeping genes identified. Conclusions: This detailed WGS analysis provides valuable insights into the genetic composition, potential virulence factors, and resistance profiles of B. cereus and B. subtilis, enhancing the understanding of their pathogenicity and epidemiology. The genomic analysis of B. cereus and B. subtilis revealed potential genomic applications in the context of food safety. [ABSTRACT FROM AUTHOR]

Background: In the present study, we aimed to determine the frequency of the csgA, fimH, mrkD, foc, papaGI, papGII and papGIII genes, to provide and to design fimbrial adhesin gene (FAG) patterns and profiles for the isolated uropathogenic Escherichia coli (UPEC) strains. Methods: The enrollment of 108 positive urine samples was performed during seven months, between January 2022 and July 2022. The UPEC strains were confirmed through the standard microbiological and biochemical tests. The antimicrobial susceptibility test was performed through the Kirby–Bauer disc diffusion method. Molecular screening of FAGs was done through the polymerase chain reaction technology. The statistical analyses including chi square and Fisher's exact tests were performed to interpret the obtained results in the present study. Results: As the main results, the antimicrobial resistance (AMR) patterns, multi- (MDR) and extensively drug-resistance (XDR) patterns and FAG patterns were designed and provided. fimH (93.3%), csgA (90.4%) and papG (37.5%) (papGII (30.8%)) genes were recognized as the top three FAGs, respectively. Moreover, the frequency of csgA-fimH gene profile was identified as the top FAG pattern (46.2%) among the others. The isolates bearing csgA-fimH gene profile were armed with a versatile of phenotypic AMR patterns. In the current study, 27.8%, 69.4% and 1.9% of the UPEC isolates were detected as extended-spectrum ß-lactamases (ESBLs) producers, MDR and XDR strains, respectively. Conclusions: In conclusion, detection, providing and designing of patterns and profiles in association with FAGs, AMR feature in UPEC strains give us an effective option to have a successful and influential prevention for both of UTIs initiation and AMR feature. [ABSTRACT FROM AUTHOR]

1. Salmonella Gallinarum strains isolated from a southern Brazil fowl typhoid outbreak were subjected to phenotypic and genotypic analyses to identify genetic elements that could improve prevention and control strategies.2. Whole-genome sequencing revealed the presence of the aac(6’)-Iaa gene, conferring aminoglycoside resistance, along with novel chromosomal point mutations, including the first detection of parE p.S451F in Salmonella Gallinarum.3. Additionally, IncFII(S) plasmid replicons, Salmonella pathogenicity islands and 105 virulence genes associated with cell adhesion, invasion and antimicrobial peptide resistance were identified.4. These findings shed light on the molecular mechanisms of fowl typhoid and provide crucial insights into emerging antimicrobial resistance and virulence factors. [ABSTRACT FROM AUTHOR]

RESEARCH HIGHLIGHTSAvian pathogenic Escherichia coli (APEC) is a significant cause of morbidity, mortality, and production loss to the poultry industry worldwide. Here, we characterized 569 E. coli isolates from avian-diagnosed colibacillosis cases from the state of Georgia, USA. In total, 339 isolates were assigned into 32 serogroups with the majority classifying as O78, O2, O25, O8, O1, O86, O18, and O15. Serogroup O25 was found to link with broilers, while broiler breeders were more often associated with serogroup O1 and pet/ hobby birds with serogroup O8. In addition, some serogroups (O1) were more prevalent in the summer and fall. Analysis for virulence-associated genes (VAGs) found 23.20% of isolates did not harbour any genes linked with the APEC pathotype, while ColV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ) were frequently detected among most isolates (with 80–96% prevalence) and some of these genes were linked with serogroup. Phylogenetic analysis, classified isolates into phylogenetic groups B2 (34%), F (19%), A (15%), and G (9%). The phylogenetic group B2 isolates also harboured the highest number of VAGs. This study highlights that the current APEC-causing disease in birds in the State of Georgia has identified several emerging serogroups possessing several VAGs that could potentially lead to challenges in colibacillosis control.Several emerging APEC serogroups were observed in Georgia poultry populations.An association between APEC serogroups and bird type was observed.The prevalence of different APEC serogroups was influenced by season.A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed.Several emerging APEC serogroups were observed in Georgia poultry populations.An association between APEC serogroups and bird type was observed.The prevalence of different APEC serogroups was influenced by season.A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed. [ABSTRACT FROM AUTHOR]

Since foodborne diseases are one of the major causes of human hospitalization and death, one of the main challenges to food safety is the elimination or reduction of pathogens from food products throughout the food production chain. Pathogens, such as Salmonella species, Escherichia coli, Bacillus cereus, Clostridium species, Staphylococcus aureus, Listeria monocytogenes, Campylobacter species, etc., enter the consumer's body through the consumption of contaminated food and eventually cause disease, disability, and death in humans. In particular, the expression of virulence genes of these pathogens in various food environments containing them has been repeatedly reported, which is a key issue for the survival and pathogenicity of the pathogen. Hence, in this review, the interventions to prevent and control foodborne diseases, such as the application of natural preservatives, redox potential, heat treatments, high‐pressure processing, and gaseous atmosphere, are discussed based on the literature. Moreover, the effects of various environmental conditions on bacterial gene expression are comprehensively reviewed. In conclusion, the effects of intrinsic and extrinsic factors on the growth and pathogenicity of bacteria are very complicated. The information obtained from the current study can be used to develop new control strategies, improve food safety, and ensure human health. [ABSTRACT FROM AUTHOR]

Introduction: Drug-resistant tuberculosis is a severe global public health threat. Virulence factors and antibiotic resistance are generally considered to play a significant role in bacterial pathogenesis. However, the interaction between resistance and virulence in Mycobacterium tuberculosis (MTB) remains unclear. Methodology: Here, we used whole genome sequences from 667 MTB isolates from 14 countries to complete an in silico evaluation of the correlations between virulence gene mutations, drug resistance, and lineage classification. The chi-square (χ2) test was used to determine whether specific virulence gene mutations and drug resistance were related. Results: Our results showed that Mce1R_G171R and Pks15_V333A, were positively correlated with streptomycin and ethambutol resistance, respectively, and Pks15_T46I was correlated with isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin resistance. We also identified an additional 24 and 40 single nucleotide polymorphisms as well as 6 and 2 insertions or deletions in various virulence genes that are likely to be associated with changes in drug susceptibility in L2 and L4, respectively. Conclusions: Taken together our data suggest that there may be some degree of co-selection between virulence and resistance factors, which may help MTB more easily adapt to new environments. [ABSTRACT FROM AUTHOR]

Background: Several Acinetobacter species live in different ecosystems, such as soil, freshwater, wastewater, and solid wastes, which has attracted considerable research interests in public health and agriculture. Methods: We assessed the distribution of Acinetobacter baumannii and Acinetobacter nosocomialis in three freshwater resources (Great Fish, Keiskemma, and Tyhume rivers) in South Africa between April 2017–March 2018. Molecular identification of Acinetobacter species was performed using Acinetobacter-specific primers targeting the recA gene, whilst confirmed species were further delineated into A. baumannii and A. nosocomialis. Similarly, virulence genes; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were assessed. Results: Our finding revealed that 410 (48.58%) and 23 (2.7%) of the isolates were confirmed as A. baumannii and A. nosocomalis, respectively. Additionally, three hundred and eight (75.12%) A. baumannii and three (13.04%) A. nosocomialis exhibited one or more of the virulence genes among the seven tested. OmpA was the most prevalent virulence gene in A. baumannii in freshwater sources. Conclusions: The distribution of clinically important Acinetobacter species in the freshwater sources studied suggests possible contamination such as the release of hospital wastewater and other clinical wastes into the environment thereby posing a risk to public health. [ABSTRACT FROM AUTHOR]

According to a report by the World Health Organization (WHO), each year, over 550 million individuals worldwide suffer from and 230,000 die from diarrheal illnesses, which accounts for more than half of the global foodborne disease burden. Among them, children face a heightened vulnerability, with approximately 220 million falling ill and 96,000 succumbing to these diseases annually. This work aimed to study the genomic characterization of selected E. coli strains from catfish (Clarias (C.) gariepinus) caught from the Onitsha North axis of the River Niger in Anambra state, Nigeria. A total of 50 fish were randomly purchased from different fishermen over a period of four months. Samples that comprised six different organs (skin, flesh, gills, gonads, guts, and liver) were screened for E. coli strains using cultural and biochemical methods. Multilocus sequence typing (MLST) and core genome (cg)MLST were performed using Ridom SeqSphere+ software. The aerobic plate count (APC) and coliform count ranged from 0.5 × 104 to 3.7 × 104 cfu/g and 0 to 3.0 × 104 cfu/g, respectively. Whole-genome sequencing (WGS) confirmed the presence of E. coli and Klebsiella quasipneumoniae isolates in our samples. We could identify only two serotypes (O102:H7 and O40:H4) of E. coli. Antimicrobial resistance genes (ARGs) and point mutations that conferred antibiotic resistance were extracted from the genome assemblies. Good hygiene is recommended to avoid the cross-contamination of raw C. gariepinus with ready-to-eat food. [ABSTRACT FROM AUTHOR]

Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host–pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions. [ABSTRACT FROM AUTHOR]

In the present study, a total of 102 samples were collected from chickens of different flocks, died due to suspected colibacillosis. Bacteriological and PCR methods were applied to detect avian pathogenic Escherichia coli (APEC). Phenotypic antimicrobial resistance (AMR) was determined by disk diffusion method. Extended spectrum beta lactamases (ESBL) detection was carried out via PCR by targeting blaTEM, blaSHV, blaOXA, and blaCTX-M groups 1, 2, and 9. Genes of eight virulence factors and class I integrons were also detected by PCR using gene specific primers. Culture, microscopic, biochemical tests and PCR recognised 69/102 (67.64%) samples as E. coli. Phenotypic AST revealed higher resistance against fluoroquinolone antibiotics, i.e., enrofloxacin (72.46%), levofloxacin (69.56%) & ciprofloxacin (66.66%), followed by amoxyclav (63.77%) and tetracycline (59.42%). Six isolates were found as pan-drug-resistant E. coli. A total of 48 (69.56%) and 7 (10.14%) isolates were positive for the presence of blaTEM and blaCTX-M-G9 genes, respectively, whereas 2 (2.90%) isolates each were found positive for blaSHV, blaOXA, and blaCTX-M-G1 genes. Among APEC associated virulence genes, iss (79.71%) was the most predominant, followed by tsh (50.72%), ast (30.43%), cvaf (26.08%), pap (23.18%), vat (8.69%) and stx-1 (1.44%). Thirty-two isolates harboured class I integrons, either with or without ESBL genes. Conclusively, the isolates under study showed pan and multiple-drug resistance, specifically against fluoroquinolone drugs. ESBL production was mediated principally through blaTEM and blaCTX-M-G9. Multiple virulence factors, toxins, and carriage & spread factor render these as zoonotically potential pathogens for humans. [ABSTRACT FROM AUTHOR]

Background: Vancomycin-resistant enterococci (VRE) have become an increasing public health concern in the past few decades, being associated with serious multidrug-resistant (MDR) infections. This study was conducted to investigate the role of diarrheic pet animals as potential reservoirs for virulent extensively drug-resistant (XDR) VRE and their threat on human health. Materials and Methods: Rectal swabs were collected from 153 diarrheic pet animals (80 dogs and 73 cats). The collected swabs were cultured on CHROMagarTMVRE for the isolation of vancomycin-resistant Enterococcus faecalis and Enterococcus faecium, and then suspected colonies were identified as enterococci after Gram staining, conventional biochemical tests, and molecular techniques. VRE were basically identified using the disk diffusion method; however, molecular identification of vanA and vanB genes was carried out among confirmed VRE isolates. Moreover, three virulence genes (cytolysin A, cylA; enterococcal surface protein, esp; and hyaluronidase, hyl) were investigated in VRE isolates. Thereafter, VRE strains that harbored virulence genes were tested for antimicrobial susceptibility. Results: Eighteen out of 153 animals (11.8%) were positive for VRE, which were obtained from 15% and 8.2% of the examined dogs and cats, respectively. None of the obtained isolates carried the vanA gene, whereas the vanB gene was detected in E. faecalis (4/10) with a prevalence rate (40%). Of the obtained VRE isolates, five possessed esp and/or cylA, while all strains were negative for the hyl gene. Furthermore, four virulent VRE isolates exhibited an XDR pattern, and one isolate was MDR. Conclusion: Diarrheic pet animals could represent a potential zoonotic reservoir for virulent XDR vancomycin-resistant E. faecalis, which may have serious public health implications. [ABSTRACT FROM AUTHOR]

This study aims to investigate the association between antimicrobial resistance genes and virulence factors in ST11 and non-ST11 types of CR-KP in bloodstream infections in the intensive care unit, providing a theoretical basis for infection control and clinical diagnosis and treatment. Methods: From January 2021 to June 2023, samples of Klebsiella pneumoniae from bloodstream infections were collected at our hospital, focusing on those resistant to carbapenems. The resistance genes, housekeeping genes, and virulence genes were identified through PCR and analyzed using the GrapeTree software to perform MLST-based minimum spanning tree typing. Results: Among the 85 CR-KP cases, 61.18% were of the ST11 type, predominantly of the KL64 capsular type; non-ST11 types were mainly ST15, accounting for 25.88%, predominantly of the KL5 capsular type. The carriage rates of virulence genes such as rmpA2, entB, silS, kpn, iucA, peg-344, and terB were significantly higher in the ST11 group than in the non-ST11 group. The primary carbapenemase identified was class A enzyme blaKPC-2, with a higher carriage rate in the ST11 group. Drug susceptibility tests showed that the resistance rates for cefepime, ertapenem, nitrofurantoin, amikacin, and gentamicin were also higher in the ST11 group, consistent with the resistance genotype findings. Conclusion: The study reveals that ST11 type CR-KP in intensive care unit bloodstream infections exhibits stronger resistance and higher virulence compared to non-ST11 types, posing significant challenges to clinical treatment. Thus, strict control over the use of carbapenem antibiotics is essential to prevent the spread of resistant plasmids. [ABSTRACT FROM AUTHOR]

Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health—a concept known as One Health—there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile. [ABSTRACT FROM AUTHOR]

Recent genomic characterisation of translocating Escherichia coli HMLN-1 isolated from mesenteric lymph nodes (MLNs) and blood of a patient with a fatal case of pancreatitis revealed the presence of a type 6 secretion system (T6SS) that was not present in non-translocating E. coli strains. This strain was also genomically similar to adherent-invasive E. coli (AIEC) LF82 pathotype. We aimed to identify the role of T6SS-1 in the pathogenesis of this strain and other pathogenic E. coli. The HMLN-1 strain was initially tested for the presence of six virulence genes (VGs) associated with AIEC strains and an iron sequestering system. Additionally, HMLN-1's interaction with a co-culture of Caco-2:HT29-MTX cells and its intra-macrophagic survival was evaluated. We subsequently screened a collection of 319 pathogenic E. coli strains isolated from patients with urinary tract infection (UTI), diarrhoea, inflammatory bowel disease (IBD) and septicaemia for the presence of T6SS-1 and its expression related to adhesion, invasion and translocation via the above co-culture of the intestinal cell lines. The results showed that HMLN-1 harboured four of the AIEC-associated VGs (dsbA, htrA, ompC and afaC). Screening of the pathogenic E. coli collection detected the presence of the T6SS-1 genes in septicaemic and UTI E. coli strains at a significantly higher level than diarrhoea and IBD strains (p < 0.0001). The high expression of T6SS-1 in E. coli HMLN-1 upon adhesion and invasion, as well as its high prevalence among extra-intestinal E. coli strains, suggests a role for T6SS-1 in the pathogenesis of translocating E. coli. [ABSTRACT FROM AUTHOR]

Abstract Mycobacteria is a diverse genus that includes both innocuous environmental species and serious pathogens like Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium ulcerans, the causative agents of tuberculosis, leprosy, and Buruli ulcer, respectively. This study focuses on Mycobacterium marinum, a closely related species known for its larger genome and ability to infect ectothermic species and cooler human extremities. Utilizing whole-genome sequencing, we conducted a comprehensive pan-genome analysis of 100 M. marinum strains, exploring genetic diversity and its impact on pathogenesis and host specificity. Our findings highlight significant genomic diversity, with clear distinctions in core, dispensable, and unique genes among the isolates. Phylogenetic analysis revealed a broad distribution of genetic lineages, challenging previous classifications into distinct clusters. Additionally, we examined the synteny and diversity of the virulence factor CpnT, noting a wide range of C-terminal domain variations across strains, which points to potential adaptations in pathogenic mechanisms. This study enhances our understanding of M. marinum's genomic architecture and its evolutionary relationship with other mycobacterial pathogens, providing insights that could inform disease control strategies for M. tuberculosis and other mycobacteria.

Abstract Background Coagulase-negative staphylococci (CoNS) have been linked to severe conditions such as bloodstream infection, with biofilm formation regarded as the major virulence mechanism. This study determined virulence genes (VGs) (icaA, icaB, icaC, and icaD) responsible for biofilm formation and antibiotic resistance genes (ARGs) (blaZ, mecA, and aac(6’)-Ie-aph(2’’)-Ia) in CoNS isolated from blood samples of 70 neonates with sepsis in Dar es Salaam, Tanzania. We used VITEK®MS (BioMérieux, France) for speciation and phenotypically detected biofilm production using the Congo red agar. Polymerase chain reaction was performed for ARGs and VGs detection; principal component analysis was used to ascertain their relationship. Results Out of 70 CoNS, Staphylococcus epidermidis, 27 (36.8%) was the most commonly isolate, subsequently to Staphylococcus haemolyticus, 24 (34.3%). The intercellular adhesion genes (ica) were detected in all isolates, with IcaD found in 70 (100.0%), followed by icaB 69 (98.6%), icaC 69 (98.6%), and icaA 65 (92.9%). Four virulence gene combinations (icaADBC, icaBCD, icaACD, and icaABD) were detected, predominantly icaADBC 63 (90.0%). Sixty-one (87.1%) isolates harbored three ARGs, mostly the mecA gene 69 (98.6%), followed by blaZ 67 (95.7%) and aac (6’)-Ie-aph (2’’)-Ia, 65 (92.7%). We observed a moderate positive correlation between mecA and icaA genes (r = 0.4341). Sixty-five (97.0%) isolates resistant to penicillin harbored blaZ genes, and all 62 (100%) resistant to oxacillin harbored mecA genes. Of the 66 isolates resistant to gentamycin, 62 (93.9%) harbored the aac (6’)-Ie-aph (2’’)-Ia gene. The mecA gene contributed most of the resistance, followed by aac(6’)-Ie-aph(2’’)-Ia genes. However, the icaA and icaD genes significantly influenced the virulence of CoNS. Conclusions Most CoNS isolated from blood samples of neonates with sepsis harbor a variety of clinically relevant virulence and resistance genes, indicating their ability to cause severe infections that are difficult to treat. Significantly, 59 (84.3%) isolates were phenotypically penicillin, gentamycin, and oxacillin resistant; the antibiotics recommended in the national guidelines for empiric treatment of neonatal sepsis.

Abstract Background Daycare centres play a critical role in early childhood development but are high-risk environments for infectious disease transmission due to close physical contact, shared toys, inadequate hygiene, and poor ventilation. These risks are especially concerning in low- and middle-income countries (LMICs) like Nigeria, where resources for infection control may be limited. This study aimed to identify and characterise virulence genes in bacterial isolates from daycare centres in Ile-Ife, Nigeria, to assess infection risks. Methods Between November 2017 and July 2019, 233 samples were collected from 76 children, 33 daycare workers, and 124 fomites in 17 daycare centres. The bacterial isolates were analysed using conventional PCR and RAPD analysis to detect the presence of virulence genes. The frequency of crucial virulence genes and the prevalence of each bacterial species were recorded. Results Key virulence genes were detected, including fimH in Klebsiella species (22.73% of Gram-negative isolates), algD in Pseudomonas aeruginosa (50%), and icaA and cna in Staphylococcus aureus (16.67%). Staphylococcus aureus was the most prevalent species (35%), followed by Klebsiella (28%) and Pseudomonas aeruginosa (20%). Conclusion This study highlights the presence of virulent bacterial pathogens in daycare environments, posing a severe infection risk to children. To mitigate these risks, it is essential to implement enhanced infection control measures, such as regular microbial screening, improved hand hygiene practices, and disinfection protocols for fomites. Training programs for daycare workers on hygiene practices and routine monitoring could also significantly reduce infection transmission. These interventions are vital for safeguarding the health of daycare children in Nigeria and similar settings globally.

Abstract Salmonella enterica, a prominent foodborne pathogen, contributes significantly to global foodborne illnesses annually. This species exhibits significant genetic diversity, potentially impacting its infectivity, disease severity, and antimicrobial resistance. Whole genome sequencing (WGS) offers comprehensive genetic insights that can be utilized for virulence assessment. However, existing bioinformatic tools for studying Salmonella virulence have notable limitations. To address this gap, a Salmonella Virulence Database with a non-redundant, comprehensive list of putative virulence factors was constructed. Two bioinformatic analysis tools, Virulence Factor Profile Assessment and Virulence Factor Profile Comparison tools, were developed. The former provides data on similarity to the reference genes, e-value, and bite score, while the latter assesses the presence/absence of virulence genes in Salmonella isolates and facilitates comparison of virulence profiles across multiple sequences. To validate the database and associated bioinformatic tools, WGS data from 43,853 Salmonella isolates spanning 14 serovars was extracted from GenBank, and WGS data previously generated in our lab was used. Overall, the Salmonella Virulence database and our bioinformatic tools effectively facilitated virulence assessment, enhancing our understanding of virulence profiles among Salmonella isolates and serovars. The public availability of these resources will empower researchers to assess Salmonella virulence comprehensively, which could inform strategies for pathogen control and risk evaluations associated with human illnesses.

Abstract Background Clostridioides difficile has been recognized as an emerging pathogen in both humans and animals. In this context, antimicrobial resistance plays a major role in driving the spread of this disease, often leading to therapeutic failure. Moreover, recent increases in community-acquired C. difficile infections have led to greater numbers of investigations into the animal origin of the disease. The aim of this study was to evaluate the genetic similarities between 23 environmental and animal isolates by using whole-genome sequencing and to determine antimicrobial resistance and virulence factor genes in toxigenic C. difficile strains to provide important data for the development of diagnostic methods or treatment guidelines. Results The most common sequence type was ST11 (87%), followed by ST2 (9%) and ST19 (4%). In addition, 86.95% of the strains exhibited multidrug resistance, with antimicrobial resistance to mainly aminoglycosides, fluoroquinolones, tetracycline and B-lactams; nevertheless, one strain also carried other resistance genes that conferred resistance to lincosamide, macrolides, streptogramin a, streptogramin b, pleuromutilin, oxazolidinone and amphenicol. In addition, a wide range of virulence factor genes, such as those encoding adherence factors, exoenzymes and toxins, were found. However, we observed variations between toxinotypes, ribotypes and sequence types. Conclusions The results of this study demonstrated significant genetic similarity between ST11 strains isolated from environmental sampling and from animal origin; these strains may represent a reservoir for community-acquired C. difficile infection, which is becoming a growing public health threat due to the development of multridug resistant (MDR) bacteria and the number of virulence factors detected.

Abstract Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic bacterium that is widely distributed in aquatic environments and causes major economic losses in fish and public health hazards.This study aimed to identify the occurrence of P. aeruginosa in samples collected from fish and fish handlers, and to investigate the antimicrobial susceptibility, virulence determinants, and biofilm genes of P. aeruginosa isolates. A total of 276 samples were cross-sectionally collected from Nile tilapia (53), Golden grey mullet (52), Mediterranean horse mackerel (50), Striped red mullet (71), and fish handlers (50) at five different retail fish markets in Damietta Governorate, Egypt. Pseudomonas species (spp.) were biochemically identified in 57.9% of the total examined samples. Peudomonas aeruginosa were the most prevalent species isolated from the fish and human samples via PCR technique. Peudomonas aeruginosa isolates exhibited full resistance (100%) to tobramycin (TOB), gentamicin (CN), and colistin (CL), with a high level of susceptibility (88.5%) to imipenem (IPM) using the disk diffusion method. Most P. aeruginosa isolates (84.6%) exhibited drug resistance, with 61.5% were multidrug resistance (MDR) and 23.1% were extensive drug resistance (XDR). Most isolates had at least four virulence-associated genes (lasB, toxA, exoU, and oprL) and three biofilm genes (psIA, peIA, and lasR) by using uniplex PCR. The lasI, and rhlR Quorum Sensing (QS) genes were identified in 84.6% and 61.5% in the examined P. aeruginosa isolates, respectively. The highest mortality rate in Nile tilapia experimentally infected with P. aeruginosa isolate encoding most of virulent genes. Multivariate analyses revealed high heterogeneity among the examined isolates. This study revealed the emergence of virulent and drug resistant P. aeruginosa isolates in fish, poses high risks to consumers and food. Thus, strict hygienic measures should be considered when catching, handling, and storing fish, in addition to the routine application of antimicrobial susceptibility testing.

Abstract Listeria monocytogenes is an important foodborne pathogen known for causing listeriosis. To gain insights into the pathogenicity, genetic characterization, and evolution of various Listeria species, in vitro cell adhesion and invasion ability assays and whole-genome sequencing were performed using four Listeria strains isolated from livestock and poultry slaughterhouses. The four Listeria strains exhibited adhesion and invasion abilities in Caco-2 and RAW264.7 cells. Pathogenic Liv1-1 and Lm2-20 had higher adhesion ability, but non-pathogenic Lin4-99 was more invasive than Lm2-20 (p

Abstract Background This study investigated Bacillus cereus and Bacillus subtilis from food vendors in Ondo State, Nigeria. Methods A comprehensive whole-genome sequencing (WGS) analysis of Bacillus genomes, including genome assembly, plasmid prediction, species identification, antimicrobial resistance (AMR) gene identification, virulence gene identification, and multilocus sequencing typing, was conducted. Results The genome assembly revealed a B. cereus genome with 87 contigs, a length of 5,798,917 base pairs, and a GC content of 34.79%, whereas B. subtilis had a genome length of 4,238,143 bp and was composed of 253 contigs with a contig L50 of 24, a contig N50 of 55,053, and a GC content of 43.14904%. Plasmid prediction revealed the absence of prominent plasmids in the assembled B. cereus genome, whereas the repUS12 plasmid was recognized with an identity of less than 95.63% for the B. subtilis genome. Species identification via the average nucleotide identity (ANI) calculation confirmed that Bacillus cereus had a 98.97% ANI value, whereas a 98.39% ANI value was confirmed for B. subtilis WAUSV36. AMR genes were identified, with virulence genes such as the alo, cytK, and hbl genes also detected in B. cereus, whereas clpX, codY, purA, and purB genes were detected in B. subtilis. Multiple-locus sequence typing (MLST) revealed that B. cereus belongs to sequence type 73 with 100% identity, identifying housekeeping gene alleles, including glp_13, gmk_8, and ilv_9, whereas B. subtilis belongs to sequence type 130, with the ilvD gene showing a perfect match and the highest allele length of 471 for the housekeeping genes identified. Conclusions This detailed WGS analysis provides valuable insights into the genetic composition, potential virulence factors, and resistance profiles of B. cereus and B. subtilis, enhancing the understanding of their pathogenicity and epidemiology. The genomic analysis of B. cereus and B. subtilis revealed potential genomic applications in the context of food safety.

Abstract Background In the present study, we aimed to determine the frequency of the csgA, fimH, mrkD, foc, papaGI, papGII and papGIII genes, to provide and to design fimbrial adhesin gene (FAG) patterns and profiles for the isolated uropathogenic Escherichia coli (UPEC) strains. Methods The enrollment of 108 positive urine samples was performed during seven months, between January 2022 and July 2022. The UPEC strains were confirmed through the standard microbiological and biochemical tests. The antimicrobial susceptibility test was performed through the Kirby–Bauer disc diffusion method. Molecular screening of FAGs was done through the polymerase chain reaction technology. The statistical analyses including chi square and Fisher’s exact tests were performed to interpret the obtained results in the present study. Results As the main results, the antimicrobial resistance (AMR) patterns, multi- (MDR) and extensively drug-resistance (XDR) patterns and FAG patterns were designed and provided. fimH (93.3%), csgA (90.4%) and papG (37.5%) (papGII (30.8%)) genes were recognized as the top three FAGs, respectively. Moreover, the frequency of csgA-fimH gene profile was identified as the top FAG pattern (46.2%) among the others. The isolates bearing csgA-fimH gene profile were armed with a versatile of phenotypic AMR patterns. In the current study, 27.8%, 69.4% and 1.9% of the UPEC isolates were detected as extended-spectrum ß-lactamases (ESBLs) producers, MDR and XDR strains, respectively. Conclusions In conclusion, detection, providing and designing of patterns and profiles in association with FAGs, AMR feature in UPEC strains give us an effective option to have a successful and influential prevention for both of UTIs initiation and AMR feature.

Green tide is a harmful ecological phenomenon caused by the explosive proliferation or high aggregation of certain large green algae (such as Ulva prolifera) in seawater under specific environmental conditions, leading to discoloration of the water. The green tide formed by a large number of floating algae can not be effectively disposed of in a short period of time, which will lead to the accumulation and decay of green algae, thereby affecting the coastal ecological landscape. The outbreak of U. prolifera has been one of the main causes of green tide occurrences in the Yellow Sea since 2008. U. prolifera is an algal plant belonging to the family Ulvaceae, which has the characteristics of high nutrient absorption efficiency, fast growth rate and strong reproductive ability, and is more competitive than other species. The explosive proliferation of a large number of U. prolifera during a short period of time has a serious impact on marine environmental ecology, aquaculture, tourism and public health and safety. The study mainly investigated the environmental physicochemical parameters, cultivable microorganisms, dominant culture bacteria, and virulence and resistance genes of dominant bacteria in water and algae samples collected before and after the outbreak of U. prolifera in the main coastal areas of Qingdao were investigated. Environmental physicochemical factors, including the coliform and fecal coliform contents, chemical oxygen demand (COD), biochemical oxygen demand (BOD5), ammonia nitrogen (NH3-N) levels, nitrite, active phosphate, inorganic nitrogen, cyanide, sulfide, arsenic, mercury, copper, zinc, selenium, total chromium, nickel, cadmium, and lead ion levels, in the seawater were assessed. At the same time, the levels of organic carbon, sulfides, coliforms, fecal coliforms, and mercury, arsenic, cadmium, lead, zinc, copper, and chromium ions in the algae were measured. Research on cultivable microorganisms included an assessment of the abundance and composition of cultivable bacteria and Vibrio species in seawater and algae. The distribution of common virulence genes (VAC, vhh, chxA, tlh, and flaA) and resistance genes (strA, strB, QnrVC, and sul2) in the dominant Vibrio bacteria was examined to evaluate the potential virulence risk of the dominant Vibrio bacteria. Comparative analysis results showed that after the outbreak of U. prolifera, the COD, NH3-N, inorganic nitrogen, arsenic ion, and active phosphate levels in the coastal waters of Qingdao increased significantly (P < 0.05), and the levels of dissolved oxygen and cadmium, lead, chromium, copper, and other metal ions decreased significantly (P < 0.05). The organic carbon content in the algal samples from the aggregated areas of U. prolifera was lower than that from non-aggregated areas. In contrast, the content of coliforms, fecal coliforms, sulfide, mercury, cadmium, zinc, and copper ions significantly increased compared to that in open areas (P < 0.05). Moreover, the proportion of Vibrio bacteria increased from 7% to 45%, representing an increase of 38%. The bacterial identification results based on 16S rDNA showed that before the outbreak of U. prolifera, there were 79 dominant bacterial and 62 Vibrio strains in the coastal waters and algae bodies of Qingdao, belonging to 22 species. The main Vibrio species were V. gigantis, V. tasmaniensis, and V. atlanticus. After the outbreak of U. prolifera, 79 dominant bacterial and 65 Vibrio strains were isolated, belonging to 24 species, with the main Vibrio species being V. fortis, V. alginolyticus, and V. owensii. The distribution of virulence genes (VAC, vhh, chxA, tlh, and flaA) and resistance genes (strA, strB, QnrVC, and sul2) in dominant Vibrio bacteria isolated from water bodies and algae before and after the outbreak of U. prolifera was tested. The results showed that only two virulence genes, tlh and flaA, were detected before the outbreak of U. prolifera, and no resistance genes were detected. Five virulence genes and four resistance genes were identified after the outbreak of U. prolifera. Correlation analysis between the number of cultivable bacteria and the environmental physicochemical factors in the water and algae of Qingdao coastal waters before and after the outbreak of U. prolifera showed that the abundance of cultivable bacteria and Vibrio species in the water and algae was correlated with environmental factors such as temperature, pH, NH3-N, nitrite, inorganic nitrogen, active phosphate, total chromium, and nickel. The results revealed the impact of the outbreak of U. prolifera on the bacterial community structure and environmental ecology in the coastal environment of Qingdao. At the same time, the harmful microbial species caused by the outbreak of U. prolifera and the risk of virulence genes and drug resistance genes carried by the outbreak of U. prolifera were evaluated. The relevant research results provide a theoretical basis for the prevention and control of green tide, marine ecological protection, healthy aquaculture in the coastal waters of the Yellow Sea and Bohai Sea.

AbstractStaphylococcus pseudintermedius is a significant bacterial pathogen that frequently colonizes different body sites and mucous membranes of pets. The objectives of the cross-sectional study were to estimate the prevalence, antimicrobial resistance pattern, and detection of diverse resistance as well as virulence genes of S. pseudintermedius in cats. A standard bacteriological method, species-specific gene and different antimicrobial resistance as well as virulence genes were confirmed by PCR assay. A total of 233 swab samples were collected from different body sites of 102 cats, among them 146 swabs from 73 healthy cats, and 87 from 29 diseased cats. Overall, prevalence of S. pseudintermedius in cats was 12.01%, while dermatitis and otitis affected cats were 26.08% and 33.33%, respectively. The highest antimicrobial resistance was observed against penicillin (96.42%) followed by streptomycin (85.71%) and erythromycin (78.57%). Moreover, 89.28% of S. pseudintermedius isolates exhibit multi-drug resistance (MDR) (≥ 3 classes’ antimicrobial resistant). In addition, 17.86% isolates harbored the mecA gene; thus, were classified as methicillin-resistant S. pseudintermedius (MRSP). Furthermore, the erythromycin resistance genes ermA and ermB were harbored by 25% and 10.71% of isolates, while 42.86% and 17.86% of isolates carried tetK and tetL (tetracycline resistance) genes, respectively. In virulence profiling, 32.14% (sea) and 10.71% (seb) of isolates were found positive for enterotoxin genes, whereas, the toxic shock syndrome toxin-1 (tst-1) gene and the Panton-Valentine leukocidin gene (pvl) were detected in 25% and 14.29% of isolates, respectively. To our knowledge, this is the first report of cats in Bangladesh for MDR S. pseudintermedius, MRSP, and their virulence profiling.

Vibrio parahaemolyticus is associated with severe food-borne illness in humans as well as substantial financial setbacks in the fishing sector. To investigate the prevalence, pathogenicity, virulence, as well as the resistance patterns of V. parahaemolyticus retrieved from Oreochromis niloticus, 180 O. niloticus (moribund fish; n = 120 and apparently healthy; n = 60) were indiscriminately collected from Lake Manzala, Egypt. Consequently, the clinical inspection, necropsy finding, and bacteriological analysis were performed. All the retrieved isolates tested positive for the groEL species-specific gene. Herein, the prevalence of V. parahaemolyticus in the collected fish was 8.9% (16/180), whereas the liver was the organ most prominently affected. PCR revealed that the most prevalent virulence-determinant genes associated with V. parahaemolyticus were the toxR and tlh genes (100% for each), then tdh (73.3%) and trh (26.7%) genes. Furthermore, 40% (18/45) of isolated V. parahaemolyticus were extensively drug-resistant (XDR) to seven antimicrobial classes and have blaTEM, blaOXA, sul1, aadA, ermB, and tetA genes. Additionally, 17.8% (8/45) of the obtained V. parahaemolyticus were multidrug-resistant (MDR) to three antimicrobial classes and owned blaTEM, ermB, and aadA genes. The pathogenicity assay accentuated the correlation between cumulative mortality and the virulent characteristics exhibited by the inoculated strain. Definitely, 77% mortality was recorded within eight days in fish injected with a virulent V. parahaemolyticus strain. Briefly, this research accentuated the occurrence of XDR V. parahaemolyticus in fish specifying a public health concern. The emerging MDR and XDR V. parahaemolyticus frequently harbored toxR, tlh, and tdh virulence genes, and blaTEM, blaOXA, sul1, aadA, ermB, and tetA or tetB antimicrobial resistance genes. [ABSTRACT FROM AUTHOR]

Klebsiellapneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over the world. In this study, we investigated the antibiotic resistance profile and the ability to produce extended-spectrum beta-lactamase (ESBL) among K. pneumoniae isolates, and then we investigated the relationship between these two factors with biofilm formation and the prevalence of different virulence genes. In this study, 130 isolates of K. pneumoniae isolated from wounds were investigated. The antibiotic resistance of the isolates was evaluated by the disk diffusion method. The microtiter plate method was used to measure biofilm formation. The prevalence of virulence genes was detected by multiplex PCR. Among the examined isolates, 85.3% showed multidrug resistance. 87.6% of the isolates were ESBL-positive. Imipenem, meropenem, and fosfomycin were the most effective drugs. The ability of the isolates to produce biofilm was strong (80%), moderate (12.3%), and weak (7.6%), respectively. fimH, mrKD, entB, and tolC virulence genes were observed in all isolates. High prevalence of antibiotic resistance (especially multidrug resistance), high prevalence of ESBL-producing isolates, the ability of all isolates to biofilm formation, and the presence of fimH, mrKD, entB, and tolC virulence genes in all isolates show the importance of these factors in the pathogenesis of K. pneumoniae isolates in Iraq. [ABSTRACT FROM AUTHOR]

Abstract Background Klebsiella pneumoniae (KP) is the second most prevalent Gram-negative bacterium causing bloodstream infections (BSIs). In recent years, the management of BSIs caused by KP has become increasingly complex due to the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP). Although numerous studies have explored the risk factors for the development of CRKP-BSIs, the mortality of patients with KP-BSIs, and the molecular epidemiological characteristics of CRKP, the variability in data across different populations, countries, and hospitals has led to inconsistent conclusions. In this single-center retrospective observational study, we utilized logistic regression analyses to identify independent risk factors for CRKP-BSIs and factors associated with mortality in KP-BSI patients. Furthermore, a risk factor-based prediction model was developed. CRKP isolates underwent whole-genome sequencing (WGS), followed by an evaluation of microbiological characteristics, including antimicrobial resistance and virulence genes, as well as epidemiological characteristics and phylogenetic analysis. Results Our study included a total of 134 patients with KP-BSIs, comprising 50 individuals infected with CRKP and 84 with carbapenem-susceptible Klebsiella pneumoniae (CSKP). The independent risk factors for CRKP-BSIs were identified as gastric catheterization (OR = 9.143; CI = 1.357–61.618; P = 0.023), prior ICU hospitalization (OR = 4.642; CI = 1.312–16.422; P = 0.017), and detection of CRKP in non-blood sites (OR = 8.112; CI = 2.130-30.894; P = 0.002). Multivariate analysis revealed that microbiologic eradication after 6 days (OR = 3.569; CI = 1.119–11.387; P = 0.032), high Pitt bacteremia score (OR = 1.609; CI = 1.226–2.111; P = 0.001), and inappropriate empirical treatment after BSIs (OR = 6.756; CI = 1.922–23.753; P = 0.003) were independent risk factors for the 28-day mortality in KP-BSIs. The prediction model confirmed that microbiologic eradication after 6.5 days and a Pitt bacteremia score of 4.5 or higher were significant predictors of the 28-day mortality. Bioinformatics analysis identified ST11 as the predominant CRKP sequence type, with bla KPC−2 as the most prevalent gene variant. CRKP stains carried multiple plasmid-mediated resistance genes along with some virulence genes. Phylogenetic analysis indicated the presence of nosocomial transmission of ST11 CRKP within the ICU. Conclusions The analysis of risk factors for developing CRKP-BSIs and the association between KP-BSIs and 28-day mortality, along with the development of a risk factor-based prediction model and the characterization of CRKP strains, enhances clinicians’ understanding of the pathogens responsible for BSIs. This understanding may help in the timely administration of antibiotic therapy for patients with suspected KP-BSIs, potentially improving outcomes.

Abstract Background Staphylococcus aureus (S. aureus) often colonizes the human skin, upper respiratory and genital tracts. In the female genital tract, it can be passed on to the newborn during vaginal delivery leading to either ordinary colonization, or neonatal infections notably umbilical stump sepsis, scalded skin syndrome, arthritis, or bacteraemia/sepsis. These infections are mediated by staphylococcal virulence factors such as (i) Staphylococcal Enterotoxins A, B, C, D, and E encoded by the sea, seb, sec, sed, see genes, (ii) Exfoliative Toxins A and B encoded by the eta and etb genes, (iii) Toxic Shock Syndrome Toxin 1 (TSST-1) encoded by the tst gene, (iv) Panton-Valentine Leukocidin (PVL) encoded by the pvl gene, and (v) Hemolysins alpha and delta encoded by the hla and hld genes, respectively. We determined the prevalence of S. aureus possessing one or more virulence factor genes and of methicillin resistant Staphylococcus aureus (MRSA) in this population. Methods This was a cross-sectional study, which used 85 S. aureus isolates from the Chlorohexidine (CHX) clinical trial study in Uganda. The isolates had been obtained by culturing vaginal swabs (VS) from 1472 women in labour, frozen at minus 80oC, then thawed, sub-cultured, and tested for the selected virulence genes sea, seb, sec, sed, see eta, etb, tst, pvl, hla and hld, and for the methicillin resistance determining gene (mecA). Data were analyzed using SPSS version 20. Results Of the 85 S. aureus isolates 13 (15.3%) were positive for one or more virulence factor genes, as follows: pvl 9/85 (10.6%), hld 5/85 (5.9%), sea 1/85 (1.2%) and seb genes 1/85 (1.2%). The other virulence genes (sec, sed, see, eta, etb, hla and tst) were not detected in any of the isolates. MRSA was detected in 55.3% (47/85) of the isolates, but only two of these carried the pvl virulence gene. Conclusion This study demonstrated that 15% of the S. aureus colonizing the female lower genital tract of mothers in labour in central Uganda carried one or more virulence genes, mostly pvl, indicating potential for newborn infection with S. aureus acquired in the maternal birth canal. More than half of the isolates were MRSA.

Abstract Background Klebsiella pneumoniae is a zoonotic opportunistic pathogen, and also one of the common pathogenic bacteria causing mink pneumonia. The aim of this study was to get a better understanding of the whole-genome of multi-drug resistant Klebsiella pneumoniae with K2 serotype in China. This study for the first time to analyze Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, resistance and virulence genes of Klebsiella pneumoniae in mink. Results The isolate was Klebsiella pneumoniae with serotype K2 and ST6189 by PCR method. The string test was positive and showed high mucus phenotype. There was one plasmid with IncFIB replicons in the genome. The virulence factors including capsule, lipopolysaccharide, adhesin, iron uptake system, urease, secretory system, regulatory gene (rcsA, rcsB), determinants of pili adhesion, enolase and magnesium ion absorption related genes. The strain was multi-drug resistant. A total of 26 resistance genes, including beta-lactam, aminoglycosides, tetracycline, fluoroquinolones, sulfonamides, amide alcohols, macrolides, rifampicin, fosfomycin, vancomycin, diaminopyrimidines and polymyxin. Multidrug-resistant efflux protein AcrA, AcrB, TolC, were predicted in the strain. Conclusion It was the first to identify that serotype K2 K. pneumonia with ST6189 isolated from mink in China. The finding indicated that hypervirulent and multi-drug resistant K. pneumoniae was exist in Chinese mink. The whole-genome of K. pneumoniae isolates have importance in mink farming practice.