High burden of multidrug resistant bacteria detected in Little Akaki River

Methicillin- and vancomycin-resistant Staphylococcus aureus in chicken carcasses, ready-to-eat chicken meat sandwiches, and buffalo milk

Methicillin-resistant Staphylococcus aureus (MRSA) is a growing public health concern; however, there is limited information about MRSA and VRSA (Vancomycin-resistant S. aureus) among animal-origin food. Therefore, this study intended to elucidate the prevalence, enterotoxin existence, antimicrobial resistance profiles, and antimicrobial resistance genes of S. aureus strains isolated from chicken carcasses, ready-to-eat (RTE) chicken meat sandwiches, and buffalo milk samples marketed in Mansoura City, Egypt. Of the 240 samples examined, 52.1 % were contaminated with S. aureus, with a mean count of 4.11 log10 CFU/g. A total of 250 isolates were verified as S. aureus by PCR targeting nuc gene, of which 39.2 % (98/250) harbored at least one S. aureus enterotoxin (SE) gene. The predominant SE genes were sea (61.2 %, 60/98), followed by sed (58.2 %, 57/98), sec (38.8 %, 38/98), and seb (27.6 %, 27/98). All isolates were resistant to at least one antimicrobial, with an average MAR (multiple antibiotic resistance) index of 0.530. Four isolates exhibited resistance to all antimicrobial agents tested. Interestingly, 100 %, 76.4 %, 35.6 %, 30.8, 10.4 %, 6 %, and 1.6 % of isolates were resistant to penicillin, azithromycin, oxacillin, ceftaroline, vancomycin, linezolid, and daptomycin, respectively. Of the 250 S. aureus strains tested, 38 % were confirmed as MRSA by mecA gene, while 10.4 % were identified as VRSA by vanA gene. The high prevalence of MRSA and VRSA isolates among samples tested is worrisome. Hence, monitoring antimicrobial usage in veterinary medicine and applying strict hygienic measures during food handling and processing is imperative to prevent the spread of such resistant bacteria and protect public health.

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

Providencia alcalifaciens is a Gram-negative bacterium found in various water and land environments and organisms, including insects and mammals. Some P. alcalifaciens strains encode gene homologs of virulence factors found in pathogenic Enterobacterales members, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are pathogenic determinants in P. alcalifaciens is not known. In this study, we investigated P. alcalifaciens-host interactions at the cellular level, focusing on the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. A large plasmid that is present in a subset of P. alcalifaciens strains, primarily isolated from diarrheal patients, encodes for T3SS1a. We show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, lyses its internalization vacuole, and proliferates in the cytosol. This triggers caspase-4-dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis, and cytosolic proliferation is host cell type-specific, playing a more prominent role in intestinal epithelial cells than in macrophages or insect cells. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa and induces mild epithelial damage with negligible fluid accumulation in a T3SS1a- and T3SS1b-independent manner. However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties

Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.

Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter

Introduction

Kluyvera is a Gram-negative, flagellated, motile bacillus within the Enterobacteriaceae. The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus Phytobacter, which often be misidentified with Kluyvera, is also an important clinically relevant member of the Enterobacteriaceae. However, the identification of Kluyvera and Phytobacter is problematic, and their phylogenetic relationship remains unclear.

Methods

Here, 81 strains of Kluyvera and 16 strains of Phytobacter were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction.

Results

Using average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new Phytobacter genomospecies-1 were defined. Phytobacter and Kluyvera show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of Kluyvera (pelX, mdtL, bglC, pcak-1, uhpB, ddpA-2, pdxY, oppD-1, cptA, yidZ, csbX) that could be served as potential identification targets. Meanwhile, the Phytobacter specific virulence genes clbS, csgA-C, fliS, hsiB1_vipA and hsiC1_vipB, were found to differentiate from Kluyvera. We concluded that the evolution rate of Kluyvera was 5.25E-6, approximately three times higher than that of Phytobacter. Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains.

Discussion

This work provided a better understanding of the differences between closely related species Kluyvera and Phytobacter. Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens Kluyvera and Phytobacter warrant close attention.

Fecal Contamination in the Wastewater Irrigation System and its Health Threat to Wastewater-Based Farming Households in Addis Ababa, Ethiopia

Due to rapidly growing demand, the production of vegetables is increasing along the Akaki Rivers. The objective of this study was to examine the degree of fecal contamination and levels of fecal contamination and dissemination throughout the wastewater irrigation system. Irrigation water, irrigated soil, and leafy vegetables were collected twice during 2 vegetable growing seasons, at the maturity period of the growing season, from 19 sampling points along the 2 Akaki Rivers. Composite samples were taken from all sampling points and E.coli was enumerated. The mean E.coli load in wastewater and non-wastewater sources were 1.1⁶±5.5³ CFU/100 ml and 2.23²±1.29² CFU/100 ml respectively. All counts of E. coli in the wastewater exceeded the WHO's standards indicating that the irrigation water quality was unacceptable. In the wastewater-irrigated and non-wastewater-irrigated soil, the mean E.coli were 3.6² ±1.58² CFU/g and 1.32²±87.1 CFU/g respectively. Meanwhile, the mean E.coli counts on the lettuce and Swiss chard were 78 ± 2 CFU/g and 44 ±3CFU/g respectively. The E.coli count on the leafy vegetables was found to be associated with the E.coli in the wastewater and soil. The production of leafy vegetables using wastewater with unacceptably high levels of E.coli and high occupational exposure introduces high levels of risk to the farming communities and to the consumers. Leafy, low-growing raw edible vegetables need careful treatment during food production and harvesting procedures or activities.

Antimicrobial Resistance Profiles and Co-Existence of Multiple Antimicrobial Resistance Genes in mcr-Harbouring Colistin-Resistant Enterobacteriaceae Isolates Recovered from Poultry and Poultry Meats in Malaysia

The co-existence of the colistin resistance (mcr) gene with multiple drug-resistance genes has raised concerns about the possibility of the development of pan-drug-resistant bacteria that will complicate treatment. This study aimed to investigate the antibiotic resistance profiles and co-existence of antibiotic resistance genes among the colistin-resistant Enterobacteriaceae isolates recovered from poultry and poultry meats. The antibiotic susceptibility to various classes of antibiotics was performed using the Kirby-Bauer disk diffusion method and selected antimicrobial resistance genes were detected using PCR in a total of 54 colistin-resistant Enterobacteriaceae isolates including Escherichia coli (E. coli) (n = 32), Salmonella spp. (n = 16) and Klebsiella pneumoniae (K. pneumoniae) (n = 6) isolates. Most of the isolates had multi-drug resistance (MDR), with antibiotic resistance against up to seven classes of antibiotics. All mcr-harbouring, colistin-resistant Enterobacteriaceae isolates showed this MDR (100%) phenotype. The mcr-1 harbouring E. coli isolates were co-harbouring multiple antibiotic resistance genes. The seven most commonly identified resistance genes (^blaTEM, tetA, floR, aac-3-IV, aadA1, fosA, aac(6_)-lb) were detected in an mcr-1-harbouring E. coli isolate recovered from a cloacal swab. The mcr-5 harbouring Salmonella spp. isolate recovered from poultry meats was positive for ^blaTEM, tetA, floR, aac-3-IV, fosA and aac(6_)-lb genes. In conclusion, the colistin-resistant Enterobacteriaceae with mcr genes co-existing multiple clinically important antimicrobial resistance genes in poultry and poultry meats may cause potential future threats to infection treatment choices in humans and animals.

Cefotaxime-, Ciprofloxacin-, and Extensively Drug-Resistant Escherichia coli O157:H7 and O55:H7 in Camel Meat

The present study aimed to explore for the first time the occurrence and the antimicrobial resistance profiles of E. coli O157:H7 and O55:H7 isolates in camel meat in Egypt. Among the 110 camel meat samples examined using standardized microbiological techniques, 10 (9.1%) and 32 (29.1%) were positive for E. coli O157:H7 and E. coli O55:H7, respectively. In total, 24 isolates were verified as E. coli O157:H7, while 102 isolates were confirmed serologically as E. coli O55:H7. Multiplex PCR revealed the existence of eaeA, stx1, stx2, and EHEC-hlyA among E. coli O157:H7 and O55:H7 isolates (n = 126) at various percentages. According to their resistance against 14 antibiotics, 16.7% and 83.3% of O157:H7 isolates and 8.6% and 76.5% of O55:H7 isolates were classified into extensively drug-resistant and multi-drug-resistant, respectively, whereas 29.4% and 22.2% of E. coli isolates were resistant to cefotaxime and ciprofloxacin, respectively. The study results emphasize that camel meat may be a vehicle for multi- and extensively drug-resistant E. coli O157:H7 and O55:H7 strains, indicating a potential threat to public health. Further studies based on the molecular evidence of the antimicrobial resistance genes and enrolling a larger number of samples are recommended for a better understanding of the antimicrobial resistance phenomenon of camel-meat-originating pathogenic E. coli strains.

Complete Genome Sequence of Kluyvera sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens)

The enterobacterium genus Kluyvera is widely distributed in the environment and a rare source of infection in humans. Kluyvera sp. strain CRP was isolated from feces of a healthy, captive Chinese red panda (Ailurus fulgens), and its complete genome (5,157,963 bp, 54.80% GC content) was established through hybrid assembly.