Detection of phylogrouping, adhesin, and extended spectrum ß-lactamases genes in hospital acquired uropathogenic Escherichia coli isolates.

BACKGROUND: It has been interesting to compare the levels of antimicrobial resistance and the virulence characteristics of uropathogenic Escherichia coli (UPEC) strains of certain phylogenetic groups. The purpose of this study was to identify the frequency of phylogenetic groups, adhesin genes, antibiotic sensitivity patterns, and extended spectrum-lactamases (ESBLs) genes in hospital-acquired UPEC. METHODS: After UPEC isolation, the disc diffusion method was used to assess its susceptibility to antibiotics. Combination disc testing confirmed the existence of ESBL producers. Polymerase chain reaction (PCR) was used to detect genes for adhesin and ESBLs. RESULTS: One hundred and twenty-eight E. coli were isolated which had the highest resistance to tetracycline (96%) followed by cefoxitin (93%), cefepime (92%), ceftazidime (79%), aztreonam (77%) and sulfamethoxazole -trimethoprim (75%). About 57% of isolates were phenotypically ESBLs positive and they were confirmed by PCR. B2 phylogroup (41%) was the most frequent in E. coli isolates then group D (30%), group A (18%), and lastly group B1 (11%). ESBLs genes were more significantly prevalent in phylogroups B2 and D than other phylogroups (P < 0.001). Regarding adhesin genes, both fim H and afa were more significantly associated with group B2 than other groups (P < 0.009, < 0.032), respectively. In ESBL-positive isolates, both genes were more significantly detected compared to negative ones (P < 0.001). CONCLUSION: Phylogroups B2 and D of UPEC are important reservoirs of antimicrobial resistance and adhesion genes. Detection of ESBL-producing E. coli is important for appropriate treatment as well as for effective infection control in hospitals.

Antibiotic resistance profile and molecular characterization of extraintestinal pathogenic Escherichia coli (ExPEC) from human clinical samples in gaza strip, palestine.

The rates of antibiotic resistance in extraintestinal pathogenic Escherichia coli (ExPEC) have increased significantly in recent years. This study aims at studying antibiotic resistance, virulence factors (VFs), and the phylogenetic background of ExPEC isolated from Palestinian patients. A total of 42 ExPEC isolates were collected from patients with extraintestinal infections in three Palestinian hospitals. Antimicrobial susceptibility was studied by the disk diffusion method. Resistance/virulence-gene profiles, phylogenetic groups, and integron profiles of these isolates were studied by PCR. The susceptibility to carbapenems was detected in 90.5% of the isolates. Half of the isolates were resistant to ampicillin and sulfamethoxazole/trimethoprim, and 33.3% of the isolates were multidrug-resistant. BlaTEM-1 was detected in seven isolates and blaOXA-1 was identified in one isolate. Sul, qnrA, and aac(6')-Ib-cr genes were found in 12, 3, and 2 isolates, respectively. Class 1 integron has been identified in 10 isolates with the gene cassette arrangement dhfr17 + aadA5. The isolates were distributed between phylogroups B2 and D. The presence of VFs, antibiotic resistance genes, and class 1 integron associated with phylogenetic groups (B2 and D) among multidrug-resistant (MDR)-ExPEC recovered from urinary tract infections (UTIs) patients will complicate infection management and increase therapy failure. Routine screening of antibiotic resistance is important for appropriate and efficient empirical treatment.

Utilization Efficiency of Human Milk Oligosaccharides by Human-Associated Akkermansia Is Strain Dependent.

Akkermansia muciniphila is a mucin-degrading bacterium found in the human gut and is often associated with positive human health. However, despite being detected by as early as 1 month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO deconstruction. Representative strains were all able to grow on HMOs with various efficiencies and growth yields. Strain CSUN-19, belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the α-fucosidases, α-sialidases, and ß-galactosidases. This study examines the utilization of individual purified HMOs by Akkermansia strains representing all known phylogroups. Further studies are required to examine how HMO ingestion influences gut microbial ecology in infants harboring different Akkermansia phylogroups. IMPORTANCE Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk and provide several benefits to developing infants, including the recruitment of beneficial bacteria to the human gut. Akkermansia strains are largely considered beneficial bacteria and have been detected in colostrum, breast milk, and young infants. A. muciniphila MucT, belonging to the AmI phylogroup, contributes to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacities of four Akkermansia phylogroups to deconstruct HMOs. Indeed, each phylogroup contained differences in their genomic capacities to deconstruct HMOs, and representative strains of each phylogroup were able to grow using HMOs. These Akkermansia-HMO interactions potentially influence gut microbial ecology in early life, a critical time for the development of the gut microbiome and infant health.

Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia.

Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::blaCTX-M-2) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.

Tracking the Transmission of Antimicrobial-Resistant Non-O157 Escherichia coli and Salmonella Isolates at the Interface of Food Animals and Fresh Produce from Agriculture Operations Using Whole-Genome Sequencing.

An increasing number of outbreaks are caused by foodborne pathogens such as Escherichia coli and Salmonella, which often harbor antimicrobial resistance (AMR) genes. We previously demonstrated the transmission of pathogens from animal operations to produce fields on sustainable farms, which illustrated an urgent need to develop and implement novel prevention methods and remediation practices such as the vegetative buffer zone (VBZ) to prevent this movement. The focus of this study was to use whole-genome sequencing (WGS) to characterize the AMR, virulence, and single-nucleotide polymorphism profile of 15 Salmonella and 128 E. coli isolates collected from small-scale dairy and poultry farms on a research station in North Carolina. Phenotypically, seven E. coli and three Salmonella isolates displayed resistance to antibiotics such as tetracycline (n = 4), ampicillin (n = 4), nalidixic acid (n = 3), chloramphenicol (n = 2), sulfisoxazole (n = 1), and streptomycin (n = 1). A single E. coli isolate was found to be resistant to five different antibiotic class types and possessed the blaTEM-150 resistance gene. Virulence genes that facilitate toxin production and cell invasion were identified. Mauve analysis of the E. coli isolates identified seven clusters (dairy-six and poultry-one) indicating that transmission is occurring from animal operations to fresh produce fields and the surrounding environment when the VBZ is denudated. This suggests that the VBZ is a useful barrier to reducing the transmission of enteric pathogens in agricultural systems. Our study demonstrates the prevalence of AMR and virulence genes on small-scale sustainable farms and highlights the advantage of using WGS to assess the impact of the VBZ to reduce the transmission of E. coli and Salmonella.

Study of the diversity of 16S-23S rDNA internal transcribed spacer (ITS) typing of Escherichia coli strains isolated from various biotopes in Tunisia.

We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550 bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550 bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.

Molecular subtyping and clonal relatedness of human and cattle verotoxin-producing Escherichia coli O157:H7 isolates.

Verotoxin-producing Escherichia coli O157:H7 is the dominant serotype isolated from patients with hemolytic-uremic syndrome (HUS) and, Argentina has the highest rate of HUS in the world. However, not all O157:H7 isolates have the same ability to infect and cause disease in humans. It has been postulated that O157:H7 strains integrate subpopulations related to the origin and virulence. In order to study the population structure and genetic diversity of VTEC O157:H7 from Argentina, a combination of molecular subtyping methods such as multiple loci VNTR analysis (MLVA), single nucleotide polymorphisms (SNP) and phylogroups assignment were used. According to MLVA, high genetic diversity was found among strains isolated from cattle, humans and food. On the other hand, 92% of the isolates presented the allele tir 255 T > A T and 95% were assigned to phylogroup E. We did not find a significant association between the isolates origin and the allele T presence (P > 0,05) postulated as significantly overrepresented in human isolates. Our results show that human and cattle VTEC O157:H7 isolates from Argentina are a homogeneous group and, although it presents high genetic diversity in relation to their MLVA and virulence profiles, it is not possible to distinguish divergent populations. The presence in all the strains of a high number of T3SS effectors genes and the no association of genetic subtypes with strain source, is an alert about the potential risk in public health that VTEC O157:H7 cattle strains possess and, at less, a partial explication about the high incidence of HUS in Argentina.

Pet dogs potential transmitters of pathogenic Escherichia coli with resistance to antimicrobials.

Escherichia coli strains are part of the normal biota of humans and animals; however, several clinical reports have implicated E. coli as the etiological agent of diarrhea in humans and companion animals. Thus, the aim of the present study was to know if companion dogs in the city of San Luis Potosi are colonized with virulent potentially harmful E. coli strains. Rectal swabs from 30 dogs, 13 with and 17 without diarrhea were analyzed. Phylogenetic and virulence genes analysis was performed to the E. coli isolates. Additionally, the Kirby-Bauer test was used to analyze the sensitivity to 32 different antimicrobials from 14 families. Eighty-five isolates were identified as E. coli and detected in 97% of healthy and diarrheic dog samples. E. coli isolates from healthy dogs carried several virulence genes, in contrast with those from diarrheic animals that presented only eaeA. In healthy dogs, phylogenetic analysis showed that 57% and 43% of E. coli isolates belonged to commensal (A and B1) and virulent (B2 and D) groups respectively. Meanwhile, diarrheic dogs showed that 69% of the isolates were identified as virulent B2 and D phylogroups. Moreover, E. coli resistant to ß-lactams, aminoglycosides, tetracycline, quinolones, and folate inhibitors were detected in both groups of dogs. The presence of E. coli with eaeA virulence gene in diarrheic dogs, suggest that these strains are associated with the animal´s condition. Finally, major attention must be drawn to the careful handling of dogs because of their capability to harbor and disseminate virulent E. coli strains.

Genetic structure and divergence of tench Tinca tinca European populations.

The tench Tinca tinca is a freshwater species with human-mediated translocations, aquaculture interest and limited information on its genetic structure. mtDNA sequencing analysis of control region and two genes in 50 individuals from five European populations identified two phylogroups, with greater variability than that reported until now, and a hybridization zone in the Danube River region. Restriction analyses of additional samples reveal the complicated genetic structure characteristics of tench's wild and translocated populations, supporting future breeding practices.

Stratified reconstruction of ancestral Escherichia coli diversification.

BACKGROUND: Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies. RESULTS: Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed. CONCLUSIONS: A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.

Arenavirus Diversity and Phylogeography of Mastomys natalensis Rodents, Nigeria.

Mastomys natalensis rodents are natural hosts for Lassa virus (LASV). Detection of LASV in 2 mitochondrial phylogroups of the rodent near the Niger and Benue Rivers in Nigeria underlines the potential for LASV emergence in fresh phylogroups of this rodent. A Mobala-like sequence was also detected in eastern Nigeria.

Bacterial defense systems exhibit synergistic anti-phage activity.

Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.

Molecular and Antimicrobial Susceptibility Characterization of Escherichia coli Isolates from Bovine Slaughterhouse Process.

Antimicrobials are routinely used in human and veterinary medicine. With repeated exposure, antimicrobials promote antibiotic resistance, which poses a threat to public health. In this study, we aimed to determine the susceptibility patterns, virulence factors, and phylogroups of E. coli isolates during the killing process in a bovine slaughterhouse. We analyzed 336 samples (from water, surfaces, carcasses, and feces), and 83.3% (280/336) were positive for E. coli. The most common phenotypic resistances that we detected were 50.7% (142/280) for tetracycline, 44.2% (124/280) for cephalothin, 34.6% (97/280) for streptomycin, and 36.7% (103/280) for ampicillin. A total of 82.4% of the isolates had resistance for at least one antimicrobial, and 37.5% presented multiresistance. We detected a total of 69 different phenotypic resistance patterns. We detected six other resistance-related genes, the most prevalent being tetA (22.5%) and strB (15.7%). The prevalence values of the virulence genes were 5.4% in hlyA, 1.4% in stx1, and 0.7% in stx2. The frequencies of the pathogenic strains (B2 and D) were 32.8% (92/280) and 67.1% (188/280) as commensals A and B1, respectively. E. coli isolates with pathogenic potential and multiresistance may represent an important source of dissemination and a risk to consumers.

Phylogeographic Aspects of Bat Lyssaviruses in Europe: A Review.

During the last few decades, bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times, rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article, we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent reg ions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones, three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroup II and the most divergent lyssaviruses generates impetus for additional phylogenetic and virological research within this geographical region.

ß-Lactamase Producing Escherichia coli Encoding blaCTX-M and blaCMY Genes in Chicken Carcasses from Egypt.

Escherichia coli with multidrug resistance and ß-lactamase genes may constitute a great public health hazard due to the potential for their transmission to humans through the food chain. This study determined the prevalence, antibiotic resistance profiles, phylogroups, and ß-lactamase genes of E. coli isolates from chicken carcasses marketed in Mansoura, Egypt. Interestingly, E. coli was detected in 98% (98/100) of the chicken carcasses examined, which seemed among the highest contamination rates by E. coli worldwide. From the 425 genetically verified uidA gene-positive E. coli, 85 isolates were further studied for antimicrobial resistance profiles, phylogroups, and ß-lactamase genes. Interestingly, 89.41% of E. coli (76/85) strains tested against 24 different antibiotics were multidrug-resistant. Of the examined 85 E. coli isolates, 22 (25.88%) isolates harbored blaCTX-M and were resistant to ampicillin, cefazoline, and ceftriaxone, while three of them were resistant to ceftazidime besides. Nine (10.59%) E. coli strains harbored AmpC- ß-lactamase blaCMY and were resistant to ampicillin. One isolate co-carried blaCMY and blaCTX-M genes, though it was negative for the blaTEM gene. Of the 35 isolates that harbored either extended-spectrum ß-lactamase (ESBL) and/or AmpC ß-lactamase genes, six strains (17.14%) were assigned to pathogenic phylogroup F and one to phylogroup E, whereas 28 (80%) isolates belonged to commensal phylogenetic groups.

Alcoholic fermentation drives the selection of Oenococcus oeni strains in wine but not in cider.

Oenococcus oeni is the predominant lactic acid bacteria species in wine and cider, where it performs the malolactic fermentation (MLF). The O. oeni strains analyzed to date form four major genetic lineages named phylogroups A, B, C and D. Most of the strains isolated from wine, cider, or kombucha belong to phylogroups A, B + C, and D, respectively, although B and C strains were also detected in wine. This study was performed to better understand the distribution of the phylogroups in wine and cider. Their population dynamics were determined by qPCR all through wine and cider productions, and the behavior of the strains was analyzed in synthetic wines and ciders. Phylogroups A, B and C were all represented in grape must and throughout the alcoholic fermentation, but on the transition to MLF, only phylogroup A remained at high levels in all wine productions. In the case of cider, phylogroups A, B and C were detected in stable levels during the process. When they were tested in synthetic wine and cider, all phylogroups performed MLF, but with different survival rates depending on the ethanol content. In this sense, ethanol and fermentation kinetics are the main agent that drives the selection of phylogroup A strains in wine, while B and C strains dominates in cider containing less ethanol.

High prevalence of Panton-Valentine Leucocidin (PVL) toxin carrying MRSA and multidrug resistant gram negative bacteria in late onset neonatal sepsis indicate nosocomial spread in a Pakistani tertiary care hospital.

BACKGROUND: Neonatal sepsis has high incidence with significant mortality and morbidity rates in Pakistan. We investigated common etiological patterns of neonatal sepsis at a tertiary care setup. METHODS: 90 pus and blood, gram negative and gram positive bacterial isolates were analyzed for virulence and antibiotic resistance gene profiling using PCR and disc diffusion methods. RESULTS: Staphylococcus aureus showed strong association with neonatal sepsis (43 %) followed by Citrobacter freundii (21 %), Pseudomonas aeruginosa (13 %), Escherichia coli (15 %) and Salmonella enterica (8 %). Molecular typing of E. coli isolates depicted high prevalence of the virulent F and B2 phylogroups, with 4 hypervirulent phylogroup G isolates. 76.9 % S. aureus isolates showed presence of Luk-PV, encoding for Panton-valentine leucocidin (PVL) toxin with majority also carrying MecA gene and classified as methicillin resistant S. aureus (MRSA). ecpA, papC, fimH and traT virulence genes were detected in E. coli and Salmonella isolates. 47 % Citrobacter freundii isolates carried the shiga like toxin SltII B. Antimicrobial resistance profiling depicted common resistance to cephalosporins, beta lactams and fluoroquinolones. CONCLUSION: Presence of PVL carrying MRSA and multidrug resistant gram negative bacteria, all isolated from late onset sepsis neonates indicate a predominant nosocomial transmission pattern which may complicate management of the disease in NICU setups.

Persistence of Antibiotic-Resistant Escherichia coli Strains Belonging to the B2 Phylogroup in Municipal Wastewater under Aerobic Conditions.

Escherichia coli is classified into four major phylogenetic groups (A, B1, B2, and D) that are associated with antibiotic resistance genes. Although antibiotic-resistant E. coli is commonly detected in municipal wastewater, little is known about the relationship between the phylogenetic groups and antibiotic-resistant E. coli in wastewater. In this study, the survival of E. coli in wastewater and the changes to the relationships between each phylogroup and the antibiotic-resistant profiles of E. coli isolates from wastewater were investigated under aerobic conditions for 14 days. The isolates were classified into the phylogroups A, B1, B2, and D or others by multiplex PCR. In addition, the susceptibility of the isolates to 11 antibiotics was assessed with the minimum inhibitory concentration (MIC) assay. While E. coli counts decreased in the wastewater with time under aerobic conditions, the prevalence of phylogroup B2 had increased to 73% on day 14. Furthermore, the MIC assay revealed that the abundance of antibiotic-resistant E. coli also increased on day 14. After batch-mixing the experiments under aerobic conditions, the surviving antibiotic-resistant E. coli included mainly multidrug-resistant and beta-lactamase-producing isolates belonging to phylogroup B2. These results suggest that the phylogroup B2 isolates that have acquired antibiotic resistance had a high survivability in the treated wastewater.

Shiga Toxin Subtypes, Serogroups, Phylogroups, RAPD Genotypic Diversity, and Select Virulence Markers of Shiga-Toxigenic Escherichia coli Strains from Goats in Mid-Atlantic US.

Understanding Shiga toxin subtypes in E. coli from reservoir hosts may give insight into their significance as human pathogens. The data also serve as an epidemiological tool for source tracking. We characterized Shiga toxin subtypes in 491 goat E. coli isolates (STEC) from the mid-Atlantic US region (stx1 = 278, stx2 = 213, and stx1/stx2 = 95). Their serogroups, phylogroups, M13RAPD genotypes, eae (intimin), and hly (hemolysin) genes were also evaluated. STEC-positive for stx1 harbored Stx1c (79%), stx1a (21%), and stx a/c (4%). Those positive for Stx2 harbored stx2a (55%) and Stx2b (32%), while stx2a/stx2d and stx2a/stx2b were each 2%. Among the 343 STEC that were serogrouped, 46% (n = 158) belonged to O8, 20% (n = 67) to 076, 12% (n = 42) to O91, 5% (n = 17) to O5, and 5% (n = 18) to O26. Less than 5% belonged to O78, O87, O146, and O103. The hly and eae genes were detected in 48% and 14% of STEC, respectively. Most belonged to phylogroup B1 (73%), followed by D (10%), E (8%), A (4%), B2 (4%), and F (1%). M13RAPD genotyping revealed clonality of 091, O5, O87, O103, and O78 but higher diversity in the O8, O76, and O26 serogroups. These results indicate goat STEC belonged to important non-O157 STEC serogroups, were genomically diverse, and harbored Shiga toxin subtypes associated with severe human disease.

High Virulence and Multidrug Resistance of Escherichia coli Isolated in Periodontal Disease.

Periodontal disease is caused by different gram-negative anaerobic bacteria; however, Escherichia coli has also been isolated from periodontitis and its role in periodontitis is less known. This study aimed to determine the variability in virulence genotype, antibiotic resistance phenotype, biofilm formation, phylogroups, and serotypes in different emerging periodontal strains of Escherichia coli, isolated from patients with periodontal disease and healthy controls. E. coli, virulence genes, and phylogroups, were identified by PCR, antibiotic susceptibility by the Kirby-Bauer method, biofilm formation was quantified using polystyrene microtiter plates, and serotypes were determined by serotyping. Although E. coli was not detected in the controls (n = 70), it was isolated in 14.7% (100/678) of the patients. Most of the strains (n = 81/100) were multidrug-resistance. The most frequent adhesion genes among the strains were fimH and iha, toxin genes were usp and hlyA, iron-acquisition genes were fyuA and irp2, and protectin genes were ompT, and KpsMT. Phylogroup B2 and serotype O25:H4 were the most predominant among the strains. These findings suggest that E. coli may be involved in periodontal disease due to its high virulence, multidrug-resistance, and a wide distribution of phylogroups and serotypes.