Defining the Genome Features of Escherichia albertii, an Emerging Enteropathogen Closely Related to Escherichia coli

Genetic distribution, characterization, and function of Escherichia coli type III secretion system 2 (ETT2)

Many Gram-negative bacteria use type Ⅲ secretion system (T3SS) to inject effector proteins and subvert host signaling pathways, facilitating the growth, survival, and virulence. Notably, some bacteria harbor multiple distinct T3SSs with different functions. An extraordinary T3SS, the Escherichia coli Type III Secretion System 2 (ETT2), is widespread among Escherichia coli (E. coli) strains. Since many ETT2 carry genetic mutations or deletions, it is thought to be nonfunctional. However, increasing studies highlight ETT2 contributes to E. coli pathogenesis. Here, we present a comprehensive overview of genetic distribution and characterization of ETT2. Subsequently, we outline its functional potential, contending that an intact ETT2 may retain the capacity to translocate effector proteins and manipulate the host's innate immune response. Given the potential zoonotic implications associated with ETT2-carrying bacteria, further investigations into the structure, function and regulation of ETT2 are imperative for comprehensive understanding of E. coli pathogenicity and the development of effective control strategies.

Detection of prolong excretion of Escherichia albertii in stool specimens of a 7-year-old child by a newly developed Eacdt gene-based quantitative real-time PCR method and molecular characterization of the isolates

Escherichia albertii is an emerging zoonotic foodborne pathogen. The clinical significance of this bacterium has increasingly been recognized worldwide. However, diagnostic method has not yet been established and its clinical manifestations are not fully understood. Here, we show that an Eacdt gene-based quantitative real-time PCR (qRT-PCR) developed in this study is 100% specific and sensitive when tested with 39 E. albertii and 36 non-E. albertii strains, respectively. Detection limit of the real-time PCR was 10 colony forming unit (CFU) and 1 pg of genomic DNA per PCR tube. When E. albertii was spiked with 4 × 100-106 CFU per mL to stool of healthy person, detection limit was 4.0 × 103 and 4.0 CFU per mL before and after enrichment culture, respectively. Moreover, the qRT-PCR was able to detect E. albertii in five children out of 246 (2%) but none from 142 adults suffering from gastroenteritis. All five E. albertii strains isolated carried eae and paa genes, however, only one strain harbored stx2f genes. Long-term shedding of stx2f gene-positive E. albertii in a child stool could be detected because of the qRT-PCR developed in this study which might have been missed if only conventional PCR and culture methods were employed. Furthermore, E. albertii isolated from siblings with diarrhea showed clonality by PFGE analysis. Taken together, these data suggest that the Eacdt gene-based qRT-PCR developed for the detection of E. albertii is useful and will assist in determining the real burden and clinical manifestation of E. albertii infections.

Escherichia albertii isolated from the bloodstream of a patient with liver cirrhosis in China: A case report

A rare case of bacteremia caused by Escherichia albertii, in a 50-year-old male with liver cirrhosis was reported. Clear, colorless, and circular colonies were recovered on blood agar after 24 h of aerobic incubation at 37 °C. The isolate was identified as E. albertii using MALDI-TOF/MS and confirmed by the diagnostic triplex-PCR targeting clpX, lysP, and mdh genes. The administration of piperacillin/tazobactam intravenously (4.5g every 8 hours) for 3 days was effective. This study suggested that specific strains of E. albertii have been implicated in causing extraintestinal infections in humans, similar to extraintestinal pathogenic E. coli (ExPEC). However, a comprehensive understanding of the underlying pathogenic mechanisms requires further exploration.

Development of a Novel Real-Time Polymerase Chain Reaction Assay to Detect Escherichia albertii in Chicken Meat

Escherichia albertii is an emerging enteropathogen. Several foodborne outbreaks of E. albertii have been reported in Japan; however, foods associated with most outbreaks remain unidentified. Therefore, polymerase chain reaction (PCR) assays detecting E. albertii specifically and sensitively are required. Primers and probe for real-time PCR assays targeting E. albertii-specific gene (EA-rtPCR) was designed. With 74 strains, including 43 E. albertii strains and several of its close relatives, EA-rtPCR specifically amplified E. albertii; therefore, the sensitivity of EA-rtPCR was then evaluated. The detection limits were 2.8 and 2.0-3.2 log colony-forming unit (CFU)/mL for E. albertii culture and enriched chicken culture inoculated with the pathogen, respectively. In addition, E. albertii was detected from 25 g of chicken meat inoculated with 0.1 log CFU of the pathogen by EA-rtPCR. The detection of E. albertii from chicken meat by EA-rtPCR was also evaluated by comparing with the nested-PCR assay, and 28 retail chicken meat and 193 dissected body parts from 21 chicken carcass were tested. One and three chicken meat were positive in the nested-PCR assay and EA-rtPCR, respectively. Fourteen carcasses had at least one body part that was positive for EA-rtPCR, and 36 and 48 samples were positive for the nested-PCR assay and EA-rtPCR, respectively. A total of 37 strains of E. albertii were isolated from seven PCR-positive samples obtained from six chicken carcass. All E. albertii isolates harbored eae gene, and were classified as E. albertii O-genotype (EAOg)3 or EAOg4 by EAO-genotyping. The EA-rtPCR developed in this study has potential to improve E. albertii detection in food and advance research on E. albertii infection.

Microbiology and Epidemiology of Escherichia albertii—An Emerging Elusive Foodborne Pathogen

Escherichia albertii, a close relative of E. coli, is an emerging zoonotic foodborne pathogen associated with watery diarrhea mainly in children and immunocompromised individuals. E. albertii was initially classified as eae-positive Hafnia alvei, however, as more genetic and biochemical information became available it was reassigned to its current novel taxonomy. Its infections are common under conditions of poor hygiene with confirmed transmission via contaminated water and food, mainly poultry-based products. This pathogen has been isolated from various domestic and wild animals, with most isolates being derived from birds, implying that birds among other wild animals might act as its reservoir. Due to the absence of standardized isolation and identification protocols, E. albertii can be misidentified as other Enterobacteriaceae. Exploiting phenotypes such as its inability to ferment rhamnose and xylose and PCR assays targeting E. albertii-specific genes such as the cytolethal distending toxin and the DNA-binding transcriptional activator of cysteine biosynthesis encoding genes can be used to accurately identify this pathogen. Several gaps exist in our knowledge of E. albertii and need to be bridged. A deeper understanding of E. albertii epidemiology and physiology is required to allow the development of effective measures to control its transmission and infections. Overall, current data suggest that E. albertii might play a more significant role in global infectious diarrhea cases than previously assumed and is often overlooked or misidentified. Therefore, simple, and efficient diagnostic tools that cover E. albertii biodiversity are required for effective isolation and identification of this elusive agent of diarrhea.

Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial

BACKGROUND

Mass drug administration (MDA) with azithromycin is the primary strategy for global trachoma control efforts. Numerous studies have reported secondary effects of MDA with azithromycin, including reductions in childhood mortality, diarrhoeal disease and malaria. Most recently, the MORDOR clinical trial demonstrated that MDA led to an overall reduction in all-cause childhood mortality in targeted communities. There is however concern about the potential of increased antimicrobial resistance in treated communities. This study evaluated the impact of azithromycin MDA on the prevalence of gastrointestinal carriage of macrolide-resistant bacteria in communities within the MORDOR Malawi study, additionally profiling changes in the gut microbiome after treatment. For faecal metagenomics, 60 children were sampled prior to treatment and 122 children after four rounds of MDA, half receiving azithromycin and half placebo.

RESULTS

The proportion of bacteria carrying macrolide resistance increased after azithromycin treatment. Diversity and global community structure of the gut was minimally impacted by treatment, however abundance of several species was altered by treatment. Notably, the putative human enteropathogen Escherichia albertii was more abundant after treatment.

CONCLUSIONS

MDA with azithromycin increased carriage of macrolide-resistant bacteria, but had limited impact on clinically relevant bacteria. However, increased abundance of enteropathogenic Escherichia species after treatment requires further, higher resolution investigation. Future studies should focus on the number of treatments and administration schedule to ensure clinical benefits continue to outweigh costs in antimicrobial resistance carriage. Trial registration ClinicalTrial.gov, NCT02047981. Registered January 29th 2014, https://clinicaltrials.gov/ct2/show/NCT02047981.

Detection of Escherichia albertii in Retail Oysters

ABSTRACT

Escherichia albertii is an emerging foodborne pathogen. Owing to its distribution in river water, it is important to determine the presence of E. albertii in aquaculture-related foods. In this study, we investigated the distribution of E. albertii in retail oyster samples. A total of 427 raw oyster samples (385 Pacific oysters and 42 Japanese rock oysters) were enriched in modified Escherichia coli broth (mEC) or mEC supplemented with novobiocin (NmEC) at 42°C. The cultures were used for E. albertii-specific nested PCR assay, as well as for E. albertii isolation using deoxycholate hydrogen sulfide lactose agar (DHL), DHL supplemented with rhamnose and xylose, and MacConkey agar supplemented with rhamnose and xylose. The population of E. albertii in nested PCR-positive samples was determined using the most-probable-number (MPN) method. E. albertii isolates were subjected to biochemical and genetic characterization. E. albertii was detected in 5 (1.6%) of 315 Pacific oyster samples (one piece each), 2 (2.9%) of 70 Pacific oyster samples (25 g each), and 2 (4.8%) of 42 Japanese rock oyster samples procured from four geographically distinct regions. A total of 64 E. albertii strains were isolated from eight of the nine nested PCR assay-positive oyster samples, and the MPN value was under the detection limit (<3 MPN/10 g). A specific season or month for detecting E. albertii was not observed in this study, suggesting that the pathogen is present in seawater. All the E. albertii isolates, except one, were positive for the virulence factor eae, indicating that these isolates have the potential to infect humans.

HIGHLIGHTS

[Prevalence of Foodborne Pathogens in Retail Meat in Saitama, Japan]

We investigated the prevalence of Campylobacter jejuni, Campylobacter coli, Salmonella, enterohemorrhagic Escherichia coli, enterotoxigenic Escherichia coli, Yersinia enterocolitica, and Escherichia albertii in domestic chicken and pork sold at retail stores in Saitama Prefecture, Japan. Campylobacter was detected in 35.7% (60/168) of chicken samples and 7.3% (14/190) of pork samples. C. jejuni and C. coli were predominant in chicken and pork, respectively. Salmonella was found in 58.1% (100/172) of chicken samples and 19.9% (41/206) of pork samples. Moreover, Salmonella Schwarzengrund was the major serovar observed in chicken isolates, whereas S. Typhimurium monophasic variant was in pork isolates. Furthermore, ETEC was found in 0.6% (1/160) of chicken samples and 2.4% (5/206) of pork samples. Y. enterocolitica was absent from all (83/83) chicken samples but was present in 9.3% (18/193) of pork samples, with a prevalence in pork tongues as high as 21.0% (13/62 samples). However, EHEC and E. albertii were not detected in our study. Therefore, the results of this study indicate that chicken was highly contaminated with Campylobacter sp. and Salmonella, and pork was with Y. enterocolitica serotype O3, Campylobacter sp., Salmonella, and ETEC.

[Genome analysis-based studies on bacterial genetic diversity]

There are a huge number of bacterial species on earth, and a huge intra-species genomic diversity are also observed in many bacteria. The high ability of bacteria to acquire foreign DNA and the presence of various mobile genetic elements contribute the generation of such genomic diversity. During the biochemical and genetic analysis of a Pseudomonas aeruginosa toxin, called cytotoxin, and its converting phage, which I first engaged in my research carrier, I became very interested in the genetic diversity of bacteria and mobile genetic elements such as bacteriophages, and realized the usefulness and power of genome analysis. Since then, I have been involved in genome analyses of various pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC), commensal bacteria of human and other animals, and bacteria or bacterial communities in natural environments. I was so lucky that I jumped in this research field at the very begging of genome analyses and experienced a very exciting time of surprisingly rapid advance in genome sequencing technologies which revolutionized a wide range of biology. In this article, I first review the main findings which our group obtained from the genome analyses on the P. aeruginosa cytotoxin converting phage and those on the evolution and genomic diversity of EHEC and related bacteria. The results of our analyses of Rickettsiaceae family genomes, which show surprisingly very low genomic diversity, and genome sequence-based analyses of an intrahospital bacterial outbreak and within-host genomic diversity are also summarized.

Molecular Study of Escherichia albertii in Pediatric Urinary Tract Infections

Background:

There are insufficient data about the presence of E. albertii as a causative organism in urinary tract infection in pediatric patients. Objective: The present study aimed to detect E. albertii by polymerase chain reaction (PCR) for detection of uidA, mdh, and lysP genes among isolated E.coli from children with urinary tract infection.

Methods:

The present study was a cross-sectional retrograde study which was carried out on 100 isolates of phenotypically confirmed E.coli detected in urine samples of children suffering from urinary tract infection. The isolates were subjected to molecular identification by PCR for uidA, mdh, and lysP genes.

Results:

E. albertii was identified by PCR in 7% of the isolates and E.coli was identified in 93% of the isolates. Two mdh and lysP genes were detected for E. albertii and the uidA gene for E. coli. E. albertii isolates had marked resistance to gentamicin (71.4%), followed by resistance to ciprofloxacin (57.1%), meropenem and imipenem (42.9% each) and ESBL activity by double discs method was reported in 57.1% of the isolates. However, none of the isolates had shown resistance to nalidixic acid and only one isolate had resistance to norfloxacin. There was a statistically insignificant difference between resistance to the used antibiotics such as aztreonam (P=0.083), ampicillin/clavulanate (P=0.5), ciprofloxacin (P=0.69), gentamicin (P=0.3) and ceftazidime (P=1.00).

Conclusion:

The present study highlights the emergence of E. albertii as a pathogen associated with urinary tract infections in children. There is marked antibiotic resistance of this pathogen, especially toward extended spectrum beta-lactams antibiotics. The identification method depends mainly on genetic studies. Further longitudinal studies with large number of patients are required to verify the accurate prevalence of this bacterium.

Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance

Escherichia albertii is a recently recognized species in the genus Escherichia that causes diarrhoea. The population structure, genetic diversity and genomic features have not been fully examined. Here, 169 E. albertii isolates from different sources and regions in China were sequenced and combined with 312 publicly available genomes (from additional 14 countries) for genomic analyses. The E. albertii population was divided into two clades and eight lineages, with lineage 3 (L3), L5 and L8 more common in China. Clinical isolates were observed in all clades/lineages. Virulence genes were found to be distributed differently among lineages: subtypes of the intimin encoding gene eae and the cytolethal distending toxin gene cdtB were lineage associated, and the second type three secretion system (ETT2) island was truncated in L3 and L6. Seven new eae subtypes and one new cdtB subtype (cdtB-VI) were identified. Alarmingly, 85.9 % of the Chinese E. albertii isolates were predicted to be multidrug-resistant (MDR) with 35.9 % harbouring genes capable of conferring resistance to 10 to 14 different drug classes. The majority of the MDR isolates were of poultry source from China and belonged to four sequence types (STs) [ST4638, ST4479, ST4633 and ST4488]. Thirty-four plasmids with some carrying MDR and virulence genes, and 130 prophages were identified from 17 complete E. albertii genomes. The 130 intact prophages were clustered into five groups, with group five prophages harbouring more virulence genes. We further identified three E. albertii specific genes as markers for the identification of this species. Our findings provided fundamental insights into the population structure, virulence variation and drug resistance of E. albertii.

The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19

Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.

ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data

Escherichia coli is a priority foodborne pathogen of public health concern and phenotypic serotyping provides critical information for surveillance and outbreak detection activities. Public health and food safety laboratories are increasingly adopting whole-genome sequencing (WGS) for characterizing pathogens, but it is imperative to maintain serotype designations in order to minimize disruptions to existing public health workflows. Multiple in silico tools have been developed for predicting serotypes from WGS data, including SRST2, SerotypeFinder and EToKi EBEis, but these tools were not designed with the specific requirements of diagnostic laboratories, which include: speciation, input data flexibility (fasta/fastq), quality control information and easily interpretable results. To address these specific requirements, we developed ECTyper (https://github.com/phac-nml/ecoli_serotyping) for performing both speciation within Escherichia and Shigella, and in silico serotype prediction. We compared the serotype prediction performance of each tool on a newly sequenced panel of 185 isolates with confirmed phenotypic serotype information. We found that all tools were highly concordant, with 92-97 % for O-antigens and 98-100 % for H-antigens, and ECTyper having the highest rate of concordance. We extended the benchmarking to a large panel of 6954 publicly available E. coli genomes to assess the performance of the tools on a more diverse dataset. On the public data, there was a considerable drop in concordance, with 75-91 % for O-antigens and 62-90 % for H-antigens, and ECTyper and SerotypeFinder being the most concordant. This study highlights that in silico predictions show high concordance with phenotypic serotyping results, but there are notable differences in tool performance. ECTyper provides highly accurate and sensitive in silico serotype predictions, in addition to speciation, and is designed to be easily incorporated into bioinformatic workflows.

Pan-Genome Reverse Vaccinology Approach for the Design of Multi-Epitope Vaccine Construct against Escherichia albertii

Escherichia albertii is characterized as an emerging pathogen, causing enteric infections. It is responsible for high mortality rate, especially in children, elderly, and immunocompromised people. To the best of our knowledge, no vaccine exists to curb this pathogen. Therefore, in current study, we aimed to identify potential vaccine candidates and design chimeric vaccine models against Escherichia albertii from the analysis of publicly available data of 95 strains, using a reverse vaccinology approach. Outer-membrane proteins (n = 4) were identified from core genome as vaccine candidates. Eventually, outer membrane Fimbrial usher (FimD) protein was selected as a promiscuous vaccine candidate and utilized to construct a potential vaccine model. It resulted in three epitopes, leading to the design of twelve vaccine constructs. Amongst these, V6 construct was found to be highly immunogenic, non-toxic, non-allergenic, antigenic, and most stable. This was utilized for molecular docking and simulation studies against six HLA and two TLR complexes. This construct can therefore be used for pan-therapy against different strains of E. albertii and needs to be tested in vitro and in vivo.

Diversification of Escherichia albertii H-Antigens and Development of H-Genotyping PCR

Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. As E. albertii sometimes causes outbreaks of gastroenteritis, rapid strain typing systems, such as the O- and H-serotyping systems widely used for E. coli, will be useful for outbreak investigation and surveillance. Although an O-genotyping system has recently been developed, the diversity of E. albertii H-antigens (flagellins) encoded by fliC genes remains to be systematically investigated, and no H-serotyping or genotyping system is currently available. Here, we analyzed the fliC genes of 243 genome-sequenced E. albertii strains and identified 73 sequence types, which were grouped into four clearly distinguishable types designated E. albertii H-genotypes 1–4 (EAHg1–EAHg4). Although there was a clear sign of intraspecies transfer of fliC genes in E. albertii, none of the four E. albertii H-genotypes (EAHgs) were closely related to any of the 53 known E. coli H-antigens, indicating the absence or rare occurrence of interspecies transfer of fliC genes between the two species. Although the analysis of more E. albertii strains will be required to confirm the low level of variation in their fliC genes, this finding suggests that E. albertii may exist in limited natural hosts or environments and/or that the flagella of E. albertii may function in a limited stage(s) in their life cycle. Based on the fliC sequences of the four EAHgs, we developed a multiplex PCR-based H-genotyping system for E. albertii (EAH-genotyping PCR), which will be useful for epidemiological studies of E. albertii infections.

[Molecular epidemiology of Escherichia albertii, emerging zoonotic enteropathogen]

Escherichia albertii is an emerging zoonotic enteric pathogen, closely related to E. coli. Several foodborne outbreaks caused by E. albertii accounting for >100 patients have recently occurred in Japan. This bacterium carries eae gene, similar to enteropathogenic E. coli. Some of them harbor Shiga toxin 2 (stx2a, stx2f) genes, primary virulence factor of enterohemorrhagic E. coli (EHEC), suggesting that the Stx2 producers could cause severe diseases such as HUS in humans. However, due to lack of the knowledges about its bacteriological characteristics and of the diagnostic methods, E. albertii-related infections might have been underestimated, and the infection sources and routes have not yet been understood. We had continuously performed molecular epidemiological studies targeting for cytolethal distending toxin-producing E. coli, and unexpectedly found that cdt-II gene-positive isolates were not E. coli but E. albertii. This finding led us to initiate research more focusing on E. albertii. We have constructed simple, efficient and reliable methods for the detection, isolation and identification of this bacterium by developing an E. albertii-specific PCR assay targeting Eacdt genes and E. albertii-selective isolation medium named XRM-MacConkey agar. We have also identified raccoons as a potential natural reservoir of E. albertii through wildlife survey using these methods. Here, I describe what I have studied with my colleagues.

Detection, isolation and molecular characterization of Escherichia albertii in wild birds in West Japan

Escherichia albertii is an emerging zoonotic foodborne pathogen. Several outbreaks of E. albertii have occurred particularly in Japan. Although birds have been considered as one of the most important reservoirs of this bacterium, information regarding the prevalence in birds is still scanty. We performed a survey of E. albertii in wild birds in Japan, and examined characteristics of the isolates. E. albertii specific gene was detected in 5 cloacal swabs out of 156 birds by PCR. Four E. albertii were isolated from a swallow with 2 different E. albertii strains and 2 pigeons in a flock by XRM-MacConkey agar. These isolates were assigned to biogroup 3, shown no resistance to any antimicrobials tested, and classified into 2 EAO-genotypes (EAOg2 and EAOg33) and untypable. Similar to clinical E. albertii strains, these isolates carried virulence genes including eae (n=4), paa (n=4), Eccdt-I (n=2) and stx2f (n=1) in addition to Eacdt. Interestingly, stx2f genes in a strain were located on an inducible bacteriophage, which can confer the ability to produce Stx2f to E. coli. In conclusion, Japanese wild birds carried E. albertii at the similar levels to the reported prevalence in birds. These isolates may have a potential to cause gastroenteritis in humans.

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota

Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect the host. The production of these molecules, mostly derived from their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite the importance of microbiome-derived primary metabolites, no tool existed to predict the gene clusters responsible for their production. For this reason, we recently introduced gutSMASH. gutSMASH can predict 41 different known pathways, including MGCs involved in bioenergetics, but also putative ones that are candidates for novel pathway discovery. To make the tool more user-friendly and accessible, we here present the gutSMASH web server, hosted at https://gutsmash.bioinformatics.nl/. The user can either input the GenBank assembly accession or upload a genome file in FASTA or GenBank format. Optionally, the user can enable additional analyses to obtain further insights into the predicted MGCs. An interactive HTML output (viewable online or downloadable for offline use) provides a user-friendly way to browse functional gene annotations and sequence comparisons with reference gene clusters as well as gene clusters predicted in other genomes. Thus, this web server provides the community with a streamlined and user-friendly interface to analyze the metabolic potential of gut microbiomes.

Prevalence of Escherichia albertii in Raccoons (Procyon lotor), Japan

Natural reservoirs of Escherichia albertii remain unclear. In this study, we detected E. albertii by PCR in 248 (57.7%) of 430 raccoons from Osaka, Japan, and isolated 143 E. albertii strains from the 62 PCR-positive samples. These data indicate that raccoons could be a natural reservoir of E. albertii in Japan.

A review of the taxonomy, genetics, and biology of the genus Escherichia and the type species Escherichia coli

Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.

Detection of Escherichia Albertii in Urinary and Gastrointestinal Infections in Kermanshah, Iran

Background: Escherichia albertii has been recently isolated from the feces of people with gastroenteritis as a pathogen that causes diarrhea. Due to insufficient information on the phenotypic and biochemical characteristics of E. albertii, it is difficult to distinguish it from other species of the Enterobacteriaceae family and, therefore, it is mistakenly identified as Escherichia coli or even Hafnia alvei. Objective: The present study which was conducted for the first time in Iran aimed to identify E. albertii in samples from individuals afflicted with urinary and gastrointestinal infections by using the polymerase chain reaction (PCR) method. The required samples were obtained from clinical laboratories in Kermanshah. Materials and Methods: Firstly, a total of 60 urinary and 40 fecal samples identified as E. coli in clinical laboratories were re-evaluated in terms of specific phenotypic and biochemical characteristics of E. coli. Then, two lysP and mdh genes were detected for E. albertii, and the uidA gene was found for E. coli by PCR using specific primers pairs. Results: The results from phenotypic and biochemical tests indicated that all samples shared common characteristics with E. coli. However, PCR findings demonstrated that out of 100 samples, 6 samples (6%) contained specific genes of E. coli while 94 remaining samples (94%) showed the uidA gene. Out of the given 6 samples, 5 samples carried urinary tract infections and only one showed gastrointestinal infection. Conclusion: Our study findings revealed that E. albertii could have been considered as one of the causes for urinary and gastrointestinal infections in Iran, and that it was mistakenly identified as E. coli in clinical laboratories.

Genomic Properties and Temporal Analysis of the Interaction of an Invasive Escherichia albertii With Epithelial Cells

Diarrhea is one of the main causes of infant mortality worldwide, mainly in the developing world. Among the various etiologic agents, Escherichia albertii is emerging as an important human enteropathogen. E. albertii promote attaching and effacing (AE) lesions due to the presence of the locus of enterocyte effacement (LEE) that encodes a type three secretion system (T3SS), the afimbrial adhesin intimin and its translocated receptor, Tir, and several effector proteins. We previously showed that E. albertii strain 1551-2 invades several epithelial cell lineages by a process that is dependent on the intimin-Tir interaction. To understand the contribution of T3SS-dependent effectors present in E. albertii 1551-2 during the invasion process, we performed a genetic analysis of the LEE and non-LEE genes and evaluated the expression of the LEE operons in various stages of bacterial interaction with differentiated intestinal Caco-2 cells. The kinetics of the ability of the 1551-2 strain to colonize and form AE lesions was also investigated in epithelial HeLa cells. We showed that the LEE expression was constant during the early stages of infection but increased at least 4-fold during bacterial persistence in the intracellular compartment. An in silico analysis indicated the presence of a new tccP/espF_U subtype, named tccP3. We found that the encoded protein colocalizes with Tir and polymerized F-actin during the infection process in vitro. Moreover, assays performed with Nck null cells demonstrated that the 1551-2 strain can trigger F-actin polymerization in an Nck-independent pathway, despite the fact that TccP3 is not required for this phenotype. Our study highlights the importance of the T3SS during the invasion process and for the maintenance of E. albertii 1551-2 inside the cells. In addition, this work may help to elucidate the versatility of the T3SS for AE pathogens, which are usually considered extracellular and rarely reach the intracellular environment.

The population genetics of pathogenic Escherichia coli

Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.

Escherichia albertii Pathogenesis

Escherichia albertii is an emerging enteropathogen of humans and many avian species. This bacterium is a close relative of Escherichia coli and has been frequently misidentified as enteropathogenic or enterohemorrhagic E. coli due to their similarity in phenotypic and genetic features, such as various biochemical properties and the possession of a type III secretion system encoded by the locus of enterocyte effacement. This pathogen causes outbreaks of gastroenteritis, and some strains produce Shiga toxin. Although many genetic and phenotypic studies have been published and the genome sequences of more than 200 E. albertii strains are now available, the clinical significance of this species is not yet fully understood. The apparent zoonotic nature of the disease requires a deeper understanding of the transmission routes and mechanisms of E. albertii to develop effective measures to control its transmission and infection. Here, we review the current knowledge of the phylogenic relationship of E. albertii with other Escherichia species and the biochemical and genetic properties of E. albertii, with particular emphasis on the repertoire of virulence factors and the mechanisms of pathogenicity, and we hope this provides a basis for future studies of this important emerging enteropathogen.

O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method

Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. In many Gram-negative bacteria, including E. coli, O-antigen variation has long been used for the serotyping of strains. In E. albertii, while eight O-serotypes unique to this species have been identified, some strains have been shown to exhibit genetic or serological similarity to known E. coli/Shigella O-serotypes. However, the diversity of O-serotypes and O-antigen biosynthesis gene clusters (O-AGCs) of E. albertii remains to be systematically investigated. Here, we analysed the O-AGCs of 65 E. albertii strains and identified 40 E. albertii O-genotypes (EAOgs) (named EAOg1–EAOg40). Analyses of the 40 EAOgs revealed that as many as 20 EAOgs exhibited significant genetic and serological similarity to the O-AGCs of known E. coli/Shigella O-serotypes, and provided evidence for the inter-species horizontal gene transfer of O-AGCs between E. albertii and E. coli. Based on the sequence variation in the wzx gene among the 40 EAOgs, we developed a multiplex PCR-based O-genotyping system for E. albertii (EAO-genotyping PCR) and verified its usefulness by genotyping 278 E. albertii strains from various sources. Although 225 (80.9 %) of the 278 strains could be genotyped, 51 were not assigned to any of the 40 EAOgs, indicating that further analyses are required to better understand the diversity of O-AGCs in E. albertii and improve the EAO-genotyping PCR method. A phylogenetic view of E. albertii strains sequenced so far is also presented with the distribution of the 40 EAOgs, which provided multiple examples for the intra-species horizontal transfer of O-AGCs in E. albertii.

Type III Secretion Effectors with Arginine N-Glycosyltransferase Activity

Type III secretion systems are used by many Gram-negative bacterial pathogens to inject proteins, known as effectors, into the cytosol of host cells. These virulence factors interfere with a diverse array of host signal transduction pathways and cellular processes. Many effectors have catalytic activities to promote post-translational modifications of host proteins. This review focuses on a family of effectors with glycosyltransferase activity that catalyze addition of N-acetyl-d-glucosamine to specific arginine residues in target proteins, leading to reduced NF-κB pathway activation and impaired host cell death. This family includes NleB from Citrobacter rodentium, NleB1 and NleB2 from enteropathogenic and enterohemorrhagic Escherichia coli, and SseK1, SseK2, and SseK3 from Salmonella enterica. First, we place these effectors in the general framework of the glycosyltransferase superfamily and in the particular context of the role of glycosylation in bacterial pathogenesis. Then, we provide detailed information about currently known members of this family, their role in virulence, and their targets.

Hypoosmotic stress induces flagellar biosynthesis and swimming motility in Escherichia albertii

Bacteria use flagella as propellers to move to favorable environments. Escherichia albertii, a growing cause of foodborne illness and diarrhea, is reportedly non-motile and lacks flagella on its surface. Here, we report that 27 out of 59 E. albertii strains, collected mainly from humans and birds, showed swimming motility when cultured at low osmotic pressure. The biosynthesis of flagella in E. albertii cells was induced under ambient temperature and hypoosmotic pressure: conditions which resemble aquatic environments. Flagellar induction increased E. albertii survival in the intestinal epithelial cell culture containing gentamicin. Although genes involved in chemotaxis are not present in the E. albertii genome, the addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augmented the proportion of swimming cells by 35-fold. These results suggest that flagellar biosynthesis and motility in E. albertii cells are controlled by their internal and external osmolarity.

Ikeda et al. report that enteropathogen E. albertii, thought to be a non-motile microorganism, may form flagella and acquire swimming motility in a hypoosmotic environment and ambient temperatures. Further addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augments the proportion of swimming cells.

Flagellum expression and swimming activity by the zoonotic pathogen Escherichia albertii

Flagella are the well-known structural appendages used by bacteria for motility. Although generally reported to be non-motile, the enteropathogenic bacterial species Escherichia albertii produces flagella intermittently. We found that E. albertii expressed flagella under specific environmental conditions. After several generations (involving 4 to 12-h incubations), six of the twelve strains we investigated displayed swimming motility in various aquatic environments, including pond water containing nutrients from pigeon droppings (10% suspension) as well as in 20 × -diluted tryptic soy broth. The most significant motility determinant was a temperature between 15 and 30 °C. At 20 °C in the 10% pigeon-dropping suspension, microscopic observations revealed that some cells (1%-95% of six strains) showed swimming motility. Electron microscopy showed that the E. albertii cells expressed flagella. Lower concentrations of some substrates (including nutrients) may be of secondary importance for E. albertii flagella expression. Interestingly, the non-motile strains (n = 6/12) contained pseudogenes corresponding to essential flagella structural proteins. After being released from its host into surface water, E. albertii may express flagella to move toward nutrient sources or new hosts.

Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands

Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.

Non-biogroup 1 or 2 Strains of the Emerging Zoonotic Pathogen Escherichia albertii, Their Proposed Assignment to Biogroup 3, and Their Commonly Detected Characteristics

Escherichia albertii, a zoonotic enteropathogen, is responsible for outbreaks of disease in humans. Identifying strains of E. albertii by phenotypic characterization tests is difficult because of its poorly defined properties. Screening its phenotypic characteristics is, nevertheless, a necessary prerequisite for further genetic analysis of its properties, and species-specific polymerase chain reaction (PCR) analysis can be used to type the pathogen. While two E. albertii biogroups (1 and 2) have been described, strains with characteristics divergent from both biogroups have been reported worldwide. The aim of the present study was to evaluate the characteristics of non-biogroup 1 or 2 strains, and discern the characteristics common to all of the E. albertii strains from this study. Altogether, 107/414 field isolates were selected for examination based on pulsed-field gel electrophoresis analysis. The 107 strains were isolated from 92 sources, including humans and pigeon feces, other wild birds, and retail chicken livers. All strains were then examined using various culture-based, biochemical (API 50CHE tests, API Zym test, and others) and molecular (virulence gene screening, multi-locus sequence analysis) testing methods. Our results revealed that all field strains (n = 107) showed non-biogroup 1 or 2 characteristics, with multiple sequence differences. Variations in indole production and the lysine decarboxylase activity profiles among the isolates made identification of E. albertii very difficult. Therefore, we propose that non-biogroup 1 or 2 of E. albertii should be assigned to biogroup 3 to make screening of them easier in public health and clinical laboratory settings. Clearly, having group criteria for indole-negative/lysine-positive, indole-positive/lysine-negative, and indole-positive/lysine-positive E. albertii biogroups 1, 2, and 3 strains, respectively, should provide for more accurate identification of E. albertii isolates. Based on our findings, we recommend that isolates displaying phenotype mobility-negativity (sulfide-indole-motility medium, 37°C), hydrogen sulfide production-negativity (triple sugar iron medium), acid production-negativity from xylose, negative β-glucuronidase activity properties, and showing indole production and lysine decarboxylase activity profiles in accordance with one of the three biogroups, should be further assessed using an E. albertii-specific PCR assay.

Draft Genome Sequence of Escherichia albertii Strain Mex-12/320a, Isolated from an Infant with Diarrhea and Harboring Virulence Genes Associated with Diarrheagenic Strains of Enteropathogenic Escherichia coli

Escherichia albertii is an emerging human enteropathogen. We report the draft genome sequence of E. albertii strain Mex-12/320a, isolated from an infant with diarrhea. The presence of the pathogenic island O122/IE6 and the nleA gene, previously found in diarrheagenic enteropathogenic Escherichia coli strains, suggests that E. albertii may cause acute diarrhea.

The Evasive Enemy: Insights into the Virulence and Epidemiology of the Emerging Attaching and Effacing Pathogen Escherichia albertii

The diarrheic attaching and effacing (A/E) pathogen Escherichia albertii was first isolated from infants in Bangladesh in 1991, although the bacterium was initially classified as Hafnia alvei Subsequent genetic and biochemical interrogation of these isolates raised concerns about their initial taxonomic placement. It was not until 2003 that these isolates were reassigned to the novel taxon Escherichia albertii because they were genetically more closely related to E. coli, although they had diverged sufficiently to warrant a novel species name. Unfortunately, new isolates continue to be mistyped as enteropathogenic E. coli (EPEC) or enterohemorrhagic E. coli (EHEC) owing to shared traits, most notably the ability to form A/E lesions. Consequently, E. albertii remains an underappreciated A/E pathogen, despite multiple reports demonstrating that many provisional EPEC and EHEC isolates incriminated in disease outbreaks are actually E. albertii Metagenomic studies on dozens of E. albertii isolates reveal a genetic architecture that boasts an arsenal of candidate virulence factors to rival that of its better-characterized cousins, EPEC and EHEC. Beyond these computational comparisons, studies addressing the regulation, structure, function, and mechanism of action of its repertoire of virulence factors are lacking. Thus, the paucity of knowledge about the epidemiology, virulence, and antibiotic resistance of E. albertii, coupled with its misclassification and its ability to develop multidrug resistance in a single step, highlights the challenges in combating this emerging pathogen. This review seeks to synthesize our current but incomplete understanding of the biology of E. albertii.

Diarrhoeagenic Escherichia coli and Escherichia albertii in Brazil: pathotypes and serotypes over a 6-year period of surveillance

Diarrhoeagenic Escherichia coli (DEC) is a leading cause of infectious diarrhoea worldwide. In recent years, Escherichia albertii has also been implicated as a cause of human enteric diseases. This study describes the occurrence of E. coli pathotypes and serotypes associated with enteric illness and haemolytic uremic syndrome (HUS) isolated in Brazil from 2011 to 2016. Pathotypes isolated included enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC) and Shiga toxin-producing E. coli (STEC). PCR of stool enrichments for DEC pathotypes was employed, and E. albertii was also sought. O:H serotyping was performed on all DEC isolates. A total of 683 DEC and 10 E. albertii strains were isolated from 5047 clinical samples. The frequencies of DEC pathotypes were 52.6% (359/683) for EPEC, 32.5% for EAEC, 6.3% for ETEC, 4.4% for EIEC and 4.2% for STEC. DEC strains occurred in patients from 3 months to 96 years old, but EPEC, EAEC and STEC were most prevalent among children. Both typical and atypical isolates of EPEC and EAEC were recovered and presented great serotype heterogeneity. HUS cases were only associated with STEC serotype O157:H7. Two E. albertii isolates belonged to serogroup O113 and one had the stx2f gene. The higher prevalence of atypical EPEC in relation to EAEC in community-acquired diarrhoea in Brazil suggests a shift in the trend of DEC pathotypes circulation as previously EAEC predominated. This is the first report of E. albertii isolation from active surveillance. These results highlight the need of continuing DEC and E. albertii surveillance, as a mean to detect changes in the pattern of pathotypes and serotypes circulation and provide useful information for intervention and control strategies.

Draft Genome Sequence of the Intimin-Positive Enteropathogenic Escherichia albertii Strain MBT-EA1, Isolated from Lettuce

The genome of the intimin (eae)-harboring Escherichia albertii strain MBT-EA1, isolated from lettuce in Germany, was sequenced. Sequence analysis showed the assembled draft genome size to be 4,560,948 bp, containing a predicted total of 4,414 protein-encoding genes, 11 rRNAs, and 82 tRNAs. Furthermore, three plasmid sequences were found.

Hierarchical sets: analyzing pangenome structure through scalable set visualizations

Motivation

The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis.

Results

We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do not correspond with the hierarchy, can be visualized using hierarchical edge bundles. When applied to pangenome data this plot shows putative horizontal gene transfers between the genomes and can highlight relationships between genomes that is not represented by the hierarchy. We illustrate the utility of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis.

Availability and Implementation

The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN (https://cran.r-project.org/web/packages/hierarchicalSets)

Supplementary information

Supplementary data are available at Bioinformatics online.

Complete Genome Sequence of Escherichia albertii Strain 1551-2, a Potential Extracellular and Intracellular Pathogen

Escherichia albertii has recently been recognized as an emerging human and bird enteric pathogen. Here, we report the complete chromosome sequence of a clinical isolate of E. albertii strain 1551-2, which may provide information about the pathogenic potential of this new species and the mechanisms of evolution of Escherichia species.

Characterization of four Escherichia albertii isolates collected from animals living in Antarctica and Patagonia

Escherichia albertii is a recently discovered species with a limited number of well characterized strains. The aim of this study was to characterize four of the E. albertii strains, which were among 41 identified Escherichia strains isolated from the feces of living animals on James Ross Island, Antarctica, and Isla Magdalena, Patagonia. Sequencing of 16S rDNA, automated ribotyping, and rep-PCR were used to identify the four E. albertii isolates. Phylogenetic analyses based on multi-locus sequence typing showed these isolates to be genetically most similar to the members of E. albertii phylogroup G3. These isolates encoded several virulence factors including those, which are characteristic of E. albertii (cytolethal distending toxin and intimin) as well as bacteriocin determinants that typically have a very low prevalence in E. coli strains (D, E7). Moreover, E. albertii protein extracts caused cell cycle arrest in human cell line A375, probably because of cytolethal distending toxin activity.

Distinctive Gut Microbiota Is Associated with Diarrheagenic Escherichia coli Infections in Chilean Children

Background: Diarrheagenic Escherichia coli (DEC) strains are a major cause of diarrhea in children under 5 years of age worldwide. DEC pathogenicity relies on the interaction of bacteria with environmental factors, including the host's resident gut microbiota. Previous reports have shown changes in the gut microbiota's composition during episodes of diarrhea, which may increase the pathogenicity of DEC strains. More intense and detailed identification of microbiota strains specifically associated with DEC infections and disease is needed to pinpoint their role in DEC pathogenicity.

Aim: To identify resident indicative bacterial taxa in DEC-positive diarrhea stool samples of Chilean children.

Methods: We analyzed 63 diarrheal stool samples from children 1–5 years of age by FilmArray® GI in order to identify a potential pathogen and to group diarrhea episodes into those caused by DEC as sole pathogen (DEC group, 32 samples) and those caused by an enteric virus as sole pathogen (viral group, 31 samples). In addition, 30 stool samples from healthy children, negative for enteric pathogens, were evaluated (healthy group). The 16S rRNA gene was amplified and sequenced using 454 pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) at 99% identity and their representatives were used to assign them to operational phylogenetic units (OPUs) using a phylogenetic inference approach.

Results: Taxa assignment using the OPU approach resulted in a lower number of units but with higher accuracy compared to the OTU approach. Data analysis indicated an increase in sequences belonging to the phylum Proteobacteria in the DEC group compared to the viral and healthy groups. Samples displayed a statistically different community structure by sample grouping by redundancy analysis and ANOVA. Escherichia albertii (p = 0.001), Citrobacter werkmanii (p = 0.001), Yersinia enterocolitica, subsp. paleartica (p = 0.048), and Haemophilus sputorum (p = 0.028) were indicative species for the DEC group as compared to the viral and healthy groups.

Conclusion: Gut microbiota in Chilean children with DEC-positive diarrhea differed from microbiota associated with enteric virus and healthy children. Indicative species found in this study may prove relevant in advancing our understanding of the relationship between resident gut microbiota and DEC leading to the occurrence of disease.

Defining the Genetic Features of O-Antigen Biosynthesis Gene Cluster and Performance of an O-Antigen Serotyping Scheme for Escherichia albertii

Escherichia albertii is a newly described and emerging diarrheagenic pathogen responsible for outbreaks of gastroenteritis. Serotyping plays an important role in diagnosis and epidemiological studies for pathogens of public health importance. The diversity of O-antigen biosynthesis gene clusters (O-AGCs) provides the primary basis for serotyping. However, little is known about the distribution and diversity of O-AGCs of E. albertii strains. Here, we presented a complete sequence set for the O-AGCs from 52 E. albertii strains and identified seven distinct O-AGCs. Six of these were also found in 15 genomes of E. albertii strains deposited in the public database. Possession of wzy/wzx genes in each O-AGC strongly suggest that O-antigens of E. albertii were synthesized by the Wzx/Wzy-dependent pathway. Furthermore, we performed an O-antigen serotyping scheme for E. albertii based on specific antisera against seven O-antigens and a high throughput xTAG Luminex assay to simultaneously detect seven O-AGCs. Both methods accurately identified serotypes of 64 tested E. albertii strains. Our data revealed the high-level diversity of O-AGCs in E. albertii. We also provide valuable methods to reliably identify and serotype this bacterium.

Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii

Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.

Escherichia albertii, a novel human enteropathogen, colonizes rat enterocytes and translocates to extra-intestinal sites

Diarrhea is the second leading cause of death of children up to five years old in the developing countries. Among the etiological diarrheal agents are atypical enteropathogenic Escherichia coli (aEPEC), one of the diarrheagenic E. coli pathotypes that affects children and adults, even in developed countries. Currently, genotypic and biochemical approaches have helped to demonstrate that some strains classified as aEPEC are actually E. albertii, a recently recognized human enteropathogen. Studies on particular strains are necessary to explore their virulence potential in order to further understand the underlying mechanisms of E. albertii infections. Here we demonstrated for the first time that infection of fragments of rat intestinal mucosa is a useful tool to study the initial steps of E. albertii colonization. We also observed that an E. albertii strain can translocate from the intestinal lumen to Mesenteric Lymph Nodes and liver in a rat model. Based on our finding of bacterial translocation, we investigated how E. albertii might cross the intestinal epithelium by performing infections of M-like cells in vitro to identify the potential in vivo translocation route. Altogether, our approaches allowed us to draft a general E. albertii infection route from the colonization till the bacterial spreading in vivo.