Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.

Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.

European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe.

The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. This work illustrates the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection.

IRIDA-ARIES Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy.

Pathogen genomics is transforming surveillance of infectious diseases, deepening our understanding of evolution and diffusion of etiological agents, host-pathogen interactions and antimicrobial resistance. This discipline is playing an important role in the development of One Health Surveillance with public health experts of various disciplines integrating methods applied to pathogen research, monitoring, management and prevention of outbreaks. Especially with the notion that foodborne diseases may not be transmitted by food only, the ARIES Genomics project aimed to deliver an Information System for the collection of genomic and epidemiological data to enable genomics-based surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface. Keeping in mind that the users of the system comprised persons with expertise in a wide variety of domains, the system was expected to be used with a low learning curve directly by the persons target of the analyses' results, keeping the information exchange chains as short as possible. As a result, the IRIDA-ARIES platform (https://irida.iss.it/) provides an intuitive web-based interface for multisectoral data collection and bioinformatic analyses. In practice, the user creates a sample and uploads the Next-generation sequencing reads, then an analysis pipeline is launched automatically performing a series of typing and clustering operations fueling the information flow. Instances of IRIDA-ARIES host the Italian national surveillance system for infections by Listeria monocytogenes (Lm) and the surveillance system for infections by Shigatoxin-producing Escherichia coli (STEC). As of today, the platform does not provide tools to manage epidemiological investigations but serves as an instrument of aggregation for risk monitoring, capable of triggering alarms on possible critical situations that might go unnoticed otherwise.

One Health surveillance-A cross-sectoral detection, characterization, and notification of foodborne pathogens.

Introduction: Several Proficiency Test (PT) or External Quality Assessment (EQA) schemes are currently available for assessing the ability of laboratories to detect and characterize enteropathogenic bacteria, but they are usually targeting one sector, covering either public health, food safety or animal health. In addition to sector-specific PTs/EQAs for detection, cross-sectoral panels would be useful for assessment of the capacity to detect and characterize foodborne pathogens in a One Health (OH) perspective and further improving food safety and interpretation of cross-sectoral surveillance data. The aims of the study were to assess the cross-sectoral capability of European public health, animal health and food safety laboratories to detect, characterize and notify findings of the foodborne pathogens Campylobacter spp., Salmonella spp. and Yersinia enterocolitica, and to develop recommendations for future cross-sectoral PTs and EQAs within OH. The PT/EQA scheme developed within this study consisted of a test panel of five samples, designed to represent a theoretical outbreak scenario. Methods: A total of 15 laboratories from animal health, public health and food safety sectors were enrolled in eight countries: Denmark, France, Italy, the Netherlands, Poland, Spain, Sweden, and the United Kingdom. The laboratories analyzed the samples according to the methods used in the laboratory and reported the target organisms at species level, and if applicable, serovar for Salmonella and bioserotype for Yersinia. Results: All 15 laboratories analyzed the samples for Salmonella, 13 for Campylobacter and 11 for Yersinia. Analytical errors were predominately false negative results. One sample (S. Stockholm and Y. enterocolitica O:3/BT4) with lower concentrations of target organisms was especially challenging, resulting in six out of seven false negative results. These findings were associated with laboratories using smaller sample sizes and not using enrichment methods. Detection of Salmonella was most commonly mandatory to notify within the three sectors in the eight countries participating in the pilot whereas findings of Campylobacter and Y. enterocolitica were notifiable from human samples, but less commonly from animal and food samples. Discussion: The results of the pilot PT/EQA conducted in this study confirmed the possibility to apply a cross-sectoral approach for assessment of the joint OH capacity to detect and characterize foodborne pathogens.

Molecular characterization of diarrheagenic Escherichia coli isolates from children with diarrhea: A cross-sectional study in four provinces of Mozambique: Diarrheagenic Escherichia coli in Mozambique.

OBJECTIVES: Analyze the frequency of diarrheagenic Escherichia coli (DEC) pathotypes and their antimicrobial resistance profiles among children aged <15 years with diarrhea in four Mozambican provinces. METHODS: A cross-sectional hospital-based surveillance program of diarrhea was implemented in Maputo, Sofala, Zambézia, and Nampula. A single stool sample was collected from each child from May 2014 to May 2017. Culture methods and biochemical characterization were performed to detect E. coli strains. DEC pathotypes were determined by conventional polymerase chain reaction targeting specific virulence genes. Antimicrobial susceptibility was assessed by the Kirby-Bauer method. RESULTS: From 723 specimens analyzed by culture, 262 were positive for E. coli. A total of 208 samples were tested by polymerase chain reaction for DEC identification, of which 101 (48.6%) were positive for a DEC pathotype. The predominant pathotypes were enteroaggregative (66.3%, 67/101), enteropathogenic (15.8%, 16/101), enterotoxigenic (13.9%, 14/101), and enteroinvasive E. coli (4.0%, 4/101). No Shiga toxin-producing E. coli was identified. Regardless of the province, the most frequent pathotype was enteroaggregative E. coli. Isolated DEC presented high frequency of resistance to ampicillin (97.8%), tetracycline (68.3%), chloramphenicol (28.4%), nalidixic acid (19.5%), and gentamicin (14.4%). CONCLUSION: Children with diarrhea in Mozambique had DEC and higher resistance to ampicillin and tetracycline.

Population Analysis of O26 Shiga Toxin-Producing Escherichia coli Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing.

Shiga toxin-producing Escherichia coli (STEC) belonging to the O26 serogroup represent an important cause of Hemolitic Uremic Syndrome (HUS) in children worldwide. The localization of STEC virulence genes on mobile genetic elements allowed the emergence of clones showing different assets of this accessory genomic fraction. A novel O26 STEC clone belonging to Sequence Type (ST) 29 and harboring stx2a, ehxA and etpD plasmid-borne genes has emerged and spread in Europe since the mid-1990s, while another ST29 clone positive for stx2d and lacking plasmid-borne virulence genes was recently described as emerging in France. In Italy, O26 has been the most frequently detected STEC serogroup from HUS cases since the late 1990s. In this study we describe the genomic characterization and population structure of 144 O26 STEC strains isolated from human sources in Italy in the period 1989-2020. A total of 89 strains belonged to ST21, 52 to ST29, two to ST396 and one to ST4944. ST29 strains started to be isolated from 1999. 24 strains were shown to harbour stx1a, alone (n=20) or in combination with stx2a (n=4). The majority of the strains (n=118) harbored stx2a genes only and the two ST396 strains harbored stx2d. A Hierarchical Clustering on Principal Components (HCPC) analysis, based on the detection of accessory virulence genes, antimicrobial resistance (AMR) genes and plasmid replicons, classified the strains in seven clusters identified with numbers from 1 to 7, containing two, 13, 39, 63, 16, 10 and one strain, respectively. The majority of the genetic features defining the clusters corresponded to plasmid-borne virulence genes, AMR genes and plasmid replicons, highlighting specific assets of plasmid-borne features associated with different clusters. Core genome Multi Locus Sequence Typing grouped ST21 and ST29 strains in three clades each, with each ST29 clade exactly corresponding to one HCPC cluster. Our results showed high conservation of either the core or the accessory genomic fraction in populations of ST29 O26 STEC, differently from what observed in ST21 strains, suggesting that a different selective pressure could drive the evolution of different populations of these pathogens possibly involving different ecological niches.

Free-ranging red deer (Cervus elaphus) as carriers of potentially zoonotic Shiga toxin-producing Escherichia coli.

Shiga toxin-producing E. coli (STEC) are zoonotic foodborne pathogens of outmost importance and interest has been raised in recent years to define the potential zoonotic role of wildlife in STEC infection. This study aimed to estimate prevalence of STEC in free-ranging red deer (Cervus elaphus) living in areas with different anthropisation levels and describe the characteristics of strains in order to evaluate the potential risk posed to humans. Two-hundred one deer faecal samples collected in 2016-2018 from animals of Central Italian Alps were examined by bacteriological analysis and PCR screening of E. coli colonies for stx1, stx2 and eae genes. STEC strains were detected in 40 (19.9%) deer, with significantly higher prevalence in offspring than in yearlings. Whole genome analysis was performed to characterise a subset of 31 STEC strains. The most frequently detected serotype was O146:H28 (n = 10, 32.3%). Virulotyping showed different stx subtypes combinations, with stx2b-only (n = 15, 48.4%) being the most prevalent. All STEC lacked the eae gene but harbored additional virulence genes, particularly adhesins, toxins and/or other colonisation factors also described in STEC isolated from disease in humans. The most frequently detected genes were astA (n = 22, 71%), subAB (n = 21, 68%), iha (n = 26, 83.9%) and lpfA (n = 24, 77%). Four hybrid STEC/Enterotoxigenic E. coli strains were also identified. According to the most recent paradigm for pathogenicity assessment of STEC issued by the European Food Safety Authority, our results suggest that red deer are carriers of STEC strains that may have zoonotic potential, regardless of the anthropisation levels. Particular attention should be drawn to these findings while handling and preparing game meat. Furthermore, deer may release STEC in the environment, possibly leading to the contamination of soil and water sources.

Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019.

Shiga toxin-producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000-2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx2 subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance-encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.

Investigation on the Evolution of Shiga Toxin-Converting Phages Based on Whole Genome Sequencing.

Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence determinants of Shiga Toxin producing E. coli, Shiga Toxins (Stx), are encoded by genes localized in the genome of lambdoid bacteriophages. Stx comprise two antigenically different types, Stx1 and Stx2, further divided into subtypes. Among these, certain Stx2 subtypes appear to be more commonly occurring in the most severe forms of the STEC disease, haemorrhagic colitis and haemolytic uremic syndrome (HUS). This study aimed at obtaining insights on the evolution of Stx2 bacteriophages, due to their relevance in public health, and we report here on the analysis of the genomic structure of Stx2 converting phages in relation with the known reservoir of the E. coli strains harboring them. Stx2-converting phages conveying the genes encoding different stx2 subtypes have been isolated from STEC strains and their whole genomes have been sequenced, analyzed and compared to those of other Stx2 phages available in the public domain. The phages' regions containing the stx2 genes have been analyzed in depth allowing to make inference on the possible mechanisms of selection and maintenance of certain Stx2 phages in the reservoir. The "stx regions" of different stx2 gene subtypes grouped into three different evolutionary lines in the comparative analysis, reflecting the frequency with which these subtypes are found in different animal niches, suggesting that the colonization of specific reservoir by STEC strains could be influenced by the Stx phage that they carry. Noteworthy, we could identify the presence of nanS-p gene exclusively in the "stx regions" of the phages identified in STEC strains commonly found in cattle. As a matter of fact, this gene encodes an esterase capable of metabolizing sialic acids produced by submaxillary glands of bovines and present in great quantities in their gastrointestinal tract.

Tracing Back the Evolutionary Route of Enteroinvasive Escherichia coli (EIEC) and Shigella Through the Example of the Highly Pathogenic O96:H19 EIEC Clone.

Enteroinvasive Escherichia coli (EIEC) cause intestinal illness through the same pathogenic mechanism used by Shigella spp. The latter species can be typed through genomic and phenotypic methods used for E. coli and have been proposed for reclassification within E. coli species. Recently the first appearance of a highly pathogenic EIEC O96:H19 was described in Europe as the causative agent of two large outbreaks that occurred in Italy and in the United Kingdom. In contrast to Shigella spp and to the majority of EIEC strains, EIEC O96:H19 fermented lactose, lacked pathoadaptive mutations, and showed good fitness in extracellular environment, similarly to non-pathogenic E. coli, suggesting they have emerged following acquisition of the invasion plasmid by a non-pathogenic E. coli. Here we describe the whole genome comparison of two EIEC O96:H19 strains isolated from severe cases of diarrhea in Uruguay in 2014 with the sequences of EIEC O96:H19 available in the public domain. The phylogenetic comparison grouped all the O96:H19 strains in a single cluster, while reference EIEC strains branched into different clades with Shigella strains occupying apical positions. The comparison of the virulence plasmids showed the presence of a complete conjugation region in at least one O96:H19 EIEC. Reverse Transcriptase Real Time PCR experiments confirmed in this strain the expression of the pilin-encoding gene and conjugation experiments suggested its ability to mobilize an accessory plasmid in a recipient strain. Noteworthy, the tra region was comprised between two reversely oriented IS600 elements, which were also found as remnants in another EIEC O96:H19 plasmid lacking the tra locus. We hypothesize that an IS-mediated recombination mechanism may have caused the loss of the conjugation region commonly observed in EIEC and Shigella virulence plasmids. The results of this study support the hypothesis of EIEC originating from non-pathogenic E. coli through the acquisition of the virulence plasmid via conjugation. Remarkably, this study showed the ability of a circulating EIEC strain to mobilize plasmids through conjugation, suggesting a mechanism for the emergence of novel EIEC clones.

Validation on milk and sprouts of EN ISO 16654:2001 - Microbiology of food and animal feeding stuffs - Horizontal method for the detection of Escherichia coli O157.

In 2006, the European Committee for standardisation (CEN)/Technical Committee 275 - Food analysis - Horizontal methods/Working Group 6 - Microbiology of the food chain (TC275/WG6), launched the project of validating the method ISO 16654:2001 for the detection of Escherichia coli O157 in foodstuff by the evaluation of its performance, in terms of sensitivity and specificity, through collaborative studies. Previously, a validation study had been conducted to assess the performance of the Method No 164 developed by the Nordic Committee for Food Analysis (NMKL), which aims at detecting E. coli O157 in food as well, and is based on a procedure equivalent to that of the ISO 16654:2001 standard. Therefore, CEN established that the validation data obtained for the NMKL Method 164 could be exploited for the ISO 16654:2001 validation project, integrated with new data obtained through two additional interlaboratory studies on milk and sprouts, run in the framework of the CEN mandate No. M381. The ISO 16654:2001 validation project was led by the European Union Reference Laboratory for Escherichia coli including VTEC (EURL-VTEC), which organized the collaborative validation study on milk in 2012 with 15 participating laboratories and that on sprouts in 2014, with 14 participating laboratories. In both studies, a total of 24 samples were tested by each laboratory. Test materials were spiked with different concentration of E. coli O157 and the 24 samples corresponded to eight replicates of three levels of contamination: zero, low and high spiking level. The results submitted by the participating laboratories were analyzed to evaluate the sensitivity and specificity of the ISO 16654:2001 method when applied to milk and sprouts. The performance characteristics calculated on the data of the collaborative validation studies run under the CEN mandate No. M381 returned sensitivity and specificity of 100% and 94.4%, respectively for the milk study. As for sprouts matrix, the sensitivity resulted in 75.9% in the low level of contamination samples and 96.4% in samples spiked with high level of E. coli O157 and specificity was calculated as 99.1%.

Characterization of a novel plasmid encoding F4-like fimbriae present in a Shiga-toxin producing enterotoxigenic Escherichia coli isolated during the investigation on a case of hemolytic-uremic syndrome.

In February 2017 a case of Hemolytic-Uremic Syndrome (HUS) was reported to the National Registry of HUS in an adult living in Northern Italy. Stool specimens from the patient and his family contacts were collected and the analyses led to the isolation of a Locus of Enterocyte Effacement (LEE)-negative Shiga toxin 2 (Stx2)-producing Escherichia coli. The epidemiological investigations performed brought to collect fecal samples from the animals reared in a farm held by the case's family and a mixture of bovine and swine feces proved positive for Shiga toxin-producing E. coli (STEC) and yielded the isolation of a LEE-negative stx2-positive E. coli strain. Further characterization by whole genome sequencing led to identify the isolates as two identical O2:H27 hybrid Enterotoxigenic Shiga toxin-producing E. coli (ETEC-STEC). Sequencing of a high molecular weight plasmid present in the human isolate disclosed a peculiar plasmid harboring virulence genes characteristic for both pathotypes, including the enterohemolysin-coding gene and sta1, encoding the heat stable enterotoxin. Moreover, a complete fae locus encoding the ETEC F4 fimbriae could be identified, including a novel variant of faeG gene responsible for the production of the main structural subunit of the fimbriae. This novel faeG showed great diversity in the nucleotidic sequence when compared with the reference genes encoding the swine F4 allelic variants, whereas at the amino acid sequence level the predicted protein sequence showed some similarity with FaeG from E. coli strains of bovine origin. Further investigation on the plasmid region harboring the newly identified faeG allelic variant allowed to identify similar plasmids in NCBI sequence database, as part of the genome of other previously uncharacterized ETEC-STEC strains of bovine origin, suggesting that the novel F4-like fimbriae may play a role in bovine host specificity.

Emergence of quinolone-resistant Shigella flexneri in Italy (March 2017).

In March 2017, a 45-year-old Italian man who has sex with men was admitted to the Infectious Diseases Department of Trieste Hospital (northeast Italy), because of fever, abdominal pain and dysentery. The patient had neither foreign travel history nor sexual contact with non-Italian partners. Stool cultures grew multidrug-resistant Shigella flexneri (resistant to ampicillin, chloramphenicol, streptomycin, tetracycline, trimethoprim, amoxicillin/clavulanic acid and ciprofloxacin) and whole genome sequencing detailed the resistance features. The phylogenetic analysis showed that the strain was unrelated to any previously reported strain. The patient was treated successfully with ceftriaxone. We hereby report the first case of locally-acquired, multidrug-resistant S. flexneri infection in Italy and also the emergence of a new clone.

A case of haemolytic uraemic syndrome (HUS) revealed an outbreak of Shiga toxin-2-producing Escherichia coli O26:H11 infection in a nursery, with long-lasting shedders and person-to-person transmission, Italy 2015.

Purpose. Shiga toxin-producing Escherichia coli (STEC) represents a major issue for public health because of the severity of the associated illnesses, including haemolytic uraemic syndrome (HUS). In 2015, investigation of a case of HUS revealed an outbreak of Shiga toxin-2-producing E. coli O26 : H11 infection in a nursery in Italy. The investigation showed that the infection was transmitted to cases' contacts via person to person.Methods. The case finding was performed by testing for STEC stool samples of the HUS case's contacts within the family and the nursery. STEC O26 isolates were characterized by whole genome sequencing. Confirmed cases were repeatedly tested to monitor the duration of STEC shedding.Results. Eleven STEC O26 cases were identified, including adults and asymptomatic patients. Clinical illness was only observed in children. Strain characterization revealed that a single clone harbouring the stx2a and eae genes and the complete array of STEC-associated virulence genes, belonging to ST(21), was implicated in the outbreak. To reduce bacterial shedding, patients were treated with cefixime following clinical recovery. This antibiotic was well tolerated and did not induce any apparent consequences on patients' health.Conclusions. This study confirms that Stx2-producing E. coli O26 represents an emerging public health problem. The occurrence of outbreaks of infection by Stx2-producing E. coli O26 in nurseries is of particular concern, given the high probability of infection progressing in severity and resulting in secondary cases.

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.

The Intriguing Evolutionary Journey of Enteroinvasive E. coli (EIEC) toward Pathogenicity.

Among the intestinal pathogenic Escherichia coli, enteroinvasive E. coli (EIEC) are a group of intracellular pathogens able to enter epithelial cells of colon, multiplicate within them, and move between adjacent cells with a mechanism similar to Shigella, the ethiological agent of bacillary dysentery. Despite EIEC belong to the same pathotype of Shigella, they neither have the full set of traits that define Shigella nor have undergone the extensive gene decay observed in Shigella. Molecular analysis confirms that EIEC are widely distributed among E. coli phylogenetic groups and correspond to bioserotypes found in many E. coli serogroups. Like Shigella, also in EIEC the critical event toward a pathogenic life-style consisted in the acquisition by horizontal gene transfer of a large F-type plasmid (pINV) containing the genes required for invasion, intracellular survival, and spreading through the intestinal mucosa. In Shigella, the ample gain in virulence determinants has been counteracted by a substantial loss of functions that, although important for the survival in the environment, are redundant or deleterious for the life inside the host. The pathoadaptation process that has led Shigella to modify its metabolic profile and increase its pathogenic potential is still in infancy in EIEC, although maintenance of some features typical of E. coli might favor their emerging relevance as intestinal pathogens worldwide, as documented by recent outbreaks in industrialized countries. In this review, we will discuss the evolution of EIEC toward Shigella-like invasive forms going through the epidemiology, including the emergence of new virulent strains, their genome organization, and the complex interactions they establish with the host.

Molecular characterisation of human Shiga toxin-producing Escherichia coli O26 strains: results of an outbreak investigation, Romania, February to August 2016.

IntroductionAt the beginning of 2016, an increase in paediatric haemolytic uremic syndrome (HUS) cases was observed in Romania. The microbiological investigations allowed isolation of Shiga toxin-producing Escherichia coli (STEC) O26 as the causative agent from most cases. Methods: An enhanced national surveillance of HUS and severe diarrhoea was established across the country following the identification of the first cases and was carried out until August 2016. A total of 15 strains were isolated from 10 HUS and five diarrhoea cases. Strains were characterised by virulence markers (i.e. stx type/subtype, eae, ehxA genes), phylogroup, genetic relatedness and clonality using PCR-based assays, PFGE and multilocus sequence typing (MLST). The first six strains were further characterised by whole genome sequencing (WGS). Results: Five PCR-defined genotypes were distinguished. All strains from HUS cases harboured stx2a and eae, with or without stx1a, while strains from diarrhoea cases carried exclusively stx1a and eae genes. PFGE resolved strains into multiple pulsotypes, compatible with a certain geographic segregation of the cases, and strains were assigned to phylogroup B1 and sequence type (ST) 21. WGS confirmed the results of conventional molecular methods, brought evidence of O26:H11 serotype, and complemented the virulence profiles. Discussion/conclusion: This first description of STEC O26 strains from cases in Romania showed that the isolates belonged to a diverse population. The virulence content of most strains highlighted a high risk for severe outcome in infected patients. Improving the national surveillance strategy for STEC infections in Romania needs to be further considered.

The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells.

Locus of enterocyte effacement (LEE)-negative Shiga toxin (Stx)-producing Escherichia coli (STEC) strains are human pathogens that lack the LEE locus, a pathogenicity island (PAI) involved in the intimate adhesion of LEE-positive strains to the host gut epithelium. The mechanism used by LEE-negative STEC strains to colonize the host intestinal mucosa is still not clear. The cell invasion determinant tia, previously described in enterotoxigenic E. coli strains, has been identified in LEE-negative STEC strains that possess the subtilase-encoding pathogenicity island (SE-PAI). We evaluated the role of the gene tia, present in these LEE-negative STEC strains, in the invasion of monolayers of cultured cells. We observed that these strains were able to invade Caco-2 and HEp-2 cell monolayers and compared their invasion ability with that of a mutant strain in which the gene tia had been inactivated. Mutation of the gene tia resulted in a strong reduction of the invasive phenotype, and complementation of the tia mutation with a functional copy of the gene restored the invasion activity. Moreover, we show that the gene tia is overexpressed in bacteria actively invading cell monolayers, demonstrating that tia is involved in the ability to invade cultured monolayers of epithelial cells shown by SE-PAI-positive E. coli, including STEC, strains. However, the expression of the tia gene in the E. coli K-12 strain JM109 was not sufficient, in its own right, to confer to this strain the ability to invade cell monolayers, suggesting that at least another factor must be involved in the invasion ability displayed by the SE-PAI-positive strains.

Comparative analysis of metagenomes of Italian top soil improvers.

Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E. coli pathotypes as well as of different antimicrobial resistance-associated genes. The genes conferring resistance to Fluoroquinolones was the most relevant class of antimicrobial resistance genes observed in all the samples tested. To a lesser extent traits associated with the resistance to Methicillin in Staphylococci and genes conferring resistance to Streptothricin, Fosfomycin and Vancomycin were also identified. The most represented metal resistance genes were cobalt-zinc-cadmium related, accounting for 15-50% of the sequence reads in the different metagenomes out of the total number of those mapping on the class of resistance to compounds determinants. Moreover the taxonomic analysis performed by comparing compost-based samples and biosolids derived from municipal sewage-sludges treatments divided the samples into separate populations, based on the microbiota composition. The results confirm that the metagenomics is efficient to detect genomic traits associated with pathogens and antimicrobial resistance in complex matrices and this approach can be efficiently used for the traceability of TSI samples using the microorganisms' profiles as indicators of their origin.

Whole-Genome Characterization and Strain Comparison of VT2f-Producing Escherichia coli Causing Hemolytic Uremic Syndrome.

Verotoxigenic Escherichia coli infections in humans cause disease ranging from uncomplicated intestinal illnesses to bloody diarrhea and systemic sequelae, such as hemolytic uremic syndrome (HUS). Previous research indicated that pigeons may be a reservoir for a population of verotoxigenic E. coli producing the VT2f variant. We used whole-genome sequencing to characterize a set of VT2f-producing E. coli strains from human patients with diarrhea or HUS and from healthy pigeons. We describe a phage conveying the vtx2f genes and provide evidence that the strains causing milder diarrheal disease may be transmitted to humans from pigeons. The strains causing HUS could derive from VT2f phage acquisition by E. coli strains with a virulence genes asset resembling that of typical HUS-associated verotoxigenic E. coli.