José Francisco Santos-Neto

Universidade Federal de São Paulo

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Tânia A. T. Gomes

Universidade Federal de São Paulo

Ana Carolina de Mello Santos

Universidade Federal de São Paulo

Tiago Barcelos Valiatti

Universidade Federal de São Paulo

Rosa Maria Silva

Universidade Federal de São Paulo

Ana Cristina Gales

Universidade Federal de São Paulo

Fernanda Fernandes Santos

Universidade Federal de São Paulo

Júllia A. S. Nascimento

Universidade Federal de São Paulo

Brenda Cardoso

Universidade de São Paulo

Fernanda Esposito

Universidade de São Paulo

Nilton Lincopán

Universidade de São Paulo

Cooperative Institutions

Universidade Federal de São Paulo

Universidade de São Paulo

Fundação de Apoio à Universidade Federal de São Paulo

Instituto Butantan

Hospital São Paulo

Hospital Universitário da Universidade de São Paulo

Monash University

Fundação Oswaldo Cruz

Universidade Estadual de Campinas (UNICAMP)

Instituto de Ciências Ambientais, Químicas e Farmacêuticas

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Data set 1 - uidA gene multifasta file

Figshare (2021)

Ana Carolina de Mello Santos Bruna Fuga Fernanda Esposito Brenda Cardoso Fernanda Fernandes Santos

Multi-FASTA file containing the uidA gene of all the E. coli strains used in the study.

Data set

10.6084/m9.figshare.14403800

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Frequency and Diversity of Hybrid Escherichia coli Strains Isolated from Urinary Tract Infections

Microorganisms (2021)

Júllia A. S. Nascimento Fernanda Fernandes Santos Tiago Barcelos Valiatti José Francisco Santos-Neto Ana Carolina de Mello Santos

(1) Background: Hybrid uropathogenic Escherichia coli (UPEC) strains carry virulence markers of the diarrheagenic E. coli (DEC) pathotypes, which may increase their virulence potential. This study analyzed the frequency and virulence potential of hybrid strains among 452 UPEC strains. (2) Methods: Strains were tested for the DEC virulence diagnostic genes’ presence by polymerase chain reaction (PCR). Those carrying at least one gene were classified as hybrid and further tested for 10 UPEC and extraintestinal pathogenic E. coli (ExPEC) virulence genes and phylogenetic classification. Also, their ability to produce hemolysis, adhere to HeLa and renal HEK 293T cells, form a biofilm, and antimicrobial susceptibility were evaluated. (3) Results: Nine (2%) hybrid strains were detected; seven of them carried aggR and two, eae, and were classified as UPEC/EAEC (enteroaggregative E. coli) and UPEC/aEPEC (atypical enteropathogenic E. coli), respectively. They belonged to phylogroups A (five strains), B1 (three), and D (one), and adhered to both cell lineages tested. Only the UPEC/EAEC strains were hemolytic (five strains) and produced biofilm. One UPEC/aEPEC strain was resistant to third-generation cephalosporins and carried blaCTX-M-15. (4) Conclusions: Our findings contribute to understanding the occurrence and pathogenicity of hybrid UPEC strains, which may cause more severe infections.

Pathogenicity island

10.3390/microorganisms9040693

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Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection

Microorganisms (2020)

Ana Carolina de Mello Santos Rosa Maria Silva Tiago Barcelos Valiatti Fernanda Fernandes Santos José Francisco Santos-Neto

Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.

Galleria mellonella

Multilocus sequence typing

10.3390/microorganisms8060827

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Unveiling the Virulent Genotype and Unusual Biochemical Behavior of Escherichia coli ST59

Applied and Environmental Microbiology (2021)

Ana Carolina de Mello Santos Bruna Fuga Fernanda Esposito Brenda Cardoso Fernanda Fernandes Santos

Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of human and animal infections worldwide. The utilization of selective and differential media to facilitate the isolation and identification of E. coli from complex samples, such as water, food, sediment, and gut tissue, is common in epidemiological studies. During a surveillance study, we identified an E. coli strain isolated from human blood culture that displayed atypical light cream-colored colonies in chromogenic agar and was unable to produce β-glucuronidase and β-galactosidase in biochemical tests. Genomic analysis showed that the strain belongs to sequence type 59 (ST59) and phylogroup F. The evaluation

10.1128/aem.00743-21

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Carriage prevalence of Neisseria meningitidis in the Americas in the 21st century: a systematic review

The Brazilian Journal of Infectious Diseases (2019)

José Francisco Santos-Neto Viviane Matos Ferreira Caroline Alves Feitosa Martha Sílvia Martinez-Silveira Leila Carvalho Campos

Neisseria meningitidis is a bacterium that colonizes the human nasopharynx and is transmitted by respiratory droplets from asymptomatic or symptomatic carriers. Occasionally, the pathogen invades the mucosa and enters the bloodstream, causing invasive meningococcal disease, a life-threatening infection. While meningococcal colonization is the first step in the development of invasive disease, the risk factors that predict progression from asymptomatic to symptomatic status are not well-known. The present report aimed to describe the prevalence of N. meningitidis carriers throughout the Americas, emphasizing the risk factors associated with carrier status, as well as the most prevalent serogroups in each studied population. We conducted a systematic review by searching for original studies in the MEDLINE/PubMed, Embase, LILACS and SciELO databases, published between 2001 and 2018. Exclusion criteria were articles published in a review format, case studies, case control studies, investigations involving animal models, and techniques or publications that did not address the prevalence of asymptomatic carriers in an American country. A total of 784 articles were identified, of which 23 were selected. The results indicate that the highest prevalence rates are concentrated in Cuba (31.9%), the United States (24%), and Brazil (21.5%), with increased prevalence found among adolescents and young adults, specifically university students and males. The present systematic review was designed to support epidemiological surveillance and prevention measures to aid in the formulation of strategies designed to control the transmission of meningococci in a variety of populations and countries throughout the Americas.

Asymptomatic carrier

Carriage

10.1016/j.bjid.2019.06.006

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Data set 2 - uidB protein multifasta file

Figshare (2021)

Ana Carolina de Mello Santos Bruna Fuga Fernanda Esposito Brenda Cardoso Fernanda Fernandes Santos

MultiFASTA file contaning uidB protein used

Data set

10.6084/m9.figshare.14403809

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Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients

Pathogens (2022)

José Francisco Santos-Neto Ana Carolina de Mello Santos Júllia A. S. Nascimento Liana O. Trovão Fernanda Fernandes Santos

Extra-intestinal pathogenic Escherichia coli (ExPEC) may inhabit the human gut microbiota without causing disease. However, if they reach extra-intestinal sites, common cystitis to bloodstream infections may occur, putting patients at risk. To examine the human gut as a source of endogenous infections, we evaluated the E. coli clonal diversity of 18 inpatients’ guts and their relationship with strains isolated from urinary tract infection (UTI) in the same hospital. Random amplified polymorphic DNA evaluated the clonal diversity, and the antimicrobial susceptibility was determined by disk diffusion. One isolate of each clone detected was sequenced, and their virulome and resistome were determined. Overall, 177 isolates were screened, among which 32 clones were identified (mean of two clones per patient), with ExPEC strains found in over 75% of the inpatients’ guts. Endogenous infection was confirmed in 75% of the cases. ST10, ST59, ST69, ST131, and ST1193 clones and critical mobile drug-resistance encoding genes (blaCTX-M-15, blaOXA-1, blaDHA-1, aac(6′)-lb-cr, mcr-1.26, qnrB4, and qnrB19) were identified in the gut of inpatients. The genomic analysis highlighted the diversity of the fecal strains, colonization by lactose-negative E. coli, the high frequency of ExPEC in the gut of inpatients without infections, and the presence of β-lactamase producing E. coli in the gut of inpatients regardless of the previous antibiotics’ usage. Considering that we found more than one ExPEC clone in the gut of several inpatients, surveillance of inpatients’ fecal pathogens may prevent UTI caused by E. coli in the hospital and dissemination of risk clones.

Resistome

clone (Java method)

10.3390/pathogens11121528

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Molecular Epidemiology and Presence of Hybrid Pathogenic Escherichia coli among Isolates from Community-Acquired Urinary Tract Infection

Microorganisms (2022)

Júllia A. S. Nascimento Fernanda Fernandes Santos José Francisco Santos-Neto Liana O. Trovão Tiago Barcelos Valiatti

Urinary tract infections (UTI) affect community and healthcare patients worldwide and may have different clinical outcomes. We assessed the phylogenetic origin, the presence of 43 virulence factors (VFs) of diarrheagenic and extraintestinal pathogenic Escherichia coli, and the occurrence of hybrid strains among E. coli isolates from 172 outpatients with different types of UTI. Isolates from phylogroup B2 (46%) prevailed, followed by phylogroups A (15.7%) and B1 (12.2%), with similar phylogenetic distribution in symptomatic and asymptomatic patients. The most frequent VFs according to their functional category were fimA (94.8%), ompA (83.1%), ompT (63.3%), chuA (57.6%), and vat (22%). Using published molecular criteria, 34.3% and 18.0% of the isolates showed intrinsic virulence and uropathogenic potential, respectively. Two strains carried the eae and escV genes and one the aggR gene, which classified them as hybrid strains. These hybrid strains interacted with renal and bladder cells, reinforcing their uropathogenic potential. The frequency of UPEC strains bearing a more pathogenic potential in the outpatients studied was smaller than reported in other regions. Our data contribute to deepening current knowledge about the mechanisms involved in UTI pathogenesis, especially among hybrid UPEC strains, as these could colonize the host's intestine, leading to intestinal infections followed by UTI.

Pathogenesis

Pathogenic Escherichia coli

Molecular Epidemiology

10.3390/microorganisms10020302

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Characterization of unconventional pathogenic Escherichia coli isolated from bloodstream infection: virulence beyond the opportunism

Brazilian Journal of Microbiology (2022)

Ana Carolina de Mello Santos José Francisco Santos-Neto Liana O. Trovão Ricardo Francisco Tavares Romano Rosa Maria Silva

Galleria mellonella

10.1007/s42770-022-00884-1

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Virulence potential of a multidrug-resistant Escherichia coli strain belonging to the emerging clonal group ST101-B1 isolated from bloodstream infection

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Ana Carolina de Mello Santos Rosa Maria Silva Tiago Barcelos Valiatti Fernanda Fernandes Santos José Francisco Santos-Neto

Abstract Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from bloodstream infection of an inpatient with persistent gastroenteritis and Zone T lymphoma, that died due to septic shock. Despite causing an extraintestinal infection, it harbors few known virulence factors and was assigned into phylogenetic group B1. To evaluate if the EC121 was pathogenic or opportunistic, its genome was sequenced, and an in vitro characterization of some pathogenicity-associated properties was performed. The data retrieved from genome analysis showed that E. coli strain EC121 belongs to the O154:H25 serotype, and to ST101-B1, which was epidemiologically linked to extraintestinal infections and antimicrobial resistance spread as well. Moreover, it was closely related to Shiga-toxin producing E. coli (STEC). Besides, strain EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including bla CTX-M-2 , and more than 50 complete virulence genetic clusters, which are reported to be associated either with DEC or ExPEC. The strain also displays the capacity to adhere to a variety of cell lineages, and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, it is virulent in the Galleria mellonella model. Altogether, E. coli EC121 unveiled to be a pathogen powered by its multi-drug resistance characteristic. Carry out studies providing accurate information about the virulence potential of all kinds of MDR strains are essential because these studies will help in the development of alternative therapies of infection management and spread control of MDR strains. Authors summary The phylogenetic origin of extraintestinal pathogenic Escherichia coli is mostly associated with phylogroup B2, and the majority of the studies regarding extraintestinal infection focus on the most virulent strains, which might also present multidrug-resistant (MDR) phenotype. Strains belonging to phylogroup B1 and isolated from extraintestinal infections are considered as opportunist pathogens and have their virulence neglected. We focus our study in one MDR strain isolated from bloodstream infection that belongs to phylogenetic group B1 to enlarge the knowledge about the virulence of this kind of strain. We demonstrated that the EC121 is capable of adheres to intestinal and bladder human cells, and invades the latter one; it survives to human serum bactericidal effects and produces biofilm. Additionally, the in vivo assay confirmed the EC121 virulence, showing that it should be considered a pathogenic strain. The genetic analyzes highlighted important aspects of EC121 which are typical from strains of sequence type 101, like its involvement in the spread of antimicrobial resistance genes and its relationship with extraintestinal infection from diverse sources. Information concerning the virulence of MDR strains is important for the development of global actions treating the spread of antimicrobial resistance, as well as to elucidate the pathogenesis of strains that were considered as an opportunist.

10.1101/797928

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