Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential.

C. difficile induces antibiotic-associated diarrhea due to the action of two secreted toxins, TcdA and TcdB. A considerable range of virulence among C. difficile strains has been widely reported. During a hospital outbreak, 46 isolates were collected that belonged to different genotypes. Of those, the majority corresponded to two virulent strains, the globally distributed Sequence Type 1 (ST1)_North American Pulsotype 1 (NAP1) and the endemic ST54_NAPCR1 genotypes, respectively. Whereas the virulence of the latter has been attributed to increased secretion of toxins and production of a highly cytotoxic TcdB, these characteristics do not explain the increased lethality of the former. We undertook a proteomic comparative approach of the isolates participating in the outbreak to look for proteins present in the exoproteome of the ST1_NAP1and ST54_NAPCR1 strains. We used a low virulent ST2_NAP4 strain isolated also in the outbreak as control. Dendrograms constructed using the exoproteomes of the strains were very similar to those created using genomic information, suggesting an association between secreted proteins and relative virulence of the strains. By 2D electrophoresis and mass spectrometry it was found that approximately half of the proteins are shared among strains of different genotypes. From the identified proteins, the surface-located SlpA draw our attention due to its detection in ST54_NAPCR1 exoproteomes. Biochemical analysis indicated that the processing of SlpA is different in the ST54_NAPCR1 strain and confirmed that this strain secretes more SlpA than its counterparts. Furthermore, SlpA from the ST54_NAPCR1 strain exerted an increased proinflammatory activity. Altogether, these results indicate that the exoproteome composition correlates with the C. difficile genotype and suggest that particular proteins secreted by some strains could synergize with the effects of TcdA and TcdB increasing their virulence.

Helicobacter pylori modulates host cell responses by CagT4SS-dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis.

Highly virulent Helicobacter pylori cause proinflammatory signaling inducing the transcriptional activation and secretion of cytokines such as IL-8 in epithelial cells. Responsible in part for this signaling is the cag pathogenicity island (cagPAI) that codetermines the risk for pathological sequelae of an H. pylori infection such as gastric cancer. The Cag type IV secretion system (CagT4SS), encoded on the cagPAI, can translocate various molecules into cells, the effector protein CagA, peptidoglycan metabolites and DNA. Although these transported molecules are known to contribute to cellular responses to some extent, a major part of the cagPAI-induced signaling leading to IL-8 secretion remains unexplained. We report here that biosynthesis of heptose-1,7-bisphosphate (HBP), an important intermediate metabolite of LPS inner heptose core, contributes in a major way to the H. pylori cagPAI-dependent induction of proinflammatory signaling and IL-8 secretion in human epithelial cells. Mutants defective in the genes required for synthesis of HBP exhibited a more than 95% reduction of IL-8 induction and impaired CagT4SS-dependent cellular signaling. The loss of HBP biosynthesis did not abolish the ability to translocate CagA. The human cellular adaptor TIFA, which was described before to mediate HBP-dependent activity in other Gram-negative bacteria, was crucial in the cagPAI- and HBP pathway-induced responses by H. pylori in different cell types. The active metabolite was present in H. pylori lysates but not enriched in bacterial supernatants. These novel results advance our mechanistic understanding of H. pylori cagPAI-dependent signaling mediated by intracellular pattern recognition receptors. They will also allow to better dissect immunomodulatory activities by H. pylori and to improve the possibilities of intervention in cagPAI- and inflammation-driven cancerogenesis.

A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.

The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.

Epidemiological, virological and clinical characterization of a Dengue/Zika outbreak in the Caribbean region of Costa Rica 2017-2018.

The increase in incidence and geographical expansion of viruses transmitted by the Aedes mosquitoes, such as dengue (DENV) and zika (ZIKV) in the Americas, represents a burden for healthcare systems in tropical and subtropical regions. These and other under-detected arboviruses co-circulate in Costa Rica, adding additional complexity to their management due to their shared epidemiological behavior and similarity of symptoms in early stages. Since diagnostics of febrile illness is mostly based on clinical symptoms alone, we gathered acute-phase serum and urine from 399 samples of acute dengue-like cases from two healthcare facilities of Costa Rica, during an outbreak of arboviruses from July 2017 to May 2018, and tested them using molecular and serological methods. The analyses showed that of the clinically presumptive arbovirus cases that were reported, only 39.4% (n=153) of the samples were confirmed positive by RT-PCR to be DENV (DENV (10.3%), CHIKV (0.2%), ZIKV (27.3%), or mixed infections (1.5%). RT-PCR for other alphaviruses and flaviviruses, and PCR for Leptospira sp were negative. Furthermore, to assess flavivirus positivity in post-acute patients, the negative sera were tested against Dengue-IgM. 20% of sera were found positive, confounding even more the definitive number of cases, and emphasizing the need of several distinct diagnostic tools for accurate diagnostics. Molecular characterization of the prM and E genes from isolated viruses revealed that the American/Asian genotype of DENV-2 and the Asian lineage of ZIKV were circulating during this outbreak. Two different clades of DENV-2 American/Asian genotype were identified to co-circulate in the same region and a difference in the platelet and leukocyte count was noted between people infected with each clade, suggesting a putative distinct virulence. Our study sheds light on the necessity for healthcare strategies in managing arbovirus outbreaks, emphasizing the importance of comprehensive molecular and serological diagnostic approaches, as well as molecular characterization. This approach aids in enhancing our understanding of the clinical and epidemiological aspects of arboviral diseases during outbreaks. Our research highlights the need to strengthen training programs for health professionals and the need to increase research-based on laboratory evidence for diagnostic accuracy, guidance, development and implementation of public health interventions and epidemiological surveillance.

Dietary shifts and social interactions drive temporal fluctuations of the gut microbiome from wild redfronted lemurs.

Animals living in highly seasonal environments adapt their diets accordingly to changes in food availability. The gut microbiome as an active participant in the metabolization of the host's diet should adapt and change with temporal diet fluctuations, but dietary shifts can be short-term and, hence, difficult to detect in cross-sectional studies. Therefore, we performed a longitudinal study combining repeated sampling of fecal samples with observations of feeding behavior in wild redfronted lemurs. We amplified taxonomical marker genes for assessing the bacteria, archaea, protozoa, helminths, and fungi, as well as the active bacterial community inhabiting their gut. We found that the most abundant protozoans were Trichostomatia and Trichomonadida, and the most abundant helminths were Chromadorea. We detected known members of the gut mycobiome from humans but in low abundances. The archaeal community is composed only of members of Methanomethylophilaceae. The predominant phyla in the entire bacterial community were Bacteroidota and Firmicutes while the most abundant genera harbor so far unknown bacteria. Temporal fluctuations at the entire community level were driven by consumption of fruits and flowers, and affiliative interactions. Changes in alpha diversity correlated only with the consumption of flowers and leaves. The composition of the entire and active bacterial community was not significantly different, but the most abundant taxa differed. Our study revealed that monthly changes in the bacterial community composition were linked to fruit and flower consumption and affiliative interactions. Thus, portraying the importance of longitudinal studies for understanding the adaptations and alterations of the gut microbiome to temporal fluctuations.

Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis.

The gut microbiome influences host's immunity, development, and metabolism and participates in the gut-brain axis, thus impacting the health of the host. It is a dynamic community varying between individuals and within individuals at different time points. Hence, determining the factors causing this variability may elucidate their impact on host's health. However, understanding the drivers of variation has proven difficult particularly as multiple interactions occur simultaneously in the gut microbiome. We investigated the factors shaping the gut microbiome by applying the metacommunity concept where the gut microbiome is considered as a microbial community shaped by the interactions within the community, with the host and microbial communities outside the host, this through a longitudinal study in a wild primate. Focal behavioral data were collected for 1 year in four groups of redfronted lemurs to determine individual social and feeding behaviors. In addition, regular fecal samples were collected to assess bacteria, protozoa, and helminths through marker gene analysis and to measure fecal glucocorticoid metabolite (fGCM) concentrations to investigate the impact of physiological stress on the gut microbiome. Higher consumption of leaves and elevated fGCM concentrations correlated with higher alpha diversity, which also differed among groups. The major drivers of variation in beta diversity were group membership, precipitation and fGCM concentrations. We found positive and negative associations between bacterial genera and almost all studied factors. Correlations between bacterial indicator networks and social networks indicate transmission of bacteria between interacting individuals. We detected that processes occurring inside the gut environment are shaping the gut microbiome. Host associated factors such as, HPA axis, dietary changes, and fluctuations in water availability had a greater impact than interactions within the microbial community. The interplay with microbial communities outside the host also shape the gut microbiome through the exchange of bacteria through social relationships between individuals and the acquisition of microorganisms from environmental water sources.

Estandarización y evaluación del desempeño de un inmunoensayo para la detección de anticuerpos contra el dominio de unión a receptor de la proteína de espícula del virus SARS-CoV-2 / Establishment and performance evaluation of an immunoassay for the antibody detection against the receptor binding domain of the SARS-CoV-2 spike protein

Resumen Objetivo: Establecer un inmunoensayo semicuantitativo para la detección de anticuerpos contra el dominio de unión al receptor de la proteína de espícula del coronavirus del síndrome respiratorio agudo grave tipo 2 y la evaluación de su desempeño como herramienta de apoyo diagnóstico. Métodos: Se generó una proteína recombinante del dominio de unión a receptor de la proteína de espícula del coronavirus del síndrome respiratorio agudo grave tipo 2. Dicha proteína se empleó como sustrato antigénico en la estandarización de dos ensayos semicuantitativos por inmunoadsorción ligados a enzima para la detección de inmunoglobulinas M e inmunoglobulinas G humanas. Se utilizó un conjunto de muestras de suero positivas (n=129), provenientes de donantes voluntarios con infección previa por el virus SARS-CoV-2, confirmada mediante reacción en cadena de la polimerasa con transcriptasa reversa, y tomadas entre agosto de 2020 y noviembre de 2021. Además, se empleó un panel de muestras prepandémicas negativas (n=196) obtenidas antes de diciembre de 2019 para la evaluación del desempeño de los ensayos; se recibieron muestras múltiples seriadas de 99 donantes voluntarios para examinar la respuesta de la prueba ante la seroconversión y se estudió la posible asociación entre las seropositividades por coronavirus del síndrome respiratorio agudo grave tipo 2 y por el virus del dengue para la evaluación de reacciones cruzadas inespecíficas. Resultados: El ensayo de detección de inmunoglobulina G mostró 81.4 % de sensibilidad, 86.2 % de especificidad y valores predictivos positivos y negativos de 79.5 % y 87.6 % respectivamente. Por su parte, el ensayo de detección de inmunoglobulina M mostró solamente 72.1 % de sensibilidad, 54.1 % de especificidad y valores predictivos positivos y negativos de 25.6 % y 89.8 % respectivamente. No se encontraron diferencias significativas entre las mediciones semicuantitativas según sexo ni correlación lineal entre esta variable y la edad. Los valores obtenidos para el inmunoensayo presentaron diferencias significativas según el autorreporte de presencia o ausencia de síntomas compatibles con COVID-19. No se encontró correlación entre las seropositividades contra el coronavirus del síndrome respiratorio agudo grave tipo 2 y el virus del dengue. El ensayo de detección de inmunoglobulina G generó valores inferiores pero constantes en muestras de donantes voluntarios que autorreportaron no haber tenido contacto con el virus SARS-CoV-2. En contraste, las muestras de donantes expuestos al virus SARS-CoV-2 mostraron valores elevados pero variables en magnitud. Además, se observaron valores elevados y variables en muestras de voluntarios vacunados o con infección previa. Conclusiones: Nuestro ensayo de detección de inmunoglobulina M presenta escaso valor diagnóstico. Por el contrario, el ensayo de detección de inmunoglobulina G muestra un rendimiento satisfactorio y se apega al comportamiento reportado para este tipo de prueba según las características demográficas y clínicas de los usuarios; por lo tanto, este ensayo podría ser empleado como herramienta fiable y práctica en aplicaciones clínicas y como apoyo al diagnóstico. Es necesario desarrollar más estudios sobre reacciones cruzadas entre los anticuerpos contra el coronavirus del síndrome respiratorio agudo grave tipo 2 con aquellos de otras entidades de interés clínico, sobre todo las presentes en países tropicales como el nuestro.

Abstract Aim: To establish a semiquantitative immunoassay for antibody detection against the RBD of the severe acute respiratory syndrome coronavirus 2 spike protein and to evaluate its performance to be used as a diagnostic supporting tool. Methods: A recombinant severe acute respiratory syndrome coronavirus 2 spike protein was produced. This protein was used as antigenic substrate in two semiquantitative enzyme-linked immunoassays for the detection of human immunoglobulins M and immunoglobulins G. A set of serum samples (N=129) from patients with prior viral infection confirmed by reverse transcription polymerase chain reaction, processed between August 2020 and November 2021, were used as positive samples. A panel of pre-pandemic samples (N=196), obtained prior to December 2019, were used as negative samples to evaluate the assay performance. Multiple samples from 99 volunteers were used to examine test response to seroconversion. The interference between seropositivity against severe acute respiratory syndrome coronavirus 2 and dengue virus was also evaluated. Results: The immunoglobulin G detection assay showed 81.4% sensitivity, 86.2% specificity, and positive and negative predictive values of 79.5% and 87.6% respectively. The immunoglobulin M detection assay yielded 72.1% sensitivity, 54.1% specificity, and positive and negative predictive values of 25.6% and 89.8% respectively. No significant differences were found between the measurements according to sex or linear correlation between this variable and age. The values presented significant differences according to the condition of self-reported presence or absence of COVID-19 like symptoms. No correlation was found between seropositivity for severe acute respiratory syndrome coronavirus 2 and dengue virus. The immunoglobulin G detection assay generated lower but constant values on samples from voluntary donors who reported not having any contact with the virus compared to samples from donors exposed to it, and high but variable values in magnitude on samples from vaccinated volunteers or those with previous severe acute respiratory syndrome coronavirus 2 infection compared to samples from donors without exposure to the viral antigen. Conclusions: Our established immunoglobulin M detection assay presents poor diagnostic value. On the other hand, the immunoglobulin G detection assay shows satisfactory performance, and coheres to the behavior reported for this type of test according to the demographic and clinic characteristics of the volunteer, so it could be used as a reliable and practical tool in clinical applications and as diagnostic complement. It is necessary to develop more studies on cross-reactions of antibodies against severe acute respiratory syndrome coronavirus 2 with other entities of clinical interest and present in our tropical area.

Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.

Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.

Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements.

The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.