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Oropouche fever is an infectious disease caused by the Oropouche virus (OROV). The diagnosis and prediction of the clinical picture continue to be a great challenge for clinicians who manage patients with acute febrile syndrome. Several symptoms have been associated with OROV virus infection in patients with febrile syndrome; however, to date, there is no clinical prediction rule, which is a fundamental tool to help the approach of this infectious disease. To assess the performance of a prediction model based solely on signs and symptoms to diagnose Oropouche virus infection in patients with acute febrile syndrome. Validation study, which included 923 patients with acute febrile syndrome registered in the Epidemiological Surveillance database of three arbovirus endemic areas in Peru. A total of 97 patients (19%) were positive for OROV infection in the development group and 23.6% in the validation group. The area under the curve was 0.65 and the sensitivity, specificity, PPV, NPV, LR + and LR- were 78.2%, 35.1%, 27.6%, 83.6%, 1.20 and 0.62, respectively. The development of a clinical prediction model for the diagnosis of Oropouche based solely on signs and symptoms does not work well. This may be due to the fact that the symptoms are nonspecific and related to other arbovirus infections, which confuse and make it difficult to predict the diagnosis, especially in endemic areas of co-infection of these diseases. For this reason, epidemiological surveillance of OROV in various settings using laboratory tests such as PCR is important.

Tuberculosis (TB), caused by Mycobacterium tuberculosis , is one of the deadliest infectious diseases worldwide. Multidrug and extensively drug-resistant strains are making disease control difficult, and exhausting treatment options. New anti-TB drugs bedaquiline (BDQ), delamanid (DLM) and pretomanid (PTM) have been approved for the treatment of multi-drug resistant TB, but there is increasing resistance to them. Nine genetic loci strongly linked to resistance have been identified ( mmpR5 , atpE , and pepQ for BDQ; ddn , fgd1 , fbiA , fbiB , fbiC , and fbiD for DLM/PTM). Here we investigated the genetic diversity of these loci across >33,000  M . tuberculosis isolates. In addition, epistatic mutations in mmpL5-mmpS5 as well as variants in ndh , implicated for DLM/PTM resistance in M. smegmatis , were explored . Our analysis revealed 1,227 variants across the nine genes, with the majority (78%) present in isolates collected prior to the roll-out of BDQ and DLM/PTM. We identified phylogenetically-related mutations, which are unlikely to be resistance associated, but also high-impact variants such as frameshifts (e.g. in mmpR5 , ddn ) with likely functional effects, as well as non-synonymous mutations predominantly in MDR-/XDR-TB strains with predicted protein destabilising effects. Overall, our work provides a comprehensive mutational catalogue for BDQ and DLM/PTM associated genes, which will assist with establishing associations with phenotypic resistance; thereby, improving the understanding of the causative mechanisms of resistance for these drugs, leading to better treatment outcomes.

Whole Genome Sequencing (WGS) is a promising tool in the global fight against tuberculosis (TB). The aim of this study was to evaluate the use of WGS in routine conditions for detection of drug resistance markers and transmission clusters in a multidrug-resistant TB hot-spot area in Peru. For this, 140 drug-resistant Mycobacterium tuberculosis strains from Lima and Callao were prospectively selected and processed through routine (GenoType MTBDR sl and BACTEC MGIT) and WGS workflows, simultaneously. Resistance was determined in accordance with the World Health Organization mutation catalogue. Agreements between WGS and BACTEC results were calculated for rifampicin, isoniazid, pyrazinamide, moxifloxacin, levofloxacin, amikacin and capreomycin. Transmission clusters were determined using different cut-off values of Single Nucleotide Polymorphism differences. 100% (140/140) of strains had valid WGS results for 13 anti-TB drugs. However, the availability of final, definitive phenotypic BACTEC MGIT results varied by drug with 10–17% of invalid results for the seven compared drugs. The median time to obtain results of WGS for the complete set of drugs was 11.5 days, compared to 28.6–52.6 days for the routine workflow. Overall categorical agreement by WGS and BACTEC MGIT for the compared drugs was 96.5%. Kappa index was good (0.65≤k≤1.00), except for moxifloxacin, but the sensitivity and specificity values were high for all cases. 97.9% (137/140) of strains were characterized with only one sublineage (134 belonging to “lineage 4” and 3 to “lineage 2”), and 2.1% (3/140) were mixed strains presenting two different sublineages. Clustering rates of 3.6% (5/140), 17.9% (25/140) and 22.1% (31/140) were obtained for 5, 10 and 12 SNP cut-off values, respectively. In conclusion, routine WGS has a high diagnostic accuracy to detect resistance against key current anti-TB drugs, allowing results to be obtained through a single analysis and helping to cut quickly the chain of transmission of drug-resistant TB in Peru.

Peru has the highest burden of multidrug-resistant tuberculosis in the Americas region. Since 1999, the annual number of extensively drug-resistant tuberculosis (XDR-TB) Peruvian cases has been increasing, becoming a public health challenge. The objective of this study was to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Peruvian patients with XDR-TB diagnosed from 2011 to 2015 in Peru. Whole genome sequencing (WGS) was performed on 68 XDR-TB strains from different regions of Peru. 58 (85.3%) strains came from the most populated districts of Lima and Callao. Concerning the lineages, 62 (91.2%) strains belonged to the Euro-American Lineage, while the remaining 6 (8.8%) strains belonged to the East-Asian Lineage. Most strains (90%) had high-confidence resistance mutations according to pre-established WHO-confident grading system. Discordant results between microbiological and molecular methodologies were caused by mutations outside the hotspot regions analysed by commercial molecular assays ( rpoB I491F and inhA S94A). Cluster analysis using a cut-off ≤ 10 SNPs revealed that only 23 (34%) strains evidenced recent transmission links. This study highlights the relevance and utility of WGS as a high-resolution approach to predict drug resistance, analyse transmission of strains between groups, and determine evolutionary patterns of circulating XDR-TB strains in the country.

Acute infective gastroenteritis (AIG) is a leading cause of mortality in children worldwide. In Peru, more than 40% of cases of AIG occurring in children under 5 years old. The disruption of the gut microbiota can increase risk for several health complications especially in patients with gastric infections caused by viruses or bacteria. The main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis. The most commonly isolated bacteria from the GM were (63.2% 74/117) (62.4%; 73/117), (59.8%; 70/117), (57.2%; 67/117), (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of , , and across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria-bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed.

Background A substantial number of children in the world are regularly subjected to physical punishment by their parents as a method of upbringing. Evidence suggests that it has negative effects on the development of brain function. However, evidence regarding its association with verbal communication is limited and heterogeneous. It is also unknown whether the effects are the same in both boys and girls; especially in the contexts of developing countries, where the highest rates of physical punishment are found. Objective This investigation aimed at analyzing the association between physical punishment administered by both fathers and mothers and effective verbal communication among children aged 9–36 months according to sex. Methods A secondary analytical cross-sectional study was conducted based on the 2018–2019 Peruvian Demographic and Family Health Survey. Physical punishment, based on the mother’s report of the use of hitting and/or slapping, was considered as a method to correct children by the father and/or mother. Effective verbal communication (EVC) was measured using the Battle scale which consists of age-appropriate questions included in the early childhood development module. A generalized linear model of the family and Log Poisson link option was used to identify the association between them, using the crude, general adjusted, and sex-stratified models. Results Of all the children, 16.31% received physical punishment from their father and/or mother, wherein 16.65% were boys and 15.97% were girls. Moreover, 36.48% exhibited EVC, wherein 32.55% were boys and 40.50% were girls. Adjusting for socioeconomic level, witnessing violence, mother’s marital status, age, occupation, education level, language, number of children, and moderate-to-severe depressive symptoms, it was found that boys who received physical punishment from their father and/or mother have a 31% lower probability of EVC (adjusted prevalence ratio (aPR) 0.69, 95% confidence interval (CI) 0.58–0.83, p  < 0.001), whereas no association was found in girls who received physical punishment from their father and/or mother and EVC (aPR 0.93, 95% CI 0.81–1.06, p  = 0.278). Conclusions An association was found between physical punishment administered by father and/or mother and reduced EVC among boys, whereas no such association was found among girls. It is possible that even though a significant impact has not been observed in girls during this early stage, they may experience consequences in later stages of life, further research is needed.

Background Acute appendicitis may be uncomplicated or may present with life threatening complications. Since the outbreak of the COVID-19 pandemic, there has been an increase in the number of cases of complicated appendicitis, suggesting a possible association between them. Therefore, we aimed to determine the association between SARS-CoV-2 infection and complicated appendicitis in surgical patients in Lima, Peru, from March 2020 to December 2021. Methods A matched case-control study was conducted. Clinical records of patients ≥ 18 years old who underwent surgery for appendicitis and had at least one positive SARS-CoV-2 diagnostic test were selected. Patients undergoing surgery for complicated appendicitis were considered cases, and patients undergoing surgery for uncomplicated appendicitis were controls. A 1:1 matching by sex, age, and month of surgery was performed. Conditional logistic regression modeling was performed to calculate crude and adjusted conditional odds ratios (cOR). Results The positivity rate for COVID-19 tests was 73.6% for cases and 26.4% for controls. The crude cOR was 4.88 (95% IC 2.89–8.23, p  < 0.001), and the adjusted cOR was 3.52 (95%IC 1.82–6.81, p  = 0.001), after controlling for onset time of symptoms and awaiting time before surgery. Conclusions Surgery for complicated appendicitis was associated with SARS-CoV-2 infection. Patients with this infection may be at higher risk of complicated appendicitis and thus may need additional clinical monitoring.

Background Tuberculosis (TB) is a communicable, preventable and curable disease caused by the bacterium Mycobacterium tuberculosis (MTB). Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis (MDR-TB) worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microdilution plate was developed and validated by the CRyPTIC project. The objective of the study was to evaluate the use of the broth microdilution (BMD) plate methodology for susceptibility testing of drug-resistant MTB strains in Peru. Methods MTB strains isolated between 2015 and 2018 in Peru were used. 496 nationally-representative strains determined as drug-resistant by the routine 7H10 Agar Proportion Method (APM) were included in the present study. The Minimum Inhibitory Concentration (MIC) of 13 antituberculosis drugs were determined for each strain using the UKMYC6 microdilution plates. Diagnostic agreement between APM and BMD plate methodology was determined for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. Phenotypes were set using binary (or ternary) classification based on Epidemiological cut-off values (ECOFF/ECV) proposed by the CRyPTIC project. Whole Genome Sequencing (WGS) was performed on strains with discrepant results between both methods. Results MIC distributions were determined for 13 first- and second-line anti-TB drugs, including new (bedaquiline, delamanid) and repurposed (clofazimine, linezolid) agents. MIC results were available for 80% (397/496) of the strains at 14 days and the remainder at 21 days. The comparative analysis determined a good agreement (0.64 ≤ k ≤ 0.79) for the drugs rifampicin, ethambutol, ethionamide and kanamycin, and the best agreement (k > 0.8) for isoniazid and levofloxacin. Overall, 12% of MIC values were above the UKMYC6 plate dilution ranges, most notably for the drugs rifampicin and rifabutin. No strain presented MICs higher than the ECOFF/ECV values for the new or repurposed drugs. Discrepant analysis using genotypic susceptibility testing by WGS supported half of the results obtained by APM (52%, 93/179) and half of those obtained by BMD plate methodology (48%, 86/179). Conclusions The BMD methodology using the UKMYC6 plate allows the complete susceptibility characterization, through the determination of MICs, of drug-resistant MTB strains in Peru. This methodology shows good diagnostic performances for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. It also allows for the characterization of MICs for other drugs used in previous years against tuberculosis, as well as for new and repurposed drugs recently introduced worldwide.

In previous studies, our group developed a method based on Confocal Laser Scanning Microscopy and Image Analysis (CLSM-IA) to analyze the diversity and biomass of cyanobacteria in microbial mats. However, this method cannot be applied to heterotrophic microorganisms, as these do not have autofluorescence. In this article, we present a method that combines CLSM-IA and Hoechst 33342 and SYTOX Green fluorochromes (FLU-CLSM-IA) to determine the viability and biomass of Micrococcus luteus DE2008, isolated from a saline microbial mat (Ebro Delta, Tarragona, Spain). The method has been applied to assess the effect of salinity on this microorganism. A reduction in viability and biomass (live cells) was observed as the salt concentration increases. The largest effect was at 100‰ NaCl with a cell death of 27.25% and a decrease in total and individual biomass of 39.75 and 0.009 mgC/cm3, respectively, both with respect to optimal growth (10 ‰ NaCl). On the other hand, another important contribution of this article was that combining the FLU-CLSM-IA results with those achieved by plate counts enabled us to determine, for first time, the viability and the total biomass of the “dormant cells” (66.75% of viability and 40.59 mgC/cm3 of total biomass at 100‰ NaCl). FLU-CLSM-IA is an efficient, fast, and reliable method for making a total count of cells at pixel level, including the dormant cells, to evaluate the viability and the biomass of a hetetrophic microorganism, M. luteus DE2008.

A bacterial strain (DE2008) was isolated from a consortium of microorganisms living in the microbial mats of the Ebro Delta with the ability to grow under conditions of high concentrations of lead and copper. Strain DE2008 has been characterized by microscopic and metabolic techniques and identified by sequencing of PCR-amplified 16S rRNA gene fragments as Micrococcus luteus . The strain is highly resistant to lead and copper. Micrococcus luteus DE2008 grew optimally until levels of 1 mM of Pb(NO 3 ) 2 and CuSO 4 , respectively, and was completely inhibited at 3 mM Pb(NO 3 ) 2 and at 1.5 mM CuSO 4 . Elemental analysis determined by energy-dispersive X-ray spectroscopy (EDX) coupled with scanning electron microscopy and transmission electron microscopy from polluted cultures of DE2008 show that this microorganism can biosorpt Pb and Cu in exopolysaccharide envelopes, without accumulating them inside the cells.