Parasitosis by Fasciola hepatica and Variations in Gut Microbiota in School-Aged Children from Peru.

(1) Background: Human fascioliasis is considered an endemic and hyper-endemic disease in the Peruvian Andean valleys. Our objective was to determine variations in the composition of the gut microbiota among children with Fasciola hepatica and children who do not have this parasitosis. (2) Method: A secondary analysis was performed using fecal samples stored in our biobank. The samples were collected as part of an epidemiological Fasciola hepatica cross-sectional study in children from 4 through 14 years old from a community in Cajamarca, Peru. (3) Results: In a comparison of the bacterial genera that make up the intestinal microbiota between the F. hepatica positive and negative groups, it was found that there are significant differences in the determination of Lactobacillus (p = 0.010, CI: 8.5-61.4), Bacteroides (p = 0.020, CI: 18.5-61.4), Clostridium (p < 0.001, CI: 3.5-36.0), and Bifidobacterium (p = 0.018, CI: 1.1-28.3), with each of these genera being less frequent in children parasitized with F. hepatica. (4) Conclusions: These results show that F. hepatica may be associated with direct or indirect changes in the bacterial population of the intestinal microbiota, particularly affecting three bacterial genera.

Estimación de casos de VIH no diagnosticados en la región Cajamarca, Perú: vinculación probabilística entre bases de datos / Estimate of undiagnosed HIV cases in the Cajamarca region of Peru: probabilistic linkage between databases

Resumen Los casos de VIH no diagnosticados contribuyen al incremento de nuevas infecciones, estimar esta cifra es importante para evaluar estrategias en los programas de control de VIH. El objetivo de este estudio fue estimar el número de casos de VIH no diagnosticados en la Región Cajamarca, Perú entre el 2015 y 2021. Los casos de VIH se obtuvieron de tres fuentes de información: La Estrategia Sanitaria Regional de Prevención y Control de VIH (ESPC-VIH); el aplicativo de notificación epidemiológica de VIH (Noti-VIH) y el sistema de información de laboratorio (Netlab). Se vincularon las tres bases de datos; un análisis de captura recaptura mediante un modelo log-linear, proporcionó estimaciones del número de casos de VIH no diagnosticados, tomando en cuenta las interacciones y el criterio de información de Akaike. Después de la vinculación se obtuvo 991 casos de VIH registrados. Se estimaron 1388 casos (IC 95%: 1265,6-1542,8) de personas viviendo con VIH, de los cuales 393 (28,4%) no fueron diagnosticados. El subregistro de cada fuente fue 51,9% en la ESPC-VIH, 63,6% en Netlab y 88% en Noti-VIH. Se concluyó que un número elevado de casos de VIH no fueron diagnosticados, siendo necesario replantear estrategias para incrementar la detección sistemática de casos de VIH.

Abstract Undiagnosed HIV cases contribute to the increase in new infections, therefore estimating this figure is important in order to assess strategies in HIV control programs. The objective of this study was to estimate the number of undiagnosed HIV cases in the Cajamarca region in Peru between 2015 and 2021. HIV cases were obtained from three sources of information: The Regional Health Strategy for HIV Prevention and Control (ESPC-HIV); the HIV epidemiological notification application (Noti-HIV), and the laboratory information system (Netlab). The three databases were linked; a capture-recapture analysis using a log-linear model provided estimates of the number of undiagnosed HIV cases, taking into account interactions and the Akaike information criterion. After linkage, 991 registered HIV cases were obtained. An estimated 1388 cases (95%CI: 1265.6-1542.8) of people living with HIV were estimated, of which 393 (28.4%) were not diagnosed. The underreporting of each source was: 51.9% in the ESPC-HIV; 63.6% in Netlab; and 88% in Noti-HIV. The conclusion drawn was that a high number of HIV cases went undiagnosed, and strategies need to be reconsidered to increase the systematic detection of HIV cases.

[Estimate of undiagnosed HIV cases in the Cajamarca region of Peru: probabilistic linkage between databases]. / Estimación de casos de VIH no diagnosticados en la región Cajamarca, Perú: vinculación probabilística entre bases de datos.

Undiagnosed HIV cases contribute to the increase in new infections, therefore estimating this figure is important in order to assess strategies in HIV control programs. The objective of this study was to estimate the number of undiagnosed HIV cases in the Cajamarca region in Peru between 2015 and 2021. HIV cases were obtained from three sources of information: The Regional Health Strategy for HIV Prevention and Control (ESPC-HIV); the HIV epidemiological notification application (Noti-HIV), and the laboratory information system (Netlab). The three databases were linked; a capture-recapture analysis using a log-linear model provided estimates of the number of undiagnosed HIV cases, taking into account interactions and the Akaike information criterion. After linkage, 991 registered HIV cases were obtained. An estimated 1388 cases (95%CI: 1265.6-1542.8) of people living with HIV were estimated, of which 393 (28.4%) were not diagnosed. The underreporting of each source was: 51.9% in the ESPC-HIV; 63.6% in Netlab; and 88% in Noti-HIV. The conclusion drawn was that a high number of HIV cases went undiagnosed, and strategies need to be reconsidered to increase the systematic detection of HIV cases.

Los casos de VIH no diagnosticados contribuyen al incremento de nuevas infecciones, estimar esta cifra es importante para evaluar estrategias en los programas de control de VIH. El objetivo de este estudio fue estimar el número de casos de VIH no diagnosticados en la Región Cajamarca, Perú entre el 2015 y 2021. Los casos de VIH se obtuvieron de tres fuentes de información: La Estrategia Sanitaria Regional de Prevención y Control de VIH (ESPC-VIH); el aplicativo de notificación epidemiológica de VIH (Noti-VIH) y el sistema de información de laboratorio (Netlab). Se vincularon las tres bases de datos; un análisis de captura recaptura mediante un modelo log-linear, proporcionó estimaciones del número de casos de VIH no diagnosticados, tomando en cuenta las interacciones y el criterio de información de Akaike. Después de la vinculación se obtuvo 991 casos de VIH registrados. Se estimaron 1388 casos (IC 95%: 1265,6-1542,8) de personas viviendo con VIH, de los cuales 393 (28,4%) no fueron diagnosticados. El subregistro de cada fuente fue 51,9% en la ESPC-VIH, 63,6% en Netlab y 88% en Noti-VIH. Se concluyó que un número elevado de casos de VIH no fueron diagnosticados, siendo necesario replantear estrategias para incrementar la detección sistemática de casos de VIH.

[Correlation between real-time PCR cycle threshold and clinical classification of COVID-19]. / Correlación entre el umbral de ciclo de la RPC en tiempo real y la clasificación clínica de la COVID-19.

BACKGROUND: The cycle threshold (Ct) of real-time reverse transcription PCR (RT-qPCR) indicates the relative concentration of an RNA sequence, this value has been related to clinical profile in viral infections. AIM: To determine the correlation between the Ct value and the clinical classification of COVID-19. METHOD: A correlational cross-sectional study was carried out, the Ct values were obtained by RT-qPCR directed to the N gene of SARS-CoV-2, grouping them by means of a central robust estimator and related to the clinical classification of COVID-19. RESULTS: Of the 718 cases included in the study; 77.7% (558) were mild; 21.3% (153) moderate and 1% (7) severe. The Ct value was grouped into levels: low Ct < 18.83; medium Ct> 18.83-30.10 and high Ct> 30.10. There was a weak inverse significant correlation (p = 0.002; Spearman's rho = -0.117) between the Ct value and the clinical classification. The characteristics: sex, age under 65 years, fever, chills, diarrhea, anosmia, and overweightobesity were associated with the Ct value. CONCLUSION: The lower the Ct value, a classification of greater severity of COVID-19 is expected, however, because the correlation is weak, its usefulness as a severity predictor is limited.

Correlación entre el umbral de ciclo de la RPC en tiempo real y la clasificación clínica de la COVID-19 / Correlation between real-time PCR cycle threshold and clinical classification of COVID-19

INTRODUCCIÓN: El umbral de ciclo (en inglés cycle threshold-Ct) de la reacción de polimerasa en cadena en tiempo real con transcripción reversa (RT-qPCR) indica la concentración relativa de una secuencia de ARN; este valor se ha relacionado con la expresión de cuadros clínicos en infecciones virales. OBJETIVO: Determinar la correlación entre el valor Ct y la clasificación clínica de la COVID-19. MÉTODO: Se realizó un estudio transeccional correlacional; los valores Ct se obtuvieron mediante RT-qPCR dirigida al gen N del SARS-CoV-2 agrupándolos mediante un estimador robusto central y relacionándose con la clasificación clínica de la COVID-19. RESULTADOS: De los 718 casos incluidos en el estudio; 77,7% (558) fueron leves; 21,3% (153) moderados y 1% (7) graves. El valor Ct se agrupó en niveles: Ct bajo 18,83 - 30,10 y Ct alto > 30,10. Existió correlación significativa inversa débil (p = 0,002; rho de Spearman = -0,117) entre el valor Ct y la clasificación clínica. Las características: sexo, edad menor a 65 años, fiebre, escalofrío, diarrea, anosmia y sobrepeso-obesidad estuvieron asociadas al valor de Ct. CONCLUSIÓN: A menor valor Ct se espera una clasificación de mayor gravedad de la COVID-19; no obstante, debido a que la correlación es débil, su utilidad como predictor de gravedad es limitada.

BACKGROUND: The cycle threshold (Ct) of real-time reverse transcription PCR (RT-qPCR) indicates the relative concentration of an RNA sequence, this value has been related to clinical profile in viral infections. AIM: To determine the correlation between the Ct value and the clinical classification of COVID-19. METHOD: A correlational cross-sectional study was carried out, the Ct values were obtained by RT-qPCR directed to the N gene of SARS-CoV-2, grouping them by means of a central robust estimator and related to the clinical classification of COVID-19. RESULTS: Of the 718 cases included in the study; 77.7% (558) were mild; 21.3% (153) moderate and 1% (7) severe. The Ct value was grouped into levels: low Ct 18.83-30.10 and high Ct> 30.10. There was a weak inverse significant correlation (p = 0.002; Spearman's rho = -0.117) between the Ct value and the clinical classification. The characteristics: sex, age under 65 years, fever, chills, diarrhea, anosmia, and overweightobesity were associated with the Ct value. CONCLUSION: The lower the Ct value, a classification of greater severity of COVID-19 is expected, however, because the correlation is weak, its usefulness as a severity predictor is limited.

Clinical characteristics and molecular detection of Bordetella pertussis in hospitalized children with a clinical diagnosis of whooping cough in Peru.

BACKGROUND AND OBJECTIVES: Pertussis is an infectious disease caused by the Gram-negative bacterium Bordetella pertussis. In Peru, actual public health programs indicate that vaccination against B. pertussis must be mandatory and generalized, besides all detected cases must be reported. The objective of this study was to determine the prevalence of B. pertussis among children under five years of age with a presumptive diagnosis of whopping cough in Cajamarca, a region located in northern Peru. MATERIALS AND METHODS: The population of this cross-sectional study were children under 5 years old hospitalized as presumptive cases of pertussis during December 2017 to December 2018. The nasopharyngeal samples were analyzed by real-time PCR for the detection of B. pertussis. RESULTS: B. pertussis was identified as PCR + in 42.3% of our sample (33/78). The clinical presentation that was observed most frequently includes paroxysmal coughing (97%), difficulty breathing (69.7%), cyanosis (72.7%) and post-tussive emesis (60.6%). Additionally, pneumonia was the most observed complication (33.3%). Four of the patients with PCR+ for B. pertussis presented only lymphocytosis, five only leukocytosis, two patients with decreased leukocytosis and lymphocytes and only one patient with leukopenia and relative lymphocytosis. There was a percentage of 84.8% of unvaccinated children in the PCR+ group. Finally, the mother was the most frequent symptom carrier (18.2%). CONCLUSION: In conclusion, in the studied population there is a high rate of PCR+ cases for B. pertussis. Laboratory values may show leukopenia or lymphopenia in patients with pertussis. It is necessary to use appropriate laboratory diagnostic tests in all infants with respiratory symptoms for B. pertussis. Since, the clinical diagnosis overestimates the diagnosis of pertussis.

Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital.

BACKGROUND: 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. OBJECTIVE: 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. RESULTS: The most commonly isolated bacteria from the GM were Firmicutes (63.2% 74/117) Bacteriodetes (62.4%; 73/117), Lactobacillus (59.8%; 70/117), Prevotella (57.2%; 67/117), Proteobacterium (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus and Prevotella 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.

Unidentified dengue serotypes in DENV positive samples and detection of other pathogens responsible for an acute febrile illness outbreak 2016 in Cajamarca, Peru.

OBJECTIVE: To describe the prevalence of dengue virus serotypes, as well as other viral and bacterial pathogens that cause acute febrile illness during an outbreak in Cajamarca in 2016. RESULTS: Dengue virus (DENV) was the most frequent etiologic agent detected in 25.8% of samples (32/124), followed by Rickettsia spp. in 8.1% (10/124), Zika virus in 4.8% (6/124), Chikungunya virus 2.4% (3/124) and Bartonella bacilliformis 1.6% (2/124) cases. No positive cases were detected of Oropouche virus and Leptospira spp. DENV serotypes identification was only achieved in 23% of the total positive for DENV, two samples for DENV-2 and four samples for DENV-4. During the 2016 outbreak in Cajamarca-Peru, it was observed that in a large percentage of positive samples for DENV, the infecting serotype could not be determined by conventional detection assays. This represents a problem for the national surveillance system and for public health due to its epidemiological and clinical implications. Other viral and bacterial pathogens responsible for acute febrile syndrome were less frequently identified.

An emerging public health threat: Mayaro virus increases its distribution in Peru.

BACKGROUND: The infection caused by Mayaro virus (MAYV), which presents as an acute febrile illness, is considered a neglected tropical disease. The virus is an endemic and emerging pathogen in South America and the Caribbean, responsible for occasional and poorly characterized outbreaks. Currently there is limited information about its expansion and risk areas. METHODS: A cross-sectional study was performed in 10 urban primary care health centers in the Cajamarca region of Peru from January to June 2017. A total of 359 patients with suspected febrile illness were assessed. RNA was extracted from serum samples, following which MAYV real-time reverse transcriptase PCR (RT-PCR) for the detection of the nsP1 gene was performed. RESULTS: MAYV was detected in 11.1% (40/359) of samples after RT-PCR amplification and confirmatory DNA sequencing. Most infections were detected in the adult population aged 18-39 years (40%) and 40-59 years (32.5%). Headache was the most frequent symptom in patients with MAYV infection (77.5%), followed by fever (72.5%), myalgia (55.0%), and arthralgia (50.0%). During the study, most of the MAYV cases were seen in May (47.5%) and April (35.0%), corresponding to the dry season (months without rain). CONCLUSIONS: This study is novel in describing the presence of MAYV in Cajamarca, an Andean region of Peru. Symptoms are non-specific and can be confused with those of other arbovirus or bacterial infections. Molecular biology methods such as RT-PCR allow the timely and accurate detection of MAYV and could thus be considered as a tool for surveillance in endemic areas.

Highly clarithromycin-resistant Helicobacter pylori infection in asymptomatic children from a rural community of Cajamarca-Peru.

OBJECTIVE: The objective of this study was to determine the prevalence of clarithromycin-resistant Helicobacter pylori in asymptomatic children in a rural community of Cajamarca (northern Peru). RESULTS: Helicobacter pylori was detected in 17.2% (49/285) of the samples. Unboiled water consumption the most frequent associated factor in patients with positive PCR for H. pylori infection (93.9%). Clarithromycin resistant mutations were found in 79.6% (39/49) of the positive samples for H. pylori. The most frequent mutation was A2142G (46.9%), followed by the double-mutation A2142G-A2143G (28.6%).

Frequency and coinfection between genotypes of human papillomavirus in a population of asymptomatic women in northern Peru.

OBJECTIVE: Describe the prevalence of HPV genotypes via PCR and DNA sequencing in 397 women who attended to the gynecological outpatient center in the Hospital Regional Docente de Cajamarca from March to September 2017. RESULTS: A positive PCR result for HPV was observed in 121 cervical samples. A high-risk genotype was found in 63.6% (77/121) of patients, a probably oncogenic type in 23.1% (28/121) and a low-risk type in 7.4%. Among the high-risk genotypes, HPV-31 was the most common one present in 20% (21/77), followed by HPV-16 in 11.4% (12/77). Coinfections between two or more genotypes were observed in 12 cases.

Bordetella pertussis in children hospitalized with a respiratory infection: clinical characteristics and pathogen detection in household contacts.

OBJECTIVE: Describe the prevalence of Bordetella pertussis via PCR in children under 5 years old hospitalized as probable cases of pertussis and report the most common clinical features among them. RESULTS: A positive PCR result for B. pertussis was observed in 20.5% of our samples (18/88), one-third of them were from infants between 2 and 3 months old. The most common symptoms were paroxysms of coughing (88.9%), difficulty breathing (72.2%), cyanosis (77.8%) and fever (50%). The mother was the most common symptomatic carrier (27.8%), followed by uncles/aunts (22.2%) among children with pertussis.

Etiology, epidemiology and clinical characteristics of acute diarrhea in hospitalized children in rural Peru.

INTRODUCTION: Diarrhea remains one of the main causes of morbidity and mortality in children under five years of age especially in low-income countries. In Peru, epidemiological reports about enteropathogens related to acute diarrhea are scarce in rural areas. The aim of this study was to describe the etiology, epidemiology, and clinical characteristics of the principal causes of acute infectious diarrhea in in a northern rural region of Peru. METHODOLOGY: A prospective study was conducted from January 2011 to December 2012 to describe the main pathogens causing acute diarrhea using PCR assay. RESULTS: A total of 117 children diagnosed with acute diarrhea were included in the study. A single etiological agent was identified in 41.03% of samples, being rotavirus followed by norovirus and Shigella. Co-infections containing virus and bacteria were found in 22.22% of samples. Vomiting was most commonly found symptoms in 58.97% cases followed by fever (54.70%). Malnutrition was detected in 14.53% of the children. CONCLUSIONS: High prevalence of rotavirus, as well as adenovirus and norovirus, was observed in the present study. Shigella was the most common bacteria found in acute diarrhea in the area. The implementation of a better surveillance system is mandatory in order to identify the principal etiologies of gastroenteritis in the rural areas of Peru and to develop of better prevention strategies and reduce diarrhea-associated mortalities.

Bordetella pertussis diagnosis in children under five years of age in the Regional Hospital of Cajamarca, Northern Peru.

INTRODUCTION: Bordetella pertussis is an important human pathogen that causes whooping cough (pertussis), an endemic illness responsible of significant morbidity and mortality, especially in infants and children. Worldwide, there are an estimated of 16 million cases of pertussis, resulting in about 195,000 child deaths per year. In Peru, pertussis is a major health problem that has been on the increase despite immunization efforts. The objective of this study was to determine the prevalence of B. pertussis among children under five years of age suspected to have whopping cough in Cajamarca, Peru. METHODOLOGY: Children diagnosed with whooping cough admitted to the Hospital Regional de Cajamarca from August 2010 to July 2013 were included. Nasopharyngeal samples were obtained for B. pertussis culture and polymerase chain reaction (PCR) detection. RESULTS: In 133 children, the pertussis toxin and IS481 gene were detected in 38.35% (51/133) of the cases by PCR, while only 9.02% (12/133) of the Bordetella cultures were positive. The most frequent symptoms in patients with positive B. pertussis were paroxysm of coughing 68.63% (35/51), cyanosis 56.86% (29/51), respiratory distress 43.14% (22/51), and fever 39.22% (20/51). Pneumonia and acute bronchial obstructive syndrome were present in 17.65% (9/51) and 13.72% (7/51) of the cases, respectively. CONCLUSIONS: B. pertussis is responsible for an important proportion of whooping cough in hospitalized children in Cajamarca. Epidemiologic surveillance programs for B. pertussis are essential in Peru, especially in children who could most benefit from the vaccine.