Características clínicas y laboratoriales de los diez primeros pacientes con diagnóstico de Guillain-Barré en Piura, 2023

El síndrome de Guillain Barré es una enfermedad derivada del compromiso en las neuronas del sistema nervioso periférico por una respuesta descontrolada del sistema inmune que conduce daño axonal y/o desmielinización. El objetivo de este reporte fue describir los 10 primeros casos sospechosos de Síndrome de Guillain Barré en Piura. Se logró identificar la presencia de Campylobacter jejuni en las muestras de heces del 80% de los pacientes reportados. Es muy importante reconocer rápida y oportunamente al paciente con diagnóstico sospechoso de Guillain Barré, y realizar los estudios necesarios en un brote para identificar los agentes desencadenantes del cuadro.

Guillain Barré syndrome is a disease derived from compromise in neurons of the peripheral nervous system by an uncontrolled response from the immune system that leads to axonal damage and/or demyelination. The objective of this report was to describe the first 10 suspected cases of Guillain Barre Syndrome in Piura. It was possible to identify the presence of Campylobacter jejuni in the stool samples of 80% of the reported patients. It is very important to quickly and opportunely recognize the patient with a suspected diagnosis of Guillain Barré, and to carry out the necessary studies in an outbreak to identify the triggering agents of the condition.

Trends in antimicrobial resistance of Shigella species in Peru, 2011-2020.

Objective: To describe the frequency of antimicrobial resistance rates and spatial-temporal distribution of Shigella species from the last 10 years in Peru. Methods: A cross-sectional descriptive study was carried out. A total of 1668 Shigella strains, remitted as part of the national enteric pathogen surveillance from 2011 to 2020, were analysed. The strains were confirmed by conventional tests and serotyped with polyvalent and monovalent antibodies. Also, antimicrobial susceptibility was performed according to the Kirby-Bauer method. Results: The most frequent Shigella species was S. sonnei (49.2%), followed by S. flexneri (42.2%), S. boydii (7.9%) and S. dysenteriae (0.7%). Phase II (46.29%) was the most frequent serotype in S. sonnei, serotype 2a (43.61%) in S. flexneri, serotype 2 in S. boydii and serotype 4 in S. dysenteriae. High rates of resistance were detected for trimethoprim/sulfamethoxazole (91.0%), tetracycline (88.4%), ampicillin (73.9%) and chloramphenicol (64.9%), moderate rates for amoxicillin/clavulanic acid (25.1%), ciprofloxacin (16.7%) and nalidixic acid (14.8%), and low rates for cefotaxime (1.74%), nitrofurantoin (0.7%) and ceftazidime (0.6%). Moreover, antimicrobial resistance to fluoroquinolones increased considerably from 2017 to 2020. Conclusion: S. sonnei was the most frequent species, which have a large proportion of strains resistant to trimethoprim/sulfamethoxazole, and a growing trend of resistance to ciprofloxacin and nalidixic acid. This increase in resistance to commonly used antibiotics in treatments is alarming, threatening the control and management of these currently treatable infections.

Evaluation of the SMARTCHEK Genesystem RT-qPCR assay for the detection of SARS-CoV-2 in clinical samples.

BACKGROUND: The COVID-19 pandemic remains the main public health problem, due to the quick and easy dissemination of the causal agent, SARS-CoV-2 virus, around the world. Since the beginning of the pandemic, an opportune laboratory diagnosis has been critical to respond this emergency, and RT-qPCR has been used as reference molecular tests for detection of SARS-CoV-2. METHODS: In this study, we performed the evaluation of a RT-qPCR SMARTCHEK platform (SMARTCHEK, Genesystem) for SARS-CoV-2 detection based on the amplification of RdRp and N gene markers. The platform was evaluated with nasopharyngeal swab samples corresponding to 360 suspected cases of COVID-19 which were remitted to Instituto Nacional de Salud in Peru. This quick method was compared with conventional RT-qPCR as gold standard. RESULTS: The RT-qPCR SMARTCHEK showed a 98.1% sensitivity (CI: 93.3-99.8%), a 98.8% specificity (CI: 96.6-99.8%), a 97.2% positive predictive value (CI: 92-99.4%) and a 99.2% negative predictive value (CI: 97.2-99.9%). The assay demonstrated a strong agreement between the RT-qPCR SMARTCHEK and conventional RT-qPCR (kappa value ≥ 0.966). CONCLUSION: The RT-qPCR SMARTCHEK is a platform that gives reliable and fast results, with high sensitivity and specificity for the detection of SARS-CoV-2, and it will be considered a suitable alternative to COVID-19 diagnosis in low-resource settings.

Evaluation of reverse transcription-loop-mediated isothermal amplification for rapid detection of SARS-CoV-2.

The main strategy for response and control of COVID-19 demands the use of rapid, accurate diagnostic tests aimed at the first point of health care. During the emergency, an increase in asymptomatic and symptomatic cases results in a great demand for molecular tests, which is promoting the development and application of rapid diagnostic technologies. In this study, we describe the development and evaluation of RT-LAMP to detect SARS-CoV-2 based on three genes (ORF1ab, M and N genes) in monoplex and triplex format. RT-LAMP assays were compared with the gold standard method RT-qPCR. The triplex format (RdRp, M and N genes) allowed obtaining comparable results with de RT-qPCR (RdRp and E genes), presented a sensitivity of 98.9% and a specificity of 97.9%, opening the opportunity to apply this method to detect SARS-CoV-2 at primary health-care centers.

Molecular Characterization of Fluoroquinolone-Resistant Bartonella bacilliformis.

The presence of amino acid changes in GyrA, GyrB, ParC, ParE, and in a proposed chromosomal chloramphenicol acetyl transferase (CAT), as well as mutations at 23S rRNA, were established by PCR and sequencing in 38 B. bacilliformis clinical isolates from four different areas in Peru. Eighteen out of 24 (75%) isolates showing ciprofloxacin resistance for both disk-diffusion and e-test presented amino acid substitutions in GyrA (G89C, six isolates, A91V, 1 isolate) GyrB (S474F, 10 isolates) or both (GyrA D95N and GyrB S474F, one isolate). Two out of 14 susceptible isolates presented amino acid substitutions at GyrB (S474F) or a double substitution GyrA D95N and GyrB S474F. Of note, ciprofloxacin-resistant isolates were recovered in the four areas studied. No amino acid change was observed at ParC or ParE. Only one isolate showed chloramphenicol resistance, but no alteration was present in either 23S rRNA or CAT. B. bacilliformis resistant to quinolones are extended throughout Peru, with amino acid substitutions at GyrA or GyrB as the main, albeit not exclusive, cause. B. bacilliformis seems to have an apparent facility to develop mutations on GyrB outside the classical positions 91, 95 of GyrA and 85, 88 of ParC.

Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru.

OBJECTIVES: The role of the environment and climate in the transmission and case fatality rates of SARS-CoV-2 is still being investigated a year into the pandemic. Elevation and air quality are believed to be significant factors in the development of the pandemic, but the influence of additional environmental factors remains unclear. METHODS: We explored the relationship between the cumulative number of infections and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, normalized difference vegetation index or NDVI, particulate matter at 2.5 µm or PM2.5 and NO2 concentration), and population density in Peru. We use confirmed cases of infection from 1,287 districts and mortality in 479 districts, we used Spearman's correlations to assess the bivariate correlation between environmental and climatic factors with cumulative infection cases, cumulative mortality and case-fatality rate. We explored district cases within the ecozones of coast, sierra, high montane forest and lowland rainforest. RESULTS: Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green vegetation cover, as a socioeconomic proxy, are influential factors in the distribution of infection and mortality of SARS-CoV-2 in Peru. Case-fatality rate was weakly associated with elevation. CONCLUSIONS: Our results also strongly suggest that exposure to poor air quality is a significant factor in the mortality of individuals below the age of 30. We conclude that environmental and climatic factors do play a significant role in the transmission and case fatality rates in Peru, however further study is required to see if these relationships are maintained over time.

Primer reporte de Candida auris en Perú

Candida auris es un hongo emergente, con gran relevancia en corto tiempo, como problema de salud pública mundial. Se reporta por primera vez en el Perú la presencia de Candida auris en 3 pacientes adultos internados en un hospital nacional de alta complejidad en el último trimestre del año 2020, durante la pandemia COVID-19. Los pacientes fueron hospitalizados en UCI; sin embargo, solo en 2 pacientes se aisló dicho germen durante su internamiento en UCI. Los pacientes tuvieron varias comorbilidades y tiempos prolongados de hospitalización desde su admisión hasta tener el primer cultivo positivo a C. auris. Todos los pacientes adquirieron una infección nosocomial bacteriana en algún momento de su hospitalización y recibieron antibióticos de amplio espectro. Todas las cepas aisladas fueron resistentes a fluconazol. El equipo de control de infecciones del hospital reforzó las medidas de contención y el Ministerio de Salud del Perú emitió una alerta epidemiológica.

Candida auris is an emerging fungus that has gained great relevance as a global public health problem in a short time. The presence of Candida auris in 3 adult patients admitted to a national hospital of high complexity in the last quarter of 2020 in the midst of the COVID-19 pandemic is reported for the first time in Peru. The patients were hospitalized in the ICU, however, this germ was isolated in only 2 patients while they were hospitalized in the ICU. The patients had various comorbidities and long hospitalization times from admission to having their first culture positive for C. auris. All patients acquired a bacterial nosocomial infection at some point during their hospitalization and received broad-spectrum antibiotics. All isolates were resistant to fluconazole. The hospital's infection control team reinforced containment measures and the Ministry of Health of Peru issued an epidemiological alert.

Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru.

Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (blaoxa-61 ), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.

[Multidrug resistance of Salmonella infantis in Peru: a study through next generation sequencing]. / Multidrogorresistencia de Salmonella infantis en Perú: un estudio mediante secuenciamiento de nueva generación.

OBJECTIVES.: To describe the phenotypic and genotypic patterns of the antimicrobial resistance of Salmonella Infantis in Peru. MATERIALS AND METHODS.: Two hundred and ninety-seven strains of Salmonella sp. submitted to the National Institute of Health (INS, in Spanish) during 2014-2016 were analyzed. The strains were phenotypically characterized by microbiological, serological, and antimicrobial susceptibility tests. Based on antimicrobial resistance patterns, 46 strains were selected and genetically characterized by next generation sequencing. RESULTS.: 193/297 (65%) strains of Salmonella Infantis were identified, of which 143 (74.1%) were multidrug-resistant producers of extended spectrum beta-lactamases (ESBL). The genomic sequencing evidenced a new profile for Salmonella Infantis; additionally, it identified the presence of 15 different genetic determinants of antimicrobial resistance coded in bacterial chromosome and five coded in a megaplasmid. The phenotypic and genotypic resistance patterns matched, with the exception of ceftazidime. Moreover, the 46 strains presented resistance and/or decreased sensitivity to quinolones. CONCLUSIONS.: Salmonella Infantis has become one of the sero-varieties most frequently referred to the INS, which includes ESBLproducing multidrug-resistant strains with resistance to quinolones. Finally, the relevance of next generation sequencing is reasserted in the characterization of new variants of pathogens that are important for public health, and their potential use in antimicrobial resistance surveillance systems.

OBJETIVOS.: Describir los patrones fenotípicos y genotípicos de la resistencia antimicrobiana de Salmonella Infantis en Perú. MATERIALES Y MÉTODOS.: Se analizaron 297 cepas de Salmonella sp. remitidas al Instituto Nacional de Salud (INS) en el periodo 2014-2016. Las cepas fueron caracterizadas fenotípicamente mediante pruebas microbiológicas, serológicas y de susceptibilidad antimicrobiana. En base a los patrones de resistencia antimicrobiana se seleccionaron 46 cepas que fueron caracterizadas genéticamente mediante secuenciamiento de nueva generación. RESULTADOS.: Se identificaron 193/297 (65,0%) cepas de Salmonella Infantis, de la cuales 143 (74,1%) fueron multidrogorresistentes productoras de betalactamasas de espectro extendido (BLEE). Con el secuenciamiento genómico se evidenció un nuevo perfil para Salmonella Infantis, además, se identificó la presencia de 15 diferentes determinantes genéticos de resistencia a los antimicrobianos codificados en cromosoma bacteriano y cinco codificados en un megaplásmido. Los patrones de resistencia fenotípicos y genotípicos coincidieron, a excepción de la ceftazidima. Asimismo, las 46 cepas presentaron resistencia y/o sensibilidad disminuida a las quinolonas. CONCLUSIONES.: Salmonella Infantis se ha convertido en una de las serovariedades más frecuentemente referidas al INS, la cual incluye cepas multidrogoresistentes productoras de BLEE con resistencia a las quinolonas. Finalmente, se reafirma la relevancia del secuenciamiento de nueva generación en la caracterización de nuevas variantes de patógenos de importancia para la salud pública y su uso potencial en los sistemas de vigilancia de resistencia antimicrobiana.

Multidrogorresistencia de Salmonella infantis en Perú: un estudio mediante secuenciamiento de nueva generación / Multidrug resistance of Salmonella infantis in Peru: a study through next generation sequencing

RESUMEN Objetivos. Describir los patrones fenotípicos y genotípicos de la resistencia antimicrobiana de Salmonella Infantis en Perú. Materiales y Métodos. Se analizaron 297 cepas de Salmonella sp. remitidas al Instituto Nacional de Salud (INS) en el periodo 2014-2016. Las cepas fueron caracterizadas fenotípicamente mediante pruebas microbiológicas, serológicas y de susceptibilidad antimicrobiana. En base a los patrones de resistencia antimicrobiana se seleccionaron 46 cepas que fueron caracterizadas genéticamente mediante secuenciamiento de nueva generación. Resultados. Se identificaron 193/297 (65,0%) cepas de Salmonella Infantis, de la cuales 143 (74,1%) fueron multidrogorresistentes productoras de betalactamasas de espectro extendido (BLEE). Con el secuenciamiento genómico se evidenció un nuevo perfil para Salmonella Infantis, además, se identificó la presencia de 15 diferentes determinantes genéticos de resistencia a los antimicrobianos codificados en cromosoma bacteriano y cinco codificados en un megaplásmido. Los patrones de resistencia fenotípicos y genotípicos coincidieron, a excepción de la ceftazidima. Asimismo, las 46 cepas presentaron resistencia y/o sensibilidad disminuida a las quinolonas. Conclusiones. Salmonella Infantis se ha convertido en una de las serovariedades más frecuentemente referidas al INS, la cual incluye cepas multidrogoresistentes productoras de BLEE con resistencia a las quinolonas. Finalmente, se reafirma la relevancia del secuenciamiento de nueva generación en la caracterización de nuevas variantes de patógenos de importancia para la salud pública y su uso potencial en los sistemas de vigilancia de resistencia antimicrobiana.

ABSTRACT Objectives. To describe the phenotypic and genotypic patterns of the antimicrobial resistance of Salmonella Infantis in Peru. Materials and Methods. Two hundred and ninety-seven strains of Salmonella sp. submitted to the National Institute of Health (INS, in Spanish) during 2014-2016 were analyzed. The strains were phenotypically characterized by microbiological, serological, and antimicrobial susceptibility tests. Based on antimicrobial resistance patterns, 46 strains were selected and genetically characterized by next generation sequencing. Results. 193/297 (65%) strains of Salmonella Infantis were identified, of which 143 (74.1%) were multidrug-resistant producers of extended spectrum beta-lactamases (ESBL). The genomic sequencing evidenced a new profile for Salmonella Infantis; additionally, it identified the presence of 15 different genetic determinants of antimicrobial resistance coded in bacterial chromosome and five coded in a megaplasmid. The phenotypic and genotypic resistance patterns matched, with the exception of ceftazidime. Moreover, the 46 strains presented resistance and/or decreased sensitivity to quinolones. Conclusions. Salmonella Infantis has become one of the sero-varieties most frequently referred to the INS, which includes ESBLproducing multidrug-resistant strains with resistance to quinolones. Finally, the relevance of next generation sequencing is reasserted in the characterization of new variants of pathogens that are important for public health, and their potential use in antimicrobial resistance surveillance systems.

Resistencia antimicrobiana de cepas de Bartonella bacilliformis procedentes de regiones endémicas de la enfermedad de Carrión en el Perú / Antimicrobial resistance of Bartonella bacilliformis strains from regions endemic to bartonellosis in Peru

Evaluar la susceptibilidad antimicrobiana in vitro a cloranfenicol (CHL) y ciprofloxacino (CIP) de cepas de Bartonella bacilliformis procedentes de áreas endémicas de la enfermedad de Carrión (EC) en el Perú, mediante tres métodos de laboratorio. Materiales y métodos. Se evaluó la susceptibilidad antimicrobiana a CHL y CIP de 100 cepas de Bartonella bacilliformis, los aislamientos procedieron de pacientes de los departamentos de Ancash, Cusco, Cajamarca, Lima y La Libertad; las cepas se evaluaron mediante: disco difusión, E-Test y dilución en agar. Resultados. El 26% de las cepas de Bartonella bacilliformis evaluadas, presentaron resistencia a CIP y 1% a CHL. Se obtuvieron patrones similares de sensibilidad/resistencia antimicrobiana en los tres métodos utilizados. Conclusiones. Las cepas de Bartonella bacilliformis circulantes en el Perú, presentan elevados niveles de resistencia in vitro a CIP, por lo que se recomienda ampliar la investigación sobre la utilización del fármaco en los esquemas de tratamiento de la EC. Los métodos de E-test y disco difusión resultaron más convenientes para la evaluación de la susceptibilidad antimicrobiana in vitro del microorganismo...

To evaluate in vitro antimicrobial susceptibility to chloramphenicol (CHL) and ciprofloxacin (CIP) in strains of Bartonella bacilliformis from areas that are endemic to Bartonellosis in Peru, through three laboratory methods. Materials and methods. Antimicrobial susceptibility to CHL and CIP from 100 strains of Bartonella bacilliformis isolated in patients from the regions of Ancash, Cusco, Cajamarca, Lima and La Libertad were evaluated. Strains were evaluated by: disk diffusion, E-test and agar dilution. Results. 26% of the strains of Bartonella bacilliformis evaluated were resistant to CIP and 1% to CHL. Similar patterns of antimicrobial sensitivity / resistance were obtained in all three methods. Conclusions. Bartonella bacilliformis strains circulating in Peru have high levels of in vitro resistance to CIP, so it is advisable to expand research on the use of drug treatment regimens of the Bartonellosis. The methods of E-test and disk diffusion were the most suitable for assessment in vitro of antimicrobial susceptibility of the microorganism...

[Antimicrobial resistance of Bartonella bacilliformis strains from regions endemic to bartonellosis in Peru]. / Resistencia antimicrobiana de cepas de Bartonella bacilliformis procedentes de regiones endémicas de la Enfermedad de Carrión en EL Perú.

OBJECTIVES: To evaluate in vitro antimicrobial susceptibility to chloramphenicol (CHL) and ciprofloxacin (CIP) in strains of Bartonella bacilliformis from areas that are endemic to Bartonellosis in Peru, through three laboratory methods. MATERIALS AND METHODS: Antimicrobial susceptibility to CHL and CIP from 100 strains of Bartonella bacilliformis isolated in patients from the regions of Ancash, Cusco, Cajamarca, Lima and La Libertad were evaluated. Strains were evaluated by: disk diffusion, E-test and agar dilution. RESULTS: 26% of the strains of Bartonella bacilliformis evaluated were resistant to CIP and 1% to CHL. Similar patterns of antimicrobial sensitivity / resistance were obtained in all three methods. CONCLUSIONS: Bartonella bacilliformis strains circulating in Peru have high levels of in vitro resistance to CIP, so it is advisable to expand research on the use of drug treatment regimens of the Bartonellosis. The methods of E-test and disk diffusion were the most suitable for assessment in vitro of antimicrobial susceptibility of the microorganism.