Presence of Zonula Occludens Toxin-Coding Genes among Vibrio parahaemolyticus Isolates of Clinical and Environmental Origin.

In recent studies, emphasis has been placed on the zonula occludens toxin (Zot) from the non-toxigenic Vibrio parahaemolyticus strain PMC53.7 as an agent inducing alterations in the actin cytoskeleton of infected Caco-2 cells and which appears as a relevant virulence factor. Universal zot primers were designed by the alignment of different types of zot gene and identification of conserved sequences to investigate the presence in diverse environmental and clinical V. parahaemolyticus isolates, in co-occurrence with virulence factors, such a hemolysins and secretion systems. The study screened a total of 390 isolates from environmental sources from Chile and Italy and 95 Chilean clinical isolates. The results revealed that around 37.2% of Chilean environmental strains and 25.9% of Italian strains, and 24.2% of clinical isolates carried the zot gene. The Zot-C2 cluster was present in 71.4% of Chilean environmental strains but absent in clinical isolates, while the Zot-C4 cluster was identified in 28.6% of environmental and 100% of clinical isolates. Understanding the role of zot in V. parahaemolyticus virulence is crucial, especially considering the risk associated with consuming diverse isolates from bivalves and the co-occurrence with virulence factors such as TDH, TRH or T3SS2.

Development and characterization of a bacteriophage cocktail with high lytic efficacy against field-isolated Salmonella enterica.

Salmonella spp. is a prevalent pathogen that causes great public health concern worldwide. Bacteriophage-based cocktails have arisen as an alternative to antibiotics to inhibit the growth of Salmonella. However, the bactericidal effect of bacteriophage cocktails in vivo largely differs from their observed effect in vitro. This is partly because in vitro developments of cocktails do not always consider the bacterial diversity nor the environmental conditions where bacteriophages will have to replicate. Here, we isolated and sequenced 47 bacteriophages that showed variable degrees of lytic activity against 258 Salmonella isolates from a commercial broiler company in Brazil. Three of these bacteriophages were characterized and selected to assemble a cocktail. In vitro quantitative assays determined the cocktail to be highly effective against multiple serovars of Salmonella, including Minnesota and Heidelberg. Remarkably, the in vitro lytic activity of the cocktail was retained or improved in conditions that more closely resembled the chicken gut, such as anaerobiosis, 42°C, and Salmonella mono-strain biofilms. Analysis of bacterial cross-resistance between the 3 bacteriophages composing the cocktail revealed limited or no generation of cross-resistance. Our results highlight the relevance of an optimized flux of work to develop bacteriophage cocktails against Salmonella with high lytic efficacy and strong potential to be applied in vivo in commercial broiler farms.

Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies.

Vaccination generates a neutralizing immune response against SARS-CoV-2. The genomic surveillance is showing the emergence of variants with mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we report the neutralization potency against alpha, gamma, and D614G SARS-CoV-2 variants in 44 individuals that received two doses of CoronaVac vaccine, an inactivated SARS-CoV-2 vaccine. Plasma samples collected at 60 days after the second dose of CoronaVac were analyzed by the reduction of cytopathic effect in Vero E6 cells with the three infectious variants of SARS-CoV-2. Plasma showed lower neutralization with alpha (geometric mean titer [GMT] = 18.5) and gamma (GMT = 10.0) variants than with D614G (GMT = 75.1) variant. Efficient neutralization against the alpha and gamma variants was not detected in 31.8% and 59.1% of plasma, respectively. These findings suggest the alpha and gamma variants could escape from neutralization by antibodies elicited by vaccination. Robust genomic and biological surveillance of viral variants could help to develop effective strategies for the control of SARS-CoV-2.

Tracing Listeria monocytogenes contamination in artisanal cheese to the processing environments in cheese producers in southern Chile.

Artisanal cheese from southern Chile is made primarily by rural families who raise dairy cows and produce cheese as a way to add value to their milk. The most common cheese produced is chanco, a semi-hard cheese that is typically sold in unauthorized markets. The methods of chanco production do not always follow good manufacturing practices; however, the presence of Listeria monocytogenes contamination in this cheese has not been previously documented. To better understand production practices and L. monocytogenes contamination, 39 cheese producers were surveyed with regard to infrastructure, cleaning and sanitation, pest control, personal hygiene, training, raw materials, and manufacturing. During four sampling trips in 2016 (March, May, August, and November), 546 samples were collected (468 cheese samples and 78 milk samples). For producers that tested positive for L. monocytogenes, environmental monitoring was also conducted, for which 130 additional samples were collected. Presumptive L. monocytogenes isolates (N = 94) were further characterized and subtyped using standard techniques and qPCR-based species/subtype verification; a subset of 52 isolates were also subtyped by Pulsed Field Gel Electrophoresis (PFGE). L. monocytogenes was found in 19 cheeses (4.1%) from five producers (12.8%). The most frequent serotypes were 1/2b (48.9%), group 4B (4b, 4d, 4e) (45.7%), and serotype 1/2a (5.4%). Although no milk samples tested positive for L. monocytogenes, all cheese samples from two producers tested positive during two of the samplings. Distinct PFGE types were recovered from each facility, demonstrating persistence of certain subtypes of the pathogen that ultimately caused end-product contamination. Environmental monitoring of the five positive producers revealed a prevalence of L. monocytogenes ranging from 0 to 30%, with food contact surfaces having the highest incidence of this organism. The findings of this study contribute to the understanding of L. monocytogenes incidence in artisanal cheese in the region of southern Chile.

Phylogenetic analysis of the first four SARS-CoV-2 cases in Chile.

The current pandemic caused by the new coronavirus is a worldwide public health concern. To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. The complete genome sequences of around 450 isolates are available, and studies about similarities and differences among them and with the close related viruses that caused similar epidemics in this century. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. Our findings reveal at least two different viral variants entries to Chilean territory, coming from Europe and Asia. We also sub-classified the isolates into variants according to punctual mutations in the genome. Our work contributes to global information about transmission dynamics and the importance to take control measures to stop the spread of the infection.

[Genetic characterization of Listeria monocytogenes strains isolated during 2007-2014 in Chile]. / Caracterización genética de cepas de Listeria monocytogenes aisladas durante los años 2007-2014 en Chile.

BACKGROUND: Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied. AIM: To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014. METHODS: We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST). RESULTS: The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II. CONCLUSIONS: A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.

Caracterización genética de cepas de Listeria monocytogenes aisladas durante los años 2007-2014 en Chile / Genetic characterization of Listeria monocytogenes strains isolated during 2007-2014 in Chile

Resumen Introducción: Listeria monocytogenes es un patógeno transmitido por alimentos que causa listeriosis, una enfermedad que puede presentarse como gastroenteritis febril o en una forma invasora que tiene altas tasas de mortalidad. Hasta el momento, ha sido poco estudiada la diversidad genética de cepas de L. monocytogenes aisladas desde pacientes, alimentos y fuentes ambientales en Chile. Objetivo: Caracterizar genéticamente cepas de L. monocytogenes de estos tres orígenes recibidas por el Instituto de Salud Pública de Chile (ISP) entre los años 2007 y 2014. Material y Métodos: Se seleccionaron 94 cepas de L. monocytogenes correspondientes a 94 pulsotipos diferentes identificados por electroforesis en gel de campo pulsado (PFGE), se extrajo ADN y se realizó serotipificación mediante reacción de polimerasa en cadena (RPC) y tipificación de secuencias multilocus (MLST). Resultados: El serotipo más común fue 4b (55,3%), seguido de 1/2a (25,5%), 1/2b (17%) y 1/2c (2,2%). Se identificaron 32 secuencias tipo (ST), de las cuales cuatro fueron nuevas, y las predominantes fueron ST1 (28,7%) y ST2 (13,8%). La totalidad de las cepas se agrupó en los Linajes I y II. Conclusiones: Se observó una gran variabilidad genética en las cepas de L. monocytogenes analizadas, siendo predominantes las secuencias tipo ST1 y ST2, ambas pertenecientes al Linaje I. Nuestros resultados contribuyen a conocer la estructura poblacional de este patógeno en Chile y su presencia en muestras clínicas, alimentos y el medio ambiente.

Background: Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied. Aim: To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014. Methods: We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST). Results: The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II. Conclusions: A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.

Genetic Platforms of blaCTX-M in Carbapenemase-Producing Strains of K. pneumoniae Isolated in Chile.

Objective: To elucidate whether the genetic platforms of blaCTX-M contribute to the phenotypes of multi-drug-resistance (MDR) in the first carbapenemase-producing K. pneumoniae strains isolated in Chile. Method: Twenty-two carbapenemase-producing K. pneumoniae strains isolated from different Chilean patients and hospitals were studied. Their genetic relatedness was assessed by PFGE and MLST. The levels of antibiotic resistance were evaluated by determining the minimum inhibitory concentration of various antimicrobials. In addition, several antibiotic resistance genes of clinical relevance in Chile were investigated. The prevalence, allelic variants, and genetic platforms of blaCTX-M were determined by PCR and sequencing. Results: Out of the 22 strains studied, 20 carry KPC, one carries NDM-1, and one carries OXA-370. The PFGE analysis showed three clades with a genetic relatedness >85%, two formed by four strains and one by eight strains. The other strains are not genetically related, and a total of 17 different pulse types were detected. Ten different STs were identified, the main ones being ST258 (five strains) and ST1161 (seven strains). The isolates presented different percentages of resistance, and 82% were resistant to all the ß-lactams tested, 91% to ciprofloxacin, 73% to colistin, 59% to gentamicin, 50% to amikacin, and only 9% to tigecycline. All isolates carried blaTEM and blaSHV, whereas 71% carried aac(6')Ib-cr, and 57% one qnr gene (A, B, C, D, or S). The blaCTX-M gene was found in 10 of the isolates (4 blaCTX-M-15 and 6 blaCTX-M-2). The characterization of the platform, in seven selected strains, revealed that the gene is associated with unusual class 1 integrons and insertion sequences such as ISCR1, ISECp1, and IS26. Conclusion: In the first carbapenemase-producing K. pneumoniae strains isolated in Chile the genetic platform of blaCTX-M-2 corresponds to an unusual class 1 integron that can be responsible for the MDR phenotype, whereas the genetic platforms of blaCTX-M-15 are associated with different IS and do not contribute to multi-drug resistance.

Novel nonsense mutation in the katA gene of a catalase-negative Staphylococcus aureus strain

Abstract We report the first description of a rare catalase-negative strain of Staphylococcus aureus in Chile. This new variant was isolated from blood and synovial tissue samples of a pediatric patient. Sequencing analysis revealed that this catalase-negative strain is related to ST10 strain, which has earlier been described in relation to S. aureus carriers. Interestingly, sequence analysis of the catalase gene katA revealed presence of a novel nonsense mutation that causes premature translational truncation of the C-terminus of the enzyme leading to a loss of 222 amino acids. Our study suggests that loss of catalase activity in this rare catalase-negative Chilean strain is due to this novel nonsense mutation in the katA gene, which truncates the enzyme to just 283 amino acids.

Novel nonsense mutation in the katA gene of a catalase-negative Staphylococcus aureus strain.

We report the first description of a rare catalase-negative strain of Staphylococcus aureus in Chile. This new variant was isolated from blood and synovial tissue samples of a pediatric patient. Sequencing analysis revealed that this catalase-negative strain is related to ST10 strain, which has earlier been described in relation to S. aureus carriers. Interestingly, sequence analysis of the catalase gene katA revealed presence of a novel nonsense mutation that causes premature translational truncation of the C-terminus of the enzyme leading to a loss of 222 amino acids. Our study suggests that loss of catalase activity in this rare catalase-negative Chilean strain is due to this novel nonsense mutation in the katA gene, which truncates the enzyme to just 283 amino acids.