Occurrence, antimicrobial resistance and whole genome sequence analysis of Salmonella serovars from pig farms in Ilorin, North-central Nigeria.

Salmonella enterica is a foodborne pathogen of global public health importance with developing countries mostly affected. Foodborne outbreaks are often attributed to pork consumption and Salmonella contamination of retail pork is directly linked to the Salmonella prevalence on farm. The widespread use of antimicrobials at different steps of swine production can favor resistant strains of Salmonella. The objectives of this study are to characterize the distribution, multilocus sequence typing (MLST), plasmid, virulence profiles and antimicrobial resistance of Salmonella serovars circulating in selected pig farms. Six hundred fecal samples were randomly collected from nine selected farms in Ilorin, Nigeria. Isolates were analyzed by cultural isolation using selective media, conventional biochemical characterization, serotyping, MLST and whole genome sequencing (WGS). Sixteen samples were positive for Salmonella sub-species, comprising of nine serovars. The antimicrobial susceptibility results revealed low-level resistance against 13 antimicrobial agents. Five strains exhibited resistance to nalidixic acid and intermediate resistance to ciprofloxacin with chromosomal (double) mutation at gyrA and parC while four strains possessed single mutation in parC. Salmonella Kentucky showed double mutation each at gyrA and parC. WGS analysis, revealed eight diverse sequence types (STs), the most common STs were ST-321 and ST-19 (n = 4) exhibited by S. Muenster and S. Typhimurium, respectively. Single Nucleotide Polymorphism (SNP)-based phylogeny analysis showed the 16 isolates to be highly related and fell into 8 existing clusters at NCBI Pathogen Detection. Curtailing the spread of resistant strains will require the establishment of continuous surveillance program at the state and national levels in Nigeria. This study provides useful information for further studies on antimicrobial resistance mechanisms in foodborne Salmonella species.

Seasonal and spatial occurrence of zoonotic Salmonella serotypes in griffon vultures at farmland environments: Implications in pathogen pollution and ecosystem services and disservices.

Livestock production is a large source of microbial, pharmaceutical, and antimicrobial pollution worldwide. Vultures are one group of birds with particularly high exposure to food-borne pathogens due to frequent consumption of infected livestock carcasses. The potential origin and spatial-temporal shedding patterns of livestock-adapted Salmonella serotypes of zoonotic importance were evaluated in adult and nestling Griffon vultures (Gyps fulvus). We specifically assessed the exposure source and subsequent elimination of Salmonella-infected carcasses (ecosystem services) or transmission back to livestock (ecosystem disservices) by vultures, thus contributing respectively to disease mitigation or amplification in natural and farmed environments. The results show a seasonal high occurrence and turnover of a high variety of serotypes, especially swine-adapted ones isolated at high frequency. This suggests that vultures can be reservoirs and long-distance carriers of faecal Salmonella shed in supplementary feeding stations and breeding colonies. Contrary to their conservation purposes, feeding stations can act as Salmonella hotspots and reservoirs. However, a role for vultures in the transmission back to food-producing animals seems impossible because they do not come into contact at indoor farms, while transmission to free-ranging ruminants was not supported by the presence of ruminant-adapted serotypes in the vultures. Therefore, vultures do not promote disservices associated with the re-infection of livestock with Salmonella, but can provide quantitatively important ecosystem services by removing carrion contaminated with these and other zoonotic pathogens potentially affecting their health. Sanitary vigilance of the farms authorised to provide food for avian scavengers should avoid the disposal of swine and poultry carcasses with Salmonella and the antibiotics used to treat it. Extensive free-ranging livestock and their carcasses exploited in the countryside should be a priority for the conservation of vultures and their ecological function as cleaners and disease mitigators.

[Rapid identification of 15 common S. enterica Salmonella serovars by multiplex real-time PCR].

OBJECTIVE: Multiplex real-time PCR for the identification of 15 Salmonella serovars was developed. METHODS: Through the Salmonella genome comparison, 12 membrane proteins STM4497 gene can be used to identify 15 Salmonella serovars, and these 12 genes were respectively listed as A-L genes. Then primers were designed according to A-L gene conserved sequences, and then multiplex real-time PCR was established assessed with the evaluation of the limit detection, sensitivity, specificity, and repeatability. The 206 Salmonella strains were identified using multiplex real-time PCR with the comparison of the serum slide agglutination assay. RESULTS: The limit detection of multiplex PCR ranged from 1. 1×10~(-3)-1. 2×10~(-3) ng/µL. The target genes were 100% specificity, and the relative standard deviation was lower than 2. 97%. Compared with the serum slide agglutination assay, Kappa ranged 0. 92-1. 00. CONCLUSION: The multiplex real-time PCR can be used to identify 15 Salmonella serovars, which is rapid, accurate and specific.

Prevalence, Distribution, and Diversity of Salmonella Strains Isolated From a Subtropical Lake.

This study investigated the prevalence, serovar distribution, antimicrobial resistance, and pulsed field gel electrophoresis (PFGE) typing of Salmonella enterica isolated from Lake Zapotlán, Jalisco, Mexico. Additionally, the association of the presence of Salmonella with physicochemical and environmental parameters was analyzed using Pearson correlation analysis and principal component analysis (PCA). Salmonella spp. were identified in 19 of 63 (30.15%) samples. The prevalence of Salmonella was positively correlated with air temperature, electrical conductivity, pH, and dissolved oxygen and negatively correlated with relative humidity, water temperature, turbidity, and precipitation. The predominant serotype identified was Agona (68.48%), followed by Weltevreden (5.26%), Typhimurium (5.26%), and serogroup B (21.05%). Overall, the highest detected antimicrobial resistance was toward colistin (73.68%), followed by sulfamethoxazole (63.15%), tetracycline (57.89%), nalidixic acid (52.63%), and trimethoprim (52.63%). All Salmonella strains were genetically diverse, with a total of 11 XbaI and four BlnI profiles on PFGE. The use of these two enzymes allowed differentiate strains of Salmonella of the same serotype. The results obtained in this study contribute to a better understanding of the Salmonella spp. ecology in an endorheic subtropical lake and provide information for decision makers to propose and implement effective strategies to control point and non-point sources of pathogen contamination.

Survival of Tomato Outbreak Associated Salmonella Serotypes in Soil and Water and the Role of Biofilms in Abiotic Surface Attachment.

Salmonella serotypes linked to tomato-associated outbreaks were evaluated for survival in soil and water over a 40-day period. Salmonella enterica serotypes Anatum, Baildon, Braenderup, Montevideo, Newport, and Javiana were inoculated separately into sterile soil and water, followed by plating onto TSAYE and XLT4 at 10-day intervals. Biofilm production by Salmonella serotypes was measured on both quartz particles (soil surrogate) and glass coverslips, and was evaluated using a crystal violet dye assay. Salmonella populations in soil and water over 40 days indicated no significant differences between Salmonella serotypes tested (p > 0.05). Over a 40-day period, there was a 1.84 ± 0.22 log CFU/g and 1.56 ± 0.54 CFU/mL decrease in populations of Salmonella in soil and water, respectively. Enumeration indicated that Salmonella population fluctuated in water but decreased linearly in soil. All serotypes tested produced the "red dry and rough" morphotype on Congo Red agar. Biofilm produced by all the Salmonella serotypes tested was significantly different on quartz particles than on glass coverslips (p < 0.0001), indicating that material and surface characteristics could affect biofilm development. The ability of Salmonella serotypes to persist in soil or water and attach to abiotic surfaces through biofilm formation affirms that contact surfaces, soil, water, and sediment should be considered as possible sources of cross-contamination in the farm environment.

Detection and Characterization of Salmonella Serotypes in the Production Chain of Two Pig Farms in Buenos Aires Province, Argentina.

The aim of the present study was to determine the prevalence of Salmonella in the pork production chain and to characterize Salmonella isolates. From 764 samples, 35 (4.6%) were positive for Salmonella spp., as determined by biochemical tests and the presence of the invA gene. From these, 2.6, 2.0, 8.8, and 8.0% corresponded to samples collected from farms, slaughterhouses, boning rooms and retail markets, respectively. Salmonella strains were classified into five serotypes and distributed as follows: S. Typhimurium in the pork production chain, S. Kentucky in farms and slaughterhouses, S. Brandenburg in slaughterhouses, S. Livingstone in farms and S. Agona in boning rooms and retail markets. Interestingly, the antimicrobial susceptibility testing indicated that all 35 Salmonella spp.-positive isolates were resistant to at least one antimicrobial agent, and 30 were multidrug-resistant (MDR) and resistant to different classes of antibiotics. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis showed clonal relatedness among strains isolated from farms, boning rooms and retail markets. The presence of antibiotic-resistant Salmonella in food poses a potential health hazard to consumers.

SEROTYPING AND ANTIMICROBIAL DRUG RESISTANCE OF SALMONELLA ISOLATED FROM LETTUCE AND HUMAN DIARRHEA SAMPLES IN BURKINA FASO.

BACKGROUND: In Burkina Faso dirty water in particular those of the stoppings and the gutter ones are used for vegetables irrigation in the gardens. The aim of this study was to determine the prevalence and antibiotic susceptibility of Salmonella serotypes from humans and lettuce samples inBurkina Faso. Materials and Methods:Salmonella strains isolated from patients in 2009 to 2015 and lettuce samples in 2014 in Burkina Faso were serotyped using specific antisera. All strains were subjected to a set of 14 antibiotics to study their antibiogram by using Baeur-Kirby disk diffusion method. RESULTS: Out of 154 Salmonella isolated, 60 were from human and 94 from lettuce samples. Serotyping revealed four different serotypes and 39% (60) untypeable strains from human and lettuce (14 and 46 strains). Salmonella serotypes from human and lettuce samples were: Paratyphi A (10% and 22%), Paratyphi B (34% and 8%), Paratyphi C (14% and 18%) and Typhi (21% and 1%). A high resistance of Salmonella Paratyphi B and Salmonella spp to tetracycline were 70% from human and 35 % from lettuce samples. Multiresistance was observed to tetracycline, chloramphenicol and amoxicillin/clavulanic-acid or ampicillin with Salmonella ParatyphiB 35% and Salmonella Typhi 33% from human samples and Salmonella spp 4% from lettuce samples. CONCLUSION: This study showed the diversity of Salmonella serotypes from both clinical and environmental samples and emergence of multiresistant Salmonella to antibiotics in Burkina Faso. A lettuce is a potential source of transmission of Salmonella causing diarrhea among human in Burkina Faso. List of non-standard Abbreviations : HDB: Hôpital du District de Bogodogo, LNSP: Laboratoire National de Santé Publique, DSG : District Sanitaire de Gourcy, DSB : District Sanitaire de Boromo.

Contamination of Carcasses and Utensils in Small Swine Slaughterhouses by Salmonella in the Northwestern Region of the State of Rio de Janeiro, Brazil.

Salmonella is a major foodborne pathogen that constantly threatens food safety in developed countries and underdeveloped countries such as Brazil, where it is responsible for 38% of notified cases of foodborne illness. Swine are one of the main meat-producing species that may asymptomatically carry Salmonella, periodically shedding the bacteria through feces. The state of Rio de Janeiro is not a major producer of swine meat, but small slaughterhouses are operational and produce meat for consumption within the state, although few studies have been conducted in the region. In this context, this study was designed to evaluate Salmonella contamination in carcasses, lymph nodes, feces, utensils, and the environment of three small slaughterhouses in the state of Rio de Janeiro. A total of 344 samples from carcasses, utensils, equipment, water, and the environment were collected from these slaughterhouses in the northwestern region of Rio de Janeiro. Salmonella was isolated from 36 (10.5%) samples: 10 of 48 carcasses, 19 of 96 lymph nodes, 4 of 48 fecal samples, 2 of 6 water samples, and 1 of 6 bleeding knives; 55 isolates were recovered. Serotyping revealed the predominance of Salmonella Typhimurium (20 isolates) followed by Salmonella Abony (10 isolates), Salmonella Give (7 isolates), Salmonella Heidelberg (4 isolates), and Salmonella Infantis (1 isolate). Ten isolates were only partially typeable, with only their O antigen identified, and three isolates had rough, nontypeable colonies. Despite the overall low prevalence of Salmonella in this study, all three slaughterhouses had poor hygienic and sanitary conditions, providing easy routes for carcass and, consequently, meat contamination. Thus, it is imperative to enforce sanitary inspections in these establishments and to apply good manufacture practices to assure the safety of the produced pork.

Heatwaves differentially affect risk of Salmonella serotypes.

OBJECTIVES: Given increasing frequency of heatwaves and growing public health concerns associated with foodborne disease, we examined the relationship between heatwaves and salmonellosis in Adelaide, Australia. METHODS: Poisson regression analysis with Generalised Estimating Equations was used to estimate the effect of heatwaves and the impact of intensity, duration and timing on salmonellosis and specific serotypes notified from 1990 to 2012. Distributed lag non-linear models were applied to assess the non-linear and delayed effects of temperature during heatwaves on Salmonella cases. RESULTS: Salmonella typhimurium PT135 notifications were sensitive to the effects of heatwaves with a twofold (IRR 2.08, 95% CI 1.14-3.79) increase in cases relative to non-heatwave days. Heatwave intensity had a significant effect on daily counts of overall salmonellosis with a 34% increase in risk of infection (IRR 1.34, 95% CI 1.01-1.78) at >41 °C. The effects of temperature during heatwaves on Salmonella cases and serotypes were found at lags of up to 14 days. CONCLUSION: This study confirms heatwaves have a significant effect on Salmonella cases, and for the first time, identifies its impact on specific serotypes and phage types. These findings will contribute to the understanding of the impact of heatwaves on salmonellosis and provide insights that could mitigate their impact.

Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance.

AIM: The purpose was to develop an analytical pipeline for specific gene analysis and biomarker discovery from next generation sequencing (NGS) data. MATERIALS & METHODS: As a test case, the fliC gene reference sequences of 24 Salmonella enterica strains of 13 serotypes and NGS reads of 32 serovar Newport, 48 Montevideo and 115 Enteritidis outbreak isolates were retrieved from the National Center for Biotechnology Information database. RESULTS: Establishment of an analytical pipeline consisting of four steps: reference sequences retrieval and template sequence determination; NGS sequence reads retrieval; multiple sequence alignments and phylogenetic analysis; data mining and biomarker discovery. CONCLUSION: The pipeline developed provides an effective bioinformatics tool for genetic diversity clarification and marker sequences discovery for pathogen characterization and surveillance.

Serotypes, antimicrobial profiles, and public health significance of Salmonella from camels slaughtered in Maiduguri central abattoir, Nigeria.

AIM: This study aimed at determining the serotypes, antimicrobial profiles, and public health importance of Salmonella strains from camels slaughtered at Maiduguri central abattoir, Nigeria. MATERIALS AND METHODS: Two hundred samples were obtained from camel comprising of intestines, feces, liver, and spleen (n=50 each). Non-lactose fermenting dark center Salmonella colonies were identified using standard biochemical techniques, serotyped and subjected to antimicrobial susceptibility test using minimum inhibition concentration method. RESULTS: Out of the 200 samples collected, 17 were Salmonella positive (spleen=7, intestine=6, feces=3, and liver=1) with a prevalence of 8.5%. Five serotypes comprising Salmonella Eko, 7 (3.5%), Salmonella Uganda, 4 (2.0%), Salmonella Amager, 2 (1.0%), Salmonella Westhampton, 2 (1.0%), and Salmonella Give, 2 (1.0%) were incriminated. Majority of the serotypes were sensitive to the antimicrobials, but one Salmonella Amager exhibited resistance to streptomycin, and one each of Salmonella Uganda and Salmonella Eko were resistant to sulfamethoxazole. CONCLUSION: This study revealed the prevalence and the antibiotic resistance profile of newly emerging Salmonella from camels in the northeast of Nigeria, which can serve as a means for the transmission of Salmonella to human. Therefore, there is a need for the establishment of national Salmonella surveillance and control programs.

Salmonella: sorotipos identificados na regiäo de Säo José do Rio Preto/SP, no período de 1990-1999 / Salmonella: serotypes identified in the Säo José do Rio Preto area, SP, during the period of 1990-1999

No período de janeiro de 1990 a dezembro de 1999, no Instituto Adolfo Lutz - Lab. I de Säo José do Rio Preto-SP, foram isoladas 324 cepas de salmonella, sendo 155 de infecçöes humanas e 169 de alimentos destinados ao consumo humano. Dos 17 diferentes sorotipos identificados a partir de infecçöes humanas, S. enterica subsp. enterica sorotipo enteritidis (S. enteritidis) foi o predominante 75,0(por cento). O material fecal representou a principal fonte de isolamento das cepas, principalmente pela ocorrência dos vários surtos de doenças veiculadas por alimentos (DVA). A partir dos alimentos, 26,6(por cento) deles envolvidos em surtos de DVA, foram identificados 30 diferentes sorotipos, também com a predominância de S. enteritidis 56,2(por cento). Os alimentos apresentando maior número de isolamentos de cepas de Salmonella foram a carne e seus derivados 59,7(por cento), seguidos por ovos e seus derivados 16,0(por cento), nos quais, S. enteritidis foi o sorotipo mais prevalente 57,4(por cento) e 81,5(por cento) respectivamente. Estes resultados demonstram que S. enteritidis permanece o sorotipo mais frequentemente isolado, tanto em infecçöes humanas quanto em alimento. Os alimentos mais comumente implicados em DVA ainda säo as carnes de aves e ovos, bem como os seus derivados, quando consumidos crus ou mal cozidos. (AU)

From January 1990 to December 1999, 324 Salmonella strains were isolated at InstitutoAdolfo Lutz ­ São José do Rio Preto­SP Lab. I, 155 from human infections and 169 from food for humanconsumption. S. enterica subsp. Enterica serotype enteritidis (S. enteritidis) was the most prevalentserotype (75.0%) among the 17 different ones identified in human infections. Fecal material representedthe main human source of the isolated strains, due to several foodborne outbreaks occurring in the periodunder study. Thirty different serotypes were identified in food, S. enteritidis being the prevailing one.About 26.6% of the analyzed foods were linked to foodborne outbreaks. Foods presenting the highest rateof isolated strains were meat and its products (59.7%), followed by eggs and egg products (16.0%). Theseresults show that S. enteritidis still remains as the most common serotype isolated from human sourcesand foods. Foods frequently implicated in foodborne outbreaks are chicken meat and eggs, as well as theirproducts, particularly raw and undercooked ones. (AU)