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Anais da Academia Brasileira de Ciências

Print version ISSN 0001-3765On-line version ISSN 1678-2690

An. Acad. Bras. Ciênc. vol.89 no.2 Rio de Janeiro Apr./June 2017  Epub May 15, 2017 

Health Sciences

Phenotypic and genotypic characterization of Salmonella spp. isolated from foods and clinical samples in Brazil






1Programa de Pós-Graduação em Ciência de Alimentos, Laboratório de Estudos em Microbiologia de Alimentos/LEMA, Faculdade de Farmácia, Universidade Federal da Bahia, Av. Adhemar de Barros, s/n, Campus de Ondina, 40170-115 Salvador, BA, Brazil

2Departamento de Análises Clínicas e Toxicológicas, Laboratório de Microbiologia Clínica, Faculdade de Farmácia, Universidade Federal da Bahia, Av. Adhemar de Barros, s/n, Campus de Ondina, 40170-115 Salvador, BA, Brazil

3Departamento de Análises Bromatológicas, Laboratório de Estudos em Microbiologia de Alimentos/LEMA, Faculdade de Farmácia, Universidade Federal da Bahia, Av. Adhemar de Barros, s/n, Campus de Ondina, 40170-115 Salvador, BA, Brazil


Increasing antimicrobial resistance in Salmonella species has been a serious problem for public health worldwide. This study examines Salmonella spp. recovered from foods and clinical samples on serotype, antimicrobial resistance and PFGE genotypes. It identified 91 salmonellae, belonging to 31 different serotypes, from 36 isolates from food and 55 clinical samples. Salmonella Infantis (16.5%) and Salmonella Enteritidis (13.7%) are the most common among food isolates, whereas Salmonella Enteritidis (29.0%) and Salmonella Typhimurium (16.0%) mainly causes human salmonellosis. Antimicrobial susceptibility data showed that 63.0% of the isolates were fully susceptible to 12 antibiotics tested. Nalidixic acid showed high resistance rates, 32.7% and 25.0% of the clinical isolates and food, respectively. Three main PFGE types: A (Salmonella Enteritidis), B (Salmonella Infantis) and C (Salmonella Schwarzengrund) comprised isolates recovered from foods and clinical samples. Our results indicate that the clonal groups were both causing diseases and food contamination, emphasizing the need to maintain a system of surveillance for foodborne disease.

Keywords: Salmonella; Salmonella Infantis; Salmonella Enteritidis; antimicrobial resistance


Salmonella is a leading cause of food-borne disease being an important health problem in industrialized and developing countries (Chu et al. 2009, Abbassi-Ghozzi et al. 2012, Yang et al. 2013). In recent years, serotypes of Salmonella isolated from foods have shown an increase in antimicrobial resistance, particularly those of animal origin. Moreover, an increased incidence of human salmonellosis due to multidrug-resistant strains have been reported (Lu et al. 2011, Wang et al. 2013).

There has been increasing concern over the past 30 years about the worldwide emergence of multidrug-resistant phenotypes among Salmonella serovars, in particular Salmonella Typhimurium and, more recently, Salmonella Newport as well as several other serovars. The levels and extent of resistance vary in different regions and are influenced by antimicrobial use in humans and animals as well as geographical differences in the epidemiology of Salmonella (Weinberger and Keller 2005, Zhao et al. 2008).

Most individuals with gastroenteritis present no serious clinical conditions and do not need hospitalization, so it is difficult to isolate the causative agents and identify the sources of contamination, thus underestimating the number of cases of salmonellosis worldwide. In Brazil, during the period of 2001 to 2006, a total of 3,749 cases of typhoid fever were reported with 30 deaths, the highest number recorded in the North and Northeast regions, especially in the states of Acre (741 cases), and Bahia (671 cases) (Brazilian Ministry of Health 2009, Souza et al. 2010).

However, sporadic studies and limited information on Salmonella food contamination and microbiological investigation in foodborne infections have not clarified uncertainties regard of the salmonellosis epidemiology in Brazil (Campioni et al. 2012). Therefore, the current study evaluates the prevalence of antimicrobial susceptibility and genotypes of Salmonella spp. isolated from food and human in the state of Bahia (Northeast region) from 1996 to 2012.



This study analyzed 91 isolates of Salmonella spp. from various cities in the State of Bahia Brazil, 36 isolated from food (meat, fish, chicken and pork, cheeses, salads, rice, ready-to-eat foods and desserts). Food Isolates came from the Laboratory for Food Microbiology Research, Federal University of Bahia and the Central Public Health Laboratory of Bahia (LACEN / BA). Merchants and local health surveillance officers sent food samples to the laboratories with suspected food infection outbreaks, isolating them for identification of Salmonella. Isolated from clinical specimens (55 isolates) were isolated from human feces (n = 43), cerebrospinal fluid - CSF (n = 10), and blood (n = 2) of patients treated at four hospitals in the city of Salvador, Bahia. Invasive CSF samples were obtained from patients with meningitis and blood and stool samples were obtained from patients with gastroenteritis suspected. The information provided by hospitals or food laboratories were referring to the year of isolation, source (feces, blood, CSF or food) and city of origin.


The isolates were serotyped by the slide agglutination method using antisera prepared at the National Reference Laboratory for Enterobacteria of the Oswaldo Cruz Foundation in Rio de Janeiro (Fundação Oswaldo Cruz - FIOCRUZ-RJ).


Antimicrobial susceptibility was assessed to ampicillin 10 µg (AMP), cephalothin 30 µg (CFL), cefotaxime 30 µg (CTX), gentamicin 10 µg (GEN), tetracycline 30 µg (TET), chloramphenicol 30 µg (CLO), trimethoprim/sulfamethoxazole 1.25/23.75 µg (TMS), ciprofloxacin 5 µg (CIP), amoxicillin/clavulanate 20/10 µg (AMC), nalidixic acid 30 µg (NLX), levofloxacin 5 µg (LEV) and ceftriaxone 30 µg (CRO). The agar diffusion method according to Clinical and Laboratory Standards Institute guidelines (CLSI 2016). The study adopted strain Escherichia coli ATCC(r) 25922 as reference for quality control.


Chromosomal digests generated by XbaI were prepared and analysed as described previously (CDC 2010). Fragments were separated in 1.0% agarose gels using using CHEF-DRII apparatus (Bio-Rad Laboratories, Hercules, CA) with pulse times of 2.2 to 63.8s for 20h at 14°C and 6 V/cm in TBE buffer. Restriction profiles were analysed using GelCompar II (Applied Maths, St. Martens, Belgium). To develop the dendrogram, the study used an unweighted pair-group with arithmetic mean (UPGMA) method and the Dice similarity coefficient, with a position tolerance coefficient of 1.5%. Isolates with ≥ 90.0% relatedness were considered a cluster.


Out of the 91 samples investigated, it was possible to identify 20 serotypes (Table I) from a set of isolates from food, of which 16.5% (6 of the 36) corresponded to serotype Salmonella Infantis (Figure 1).

TABLE -I Distribution of Salmonella spp. serotypes from food isolates (N=36). 

Serotypes Food Source Nº of Isolates Total %
Salmonella Infantis Salami 1
Cooked rice 1
Pork 1 6 16.5
Cooked chicken 1
Raw chicken 1
Uncooked seasoned pork 1
Salmonella Enteritidis Peanut pave 1
Chocolate bonbon 1
Chocolate pave 1 5 13.7
Homemade cake 1
Strawberry syrup 1
Salmonella Senftenberg Uncooked pork pepperoni 1
Charru Mussel 1 3 8.2
Raw chicken 1
Salmonella Mbandaka Raw fish 1 2 5.6
Uncooked chicken file 1
Salmonella Muenchen Fresh sausage 1 2 5.6
Uncooked seasoned chicken 1
Salmonella Newport Cheese curd 2 2 5.6
Salmonella Schwarzengrund Raw salad 1 2 5.6
Raw chicken 1
Salmonella Typhimurium Raw salad 1 2 5.6
Raw beef 1
Salmonella Agona Raw chicken 1 1 2.8
Salmonella Cubana Raw chicken 1 1 2.8
Salmonella enterica subsp. enterica (O:6,7) Raw salad 1 1 2.8
Salmonella enterica subsp. enterica (O:6,7:e,h:-) Cheese curd 1 1 2.8
Salmonella enterica subsp. enterica (O:6,7:r:-) Cheese curd 1 1 2.8
Salmonella enterica subsp. enterica (O:6,8) Uncooked ground beef 1 1 2.8
Salmonella enterica subsp. enterica (O:11) Cooked salad 1 1 2.8
Salmonella Heidelbeg Cheese curd 1 1 2.8
Salmonella Kentucky Raw salad 1 1 2.8
Salmonella Livingstone Smoked meat 1 1 2.8
Salmonella Muenster Halfbeak fish 1 1 2.8
Salmonella Orion Sausage 1 1 2.8

Figure 1 Distribution of Salmonella serotypes in food and clinical samples. 

Among isolates obtained from clinical samples, this study identified 18 different serotypes. Salmonella Enteritidis was predominant with 29.1% (Figure 1). Serotype diversity was lower among clinical isolates than in foods samples (Table II).

TABLE II Distribution of serotypes of Salmonella spp. isolated from clinical samples (N= 55). 

Serotypes Sample Source Nº of Isolates Total %
Salmonella Enteritidis Stool 11 16 29.1
Salmonella Typhimurium Stool 6 9 16.4
Salmonella Infantis Stool 6 6 10.9
Salmonella Schwarzengrund Stool 6 6 10.9
Salmonella Newport Stool 3 3 5.5
Salmonella Corvallis Stool 2 2 3.7
Salmonella enterica subsp. Houtenae Blood 1 2 3.7
Salmonella Agona Stool 1 1 1.8
Salmonella Anatum Blood 1 1 1.8
Salmonella Cerro Stool 1 1 1.8
Salmonella Derby Stool 1 1 1.8
Salmonella enterica subsp. enterica (O:6,7:e,h:-) Stool 1 1 1.8
Salmonella enterica subsp. enterica (O:4,5:-:1,6) Stool 1 1 1.8
Salmonella Indiana Stool 1 1 1.8
Salmonella Mbandaka Stool 1 1 1.8
Salmonella Montevideo Stool 1 1 1.8
Salmonella Panama Stool 1 1 1.8
Salmonella Worthington CSF 1 1 1.8

CSF (Cerebrospinal Fluid)

In regards to antimicrobial resistance, 63.0% (57/91) of the isolates were sensitive to all antibiotics tested and 37.0% (34/91) resistant to at least one of the 12 antibiotics tested (Table III). High resistance rates were seen for nalidixic acid among the isolates, 32.7% and 25.0% of the clinical isolates and food, respectively. In addition, isolates from clinical samples were more resistant than isolates from food: resistance to tetracycline (25.5% vs. 8.3%), ampicillin (21.8% vs. 5.6%) and TMS (14.5% vs. 8.3%). However, amoxicillin/clavulanate, cephalothin, chloramphenicol, ceftriaxone, cefotaxime and gentamicin showed low resistance rates. All isolates were susceptible to ciprofloxacin and levofloxacin.

TABLE III Antimicrobial resistance profiles for Salmonella isolates from food and clinical samples. 

Resistance profile Nº of strain isolated from foods (n = 12/36) Nº of strain isolated from clinical samples (n = 22/55)
NLX 6 6
NLX* 1

GEN (gentamicin); NLX (nalidixic acid); TET (tetracycline); TMS (trimethoprim/sulfamethoxazole); AMP (ampicillin); AMC (amoxicillin/clavulanate); CLO (chloramphenicol); CFL (cephalothin); CRO (ceftriaxone); CTX (cefotaxime); *Intermediate sensitivity.

Among resistant isolates, this study identified 15 patterns among resistant isolates, four of which were found only in isolates from foods (GEN, NLX/TET, NLX/TMS and AMP/TET/TMS). Nine patterns were identified only in clinical isolates (NLX, TET, NLX/TET, TET/TMS, AMP/NLX/TET, AMP/TET/TMS, AMP/NLX/TMS, AMP/AMC/CLO/TET and AMP/GEN/NLX/TET), and two patterns were common to both groups (NLX and AMP/CFL/CRO/CTX/TET/TMS/NLX). The most frequently observed pattern was NLX identified among Salmonella Enteritidis isolates from food (16.0%) and clinical samples (11.0%). Overall, antibiotic resistance between clinical and food isolates showed that clinical isolates are more resistant to antibiotics (Figure 2). The Salmonella Schwarzengrund showed multidrug resistance with resistance to phenotype AMP/CFL/CRO/CTX/TET/TMS/NLX found in both the food (3.0%) and clinical isolates (9.0%).

Figure 2 Resistance of Salmonella serotypes in food and clinical samples to a variety of antimicrobials. X-axis represents the number of antimicrobials to which strains are resistant. Isolates from human and food were grouped according to the number of antimicrobial agents they were resistant. 

The study identified 47 PFGE types, including 11 clonal groups, ranging from 2 to 20 isolates. The isolates were grouped in two major clusters designated as PFGE A (20 isolates) and PFGE B (11 isolates). In the PFGE A cluster, 19 isolates of Salmonella Enteritidis and one Salmonella Infantis exhibited similarity above 90.0% (Figure 3).

Figure 3 Dendrogram representing genetic relationships among Salmonella Enteritidis (a) strains based on PFGE. The data were sorted by the UPGMA method. NLX (nalidixic acid). 

The PFGE A cluster included isolates from food (4), feces (11) and CSF (5) identified from 1996 to 2011 in different localities of the Bahia State. The PFGE B cluster contained 11 isolates of Salmonella Infantis (food [7] and feces [4]) (Figure 4b). The PFGE C cluster contained seven isolates of Salmonella Schwarzengrund (food [1] and feces [6]) (Figure 4c). In total, 85.7% of food samples were of animal origin and identified over a three-year period (2009-2011).

Figure 4 Dendrogram representing genetic relationships among Salmonella Infantis (b) and Salmonella Schwarzengrund (c) strains based on PFGE. The data were sorted by the UPGMA method. GEN (gentamicin); NLX (nalidixic acid); TET (tetracycline); TMS (trimethoprim/sulfamethoxazole); AMP (ampicillin); CFL (cephalothin); CRO (ceftriaxone); CTX (cefotaxime). 


Salmonella is an environmentally persistent pathogen that that survives and multiplies in diverse environments, and is one of the most common bacteria in food-borne diseases in humans. The CDC estimated that, each year, there are approximately one million cases of salmonellosis caused by non-typhoidal Salmonella (CDC 2011). In Brazil, salmonellosis has been substantially underestimated, thus, this study brings important contribution to public health in Brazil and all over the world.

The most frequently observed serotypes in food samples are similar to those reported in other regions of Brazil and around the world (Murakami et al. 2007, EFSA 2011, Pulido-Landinez et al. 2013). Of 16 serotypes identified among food isolates, Salmonella Infantis was the most frequent serovar (16.0%), followed by Salmonella Enteritidis (14.0%). In regards to clinical samples, the predominant was Salmonella Enteritidis (29.0%), followed by Salmonella Typhimurium (16.0%), Salmonella Infantis (11.0%) and Salmonella Schwarzengrund (11.0%).

Derived food products such as poultry meat and eggs are the main forms of infection by Salmonella spp. in humans (Gantois et al. 2009). A large number of serovars of Salmonella are pathogenic for humans, so the ability to genus Salmonella to cause a disease depends on several virulence determinant factors. Therefore, there is a less diverse serotypes among clinical isolates than food samples. Higher frequencies of Salmonella Enteritidis and Salmonella Typhimurium were also found in other studies in Brazil and elsewhere, and they pose a threat to human health (Silva and Duarte 2002, Mürmann et al. 2009).

Salmonella Enteritidis was the most common serotype in the country. In 1993, Salmonella Enteritidis accounted for approximately 10.0% of the Salmonella serotypes isolated from human samples, and from then on it became the dominant serotype in both human and non-human samples (Taunay et al. 1996). In 1994 and 1995, it accounted for 43% and 65% of Salmonella Enteritidis isolated from humans, respectively, in Sao Paulo (Taunay et al. 1996). Modifications in serotype distribution reflect changes in animal production and the spreading of new serotypes due to world trade. Of a particular concern is the emergence of resistance to multiple antimicrobials. Resistance to quinolones, such as nalidixic acid, has become a significant problem for public health and has been increasing in recent years, mainly due to the liberal use of quinolone drugs in aquaculture and industrial animal production (Oliveira et al. 2005). In contrast, antibiotics such as aminoglycosides, florfenicol and nalidixic acid, not commonly used in animal health and production showed no resistance (Piras et al. 2011, Li et al. 2014).

Antimicrobial resistance to at least one antibiotic was identified in 40.0% and 33.0% of clinical and food isolates, respectively. In the Southern Brazil, 82.0% of Salmonella samples of fresh pork sausage were resistant to at least one antibiotic tested (Mürmann et al. 2009). In the US, 47.0% of Salmonella Heidelberg isolates from human patients were resistant to antimicrobials (Han et al. 2011). Salmonella multidrug resistance is a growing concern since it limits treatment options for invasive disease, and it could lead to the transfer of resistance to other pathogenic organisms. In this study, a relative high frequency of multidrug-resistant Salmonella (25.0% of clinical isolates and 11.0% of food isolates) represents an additional public health risk, and Salmonella Schwarzengrund, in special, seemed to be resistant to six or more antibiotics.

The current gold standard method used to evaluate relatedness among Salmonella strains is PFGE has been established as important for the discrimination, characterization, and investigation of food-borne outbreaks (CDC 2010). Thus, PFGE fingerprinting shows several foods isolates that clustered with clinical isolates, mainly Salmonella Enteritidis and Salmonella Infantis among cities more than 500 miles apart, with persistence and geographical transmission in the Bahia State. However, other studies have described the limited discriminatory power of PFGE for Salmonella Enteritidis (CDC 2010, Mezal et al. 2014). A combination of different typing methods may be better to achieve best resolution for the discrimination of highly clonal organisms.

The combined use of different patterns of resistance and genotypes to analyze pathogenic isolates from food has been a useful way to identify the origins of outbreaks, establish sources of contamination, determine the etiological agents responsible for outbreaks, understand the epidemiology of food-borne disease and facilitate further studies on the spread of antibiotic-resistant isolates. This study provides data that indicate a probable transmission of Salmonella from food sources to cause infections in humans, establishing a serious risk to public health.

In this study, the most prevalent serotype in food samples was Salmonella Infantis and clinical samples of Salmonella Enteritidis. The most frequently observed resistance profiles were the NLX (nalidixic acid) and multi-resistance AMP / CFL / CRO / CTX / TET / TMS / NLX * (ampicillin, cephalothin, ceftriaxone, cefotaxime, tetracycline and trimethoprim / sulfametazol, nalidixic acid), common to isolates from food and clinical samples. In addition, clonal groups, found among strains epidemiologically unrelated, suggested that some isolated persisted in the environment over the years in different cities of Bahia. Thus, our results indicate that the clonal groups were both causing diseases and food contamination, emphasizing the need to maintain a system of surveillance for foodborne disease.


The authors would like to thank to Dalia dos Prazeres, Laboratório de Enterobactérias da Fundação Oswaldo Cruz, Rio de Janeiro, Brazil for serotyping the Salmonella isolates.


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Received: July 13, 2016; Accepted: December 06, 2016

Correspondence to: Andrea Lobo Miranda E-mail:

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