Antimicrobial drug resistance and genetic properties of Salmonella enterica serotype Enteritidis circulating in chicken farms in Tunisia

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia

ABSTRACT

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

HIGHLIGHTS

A Public Health Insight into Salmonella in Poultry in Africa: A Review of the Past Decade: 2010-2020

Poultry is a cheap source of animal protein and constituent of diets in Africa. Poultry can serve as a reservoir for Salmonella and cause food-borne infections in humans. This review describes Salmonella contamination of food, poultry, and the farming environment, antimicrobial resistance profiles, and serotypes of Salmonella, as well as the farming systems, antimicrobial use (AMU), hygiene, and husbandry conditions used to rear poultry in Africa. Using the PRISMA (preferred reporting items for systematic reviews and meta-analysis) guidelines, PubMed, Science Direct, and Web of Science databases were searched using a set of predefined keywords. Full-length research articles in English were examined for the period 2010-2020 and relevant information extracted for the narrative synthesis. Of the articles that met the inclusion criteria, 63.1% were conducted on farms and among households, while 36.9% were undertaken at government-controlled laboratories, which quarantine imported birds, processing plants, and retail outlets. The farming systems were intensive, semi-intensive, and extensive. AMU was described in 11.5% of the studies and varied within and across countries. Multidrug-resistant (MDR) Salmonella isolates were detected in 30 studies and the prevalence ranged from 12.1% in Zimbabwe to 100% in Egypt, Ethiopia, Nigeria, Senegal, and South Africa. A total of 226 different Salmonella serotypes were reported. Twenty-four (19.7%) of the studies reported food-borne Salmonella contamination in eggs, poultry, and poultry products at retail outlets and processing plants. The apparent extensive use of antimicrobials and circulation of MDR Salmonella isolates of various serotypes in Africa is a concern. It is important to implement stricter biosecurity measures on farms, regulate the use of antimicrobials and implement surveillance systems, in addition to food safety measures to monitor the quality of poultry and poultry products for human consumption.

Antimicrobial resistance and virulence genes in Salmonella enterica serovars isolated from droppings of layer chicken in two farms in Nigeria

AIM

This study aimed to investigate the isolation rate, antibiotic resistance, and virulence genes of Salmonella enterica serovar from two commercial farms in Nigeria.

METHODS AND RESULTS

Salmonella isolation was performed according to the United States Food and Drug Agency (USFDA) method. Serotyping, antimicrobial susceptibility testing, detection of resistance and virulence genes were done using the Kauffman-White Scheme, disc diffusion, minimum inhibitory concentration, and real-time polymerase chain reaction techniques. Salmonella serovars were isolated from only farm A at 22/50 (44.0%) while none were isolated from farm B. Salmonella Typhi, 9 (40.9%); Salmonella Typhimurium, 2 (9.1%), Salmonella Enteritidis, 2 (9.1%), Salmonella Pullorum, 1 (4.5%), Salmonella Kentucky, 4 (18.2%) were identified while 4 (18.2%) were untypable. Sixteen isolates (72.7%) showed multiple drug resistance and 17 different resistance profile types with AMP-CHL-TRM-SXT as the most prevalent pattern. Resistance genes (blaTEM, 12/22 (54.5%) and virulence genes (InvA, sopB, mgtC, and spi4D, 22/22 (100.0%), ssaQ, 16/22 (72.7%), and spvC, 13/22 (59.1%) were found, while blaSHV, blaCTX-M, floR, tetA, tetB, tetG, and LJSGI-1 genes were absent.

CONCLUSION

Pathogenic Salmonella were isolated from the chicken droppings in this study. Most of these strains were resistant to antibiotics and possessed characteristics of virulence.

SIGNIFICANCE AND IMPACT OF THE STUDY

Chicken droppings from this study area contained pathogenic strains of Salmonella and a rare occurrence of Salmonella Typhi. The study revealed that the environment and the food chain could be at risk of contamination of highly virulent and antimicrobial-resistant strains of Salmonella. These could affect the profitability of the poultry industry and food consumption. There is a need for caution in indiscriminate disposal of poultry waste and the use of uncomposted chicken droppings in soil amendment.

Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing

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Antimcrobial resistance genes, virulence factors and prophage sequences were studied in WGS of 45 Salmonella Enteritidis from different sources.

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WGS is most powerful tool for determining genomic variation in S. Enteritidis.

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Two major lineages of S. Enteritidis were detected in Tunisia.

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Missense mutations identified in virulence genes were mostly detected in lineage B.

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Salmon118970_sal3 and RE_2010 phages were detected in lineage A and lineage B, respectively.

Salmonella Enteritidis causes a major public health problem in the world. Whole genome sequencing can give us a lot of information not only about the phylogenetic relatedness of these bacteria but also in antimicrobial resistance and virulence gene predictions. In this study, we analyzed the whole genome data of 45 S. Enteritidis isolates recovered in Tunisia from different origins, human, animal, and foodborne samples. Two major lineages (A and B) were detected based on 802 SNPs differences. Among these SNPs, 493 missense SNPs were identified. A total of 349 orthologue genes mutated by one or two missense SNPs were classified in 22 functional groups with the prevalence of carbohydrate transport and metabolism group. A good correlation between genotypic antibiotic resistance profiles and phenotypic analysis were observed. Only resistant isolates carried the respective molecular resistant determinants. The investigation of virulence markers showed the distribution of 11 Salmonella pathogenicity islands (SPI) out of 23 previously described. The SPI-1 and SPI-2 genes encoding type III secretion systems were highly conserved in all isolates except one. In addition, the virulence plasmid genes were present in all isolates except two. We showed the presence of two fimbrial operons sef and ste previously considered to be specific for typhoidal Salmonella. Our collection of S. Enteritidis reveal a diversity among prophage profiles. SNPs analysis showed that missense mutations identified in fimbriae and in SPI-1 and SPI-2 genes were mostly detected in lineage B.

In conclusion, WGS is a powerful application to study functional genomic determinants of S. Enteritidis such as antimicrobial resistance genes, virulence markers and prophage sequences. Further studies are needed to predict the impact of the missenses SNPs that can affect the protein functions associated with pathogenicity.

Occurrence and antimicrobial resistance of Salmonella isolated from retail meats in Anhui, China

Salmonella is considered one of the major foodborne pathogens associated with severe infections. Little attempt has been focused on the distribution of Salmonella in retail meats and the analysis of its phenotypic characteristics in Anhui Province. The aim of this study was to characterize the prevalence of Salmonella serovars, antimicrobial susceptibility, antimicrobial resistance genes, and virulence genes in Salmonella recovered from retail meats in Anhui, China. Out of the 120 samples collected from supermarket chains and open-air markets, 16 samples (13.3%) were positive for Salmonella, of which Salmonella enterica serovars Enteritidis and Typhimurium were the common serotypes. Significant differences in incidence were found between supermarket chains and open-air markets (p < 0.05). Overall, all 16 isolates were resistant to at least two tested antimicrobials, while 12 isolates showed multiple antimicrobial resistant phenotypes. High resistance was observed for ampicillin (87.5%), doxycycline (75.0%), and tetracycline (62.5%). The sul2 was detected in all isolates, and the aac(6')-Ib-cr (93.8%) and the tetA (81.3%) were predominant in 10 resistance genes conferring five classes of antimicrobials. In addition, the correlation between resistance phenotypes and genes of tetracyclines and aminoglycosides was more than 80%. Interestingly, all the Salmonella isolates contained the genes mogA, mgtC, sopB, and spvB, whereas the siiE was variably represented. The findings in this study showed high prevalence, antimicrobial resistance, and the existence of virulence genes, suggesting that effective measures are required to ensure microbial safety from retail meats.

Antimicrobial Use and Resistance in Agriculture and Food Production Systems in Africa: A Systematic Review

In Africa, there is dearth of information on antimicrobial use (AMU) in agriculture and food production systems and its consequential resistance in pathogens that affect animal, human and environmental health. Data published between 1980 and 2021 on the magnitude of AMU and AMR in agriculture and food productions systems in Africa were reviewed. Data from 13-27 countries in Africa indicate that 3558-4279 tonnes of antimicrobials were used in animals from 2015 to 2019. Tetracyclines and polypeptides contributed the largest proportion of antimicrobials used. Cattle and poultry production account for the largest consumption of antimicrobials in Africa. Although limited studies have reported AMR in crops, fish and beekeeping, AMR from a variety of farm animals has been substantially documented in Africa. Some countries in Africa have developed policies/plans to address AMU and AMR in agriculture and food production systems; however, their enforcement is challenged by weak regulations. In conclusion, although there is limited information on the quantities of antimicrobials used in agriculture and food production system, the levels of AMR are high. There is a need to strengthen regulatory authorities with a capacity to monitor AMU in agriculture and food production systems in Africa.

Identification and characterization of multidrug-resistant ESBL-producing Salmonella enterica serovars Kentucky and Typhimurium isolated in Tunisia CTX-M-61/TEM-34, a novel cefotaxime-hydrolysing β-lactamase of Salmonella

AIMS

Molecular characterization of extended-spectrum β-lactamases (ESBLs) among Salmonella Kentucky and Typhimurium isolates: partial sequence analysis of the types of β-lactamases found in these isolates, clonality, resistance and supposed emergence of ESBL-producing strains.

METHODS AND RESULTS

A retrospective study surveyed the ESBLs occurring in a total of 1404 Salmonella Kentucky and Typhimurium isolates collected over a 5-year period in Tunisia. Antimicrobial susceptibility tests, ESBL phenotype determination (double-disc synergy) were performed. Polymerase chain reaction assays were used for the detection of β-lactamase genes (bla_TEM , bla_SHV , bla_OXA-1 and bla_CTX-M ), class 1 and class 2 integrases (intI1 and intI2) and the 3' conserved segment (3'-CS) of class 1 integron (qacEΔ1+sul1). Sequencing of amplicons of β-lactamase genes was performed. Percentage of 9.8 of the isolates (S. Kentucky = 117, S. Typhimurium = 20) were either resistant to penicillin and had decreased susceptibility to cefotaxime or had a positive double-disc synergy test result. Polymerase chain reaction detected that these isolates harboured one or more β-lactamase genes (bla_TEM , bla_SHV , bla_OXA-1 or bla_CTX-M ). TEM-1, TEM-34, CTX-M15, CTX-M9 and CTX-M61 type ESBLs were identified through sequencing. The novel Salmonella cefotaxime-hydrolysing β-lactamase, CTX-M61/TEM-34, detected in this study showed the emergence of new CTX-M-type ESBLs in Tunisia. There were found 33 different multidrug resistance (MDR) patterns.

CONCLUSION

These findings highlighted the proliferation of ESBLs and MDR in Salmonella Kentucky and Typhimurium isolates from numerous regions and sources in Tunisia, indicating an emerging public health concern.

SIGNIFICANCE AND IMPACT OF THE STUDY

For the first time CTX-M-61/TEM-34, a novel cefotaxime-hydrolysing β-lactamase of Salmonella had been detected.

Virulence and resistance genes profiles and clonal relationships of non-typhoidal food-borne Salmonella strains isolated in Tunisia by whole genome sequencing

Whole genome sequencing (WGS) has made impressive progress in the field of molecular biology. Its most common application for public health is in the area of surveillance of food-borne diseases. WGS has the potential for providing a large amount of information, such as the identification of the strain type, the characterization of antibiotic resistance and virulence, and phylogeny. In our study, thirty-nine non-typhoidal Salmonella strains were isolated from diverse sources in Tunisia. Non-typhoidal Salmonella are among the most common pathogens contaminating food animals. The presence of virulence and antimicrobial resistance determinants in those strains were investigated using whole genome sequencing (WGS) and appropriate data analysis. The genomes were screened for several Salmonella virulence genes using the Virulence Factor Database VFDB. Twelve different virulence profiles, which correspond to the 12 identified serovars, were recognized. Several antimicrobial resistance genes were also detected: aac (6')-Iaa, sul1, tetA, bla-TEM and qnrS genes. Phylogenetic relationships among the strains were further assessed by a cgMLST analysis. The resulting phylogenetic tree consisted of several clusters consistently with the in silico multilocus sequence typing (MLST) and serotyping. Our findings demonstrated that WGS and subsequent data analysis provided an accurate tool for genetic characterization of bacterial strains compared to usual molecular typing techniques. To the best of our knowledge, this is the first report of an application of WGS for genetic characterization of food-borne Tunisian strains.

Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia

We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtyping Salmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175 Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-five Salmonella Enteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification of Salmonella Enteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey of Salmonella Enteritidis lineages in Tunisia using WGS.

Association of Virulence and Antibiotic Resistance in Salmonella-Statistical and Computational Insights into a Selected Set of Clinical Isolates

The acquisition of antibiotic resistance (AR) by foodborne pathogens, such as Salmonella enterica, has emerged as a serious public health concern. The relationship between the two key survival mechanisms (i.e., antibiotic resistance and virulence) of bacterial pathogens is complex. However, it is unclear if the presence of certain virulence determinants (i.e., virulence genes) and AR have any association in Salmonella. In this study, we report the prevalence of selected virulence genes and their association with AR in a set of phenotypically tested antibiotic-resistant (n = 117) and antibiotic-susceptible (n = 94) clinical isolates of Salmonella collected from Tennessee, USA. Profiling of virulence genes (i.e., virulotyping) in Salmonella isolates (n = 211) was conducted by targeting 13 known virulence genes and a gene for class 1 integron. The association of the presence/absence of virulence genes in an isolate with their AR phenotypes was determined by the machine learning algorithm Random Forest. The analysis revealed that Salmonella virulotypes with gene clusters consisting of avrA, gipA, sodC1, and sopE1 were strongly associated with any resistant phenotypes. To conclude, the results of this exploratory study shed light on the association of specific virulence genes with drug-resistant phenotypes of Salmonella. The presence of certain virulence genes clusters in resistant isolates may become useful for the risk assessment and management of salmonellosis caused by drug-resistant Salmonella in humans.

Quinolone resistance among Salmonella Kentucky and Typhimurium isolates in Tunisia: first report of Salmonella Typhimurium ST34 in Africa and qnrB19 in Tunisia

AIMS

Characterization of quinolone-resistant Salmonella Kentucky and Typhimurium isolates in Tunisia from various sources, detection of some plasmid-mediated quinolone resistance genes and the genetic relatedness.

METHODS

A total of 1404 isolates of S. Kentucky (n = 1059)/S. Typhimurium (n = 345) from various sources from all over Tunisia were tested for quinolone resistance by disk diffusion method. Minimum inhibitory concentrations of nalidixic acid, ciprofloxacin and ofloxacin were determined. Quinolone-resistant isolates were screened for plasmid-mediated quinolone-resistance genes (qnrA,qnrB,qnrS, aac(6')-Ib-cr and qepA) by polymerase chain reaction (PCR). Mutations in the quinolone-resistance-determining regions of the gyrA and parC genes were detected by PCR and DNA sequencing. Pulsed-field gel electrophoresis and multilocus sequence typing were accomplished for isolates harbouring plasmid-mediated quinolone-resistance genes.

RESULTS

According to our selection criteria (NAL = resistance phenotype; CIP = resistant with diameter 0, or intermediate), only 63 S. Kentucky/41 S. Typhimurium isolates were investigated: 49% (5/104) were multidrug resistant. Two S. Typhimurium isolates harboured qnrB19 with different PFGE profiles. A mutation was detected in the gyrA gene for each of these two isolates. MLST revealed the presence of ST313 and ST34, an endemic sequence type.

CONCLUSION

Our study highlights the presence of quinolone multidrug-resistant Salmonella in humans and animals in Tunisia. This is the first report of S. Typhimurium ST34 in Africa and qnrB19 in Tunisia.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that describes not only the current epidemiological situation of the quinolone resistance in S. Kentucky and Typhimurium isolated from various sources and regions in Tunisia, but also, the genetic resistance determinants associated with phenotypic antibiotic resistance and the molecular mechanisms of their quinolone-resistance. Also, we provide the first report of S. Typhimurium ST34 in Africa, and the first report of qnrB19 in Salmonella in Tunisia.

The complete genome of lytic Salmonella phage vB_SenM-PA13076 and therapeutic potency in the treatment of lethal Salmonella Enteritidis infections in mice

S. Enteritidis continues to be the most common pathogen of farm animals and a major public health burden worldwide. Using bacteriophages is a potential alternative to antibiotics against S. Enteritidis infection. In this study, the genome analysis of the lytic phage vB_SenM-PA13076 (PA13076) infecting S. Enteritidis revealed a linear, double-stranded DNA genome, which comprised of 52,474 bp and contained 69 ORFs. It belongs to the order Caudovirales; family Myoviridae, genus unclassified. The genes coded for DNA packaging, phage structural proteins, lysis components, DNA recombination, regulation, modification, and replication. No bacterial virulence or drug-resistance genes were detected. The phage PA13076 protected mice from a lethal dose of S. Enteritidis 13076Amp (5 × 108 CFU) by reducing the concentration of bacterial cells in blood, intestine, liver, spleen, and kidney. The phage PA13076 achieved at least 2.5 log reductions of S. Enteritidis cells in infected mice within 24 h (P < 0.05) when compared to the organs of control mice. The data also indicated that phage PA13076 could rapidly enter the blood and four organs of infected mice, remaining therein at concentrations of>104 PFU/g for at least 72 h. These results show that phage PA13076 has definite potential as an antibacterial therapeutic agent for attenuating S. Enteritidis infections.

Antimicrobial resistance and genetic diversity of Salmonella enterica from eggs

Salmonella enterica is a common foodborne pathogen responsible for major global health problems such as paratyphoid fever and gastroenteritis. Here, we report the prevalence, antibiotic resistance phenotypes, serotypes, and molecular subtyping of Salmonella isolated from eggs in Guangdong, China. Out of 1,000 egg samples, 54 (5.40%) were positive. S. Enteritidis made up the largest proportion of samples with 11 serotypes. Antimicrobial susceptibility test indicated that most strains were resistant to β-lactam, aminoglycoside, and tetracycline antibiotics (27.00%-40.00%). There were 37 STs based on MLST typing. MLST and ERIC-PCR classified 54 isolates into three and five clusters, respectively, which revealed the genetic relatedness and diversity. In conclusion, frequent monitoring of eggs for Salmonella, antibiotic resistance profiles and genetic diversity is essential for improving food safety.

Occurrence and Phenotypic and Molecular Characterization of Antimicrobial Resistance of Salmonella Isolates from Food in Tunisia

HIGHLIGHTS

Multidrug-resistant Salmonella isolates have been recovered from food in Tunisia. Salmonella isolates from food are resistant to fluoroquinolones and cephalosporins. Surveillance of the antimicrobial susceptibility of foodborne bacteria is needed in Tunisia.

Establishment of a Multiplex Loop-Mediated Isothermal Amplification Method for Rapid Detection of Sulfonamide Resistance Genes (sul1, sul2, sul3) in Clinical Enterobacteriaceae Isolates from Poultry

Antimicrobial resistance genes play an important role in mediating resistance to sulfonamide in Gram-negative bacteria. While PCR is the current method to detect sulfonamide resistance genes (sul1, sul2, sul3), it is time-consuming and costly and there is an urgent need to develop a more convenient, simpler and rapid test for the sul. In this study, we describe a multiplex loop-mediated isothermal amplification (m-LAMP) assay we developed for the rapid and simultaneous detection of three sul. This m-LAMP assay successfully detected seven reference strains with different sul genotypes, but was negative for nine sul-negative reference strains. The m-LAMP products were verified by HinfI restriction enzyme digestion and the detection limit of the test was 0.5 pg genomic DNA per reaction. Testing 307 sulfonamide-resistant Enterobacteriaceae clinical isolates with the m-LAMP revealed all were positive for the sul with sul2 (79.5%) and sul1 (64.5%) being most prevalent, and sul3 the least (12.1%). Of the Enterobacteriaceae isolates tested, the Salmonella Indiana, a newly emerging serovar resistant to numerous antimicrobials, were most commonly positive with 33% having sul3.

Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China

The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR) to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs) at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase (intI1) gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3–V4 regions using MiSeq sequencing. The results indicated Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes as the dominant phyla in the water samples from the Weihe River. Higher abundances of bla_TEM, strB, aadA, and intI1 genes (10³ to 10⁵ copies/mL) were detected in the surface water samples compared with the relatively low abundances of strA, mecA, and vanA genes (0–1.94 copies/mL). Eight bacterial genera were identified as possible hosts of the intI1 gene and three ARGs (strA, strB, and aadA) based on network analysis. The results suggested that the bacterial community structure and horizontal gene transfer were associated with the variations in ARGs.

Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda

Non-typhoidal Salmonella (NTS) are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE). Phenotypically resistant isolates (n = 54) were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4%) of the 54 resistant isolates carried at least one of the seven genes (blaTEM-1,cmlA, tetA, qnrS,sul1,dhfrI,dhfrVII) identified by PCR and six (11%) carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia

Salmonella enterica is a major cause of gastroenteritis and foodborne illness in Australia where notification rates in the state of Queensland are the highest in the country. S. Enteritidis is among the five most common serotypes reported in Queensland and it is a priority for epidemiological surveillance due to concerns regarding its emergence in Australia. Using whole genome sequencing, we have analysed the genomic epidemiology of 217 S. Enteritidis isolates from Queensland, and observed that they fall into three distinct clades, which we have differentiated as Clades A, B and C. Phage types and MLST sequence types differed between the clades and comparative genomic analysis has shown that each has a unique profile of prophage and genomic islands. Several of the phage regions present in the S. Enteritidis reference strain P125109 were absent in Clades A and C, and these clades also had difference in the presence of pathogenicity islands, containing complete SPI-6 and SPI-19 regions, while P125109 does not. Antimicrobial resistance markers were found in 39 isolates, all but one of which belonged to Clade B. Phylogenetic analysis of the Queensland isolates in the context of 170 international strains showed that Queensland Clade B isolates group together with the previously identified global clade, while the other two clades are distinct and appear largely restricted to Australia. Locally sourced environmental isolates included in this analysis all belonged to Clades A and C, which is consistent with the theory that these clades are a source of locally acquired infection, while Clade B isolates are mostly travel related.