Multiplex PCR for distinguishing the most common phase-1 flagellar antigens of Salmonella spp

Growth assessment of Salmonella enterica multi-serovar populations in poultry rinsates with commonly used enrichment and plating media

Isolation of Salmonella from enrichment cultures of food or environmental samples is a complicated process. Numerous factors including fitness in various selective enrichment media, relative starting concentrations in pre-enrichment, and competition among multi-serovar populations and associated natural microflora, come together to determine which serovars are identified from a given sample. A recently developed approach for assessing the relative abundance (RA) of multi-serovar Salmonella populations (CRISPR-SeroSeq or Deep Serotyping, DST) is providing new insight into how these factors impact the serovars observed, especially when different selective enrichment methods are used to identify Salmonella from a primary enrichment sample. To illustrate this, we examined Salmonella-positive poultry pre-enrichment samples through the selective enrichment process in Tetrathionate (TT) and Rappaport Vassiliadis (RVS) broths and assessed recovery of serovars with each medium. We observed the RA of serovars detected post selective enrichment varied depending on the medium used, initial concentration, and competitive fitness factors, all which could result in minority serovars in pre-enrichment becoming dominant serovars post selective enrichment. The data presented provide a greater understanding of culture biases and lays the groundwork for investigations into robust enrichment and plating media combinations for detecting Salmonella serovars of greater concern for human health.

Genotypic virulence profiles and associations in Salmonella isolated from meat samples in wet markets and abattoirs of Metro Manila, Philippines

BACKGROUND

Salmonella are pathogenic foodborne bacteria with complex pathogenicity from numerous virulence genes housed in Salmonella pathogenicity islands (SPIs), plasmids, and other gene cassettes. However, Salmonella virulence gene distributions and mechanisms remain unestablished. In the Philippines, studies mainly report Salmonella incidences and antimicrobial resistance, but little to none on virulence profiles, their associations to animal sources, collection sites and Salmonella serogroups. Hence, a total of 799 Salmonella isolates, previously obtained from pig, cow, and chicken meat samples in wet markets and abattoirs (wet markets: 124 chicken, 151 cow, and 352 pig meat isolates; abattoirs: 172 pig tonsil and jejunum isolates) in Metro Manila, Philippines, were revived and confirmed as Salmonella through invA gene polymerase chain reaction (PCR). Isolates were then screened for eight virulence genes, namely avrA, hilA, sseC, mgtC, spi4R, pipB, spvC and spvR, by optimized multiplex PCR and significant pair associations between virulence genes were determined through Fisher's exact test. Gene frequency patterns were also determined. Salmonella serogroups in addition to animal sources and location types were also used to predict virulence genes prevalence using binary logistic regression.

RESULTS

High frequencies (64 to 98%) of SPI virulence genes were detected among 799 Salmonella isolates namely mgtC, pipB, avrA, hilA, spi4R and sseC, from most to least. However, only one isolate was positive for plasmid-borne virulence genes, spvC and spvR. Diversity in virulence genes across Salmonella serogroups for 587 Salmonella isolates (O:3 = 250, O:4 = 133, O:6,7 = 99, O:8 = 93, O:9 = 12) was also demonstrated through statistical predictions, particularly for avrA, hilA, sseC, and mgtC. mgtC, the most frequent virulence gene, was predicted by serogroup O:9, while sseC, the least frequent, was predicted by serogroup O:4 and chicken animal source. The highest virulence gene pattern involved SPIs 1-5 genes which suggests the wide distribution and high pathogenic potential of Salmonella. Statistical analyses showed five virulence gene pair associations, namely avrA and hilA, avrA and spi4R, hilA and spi4R, sseC and spi4R, and mgtC and pipB. The animal sources predicted the presence of virulence genes, sseC and pipB, whereas location type for hilA and spi4R, suggesting that these factors may contribute to the type and pathogenicity of Salmonella present.

CONCLUSION

The high prevalence of virulence genes among Salmonella in the study suggests the high pathogenic potential of Salmonella from abattoirs and wet markets of Metro Manila, Philippines which poses food safety and public health concerns and threatens the Philippine food animal industry. Statistical associations between virulence genes and prediction analyses across Salmonella serogroups and external factors such as animal source and location type and presence of virulence genes suggest the diversity of Salmonella virulence and illustrate determining factors to Salmonella pathogenicity. This study recommends relevant agencies in the Philippines to improve standards in food animal industries and increase efforts in monitoring of foodborne pathogens.

Serological structure and antimicrobial susceptibility of Salmonella isolated from human and food items in Southern provinces of Viet Nam

The article suggests currently relevant data on the serogroup structure and antibiotic susceptibility of Salmonella strains isolated in the southern provinces of the Socialist Republic of Vietnam. The study included 189 Salmonella strains, isolated from feces of human with acute diarrhea (86 strains) and pork samples (103 strains). Serological identification to O-group was fulfilled by slide agglutination with O- and H- antisera and multiply PCR to detect H phase-1 and phase-2. Antimicrobial susceptibility testing was made by disk-diffusion method according EUCAST (version 2019). Strains isolated from human predominantly belonged to O4 group (69,8%), percentage of other serogroups fluctuated from 1,2% (rare group O16) to 11,6 % (O9). About a half of strains (44,7%) isolated from pork turned to belong to О3,10 serogroup (versus 7,0 % of strains from human beings). Such serogroups as О7, О4 and О8 happened to be less frequent (22,3%, 14,6% and 13,6%, respectively). The singular strains belonged to serogroups О9, О13 and О18. Whatever the isolation source about 80% Salmonella strains turned to be resistant to antibiotics from different antimicrobial groups (not to carbapenems): 67,0% were resistant to tetracycline, about a half of strains (54,0, 47,1 and 46,6%) - to pefloxacin, ampicillin and chloramphenicol, up to 40% - to trimetoprime/sulfametoxazole and nalidixic acid. The proportion of strains resistant to ceftriaxone and gentamycin happened to look obviously bigger in those of human origin versus those of pork origin: 12,8% vs.1,0% and 30,2 vs 1,9%, respectively. More over, 62,8% strains of human origin and 43,7% - from pork demonstrated multidrug resistance (to 3 and more antimicrobial groups). The simultaneous resistance to 6 antimicrobial groups was detected much more frequently in Salmonella strains isolated from human beings than in those isolated from pork samples (15,1% vs. 1,0%, respectively) as well. Multidrug resistance demonstrated strains of different serovars, predominantly S. Typhimurium (36,4%). Predominant multidrug resistance phenotype AMP, TE, QN, C, SXT (30,3%) was revealed in serovars S. Typhimurium, S. Bredeney, S. Corvallis, S. Give, S. London, S. Rissen, S. Meleagridis. So, Salmonella strains having been isolated in southern provinces of Viet Nam demonstrated the resistance to fluoroquinolones and cephalosporins that given the simultaneous loss of susceptibility to the old antimicrobials (ampicillin, chloramphenicol, trimethoprim/ sulfametoxazole) crucially restricts the list of medicines potent to treat complicated salmonellosis cases.

Using genetic markers for detection and subtyping of the emerging Salmonella enterica subspecies enterica serotype Muenchen

Non-typhoidal Salmonella (NTS) poses a global threat to public health. Poultry, one of the main reservoirs of NTS, is usually not clinically affected by most NTS, yet the economic losses to the poultry industry due to control and mitigation efforts, and due to negative publicity can be tremendous.

NTS strains are routinely characterized into serotypes in a time-consuming, labor-intensive multistep process that requires skilled personnel. Moreover, the discriminatory power of serotyping is limited compared to other subtyping methods. Whole-genome sequence data enable the identification of genetic variation within serotypes. However, sequencing is often limited by available resources, and analyzing and interpreting the genetic data may be time-consuming. Source tracing during epidemiological outbreak investigations requires rapid and efficient characterization of strains to control pathogen spread. Here we designed a multiplex polymerase chain reaction (PCR) assay for the detection of genetic variants of Salmonella Muenchen, a serotype that has emerged in Israel in the last 3 yr in both clinical human cases and different hosts. Test sensitivity of 99.21% and specificity of 94 to 100% were determined using in-silico PCR with a dataset of 18,282 NTS assemblies from 37 NTS serotypes. Similarly, test sensitivity of 100% and specificity of 96.2 to 100% were determined in-vitro with 120 NTS isolates of 52 serotypes. Moreover, the test enabled differentiation between the common sequence types of serotype Muenchen using both approaches. As opposed to traditional serotyping and other subtyping methods, the designed test allows for rapid and cost-efficient detection of the emerging S. Muenchen serotype and its variants in a single step. Future development of similar assays for other dominant serotypes may help reduce the time and cost required for detection and initial characterization of dominant NTS strains. Overall, these tests will be beneficial to both public health and for reducing of the economic losses to the poultry industry due to NTS infections.

Efficacy of Antimicrobial Interventions Used in Meat Processing Plants against Antimicrobial Tolerant Non-Antibiotic-Resistant and Antibiotic-Resistant Salmonella on Fresh Beef

ABSTRACT

Salmonella is a common cause of foodborne illness in the United States, and several strains of Salmonella have been identified as resistant to antibiotics. It is not known whether strains that are antibiotic resistant (ABR) and that have some tolerance to antimicrobial compounds are also able to resist the inactivation effects of antimicrobial interventions used in fresh meat processing. Sixty-eight Salmonella isolates (non-ABR and ABR strains) were treated with half concentrations of lactic acid (LA), peracetic acid (PAA), and cetylpyridinium chloride (CPC), which are used in beef processing plants to screen for tolerant strains. Six strains each from non-ABR and ABR Salmonella that were most tolerant of LA (2%), PAA (200 ppm), and CPC (0.4%) were selected. Selected strains were inoculated on surfaces of fresh beef and subjected to spray wash treatment with 4% LA, 400 ppm PAA, or 0.8% CPC for the challenge study. Tissue samples were collected before and after each antimicrobial treatment for enumeration of survivors. Spray treatment with LA, PAA, or CPC significantly reduced non-ABR Salmonella and ABR Salmonella on surfaces of fresh beef by 1.95, 1.22, and 1.33 log CFU/cm2, and 2.14, 1.45, and 1.43 log CFU/cm2, respectively. The order of effectiveness was LA > PAA = CPC. The findings also indicated that LA, PAA, and CPC were equally (P ≤ 0.05) effective against non-ABR and ABR Salmonella on surfaces of fresh beef. These data contribute to the body of work that indicates that foodborne pathogens that have acquired both antibiotic resistance and antimicrobial tolerance are still equally susceptible to meat processing antimicrobial intervention treatments.

HIGHLIGHTS

Antimicrobial Susceptibility and Frequency of bla and qnr Genes in Salmonella enterica Isolated from Slaughtered Pigs

Salmonella enterica is known as one of the most common foodborne pathogens worldwide. While salmonellosis is usually self-limiting, severe infections may require antimicrobial therapy. However, increasing resistance of Salmonella to antimicrobials, particularly fluoroquinolones and cephalosporins, is of utmost concern. The present study aimed to investigate the antimicrobial susceptibility of S. enterica isolated from pork, the major product in Philippine livestock production. Our results show that both the qnrS and the bla_TEM antimicrobial resistance genes were present in 61.2% of the isolates. While qnrA (12.9%) and qnrB (39.3%) were found less frequently, co-carriage of bla_TEM and one to three qnr subtypes was observed in 45.5% of the isolates. Co-carriage of bla_TEM and bla_CTX-M was also observed in 3.9% of the isolates. Antimicrobial susceptibility testing revealed that the majority of isolates were non-susceptible to ampicillin and trimethoprim/sulfamethoxazole, and 13.5% of the isolates were multidrug-resistant (MDR). MDR isolates belonged to either O:3,10, O:4, or an unidentified serogroup. High numbers of S. enterica carrying antimicrobial resistance genes (ARG), specifically the presence of isolates co-carrying resistance to both β-lactams and fluoroquinolones, raise a concern on antimicrobial use in the Philippine hog industry and on possible transmission of ARG to other bacteria.

An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI

Species and subspecies within the Salmonella genus have been defined for public health purposes by biochemical properties; however, reference laboratories have increasingly adopted sequence-based, and especially whole genome sequence (WGS), methods for surveillance and routine identification. This leads to potential disparities in subspecies definitions, routine typing, and the ability to detect novel subspecies. A large-scale analysis of WGS data from the routine sequencing of clinical isolates was employed to define and characterise Salmonella subspecies population structure, demonstrating that the Salmonella species and subspecies were genetically distinct, including those previously identified through phylogenetic approaches, namely: S. enterica subspecies londinensis (VII), subspecies brasiliensis (VIII), subspecies hibernicus (IX) and subspecies essexiensis (X). The analysis also identified an additional novel subspecies, reptilium (XI). Further, these analyses indicated that S. enterica subspecies arizonae (IIIa) isolates were divergent from the other S. enterica subspecies, which clustered together and, on the basis of ANI analysis, subspecies IIIa was sufficiently distinct to be classified as a separate species, S. arizonae. Multiple phylogenetic and statistical approaches generated congruent results, suggesting that the proposed species and subspecies structure was sufficiently biologically robust for routine application. Biochemical analyses demonstrated that not all subspecies were distinguishable by these means and that biochemical approaches did not capture the genomic diversity of the genus. We recommend the adoption of standardised genomic definitions of species and subspecies and a genome sequence-based approach to routine typing for the identification and definition of novel subspecies.

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A large-scale analysis of genomic data demonstrate Salmonella species and subspecies are genetically distinct.

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Biochemical analysis does not capture the genomic diversity of the Salmonella genus but routine species and subspecies identification can be achieved with rMLST

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Average Nucleotide Identify (ANI) with a 95% criteria was suitable to distinguish species and 98% to distinguish subspecies.

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Five novel S. enteric subspecies (VII-XI) type strains are defined.

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Reclassification of S. arizonae as a separate species is recommended.

Antimicrobial Resistance in U.S. Retail Ground Beef with and without Label Claims Regarding Antibiotic Use

ABSTRACT

Antibiotics used during food animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from six U.S. cities. Samples with an RWA or U.S. Department of Agriculture Organic claim (n = 299) were assigned to the RWA production system. Samples lacking these claims (n = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial-resistant bacteria. Genomic DNA was isolated from each sample, and a quantitative PCR assay was used to determine the abundance of 10 antimicrobial resistance (AMR) genes. Prevalence of tetracycline-resistant Escherichia coli (CONV, 46.3%; RWA, 34.4%; P < 0.01) and erythromycin-resistant Enterococcus (CONV, 48.0%; RWA, 37.5%; P = 0.01) was higher in CONV ground beef. Salmonella was detected in 1.2% of samples. The AMR gene blaCTX-M (CONV, 4.1 log-normalized abundance; RWA, 3.8 log-normalized abundance; P < 0.01) was more abundant in CONV ground beef. The AMR genes mecA (CONV, 4.4 log-normalized abundance; RWA, 4.9 log-normalized abundance; P = 0.05), tet(A) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), tet(B) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), and tet(M) (CONV, 5.4 log-normalized abundance; RWA, 5.8 log-normalized abundance; P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U.S. cattle production does not increase human exposure to antimicrobial-resistant bacteria via ground beef, quantitative microbiological risk assessments are required for authoritative determination of the human health impacts of the use of antimicrobial agents during beef production.

HIGHLIGHTS

Virulence and Antimicrobial Resistance Profiles of Salmonella enterica Serovars Isolated from Chicken at Wet Markets in Dhaka, Bangladesh

Virulent and multi drug resistant (MDR) Salmonellaenterica is a foremost cause of foodborne diseases and had serious public health concern globally. The present study was undertaken to identify the pathogenicity and antimicrobial resistance (AMR) profiles of Salmonellaenterica serovars recovered from chicken at wet markets in Dhaka, Bangladesh. A total of 870 cecal contents of broiler, sonali, and native chickens were collected from 29 wet markets. The overall prevalence of S. Typhimurium, S. Enteritidis, and untyped Salmonella spp., were found to be 3.67%, 0.57%, and 1.95% respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. S. Enteritidis isolates carried all virulence genes whilst S. Typhimurium isolates carried six virulence genes except sefA and spvC. A diverse phenotypic and genotypic AMR pattern was found. Harmonic descending trends of resistance patterns were observed among the broiler, sonali, and native chickens. Interestingly, virulent and MDR Salmonella enterica serovars were found in native chicken, although antimicrobials were not used in their production cycle. The research findings anticipate that virulent and MDR Salmonella enterica are roaming in the wet markets which can easily anchor to the vendor, consumers, and in the food chain.

Antimicrobial Resistance at Two U.S. Cull Cow Processing Establishments

ABSTRACT

Culled beef cows (cows that have reached the end of their productive life span in cow-calf operations) and culled dairy cows represent approximately 18% of the cattle harvested in the United States annually, but data on antimicrobial resistance (AMR) in these cull cattle are extremely limited. To address this data gap, colon contents were obtained from 180 culled conventional beef cows, 179 culled conventional dairy cows, and 176 culled organic dairy cows (produced without using antimicrobials). Sponge samples were also collected from 181 conventional beef, 173 conventional dairy, and 180 organic dairy cow carcasses. These samples were obtained on 6 days (3 days each at two beef harvest and processing establishments). At one establishment, 30 samples of beef manufacturing trimmings from conventional cows and 30 trim samples from organic dairy cows were acquired. All 1,129 samples were cultured for Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella, and 3GCrSalmonella. Metagenomic DNA was isolated from 535 colon content samples, and quantitative PCR assays were performed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For colon contents, only TETrE. coli (P < 0.01), 3GCrE. coli (P < 0.01), and erm(B) (P = 0.03) levels were higher in conventional than in organic cows. Sampling day also significantly affected (P < 0.01) these levels. Production system did not affect the levels of any measured AMR on carcasses or trim. The human health impact of the few significant AMR differences could not be determined due to the lack of standards for normal, background, safe, or basal values. Study results provide key heretofore unavailable data that may inform quantitative microbial risk assessments to address these gaps.

HIGHLIGHTS

PCR-based detection and serovar identification of Salmonella in retail meat collected from wet markets in Metro Manila, Philippines

This study aimed to detect Salmonella from retail meat collected from nine wet markets in Metro Manila, and identify the subtypes of Salmonella isolates using molecular serotyping assays from previously developed primers. Of the 720 collected meat samples, 57.64% were found to be Salmonella-contaminated. The most predominant serogroup was Salmonella O:3, and Salmonella serogroups O:4, O:6,7, O:8, O:9, and undetermined serogroups were also found. Most frequently detected isolates in bovine meat were S. 3:e,h:1,6 (putative identity: S. Anatum) and S: 4:e,h:1,2 (putative identity: S. Saintpaul), in porcine meat was S. 3:e,h:1,6 (putative identity: S. Anatum), and S. 8:i:z6 (putative identity: S. Kentucky) was common in poultry products. This study also demonstrated retail meat samples were contaminated with multiple Salmonella serogroups and serovars. This is the first Philippine study that utilized PCR-based assays to characterize Salmonella isolates down to a serovar level and provides baseline information regarding Salmonella prevalence and serovar distribution in retail meat. Molecular serotyping performed in this study can be used as an alternative approach to traditional serotyping in surveillance of Salmonella in the Philippines since the latter is expensive, time-consuming, and requires skilled technicians.

Molecular identification and antibiotic resistance profiling of Salmonella species isolated from chickens in eastern Turkey

BACKGROUND

The aim of this study was to obtain quantitative data about the frequency, genotypic characterization and antibiotic resistance profiling of Salmonella agents in chicken flocks located in eastern Turkey.

RESULTS

Feces samples representing at least 20% of the flock area were collected via sock swabs from commercial poultry flocks in the study region in addition to internal organs (liver, spleen, intestine) collected at necropsy of suspected chickens belonging to small family enterprises. The samples were analyzed by conventional bacteriological methods (ISO 6579:2002/A1:2007) for isolation, and genus specific (invA) PCR for the identification of Salmonella spp. Then, two mPCR were set up to determine Salmonella serotypes and genotypic resistance status of the field isolates against ampicillin, tetracycline, trimethoprim-sulfamethoxazole and chloramphenicol antibiotics. In the PCR analysis of the suspected colonies, 98.5% were confirmed as Salmonella spp., and, the most prevalent serotype was identified as S. Infantis with the proportion of 26.6% (17/64), followed by S. Enteritidis with 21.9% (14/64) and S. Typhimurium with 9.4% (6/64). The findings related to antibiotic resistance genes revealed that the most frequently determined gene was sul1 with approximately 58%, while the blaTEM gene was detected at the lowest proportion with 20%, among Salmonella isolates.

CONCLUSIONS

The results indicated that Salmonella infections constitute a potential risk for chicken flocks in the country and that genotypic resistance rates against various antibiotics should draw particular attention in terms of both human and animal health.

A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium

Humans are mostly contaminated by Salmonella through the consumption of pork- and poultry-derived food products. Therefore, a strict monitoring of Salmonella serotypes in food-producing animals is needed to limit the transmission of the pathogen to humans. Additionally, Salmonella can lead to economic loss in the food sector. Previously, a genoserotyping method using the MOL-PCR and Luminex technology was developed for the identification of the 6 Salmonella serotypes, and their variants, subjected to an official control in the Belgian food sector. In this study, 3 additional assays using the same technology were developed for the rapid and cost-effective detection of 13 dangerous highly invasive serotypes or other serotypes frequently isolated from the Belgian poultry and pork sector, i.e. Agona, Anatum, Brandenburg, Choleraesuis, Derby, Enteritidis vaccine strains, Gallinarum var. Gallinarum/Pullorum, Livingstone, Mbandaka, Minnesota, Ohio, Rissen and Senftenberg. Moreover, the previously developed first MOL-PCR assay was improved for S. Paratyphi B and serogroup O:3 detection. Finally, a Decision Support System hosted by a web application was created for an automatic and objective interpretation of the Luminex raw data. The 3 new assays and the modifications of the first assay were validated with a 100% accuracy, using 553 Salmonella and non-Salmonella strains in total.

Isolation and characterization of Salmonella in pork samples collected from retail and wholesale markets in each season from 2016 to 2018 in Wuhan, China

AIMS

To investigate the prevalence and characteristics of Salmonella in pork on sale in Wuhan, Central China.

METHODS AND RESULTS

A total of 4744 pork samples were collected from retail or wholesale markets in each season from 2016 to 2018. The samples showed an overall Salmonella prevalence of 19·54% (927/4744), among which the samples collected in 2017 (21·67%, 428/1975) possessed a significantly higher prevalence than those collected in 2016 (18·61%, 209/1123) (P = 0·047) or 2018 (17·51%, 290/1656) (P = 0·002), and the samples collected in winter showed the lowest prevalence (15·86%, 177/1116). The Salmonella prevalence was significantly higher among samples from retail markets (25·68%, 283/1102) than wholesale markets (17·68%, 644/3642) (P = 0·000). Antimicrobial resistance of 922 Salmonella strains was tested by determining the minimal inhibitory concentrations using a broth microdilution method. The strains revealed that 98·92% (912/922) were resistant to at least one of the antimicrobial agents, and 80·04% (738/922) were resistant to three or more antimicrobials (MDR). Resistance to sulfamethoxazole/trimethoprim (89·91%), tetracycline (87·20%) and ampicillin (71·69%) was predominant. The proportion of MDR strains in 2017 (93·62%, 396/423) was significantly higher than that in 2016 (63·16%, 132/209) (P = 0·000) or 2018 (69·66%, 202/290) (P = 0·000). No significant difference was observed in the proportions of MDR strains between wholesale markets (76·07%, 213/280) and retail markets (80·53%, 517/642) (P = 0·075). Multi-locus sequence typing for 554 of the isolates revealed 20 different sequence types (STs), among which ST40 (38·27%, 212/554), ST34 (18·41%, 102/554) and ST469 (14·46%, 79/554) were dominant.

CONCLUSIONS

A high risk of Salmonella prevalence and antimicrobial resistance was observed in pork in Wuhan. The risk varies between different sampling years, seasons and market types.

SIGNIFICANCE AND IMPACT OF THE STUDY

Providing baseline data on Salmonella contamination in pork on sale in Central China.

A real-time PCR for rapid identification of Salmonella enterica Gaminara serovar

Salmonella is one of the leading causes of foodborne illnesses in the USA. When a Salmonella outbreak occurs, rapid identification of the causative serovar is important for tracing the source of contamination and for preventing the further spread of the illness. Each serovar is characterized by the presence of a group-specific somatic O-antigen(s) and an assortment of flagellar phase-1 and phase-2 antigens. As the traditional serotyping protocol is time consuming, labor intensive, and expensive, faster and less expensive molecular diagnostic methods are needed. This report outlines the development of a rapid multiplex real-time PCR procedure that facilitates the identification of Salmonella serogroup I and the serovars of the group. Using Salmonella Gaminara serovar (O16:d:1,7) as an example, first the gene(s) responsible for expression of the somatic O antigen, O16, and the nucleotide sequence of the variable-region of genes encoding the flagellar phase-1 (d) and phase-2 (1,7) antigens were identified. Then, a multiplex real-time PCR was designed that incorporated primers and probes specific for the three target genes and confirmed the specificity. The assay had 100% inclusivity for all three gene targets, detecting 2 genomic DNA copies of O16 and 1,7 gene targets and 10 copies of d gene target. Importance: Rapid molecular methods to identify Salmonella serovars should increase the precision of routine surveillance of clinically important serovars and promote public health.

Prevalence and Characterization of Salmonella Present during Veal Harvest

Beef and veal products have been vehicles implicated in the transmission of Salmonella enterica, a gastroenteritis-causing bacteria. Recent regulatory samples collected from veal have indicated bob veal, or calves harvested within days of birth, have higher rates of Salmonella than samples collected from formula-fed veal, or calves raised 20 weeks on milk replacer formula before harvest. To investigate this problem, we collected samples from veal calf hides, preevisceration carcasses, and final carcasses at five veal processors that harvested bob or formula-fed veal or both. Prevalence and concentrations of Salmonella were determined, and then the isolates were characterized for serovar and antibiotic susceptibility. Salmonella was more prevalent (P < 0.05) among bob veal than formula-fed veal hides, preevisceration carcasses, and final carcass (84.2 versus 15.6%, 62.8 versus 10.1%, and 12.0 versus 0.4%, respectively). Concentrations of Salmonella could be estimated by using regression order statistics on hides and preevisceration carcasses at two veal plants, with one harvesting bob veal and the other bob and formula-fed veal. The concentration of Salmonella on bob veal hides at the plants was 1.45 ± 0.70 and 2.04 ± 1.00 log CFU/100 cm², greater (P < 0.05) than on formula-fed veal hides, which was 1.10 ± 1.51 log CFU/100 cm². Concentrations on carcasses, however, were very low. Seventeen Salmonella serovars were identified among 710 isolates. Salmonella serovars London, Cerro, and Muenster were most common to bob veal and made up 50.7, 18.7, and 6.3% of the isolates, respectively, while serovar Montevideo (6.8% of isolates) was most common to formula-fed veal. Although bob veal had increased prevalence and concentrations of Salmonella, one group of formula-fed veal was found to harbor human disease-related antibiotic-resistant Salmonella serovars Heidelberg and the monophasic variant of Typhimurium (1,4,[5],12:i:-). Veal processors have made changes to improve the safety of veal, but further efforts are necessary from both bob and formula-fed veal to address Salmonella.

Salmonella Typhimurium in Iran: Contribution of molecular and IS200 PCR methods in variants detection

Salmonella Typhimurium, a zoonotic pathogen, is regarded as a major health and economic concern worldwide. Recently, monophasic variants of this serovar have been significantly associated with human gastroenteritis outbreaks globally, making its accurate identification essential for epidemiological and control purposes. We have identified and analyzed 150 S. Typhimurium from 884 Salmonella genus isolated from humans, domestic animals, poultry, food items and abattoirs origins. The Salmonella isolates were obtained from Iranian National Veterinary Reference Laboratories of 9 provinces during 2007–2016, and from five hospitals in Tehran in 2015. The isolates were evaluated biochemically, serologically, and by PCR amplification of invA, mdh, STM4492, fliC, fljA, fljB, hin genes, IS200 and DT104. invA and mdh genes were used to confirm the S. Typhimurium serotype, fliC and fljB genes for determination of monophasic variants and amplification of IS200 to discriminate the monophasic variants from the closely related serotypes. We identified 78.6% (118/150) as classical S. Typhimurium (fliC, fljB and IS200 positive), 12.6% (19/150) were IS200 negative from all isolates. DT104 is another marker for S.Typhimurium serovar typing. Contrary to EFSA guidelines 20.6% (19/29) of human isolates that lacked IS200 insertion sequence, were confirmed as S.Typhimurium. Compared to the North American/European isolates the low prevalence of fljB negative 6% (9/150) and the high abundance of fliC negative 23.3% (35/150) isolates also were indicative of a different regional atypical population. Studies have shown that the prevalence of monophasic (fljB^-) S. Typhimurium worldwide is promoted by the Swine industry. Thus, one reason for this high number of different atypical strains could be inhibition of swine breeding system (house hold and industry) in Iran. These results demonstrate a need for a modified identifying protocol to overcome the regional differences.

Prevalence and molecular characterization of Salmonella enterica serovar Typhimurium from ice and beverages in Jakarta, Indonesia

OBJECTIVE

The presence of Salmonella enterica serovar Typhimurium becomes a concern in relation to the safety of drinking water and ice. We detected and enumerated the bacteria from ice and beverages collected from several areas in Jakarta. Most Probable Number (MPN) and multiplex PCR method were used. Three sets of primers were used rfbJ, fliC, and fljB. Two Multiplex PCR's were performed, the first is to detect the presence of Salmonella and the second is to confirm the positive isolate of S. enterica serovar Typhimurium.

RESULTS

A total of 50 beverages and 50 ices were collected MPN result ranged from < 3 to > 11,000 MPN/ml. The highest MPN value > 11,000 MPN/ml. The first Multiplex PCR result from beverages, 58% positively contained Salmonella spp. with amplification of fliB gene and no amplification of rfbJ and fliC genes. For ice samples, 2% positively contained Salmonella spp. with rfbJ gene amplification, 62% fliB gene and no amplification of fliC gene. The second Multiplex PCR results from beverages identified 21 positive isolates of S. enterica serovar Typhimurium. In which, 17 isolates contained fljB gene and 4 isolates contained both fljB and rfbJ genes. From ice, 17 isolates having both rfbJ and fljB genes.

Identification and phase inversion of Salmonella flagellar antigens, using immuno-discs

Disc immuno-immobilization is a simple method for typing the flagellar phase of Salmonella enterica. We re-examined this method using commercial antisera, which contains the preservative sodium azide. Originally prepared motility agar activates bacterial motility and renders S. enterica resistant to sodium azide, resulting in the formation of immuno-immobilization lines around reactive immuno-discs. Though disc immuno-immobilization serves both serotyping and phase inversion, this method is insufficient for the strains in which phase variation rarely occurs. Here, we devised a novel immuno-disc phase inversion method, and all S. enterica strains tested were identically typed. These methods would drastically simplify the task of S. enterica typing in clinical laboratories.

A simplified multiplex PCR-based typing method for common Salmonella enterica serovars supported by online server-based detection system

Background & objectives:

A rapid and simple alternative method is needed to replace the laborious, time-consuming Salmonella serotyping. The objective of the present study was to improve and simplify a previously reported multiplex polymerase chain reaction (PCR)-based method and to create an online server to enable rapid determination of serovars.

Methods:

A method of multiplex PCR-based genome typing (MPGT) was standardized using 59 Salmonella isolates of 31 serovars. Several previously reported primers were modified to obtain a more accurate performance. The screen was separated into four different multiplex reactions distinguishable on standard electrophoresis. A blind study was subsequently performed with 81 isolates of 10 serovars most prevalent in India. Whole genome information from 440 Salmonella isolates was used to confirm the usefulness of this method and concurrence of in silico predictions and PCR results were investigated. A public server (http://www.mpgt-salmonella.res.in) was established for data storage and determination of closest previously observed Salmonella isolates based on obtained MPGT patterns.

Results:

The 16 target genes amplified showed variability in their presence in strains from different serotypes. Hence, identical amplification patterns suggested genetic relatedness of strains and usually identical serological behaviour. The observed absence/presence patterns of genes were converted to an MPGT code. Altogether, 83 different codes were predicted in silico based on the whole genome information of 440 strains. Results confirmed that major serovars usually displayed unique MPGT codes.

Interpretation & conclusions:

The multiplex PCR assay resulted in specific binary codes for isolates from each of the 31 Salmonella serovars tested. The online server allowed the user to compare obtained PCR results with stored previous patterns. Simplicity, speed and cost-effectiveness make this tool useful for quick outbreak management.

Characterization of Salmonella enterica isolates causing bacteremia in Lima, Peru, using multiple typing methods

In this study, different molecular typing tools were applied to characterize 95 Salmonella enterica blood isolates collected between 2008 and 2013 from patients at nine public hospitals in Lima, Peru. Combined results of multiplex PCR serotyping, two- and seven-loci multilocus sequence typing (MLST) schemes, serotyping, IS200 amplification and RAPD fingerprints, showed that these infections were caused by eight different serovars: Enteritidis, Typhimurium, Typhi, Choleraesuis, Dublin, Paratyphi A, Paratyphi B and Infantis. Among these, Enteritidis, Typhimurium and Typhi were the most prevalent, representing 45, 36 and 11% of the isolates, respectively. Most isolates (74%) were not resistant to ten primarily used antimicrobial drugs; however, 37% of the strains showed intermediate susceptibility to ciprofloxacin (ISC). Antimicrobial resistance integrons were carried by one Dublin (dfra1 and aadA1) and two Infantis (aadA1) isolates. The two Infantis isolates were multidrug resistant and harbored a large megaplasmid. Amplification of spvC and spvRA regions showed that all Enteritidis (n = 42), Typhimurium (n = 34), Choleraesuis (n = 3) and Dublin (n = 1) isolates carried the Salmonella virulence plasmid (pSV). We conclude that the classic serotyping method can be substituted by the multiplex PCR and, when necessary, sequencing of only one or two loci of the MLST scheme is a valuable tool to confirm the results. The effectiveness and feasibility of different typing tools is discussed.

Salmonella in Peripheral Lymph Nodes of Healthy Cattle at Slaughter

To more fully characterize the burden of Salmonella enterica in bovine peripheral lymph nodes (PLN), PLN (n = 5,450) were collected from healthy cattle at slaughter in 12 commercial abattoirs that slaughtered feedlot-fattened (FF) cattle exclusively (n = 7), cattle removed (or culled) from breeding herds (n = 3), or both FF and cull cattle (n = 2). Qualitative and quantitative methods were used to estimate prevalence and concentration of Salmonella in PLN. Isolates were subjected to a variety of phenotypic, serological, and molecular assays. Overall, Salmonella prevalence in PLN from FF and cull cattle was 7.1 and 1.8%. However, burden varied by season in that observed prevalence in PLN collected in cooler or warmer seasons was 2.4 and 8.2%, respectively. Prevalence in PLN from cull cattle in the southwest region of the US was 2.1 and 1.1% for cool and warm seasons, respectively; however, prevalence in FF PLN was far greater in that it was 6.5 and 31.1%, respectively. Salmonella was recovered from 289 (5.6%) PLN and 2.9% (n = 160) of all PLN tested had quantifiable concentrations that varied from 1.6 to 4.9 log₁₀ colony forming units/PLN. The most common serotypes isolated from PLN were Montevideo (26.9%), Lille (14.9%), Cerro (13.0%), Anatum (12.8%), and Dublin (6.9%). In all, 376 unique isolates were collected from the 289 Salmonella-positive PLN. Antimicrobial susceptibility testing revealed the majority (80.6%) of these isolates were pansusceptible; however, 10.7% of isolates were found to be resistant to two or more antimicrobial classes. We were able to document an observed increased in prevalence of Salmonella in PLN during the warmer season, particularly in FF cattle from the southwest region of the US. The mechanisms underlying the observed association between season, region, and production source have yet to be elucidated. Nevertheless, these findings increase our understanding of the sources of contamination of beef products and shed light on transmission dynamics that may be useful in targeting these sources.

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

Background

The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children.

Methods

A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance.

Results

Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi.

Conclusions

These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.

Typhoid fever, a serious bloodstream infection caused by the bacterium Salmonella Typhi, is a major cause of disease and death around the world. There have been limited data on the epidemiology of typhoid in many countries in sub-Saharan African, including Nigeria. Recent evidence, however, showed that typhoid was an important cause of bacteraemia in children residing in two regions of Nigeria. Here, we analyzed the whole genome sequences of 128 S. Typhi isolates from two studies in order to elucidate the population structure and characterize the genetic components of antimicrobial resistance. We found that the multiple S. Typhi genotypes identified were closely related to other S. Typhi from neighboring regions of Africa and that multidrug resistance (MDR) was common among these isolates, and in many cases was associated with the IncHI1 plasmid known to cause MDR typhoid. These results provide evidence that typhoid was established in Nigeria as a result of several independent introductions into the country and that there has been extensive exchange of S. Typhi in and around the region of West Africa. This study emphasizes the importance of surveillance to improve our understanding of the epidemiology of typhoid, which is needed to underpin public health measures to reduce the spread of disease and facilitate patient management.

Salmonella Bacteremia Among Children in Central and Northwest Nigeria, 2008-2015

BACKGROUND

Etiologic agents of childhood bacteremia remain poorly defined in Nigeria. The absence of such data promotes indiscriminate use of antibiotics and delays implementation of appropriate preventive strategies.

METHODS

We established diagnostic laboratories for bacteremia surveillance at regional sites in central and northwest Nigeria. Acutely ill children aged <5 years with clinically suspected bacteremia were evaluated at rural and urban clinical facilities in the Federal Capital Territory, central region and in Kano, northwest Nigeria. Blood was cultured using the automated Bactec incubator system.

RESULTS

Between September 2008 and April 2015, we screened 10,133 children. Clinically significant bacteremia was detected in 609 of 4051 (15%) in the northwest and 457 of 6082 (7.5%) in the central region. Across both regions, Salmonella species account for 24%-59.8% of bacteremias and are the commonest cause of childhood bacteremia, with a predominance of Salmonella enterica serovar Typhi. The prevalence of resistance to ampicillin, chloramphenicol, and cotrimoxazole was 38.11%, with regional differences in susceptibility to different antibiotics but high prevalence of resistance to readily available oral antibiotics.

CONCLUSIONS

Salmonella Typhi is the leading cause of childhood bacteremia in central Nigeria. Expanded surveillance is planned to define the dynamics of transmission. The high prevalence of multidrug-resistant strains calls for improvement in environmental sanitation in the long term and vaccination in the short term.

Multiplex PCR-Based Serogrouping and Serotyping of Salmonella enterica from Tonsil and Jejunum with Jejunal Lymph Nodes of Slaughtered Swine in Metro Manila, Philippines

Food poisoning outbreaks and livestock mortalities caused by Salmonella enterica are widespread in the Philippines, with hogs being the most commonly recognized carriers of the pathogen. To prevent and control the occurrence of S. enterica infection in the country, methods were used in this study to isolate and rapidly detect, differentiate, and characterize S. enterica in tonsils and jejuna with jejunal lymph nodes of swine slaughtered in four locally registered meat establishments (LRMEs) and four meat establishments accredited by the National Meat Inspection Services in Metro Manila. A total of 480 samples were collected from 240 animals (120 pigs from each type of meat establishment). A significantly higher proportion of pigs were positive for S. enterica in LRMEs (60 of 120) compared with meat establishments accredited by the National Meat Inspection Services (38 of 120). More S. enterica-positive samples were found in tonsils compared with jejuna with jejunal lymph nodes in LRMEs, but this difference was not significant. A PCR assay targeting the invA gene had sensitivity that was statistically similar to that of the culture method, detecting 93 of 98 culture-confirmed samples. Multiplex PCR-based O-serogrouping and H/Sdf I typing revealed four S. enterica serogroups (B, C1, D, and E) and six serotypes (Agona, Choleraesuis, Enteritidis, Heidelberg, Typhimurium, and Weltevreden), respectively, which was confirmed by DNA sequencing of the PCR products. This study was the first to report detection of S. enterica serotype Agona in the country.

Bovine salmonellosis in northeast of Iran: frequency, genetic fingerprinting and antimicrobial resistance patterns of Salmonella spp

OBJECTIVE

To evaluate serovar and antimicrobial resistance patterns of Salmonella spp isolated from healthy, diseased and necropsied cows and calves in this observational study.

METHODS

Nineteen isolates recovered from feces and tissues of salmonellosis-affected animals of two commercial farms in north-east of Iran. In second part of the study, the two farms were sampled 4 times with an interval of 2 month. The samples included calves' feces, adult cows' feces, feeds, water, milk filters, and milk fed to calves. Five Salmonella were isolated from 332 fecal samples collected from calves and peri-parturient cows. No Salmonella was recovered from water, feed, milk filers and milk fed to calves.

RESULTS

Salmonella Typhimurium was the most frequently isolate among all sero-groups. S. Dublin was only accounted for 8% (two out of 24) of isolates. Isolated Salmonella strains were used for the ERIC PCR DNA fingerprinting assay. Our results grouped Salmonella isolates into 3 clusters, suggesting that specific genotypes were responsible for each sero-group of Salmonella. The results also revealed diversity among Salmonella isolates in cluster III (sero-group B). Eighteen out of 19 Salmonella spp. were resistant to oxytetracycline. Five isolates out of 19 showed more than one drug resistance. Multi-drug resistance was seen only among Salmonella Typhimurium isolates. Enrofloxacin was the most susceptible antibiotic against all isolates in this study.

CONCLUSION

The emergence of multiple antibiotic-resistant strains of Salmonella Typhimurium should be of great concern to the public. No correlation between ERIC fingerprinting and resistance patterns of Salmonella isolates was found, which indicates resistance to antimicrobial agents was not related to specific genetic background.

Sequence-level and dual-phase identification of Salmonella flagellum antigens by liquid chromatography-tandem mass spectrometry (LC-MS/MS)

Forty-three reference strains involving the 24 most common serovars of Salmonella enterica were examined by using a mass spectrometry-based H antigen typing platform (MS-H). The results indicate that MS-H can be used as a sensitive, rapid, and straightforward approach for the typing of Salmonella flagella at the molecular level without antiserum and phase inversion.

Repression of flagella is a common trait in field isolates of Salmonella enterica serovar Dublin and is associated with invasive human infections

The nontyphoidal Salmonella enterica serovar Dublin is adapted to cattle but infrequently infects humans, very often resulting in invasive infections with high levels of morbidity and mortality. A Salmonella-induced intestinal acute inflammatory response is postulated as a mechanism to prevent bacterial dissemination to systemic sites. In S. enterica serovar Typhimurium, flagella contribute to this response by providing motility and FliC-mediated activation of pattern recognition receptors. In this study, we found 4 Salmonella enterica isolates, with the antigenic formula 9,12:-:-, that, based on fliC sequence and multilocus sequence type (MLST) analyses, are aflagellate S. Dublin isolates. Interestingly, all were obtained from human bloodstream infections. Thus, we investigated the potential role of flagella in the unusual invasiveness exhibited by S. Dublin in humans by analyzing flagellation and proinflammatory properties of a collection of 10 S. Dublin human clinical isolates. We found that 4 of 7 blood isolates were aflagellate due to significantly reduced levels of fliC expression, whereas all 3 isolates from other sources were flagellated. Lack of flagella correlated with a reduced ability of triggering interleukin-8 (IL-8) and CCL20 chemokine expression in human intestinal Caco-2 cells and with reduced early inflammation in the ceca of streptomycin-pretreated C57/BL6 mice. These results indicate that flagella contribute to the host intestinal inflammatory response to Salmonella serovar Dublin and suggest that their absence may contribute to its systemic dissemination through dampening of the gut immune response. Analysis of FliC production in a collection of cattle isolates indicated that the aflagellate phenotype is widely distributed in field isolates of S. Dublin.

Molecular methods for serovar determination of Salmonella

Salmonella is a diverse foodborne pathogen, which has more than 2600 recognized serovars. Classification of Salmonella isolates into serovars is essential for surveillance and epidemiological investigations; however, determination of Salmonella serovars, by traditional serotyping, has some important limitations (e.g. labor intensive, time consuming). To overcome these limitations, multiple methods have been investigated to develop molecular serotyping schemes. Currently, molecular methods to predict Salmonella serovars include (i) molecular subtyping methods (e.g. PFGE, MLST), (ii) classification using serovar-specific genomic markers and (iii) direct methods, which identify genes encoding antigens or biosynthesis of antigens used for serotyping. Here, we reviewed reported methodologies for Salmonella molecular serotyping and determined the "serovar-prediction accuracy", as the percentage of isolates for which the serovar was correctly classified by a given method. Serovar-prediction accuracy ranged from 0 to 100%, 51 to 100% and 33 to 100% for molecular subtyping, serovar-specific genomic markers and direct methods, respectively. Major limitations of available schemes are errors in predicting closely related serovars (e.g. Typhimurium and 4,5,12:i:-), and polyphyletic serovars (e.g. Newport, Saintpaul). The high diversity of Salmonella serovars represents a considerable challenge for molecular serotyping approaches. With the recent improvement in sequencing technologies, full genome sequencing could be developed into a promising molecular approach to serotype Salmonella.

Simultaneous and Rapid Detection of Salmonella typhi, Bacillus anthracis, and Yersinia pestis by Using Multiplex Polymerase Chain Reaction (PCR)

BACKGROUND

Salmonella typhi, Bacillus anthracis, and Yersinia pestis are some serious human pathogens, which their early diagnosis is of great importance. Salmonella typhi, Bacillus anthracis, and Yersinia pestis cause typhoid fever, anthrax, and plague respectively. These bacteria can be used to make biologic weapons.

OBJECTIVES

In this study, we designed a new and rapid diagnostic method based on Uniplex and Multiplex PCR method.

MATERIALS AND METHODS

Uniplex and multiplex Polymerase Chain Reaction (PCR) were conducted on virulent genes of hp and invA of Salmonella typhimurium, Pa and chr of Bacillus anthracis, and pla of Yersinia pestis. A genome from other bacteria was used to study the specificity of the primer and the PCR test.

RESULTS

Standard strains used in this study showed that primers were specific. As for sensitivity, it was shown that this method can diagnose 1-10 copies of the genome, or 1-10 Colony Forming Units (CFU) for each of the bacteria. All pieces except anthrax were sequenced in PCR to validate the product. DNA fragment resulted from Bacillus anthracis was confirmed by restriction enzyme digestions.

CONCLUSION

The designed methods are accurate, rapid, and inexpensive to find and differentiate these bacteria from similar bacteria. They can be applied for rapid diagnosis of these agents in different specimens, and bioterrorism cases.

Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest

Bovine peripheral lymph nodes (LNs), including subiliac LNs, have been identified as a potential source of human exposure to Salmonella enterica, when adipose trim containing these nodes is incorporated into ground beef. In order to gain a better understanding of the burden of S. enterica in peripheral LNs of feedlot and cull cattle, a cross-sectional study was undertaken in which 3327 subiliac LNs were collected from cattle at harvest in seven plants, located in three geographically distinct regions of the United States. Samples were collected in three seasons: Fall 2010, Winter/Spring 2011, and Summer/Fall 2011. A convenience sample of 76 LNs per day, 2 days per season (approximately 1 month apart), was collected per plant, from carcasses held in the cooler for no less than 24 h. Every 10(th) carcass half on a rail was sampled, in an attempt to avoid oversampling any single cohort of cattle. Median point estimates of S. enterica contamination were generally low (1.3%); however, median Salmonella prevalence was found to be greater in subiliac LNs of feedlot cattle (11.8%) compared to those of cull cattle (0.65%). Enumeration analysis of a subset of 618 feedlot cattle LNs showed that 67% of those harboring S. enterica (97 of 144) did so at concentrations ranging from <0.1 to 1.8 log10 CFU/g, while 33% carried a higher burden of S. enterica, with levels ranging from 1.9 to >3.8 log10 CFU/g. Serotyping of S. enterica isolated identified 24 serotypes, with the majority being Montevideo (44.0%) and Anatum (24.8%). Antimicrobial susceptibility phenotypes were determined for all isolates, and the majority (86.1%) were pansusceptible; however, multidrug-resistant isolates (8.3%) were also occasionally observed. As Salmonella contained within LNs are protected from carcass interventions, research is needed to define opportunities for mitigating the risk of Salmonella contamination in LNs of apparently healthy cattle.

Substantial within-animal diversity of Salmonella isolates from lymph nodes, feces, and hides of cattle at slaughter

Lymph nodes (mandibular, mesenteric, mediastinal, and subiliac; n = 68) and fecal (n = 68) and hide (n = 35) samples were collected from beef carcasses harvested in an abattoir in Mexico. Samples were analyzed for Salmonella, and presumptive colonies were subjected to latex agglutination. Of the isolates recovered, a subset of 91 was characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility phenotyping. Salmonella was isolated from 100% (hide), 94.1% (feces), 91.2% (mesenteric), 76.5% (subiliac), 55.9% (mandibular), and 7.4% (mediastinal) of samples. From the 87 typeable isolates, eight Salmonella enterica serotypes, including Kentucky (32.2%), Anatum (29.9%), Reading (17.2%), Meleagridis (12.6%), Cerro (4.6%), Muenster (1.1%), Give (1.1%), and Mbandaka (1.1%), were identified. S. Meleagridis was more likely (P = 0.03) to be recovered from lymph nodes than from feces or hides, whereas S. Kentucky was more likely (P = 0.02) to be recovered from feces and hides than from lymph nodes. The majority (59.3%) of the Salmonella isolates were pansusceptible; however, multidrug resistance was observed in 13.2% of isolates. Typing by PFGE revealed that Salmonella strains generally clustered by serotype, but some serotypes (Anatum, Kentucky, Meleagridis, and Reading) were comprised of multiple PFGE subtypes. Indistinguishable PFGE subtypes and, therefore, serotypes were isolated from multiple sample types, and multiple PFGE subtypes were commonly observed within an animal. Given the overrepresentation of some serotypes within lymph nodes, we hypothesize that certain Salmonella strains may be better at entering the bovine host than other Salmonella strains or that some may be better adapted for survival within lymph nodes. Our data provide insight into the ecology of Salmonella within cohorts of cattle and offer direction for intervention opportunities.

Molecular identification in monophasic and nonmotile variants of Salmonella enterica serovar Typhimurium

Variant strains of Salmonella enterica serovar Typhimurium, lacking one or both flagellar phases have been widely reported. The monophasic S.1,4,[5],12:i:- variant has emerged worldwide in the past few years and has become one of the most frequently encountered in many countries. In contrast, monophasic S.1,4,[5],12:-:1,2 and nonmotile S.1,4,[5],12:-:- strains are rarely described. This study investigated seven molecular markers to identify and delineate monophasic S.1,4,[5],12:i:- (n = 90), S.1,4,[5],12:-:1,2 (n = 25), nonmotile S.1,4,[5],12:-:- (n = 17) strains, and some serovar Typhimurium strains (n = 124) collected through the French Salmonella network between 2001 and 2010. Three markers were commonly detected in serovar Typhimurium and in all variant strains: STM2757, mdh and fliA-B. Monophasic S.1,4,[5],12:i:- were genotypically confirmed by the absence of the fljB, fljA, and hin genes. Nevertheless, 13 (14.5%) of them were positive for these last three genes, revealing monophasic strains named "inconsistent" as previously described. All nonmotile 1,4,[5],12:-:- strains had the fliC, fljA, fljB, and hin genes and the fliC gene was detected in 88% of monophasic S.1,4,[5],12:-:1,2 strains. The combination of the seven markers detection enables to recognize eight different genotypes within the S.1,4,[5],12:i:- collection, among which the Spanish and the U.S. clones previously described could be distinguished and assigned to a genotype. Based on this molecular approach, 71% of the French S.1,4,[5],12:i:- collection belonged to the Spanish clone, whereas only 2% were assigned to the U.S. clone. This study highlights the usefulness of these molecular markers and genotypes for identifying lineages, especially among the epidemiologically important monophasic S.1,4,[5],12:i:- variant.

Aptamer-based impedimetric sensor for bacterial typing

The development of an aptamer-based impedimetric sensor for typing of bacteria (AIST-B) is presented. Highly specific DNA aptamers to Salmonella enteritidis were selected via Cell-SELEX technique. Twelve rounds of selection were performed; each comprises a positive selection step against S. enteritidis and a negative selection step against a mixture of related pathogens, including Salmonella typhimurium, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Citrobacter freundii, to ensure the species-specificity of the selected aptamers. After sequencing of the pool showing the highest binding affinity to S. enteritidis, a DNA sequence of high affinity to the bacteria was integrated into an impedimetric sensor via self-assembly onto a gold nanoparticles-modified screen-printed carbon electrode (GNPs-SPCE). Remarkably, this aptasensor is highly selective and can successfully detect S. enteritidis down to 600 CFU mL(-1) (equivalent to 18 CFU in 30 μL assay volume) in 10 min and distinguish it from other Salmonella species, including S. typhimurium and S. choleraesuis. This report is envisaged to open a new venue for the aptamer-based typing of a variety of microorganisms using a rapid, economic, and label-free electrochemical platform.

Multilocus sequence typing as a replacement for serotyping in Salmonella enterica

Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.

Microbiologists have used serological and nutritional characteristics to subdivide pathogenic bacteria for nearly 100 years. These subdivisions in Salmonella enterica are called serovars, some of which are thought to be associated with particular diseases and epidemiology. We used MultiLocus Sequence-based Typing (MLST) to identify clusters of S. enterica isolates that are related by evolutionary descent. Some clusters correspond to serovars on a one to one basis. But many clusters include multiple serovars, which is of public health significance, and most serovars span multiple, unrelated clusters. Despite its broad usage, serological typing of S. enterica has resulted in confusing systematics, with a few exceptions. We recommend that serotyping for strain discrimination of S. enterica be replaced by a DNA-based method, such as MLST. Serotyping and other non-sequence based typing methods are routinely used for detecting outbreaks and to support public health responses. Moving away from these methods will require a major shift in thinking by public health microbiology laboratories as well as national and international agencies. However, a transition to the routine use of MLST, supplemented where appropriate by even more discriminatory sequence-based typing methods based on entire genomes, will provide a clearer picture of long-term transmission routes of Salmonella, facilitate data transfer and support global control measures.

Prevalence, enumeration, serotypes, and antimicrobial resistance phenotypes of salmonella enterica isolates from carcasses at two large United States pork processing plants

The objective of this study was to characterize Salmonella enterica contamination on carcasses in two large U.S. commercial pork processing plants. The carcasses were sampled at three points, before scalding (prescald), after dehairing/polishing but before evisceration (preevisceration), and after chilling (chilled final). The overall prevalences of Salmonella on carcasses at these three sampling points, prescald, preevisceration, and after chilling, were 91.2%, 19.1%, and 3.7%, respectively. At one of the two plants, the prevalence of Salmonella was significantly higher (P < 0.01) for each of the carcass sampling points. The prevalences of carcasses with enumerable Salmonella at prescald, preevisceration, and after chilling were 37.7%, 4.8%, and 0.6%, respectively. A total of 294 prescald carcasses had Salmonella loads of >1.9 log CFU/100 cm(2), but these carcasses were not equally distributed between the two plants, as 234 occurred at the plant with higher Salmonella prevalences. Forty-one serotypes were identified on prescald carcasses with Salmonella enterica serotypes Derby, Typhimurium, and Anatum predominating. S. enterica serotypes Typhimurium and London were the most common of the 24 serotypes isolated from preevisceration carcasses. The Salmonella serotypes Johannesburg and Typhimurium were the most frequently isolated serotypes of the 9 serotypes identified from chilled final carcasses. Antimicrobial susceptibility was determined for selected isolates from each carcass sampling point. Multiple drug resistance (MDR), defined as resistance to three or more classes of antimicrobial agents, was identified for 71.2%, 47.8%, and 77.5% of the tested isolates from prescald, preevisceration, and chilled final carcasses, respectively. The results of this study indicate that the interventions used by pork processing plants greatly reduce the prevalence of Salmonella on carcasses, but MDR Salmonella was isolated from 3.2% of the final carcasses sampled.

One-step triplex high-resolution melting analysis for rapid identification and simultaneous subtyping of frequently isolated Salmonella serovars

Salmonellosis is one of the most important food-borne diseases worldwide. For outbreak investigation and infection control, accurate and fast subtyping methods are essential. A triplex gene-scanning assay was developed and evaluated for serotype-specific subtyping of Salmonella enterica isolates based on specific single-nucleotide polymorphisms in fragments of fljB, gyrB, and ycfQ. Simultaneous gene scanning of fljB, gyrB, and ycfQ by high-resolution melting-curve analysis of 417 Salmonella isolates comprising 46 different serotypes allowed the unequivocal, simple, and fast identification of 37 serotypes. Identical melting-curve profiles were obtained in some cases from Salmonella enterica serotype Enteritidis and Salmonella enterica serotype Dublin, in all cases from Salmonella enterica serotype Ohio and Salmonella enterica serotype Rissen, from Salmonella enterica serotype Mbandaka and Salmonella enterica serotype Kentucky, and from Salmonella enterica serotype Bredeney, Salmonella enterica serotype Give, and Salmonella enterica serotype Schwarzengrund. To differentiate the most frequent Salmonella serotype, Enteritidis, from some S. Dublin isolates, an additional single PCR assay was developed for specific identification of S. Enteritidis. The closed-tube triplex high-resolution melting-curve assay developed, in combination with an S. Enteritidis-specific PCR, represents an improved protocol for accurate, cost-effective, simple, and fast subtyping of 39 Salmonella serotypes. These 39 serotypes represent more than 94% of all human and more than 85% of all nonhuman Salmonella isolates (including isolates from veterinary, food, and environmental samples) obtained in the years 2008 and 2009 in Austria.

Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin

The Enteritidis and Dublin serovars of Salmonella enterica are closely related, yet they differ significantly in pathogenicity and epidemiology. S. Enteritidis is a broad host range serovar that commonly causes gastroenteritis and infrequently causes invasive disease in humans. S. Dublin mainly colonizes cattle but upon infecting humans often results in invasive disease.To gain a broader view of the extent of these differences we conducted microarray-based comparative genomics between several field isolates from each serovar. Genome degradation has been correlated with host adaptation in Salmonella, thus we also compared at whole genome scale the available genomic sequences of them to evaluate pseudogene composition within each serovar.Microarray analysis revealed 3771 CDS shared by both serovars while 33 were only present in Enteritidis and 87 were exclusive to Dublin. Pseudogene evaluation showed 177 inactive CDS in S. Dublin which correspond to active genes in S. Enteritidis, nine of which are also inactive in the host adapted S. Gallinarum and S. Choleraesuis serovars. Sequencing of these 9 CDS in several S. Dublin clinical isolates revealed that they are pseudogenes in all of them, indicating that this feature is not peculiar to the sequenced strain. Among these CDS, shdA (Peyer´s patch colonization factor) and mglA (galactoside transport ATP binding protein), appear also to be inactive in the human adapted S. Typhi and S. Paratyphi A, suggesting that functionality of these genes may be relevant for the capacity of certain Salmonella serovars to infect a broad range of hosts.

Emergence of Salmonella enterica serovar Potsdam as a major serovar in waterfowl hatcheries and chicken eggs

Salmonellosis is a common food-borne illness in humans caused by Salmonella-contaminated poultry and their products. In hatcheries, 110 Salmonella isolates were identified, mostly from first enrichment, and few from delayed enrichment. The Salmonella prevalence in goose and duck hatcheries was higher when measured by four multiplex PCR methods than by traditional culture (73.8% vs. 44.35%, P < 0.05); 97.3% of 110 isolates were Salmonella Potsdam of serogroup C1 and other isolates were Salmonella Montevideo of C1 and Salmonella Albany of C2. Plasmid and pulsed field gel electrophoresis genetic analysis revealed that isolates from duck hatcheries were more diverse than those from goose hatcheries. In Salmonella Potsdam, host species-specific genotypes were observed in geese for genotypes 3, 4, and 5 and in ducks for genotypes 7, 8, and 9, suggesting that Salmonella Potsdam may evolve into goose- and duck-specific isolates. An examination of 1121 eggs found that only Salmonella Potsdam was identified in 1.8% (7/591) of eggs from chickens fed on the ground, not housed in cages, and in egg content (6/7) as well as eggshell membrane (1/7). In conclusion, Salmonella Potsdam may be a major Salmonella infection in waterfowl and chicken eggs.

Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives

For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of Salmonella in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different Salmonella enterica subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping Salmonella strains at a deeper level.

Rapid genoserotyping tool for classification of Salmonella serovars

We have developed a Salmonella genoserotyping array (SGSA) which rapidly generates an antigenic formula consistent with the White-Kauffmann-Le Minor scheme, currently the gold standard for Salmonella serotyping. A set of 287 strains representative of 133 Salmonella serovars was assembled to validate the array and to test the array probes for accuracy, specificity, and reproducibility. Initially, 76 known serovars were utilized to validate the specificity and repeatability of the array probes and their expected probe patterns. The SGSA generated the correct serovar designations for 100% of the known subspecies I serovars tested in the validation panel and an antigenic formula consistent with that of the White-Kauffmann-Le Minor scheme for 97% of all known serovars tested. Once validated, the SGSA was assessed against a blind panel of 100 Salmonella enterica subsp. I samples serotyped using traditional methods. In summary, the SGSA correctly identified all of the blind samples as representing Salmonella and successfully identified 92% of the antigens found within the unknown samples. Antigen- and serovar-specific probes, in combination with a pepT PCR for confirmation of S. enterica subsp. Enteritidis determinations, generated an antigenic formula and/or a serovar designation consistent with the White-Kauffmann-Le Minor scheme for 87% of unknown samples tested with the SGSA. Future experiments are planned to test the specificity of the array probes with other Salmonella serovars to demonstrate the versatility and utility of this array as a public health tool in the identification of Salmonella.

MassCode liquid arrays as a tool for multiplexed high-throughput genetic profiling

Multiplexed detection assays that analyze a modest number of nucleic acid targets over large sample sets are emerging as the preferred testing approach in such applications as routine pathogen typing, outbreak monitoring, and diagnostics. However, very few DNA testing platforms have proven to offer a solution for mid-plexed analysis that is high-throughput, sensitive, and with a low cost per test. In this work, an enhanced genotyping method based on MassCode technology was devised and integrated as part of a high-throughput mid-plexing analytical system that facilitates robust qualitative differential detection of DNA targets. Samples are first analyzed using MassCode PCR (MC-PCR) performed with an array of primer sets encoded with unique mass tags. Lambda exonuclease and an array of MassCode probes are then contacted with MC-PCR products for further interrogation and target sequences are specifically identified. Primer and probe hybridizations occur in homogeneous solution, a clear advantage over micro- or nanoparticle suspension arrays. The two cognate tags coupled to resultant MassCode hybrids are detected in an automated process using a benchtop single quadrupole mass spectrometer. The prospective value of using MassCode probe arrays for multiplexed bioanalysis was demonstrated after developing a 14plex proof of concept assay designed to subtype a select panel of Salmonella enterica serogroups and serovars. This MassCode system is very flexible and test panels can be customized to include more, less, or different markers.

Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array

Serotyping of Salmonella has been an invaluable subtyping method for epidemiologic studies for more than 70 years. The technical difficulties of serotyping, primarily in antiserum production and quality control, can be overcome with modern molecular methods. We developed a DNA-based assay targeting the genes encoding the flagellar antigens (fliC and fljB) of the Kauffmann-White serotyping scheme. Fifteen H antigens (H:a, -b, -c, -d, -d/j, -e,h, -i, -k, -r, -y, -z, -z(10), -z(29), -z(35), and -z(6)), 5 complex major antigens (H:G, -EN, -Z4, -1, and -L) and 16 complex secondary antigens (H:2, -5, -6, -7, -f, -m/g,m, -m/m,t, -p, -s, -t/m,t, -v, -x, -z(15), -z(24), -z(28), and -z(51)) were targeted in the assay. DNA probes targeting these antigens were designed and evaluated on 500 isolates tested in parallel with traditional serotyping methods. The assay correctly identified 461 (92.2%) isolates based on the 36 antigens detected in the assay. Among the isolates considered correctly identified, 47 (9.4%) were partially serotyped because probes corresponding to some antigens in the strains were not in the assay, and 13 (2.6%) were monophasic or nonmotile strains that possessed flagellar antigen genes that were not expressed but were detected in the assay. The 39 (7.8%) strains that were not correctly identified possessed an antigen that should have been detected by the assay but was not. Apparent false-negative results may be attributed to allelic divergence. The molecular assay provided results that paralleled traditional methods with a much greater throughput, while maintaining the integrity of the Kauffmann-White serotyping scheme, thus providing backwards-compatible epidemiologic data. This assay should greatly enhance the ability of clinical and public health laboratories to serotype Salmonella.

SALMATcor: microagglutination for Salmonella flagella serotyping

Salmonella is a complex bacterial group with more than 2400 serovars widely distributed in nature; they are considered zoonotic because they can infect a variety of animals and be transmitted to humans. Usually, they cause alimentary acquired diseases such as gastroenteritis, typhoid fever, and others that can lead to severe complications and death. Serotyping is useful to differentiate among Salmonella, because it shows an important correlation with their clinical and epidemiological patterns; consequently, it is of high value for public health, animal health, agriculture, and industry. To characterize all known Kauffmann-White Salmonella serovars, over 250 antisera are required. Due to this and to high prices antisera, many laboratories worldwide have limitations in establishing Salmonella surveillance. Therefore, we developed and validated a Salmonella flagella microagglutination test (SALMATcor) that significantly reduces laboratory requirements of antisera. SALMATcor is based on scaling down, by fivefold, the antigen:antiserum volumes actually required for the reference method: flagella standard tube agglutination technique (STAT). Antigen preparation, temperatures, and incubation periods remained as established for STAT. The SALMATcor was validated according to ISO/DIS 16140:1999 protocol, which included 1187 comparisons of flagella determinations conducted by SALMATcor and STAT, on 141 Salmonella isolates of 12 common serotypes and the use of antiserum recommended for STAT. SALMATcor concordance was excellent (Cohen's kappa index 0.9982), obtaining relative accuracy >99.9% and relative specificity >99.9%. Additionally, SALMATcor has been used by CNRB-INCIENSA since 2004 to respond to all 40 Salmonella proficiency testing strains, provided by World Health Organization-Global Salmonella Surveillance Network, obtaining 100% concordance on serovar identification. On the basis of the results achieved with SALMATcor and considering that it also significantly reduces antiserum expenses, hand labor, glassware, and bench top and water bath space requirements (microtiter plates and micropipette tips are the only additional supplies), we envision that SALMATcor will contribute to establish a sustainable Salmonella serovar surveillance worldwide.

High-throughput Universal Probe Salmonella Serotyping (UPSS) by nanoPCR

Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp. is indispensable within microbiology labs. To amalgamate single tube isolate identification with Salmonella typing, we developed the high-throughput Universal Probe Salmonella Serotyping (UPSS) technique based on nano liter PCR. In comparison to the classical approach, where O- and H-antisera are applied, the UPSS relies on specific gene content amplification of Salmonella spp. by a universal TaqMan assay for all markers and identification of the specific amplicon pattern. To enable high-throughput technology we employed a chip format containing 1024 wells loaded by an automated liquid-handling system which allowed us to perform TaqMan PCR reactions in volumes of 100nL per well. Herein we present proof of principle of the UPSS method by the use of a test panel of 100 previously serotyped Salmonella isolates to successfully verify the usability, accuracy and feasibility of the newly developed UPSS approach. We found that the methodology of the UPSS technology is capable of unequivocally identifying 30 Salmonella serotypes on a single chip within 3 hours but can be highly parallelized by the use of multiple PCR machines. Therefore the UPSS method offers a robust and straightforward molecular alternative for Salmonella detection and typing that saves expensive chemistry and can be easily automated.

Identification by PCR of non-typhoidal Salmonella enterica serovars associated with invasive infections among febrile patients in Mali

Background

In sub-Saharan Africa, non-typhoidal Salmonella (NTS) are emerging as a prominent cause of invasive disease (bacteremia and focal infections such as meningitis) in infants and young children. Importantly, including data from Mali, three serovars, Salmonella enterica serovar Typhimurium, Salmonella Enteritidis and Salmonella Dublin, account for the majority of non-typhoidal Salmonella isolated from these patients.

Methods

We have extended a previously developed series of polymerase chain reactions (PCRs) based on O serogrouping and H typing to identify Salmonella Typhimurium and variants (mostly I 4,[5],12:i:-), Salmonella Enteritidis and Salmonella Dublin. We also designed primers to detect Salmonella Stanleyville, a serovar found in West Africa. Another PCR was used to differentiate diphasic Salmonella Typhimurium and monophasic Salmonella Typhimurium from other O serogroup B, H:i serovars. We used these PCRs to blind-test 327 Salmonella serogroup B and D isolates that were obtained from the blood cultures of febrile patients in Bamako, Mali.

Principal Findings

We have shown that when used in conjunction with our previously described O-serogrouping PCR, our PCRs are 100% sensitive and specific in identifying Salmonella Typhimurium and variants, Salmonella Enteritidis, Salmonella Dublin and Salmonella Stanleyville. When we attempted to differentiate 171 Salmonella Typhimurium (I 4,[ 5],12:i:1,2) strains from 52 monophasic Salmonella Typhimurium (I 4,[5],12:i:-) strains, we were able to correctly identify 170 of the Salmonella Typhimurium and 51 of the Salmonella I 4,[5],12:i:- strains.

Conclusion

We have described a simple yet effective PCR method to support surveillance of the incidence of invasive disease caused by NTS in developing countries.

The genus Salmonella has more than 2500 serological variants (serovars), such as Salmonella enterica serovar Typhi and Salmonella Paratyphi A and B, that cause, respectively, typhoid and paratyphoid fevers (enteric fevers), and a large number of non-typhoidal Salmonella (NTS) serovars that cause gastroenteritis in healthy hosts. In young infants, the elderly and immunocompromised hosts, NTS can cause severe, fatal invasive disease. Multiple studies of pediatric patients in sub-Saharan Africa have documented the important role of NTS, in particular Salmonella Typhimurium and Salmonella Enteritidis (and to a lesser degree Salmonella Dublin), as invasive bacterial pathogens. Salmonella spp. are isolated from blood and identified by standard microbiological techniques and the serovar is ascertained by agglutination with commercial antisera. PCR-based typing techniques are becoming increasingly popular in developing countries, in part because high quality typing sera are difficult to obtain and expensive and H serotyping is technically difficult. We have developed a series of polymerase chain reactions (PCRs) to identify Salmonella Typhimurium and variants, Salmonella Enteritidis and Salmonella Dublin. We successfully identified 327 Salmonella isolates using our multiplex PCR. We also designed primers to detect Salmonella Stanleyville, a serovar found in West Africa. Another PCR generally differentiated diphasic Salmonella Typhimurium and monophasic Salmonella Typhimurium variant strains from other closely related strains. The PCRs described here will enable more laboratories in developing countries to serotype NTS that have been isolated from blood.