Characterizing Salmonella enterica Serovar Choleraesuis, var. Kunzendorf: A Comparative Case Study.

Different Salmonella serovars generally display different antigenic formulae, but there are some exceptions. For instance, the same antigenic formula, 6,7:c:1,5, is shared by Salmonella enterica serovar, Paratyphi C, Typhisuis, and Choleraesuis. Moreover, three biotypes have been described within the S. Choleraesuis serovar. A distinction among such biotypes can only be based on biochemical behaviors (biotyping) posing serious concerns when rapid characterization is required. The study of an outbreak of severe epizootic salmonellosis in wild boars occurred in Italy between 2012 and 2014 and the typing of the isolates recovered from the outbreak were used to test different approaches for serovar identification. A number of 30 S. Choleraesuis var. Kunzendorf isolates from the outbreak were typed by means of four different methods to derive serovar and biotype: (i) slide agglutination method followed by biochemical tests, (ii) suspension array xMAP® Salmonella Serotyping Assay (SSA), (iii) whole genome sequencing (WGS) and data analysis using SeqSero tool, and (iv) WGS and data analysis using Salmonella TypeFinder tool. Slide agglutination, xMAP® SSA and WGS, followed by SeqSero analysis, are methods that infer the serovars according to the White-Kauffmann-Le Minor (WKL) scheme, based exclusively on antigens. Using these methods, isolates with incomplete antigenic formulae could be misleadingly excluded from an outbreak. On the contrary, WGS followed by Salmonella TypeFinder data analysis, which predicts the serotype on the basis of Multilocus sequence typing (MLST), might be able to cluster together isolates belonging to the same outbreak irrespective of the antigenic formula. Results suggest the benefit of routine use of a combination of in silico MLST and antigenic formula analysis to solve specific ambiguous case studies for outbreak investigation purposes.

Insight into an outbreak of Salmonella Choleraesuis var. Kunzendorf in wild boars.

An unusual mortality of wild boars occurred in Italy from 2012 to 2015 due to Salmonella Choleraesuis infection. In order to confirm the occurrence of an outbreak of S. Choleraesuis in wild boars and to epidemically characterise the unique S. Choleraesuis biovar, a collection of isolates belonging to wild boars was investigated from the phenotypic, molecular and genomic points of view (PFGE and WGS). Moreover, the possibility of transmission to domestic pigs and humans, temporally and geographically close to the wild boar epidemic, was tested by also including in the panel isolates from infected domestic pigs and from one human case of infection. Wild boar isolates displayed a high genetic correlation, thus suggesting they are part of the same outbreak, with a common invasiveness potential. Conversely, no correlation between pig isolates and those from the other sources (wild boars and human) was found. However, the phylogenetic and PFGE analyses suggest a high degree of similarity between the human and the investigated wild boar outbreak isolates, implying the potential for the spread of Salmonella Choleraesuis among these species.

Different Resolution Power of Multilocus Variable-Number Tandem Repeat Analysis and Whole-Genome Sequencing in the Characterization of S. 1,4,[5],12:i:- Isolates.

Salmonella enterica serovar 1,4,[5],12:i:- has emerged over the last two decades as one of the most common serovars causing human salmonellosis in Europe. It is supposed to originate from Salmonella enterica serovar Typhimurium due to antigenic and genotypic similarities between the two serovars. Due to the high level of similarity, the multilocus variable-number tandem repeat analysis (MLVA) protocol designed for Salmonella Typhimurium routine typing is commonly used also for the characterization of S. 1,4,[5],12:i. Nevertheless, the Salmonella Typhimurium-based MLVA protocol often shows poor discriminatory power for S. 1,4,[5],12:i. Indeed, only a limited number of MLVA profiles have been described for S. 1,4,[5],12:i:-. Moreover, based on the MLVA clustering, S. 1,4,[5],12:i:- is supposed to display high clonality. The aim of the present work was to assess whether the five loci of Salmonella Typhimurium investigated by MLVA are sufficiently accurate to correctly assign S. 1,4,[5],12:i:- isolates. For this purpose, 38 epidemiologically unrelated S. 1,4,[5],12:i:- were subjected to whole-genome sequencing. Isolates were selected among a collection of monophasic strains isolated in Italy from different sources over the period 2014-2016 and belonging to the five most commonly detected MLVA profiles. Results confirmed the possible clonality for S. 1,4,[5],12:i:- serovar in the light of the scarce difference observed in terms of single-nucleotide polymorphisms (SNPs) among investigated isolates. Nevertheless, unrelated isolates on the basis of the difference of SNP number were characterized as indistinguishable by MLVA profile, thus suggesting an insufficient resolution of MLVA. Hence, we can conclude that MLVA-based approach does not seem a valuable proxy to deepen into the epidemiological relationship among S. 1,4,[5],12:i:- isolates. These evidences can be useful to avoid incorrect assignment especially when surveillance data are used for outbreak investigations.

Salmonella serovars and their distribution in Nigerian commercial chicken layer farms.

Commercial poultry farms (n° 523), located in all the six regions of Nigeria were sampled with a view to generate baseline information about the distribution of Salmonella serovars in this country. Five different matrices (litter, dust, faeces, feed and water) were collected from each visited farm. Salmonella was isolated from at least one of the five matrices in 228 farms, with a farm prevalence of 43.6% (CI95[39.7-48.3%]). Altogether, 370 of 2615 samples collected (14.1%, CI95[12.8; 15.5%]) contained Salmonella. Considering the number of positive farms and the number of positive samples, it was evident that for the majority of the sampled farms, few samples were positive for Salmonella. With regard to the matrices, there was no difference in Salmonella prevalence among the five matrices considered. Of the 370 isolates serotyped, eighty-two different serotypes were identified and Salmonella Kentucky was identified as having the highest isolation rate in all the matrices sampled (16.2%), followed by S. Poona and S. Elisabethville. S. Kentucky was distributed across the country, whereas the other less frequent serovars had a more circumscribed diffusion. This is one of few comprehensive studies on the occurrence and distribution of Salmonella in commercial chicken layer farms from all the six regions of Nigeria. The relatively high prevalence rate documented in this study may be attributed to the generally poor infrastructure and low biosecurity measures in controlling stray animals, rodents and humans. Data collected could be valuable for instituting effective intervention strategies for Salmonella control in Nigeria and also in other developing countries with a similar poultry industry structure, with the final aim of reducing Salmonella spread in animals and ultimately in humans.

Molecular characterization of "inconsistent" variants of Salmonella Typhimurium isolated in Italy.

Salmonella 4,[5],12:i:- is a variant of Salmonella Typhimurium, which lacks the expression of phase-2 flagellar antigen, generally associated with the deletion of the fljB gene. Additional mechanisms involving the fljAB operon ( fljA, fljB, and hin genes) lead to the lack of expression of phase-2 flagellar antigens also in Salmonella strains harboring the fljB gene. For 20 S. 4,[5],12:i:- strains, defined as "inconsistent" Salmonella Typhimurium variants since they had phenotypically behaved as monophasic, even though the fljB gene was conserved, the fljAB operon was characterized in order to explain the ineffective expression of the phase-2 flagellar antigen. The monophasic phenotype for a first group of strains (9) was likely due to the absence of the hin gene, leading to the inhibited switch between the expression of phase-1 and phase-2 flagellar genes. For a second group of strains (5), the monophasic phenotype could be attributed to nonconservative point mutations identified in fljA and hin genes, which could hamper the proper expression of invertase gene and the fljA, acting as repressor of the phase-1 flagellar gene. Finally, for a last group of inconsistent strains (6), a plausible reason for their monophasic phenotype was not found, since the genes involved in the expression of phase-2 flagellar antigen were fully conserved. Moreover, the collection of inconsistent Salmonella Typhimurium isolates investigated were characterized by distinct molecular profiles, as demonstrated by multiple-locus variable-number tandem repeat analysis, and phenotype variability, as demonstrated by phage-typing. This study highlights the usefulness of investigating the entire fljAB operon when a definitive identification of the monophasic or biphasic status of Salmonella Typhimurium strains is needed (for instance, in the context of epidemiological investigations aimed to identify the relatedness among strains).

European validation of Real-Time PCR method for detection of Salmonella spp. in pork meat.

The classical microbiological method for detection of Salmonella spp. requires more than five days for final confirmation, and consequently there is a need for an alternative methodology for detection of this pathogen particularly in those food categories with a short shelf-life. This study presents an international (at European level) ISO 16140-based validation study of a non-proprietary Real-Time PCR-based method that can generate final results the day following sample analysis. It is based on an ISO compatible enrichment coupled to an easy and inexpensive DNA extraction and a consolidated Real-Time PCR assay. Thirteen laboratories from seven European Countries participated to this trial, and pork meat was selected as food model. The limit of detection observed was down to 10 CFU per 25 g of sample, showing excellent concordance and accordance values between samples and laboratories (100%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (100%) when the results obtained for the Real-Time PCR-based methods were compared to those of the ISO 6579:2002 standard method. The results of this international trial demonstrate that the evaluated Real-Time PCR-based method represents an excellent alternative to the ISO standard. In fact, it shows an equal and solid performance as well as it reduces dramatically the extent of the analytical process, and can be easily implemented routinely by the Competent Authorities and Food Industry laboratories.

Molecular characterization of Salmonella enterica serovar 4,[5],12:i:- DT193 ASSuT strains from two outbreaks in Italy.

Salmonella enterica subsp. enterica serovar 4,[5],12:i:- DT193 is recognized as an emerging monophasic variant of Salmonella Typhimurium in many European countries. Resistance to ampicillin, streptomycin, sulphonamides, and tetracycline (R-type ASSuT) is described as one of the most common profiles of resistance within this clone. Recently, strains presenting such features were isolated from two unrelated outbreaks in Italy. Strains were characterized by pulsed-field gel electrophoresis (PFGE), performed with XbaI, BlnI, and SpeI, and multiple-locus variable-number tandem repeat analysis (MLVA). XbaI-PFGE showed strains related to the two outbreaks as indistinguishable. Conversely, both BlnI-PFGE and MLVA characterized the strains related the two outbreaks as different. XbaI-PFGE identified two profiles, differing by one band, within strains isolated from one of the two outbreaks. Also BlnI-PFGE and MLVA generated different profiles among the strains related to that outbreak. Combining the PFGE profiles obtained by XbaI and BlnI and comparing them with the MLVA profiles, the two methods grouped the same isolates based on identity. Moreover, genomic deletions of the genes included in the operon fljAB, the flanking iroB gene, and the closely located STM2757 gene were investigated. For all strains, the same profile of deletion characterized by the absence of fljA, fljB, and hin genes and the presence of STM2757 and iroB genes was identified. This profile of deletion represents a mixture between two profiles of Salmonella 4,[5],12:i:- described as the "Spanish" and the "U.S." clones. This study demonstrated that although strains of Salmonella 4,[5],12:i:- DT193 ASSuT are highly clonal, minor differences between strains may be seen during the same outbreak by using in parallel PFGE with different restriction enzymes, MLVA, and the analysis of molecular markers related to the operon fljAB. The combination of these different molecular approaches was essential to clarify the epidemiological relationship among the strains.

A rapid and sensitive method to identify and differentiate Salmonella enterica serotype Typhimurium and Salmonella enterica serotype 4,[5],12:i:- by combining traditional serotyping and multiplex polymerase chain reaction.

Salmonella enterica subspecies enterica serotype 4,[5],12:i:- is an emerging serovar considered as a monophasic variant of Salmonella enterica serotype Typhimurium. The antigenic and genetic similarity between Salmonella 4,[5],12:i:- and Salmonella Typhimurium suggests that they may behave in a similar way and represent a comparable threat to public health. As serotyping alone does not necessarily provide for identification of Salmonella 4,[5],12:i:- and its differentiation from Salmonella Typhimurium, a method that combines traditional serotyping and a multiplex polymerase chain reaction has been tested on 208 strains serotyped as Salmonella 4,[5],12:i:-, Salmonella Typhimurium, and similar serovars of serogroup B sharing the same phase-1 antigen "i." For 191 strains, the combined method fully confirmed the results provided by traditional serotyping, whereas for 17 strains of Salmonella 4,[5],12:i:- and Salmonella Typhimurium some inconsistencies emerged between the two methods. The combined method resulted in a more accurate and faster identification of these two relevant serovars.

Multiplexed typing of Mycobacterium avium subsp. paratuberculosis types I, II, and III by Luminex xMAP suspension array.

Differentiation among types I, II, and III is the primary step in typing Mycobacterium avium subsp. paratuberculosis. We propose an innovative approach based on detection of gyrase B (gyrB) gene polymorphisms by suspension array technology, with high discriminatory power and high-throughput potential.

Fluoroquinolone resistance detection in Campylobacter coli and Campylobacter jejuni by Luminex xMAP technology.

The proportion of Campylobacter spp. isolates that are resistant to fluoroquinolones, the drugs of choice for campylobacteriosis, has been increasing worldwide. We developed an innovative method based on a Luminex xMAP DNA suspension array that allows the identification of Campylobacter species and, simultaneously, the detection of the most common point mutation in the gyrA gene (substitution from threonine 86 to isoleucine 86) that is responsible for fluoroquinolone resistance. Ninety-six Campylobacter coli and Campylobacter jejuni isolates collected from turkeys were first investigated by microdilution test to characterize the antimicrobial resistance patterns. The isolates, amplified for the quinolone resistance determining region of the gyrA gene, were then tested using Luminex suspension array. The reliability of the method was demonstrated by the total concordance between the results obtained using Luminex and those of the sequencing of gyrA polymerase chain reaction products. The genotypic characterization of fluoroquinolone resistance using Luminex was also consistent with the data on phenotypical resistance obtained by microdilution test. The results of this study strongly support the potential of Luminex xMAP technology as an efficient molecular method for the rapid and accurate identification of C. coli and C. jejuni isolates and the characterization of the major determinant of fluoroquinolone resistance.

Bacteria-eradicating therapy with doxycycline in ocular adnexal MALT lymphoma: a multicenter prospective trial.

BACKGROUND: An association between ocular adnexal MALT lymphoma (OAL) and Chlamydia psittaci (Cp) infection has been proposed, and recent reports suggest that doxycycline treatment causes tumor regression in patients with Cp-related OAL. The effectiveness of doxycycline treatment in Cp-negative OAL has not been tested. METHODS: In a prospective trial, 27 OAL patients (15 newly diagnosed and 12 having experienced relapse) were given a 3-week course of doxycycline therapy. Objective lymphoma response was assessed by computerized tomography scans or magnetic resonance imaging at 1, 3, and 6 months after the conclusion of therapy and every 6 months during follow-up. Cp infection in patients was determined by touchdown enzyme time-release polymerase chain reaction (TETR-PCR). Statistical tests were two-sided. RESULTS: Eleven patients were Cp DNA-positive and 16 were Cp DNA negative. Doxycycline was well tolerated. At a median follow-up of 14 months, lymphoma regression was complete in six patients, and a partial response (> or = 50% reduction of all measurable lesions) was observed in seven patients (overall response rate [complete and partial responses] = 48%). Lymphoma regression was observed in both Cp DNA-positive patients (seven of 11 experienced regression) and Cp DNA-negative patients (six of 16 experienced regression) (64% versus 38%; P = .25, Fisher's exact test). The three patients with regional lymphadenopathies and three of the five patients with bilateral disease achieved objective response. In relapsed patients, response was observed both in previously irradiated and nonirradiated patients. The 2-year failure-free survival rate among the doxycycline-treated patients was 66% (95% confidence interval = 54 to 78), and 20 of the 27 patients were progression free. CONCLUSIONS: Doxycycline is a fast, safe, and active therapy for Cp DNA-positive OAL that was effective even in patients with multiple failures involving previously irradiated areas or regional lymphadenopathies. The responses observed in PCR-negative OAL may suggest a need for development of more sensitive methods for Cp detection and investigation of the potential role of other doxycycline-sensitive bacteria.

Association between Helicobacter pylori infection and MALT-type lymphoma of the ocular adnexa: clinical and therapeutic implications.

BACKGROUND: The prevalence and the clinical impact of gastric Helicobacter pylori (Hp) infection, as well as its possible correlation with Chlamydia psittaci (Cps) infection and the lymphoma regression rate produced by Hp eradicating antibiotic therapy were investigated in patients with MALT-type lymphoma of the ocular adnexa (OAL). METHODS: During staging, the presence of gastric Hp infection was assessed by gastroscopy and multiple biopsies in 31 OAL patients. Immediately after, Hp-positive patients were treated with eradicating antibiotic therapy, alone or associated with other therapies. RESULTS: Gastric Hp infection was detected in 10 (32%) patients; this feature did not correlate with patients' characteristics and disease. Four Hp-positive patients were treated with Hp-eradicating antibiotics therapy as exclusive strategy (assessable for response), none of them showed lymphoma regression. Conversely, 6 Hp-positive patients were treated with antibiotic therapy concurrently with other therapies, achieving lymphoma regression in all cases. Three Hp-positive patients with Cps-positive lymphoma were treated with doxycycline at relapse, resulting in two CR and one PR, which lasted 24+, 20+, and 18+ months, respectively. One of these patients achieved a CR after doxycycline despite the chronic persistence of Hp infection, whereas Cps-eradication was confirmed in the analysis of PBMC samples. CONCLUSIONS: Gastric Hp infection, even if common among OAL patients, does not influence clinical presentation. Hp-eradicating antibiotic therapy is not active against OAL. Cps-eradicating antibiotic therapy with doxycycline induces lymphoma remission irrespectively of the persistence of Hp infection.

Regression of ocular adnexal lymphoma after Chlamydia psittaci-eradicating antibiotic therapy.

PURPOSE: Some infectious agents contributing to lymphomagenesis have been considered targets for new therapeutic strategies. Chlamydia psittaci DNA has been detected in 80% of ocular adnexal lymphomas. The present pilot study was carried out to assess whether C psittaci-eradicating antibiotic therapy is associated with tumor regression in ocular adnexal lymphomas. PATIENTS AND METHODS: Nine patients with C psittaci-positive marginal-zone B-cell lymphoma of the ocular adnexa at diagnosis or relapse were treated with doxycycline 100 mg, bid orally, for 3 weeks. The presence of C psittaci DNA in peripheral-blood mononuclear cells (PBMCs) was also assessed before and after treatment in seven patients. Objective lymphoma regression was assessed 1, 3, and 6 months after therapy conclusion and every 6 months during follow-up. RESULTS: All patients completed antibiotic therapy with excellent tolerability. At 1 month from doxycycline assumption, chlamydial DNA was no longer detectable in PBMCs of all four positive patients. Objective response was complete in two patients, partial response (> 50%) was observed in two patients, and minimal response (< 50%) was observed in three patients. Duration of response in the seven responders was 12+, 29+, 31+, 8+, 7+, 2+, and 1+ months, respectively. CONCLUSION: C psittaci-eradicating antibiotic therapy with doxycycline is followed by objective response in patients with ocular adnexal lymphoma, even after multiple relapses of the disease. A confirmatory, large, phase II trial is warranted to confirm whether this fast, cheap, and well-tolerated therapy could replace other more aggressive strategies as first-line treatment against ocular adnexal lymphomas.