Characterization of antimicrobial resistance of recent Salmonella enterica serovar Gallinarum isolates from chickens in South Korea

Strain typing and antimicrobial susceptibility of Salmonella enterica Albany isolates from duck farms in South Korea

Salmonella enterica is distributed worldwide and is a common cause of bacterial food poisoning in humans and a serious public health problem. Although duck meat consumption has recently increased in Korea, studies on the epidemiological relationship between S. enterica contamination in duck farms are scarce. Salmonella enterica serovar Albany isolates recovered from duck farms were analyzed using two typing methods - IR Biotyper® (IRBT) and multilocus variable-number tandem repeat analysis (MLVA). The clustering results were compared with the epidemiological survey findings and the antimicrobial resistance profiles. From April 2019 to October 2020, 20 individual feces per farm from 5-6-week-old ducks were collected repeatedly from 105 duck farms. Salmonella spp. isolated from duck feces were identified using PCR and multilocus sequence typing to investigate the prevalence and distribution of the Salmonella serovars. The prevalence of S. enterica was 19%, and S. enterica Albany was the predominantly recovered isolate. The S. enterica Albany isolates underwent antimicrobial susceptibility testing to determine the minimum inhibitory concentration. MLVA and IRBT methods established relatedness and diversity among the S. enterica Albany isolates. Multidrug-resistant S. enterica Albany was distributed in all the farms. Antimicrobial resistance profiles reflected the duck farm characteristics and isolates recovered from the same farm showed an identical profile. Isolates repeatedly recovered from the same farm also showed identical IRBT clusters and MLVA groups. These findings suggest that the isolates remained on the duck farm and re-infected new duck flocks. Thus, proper cleaning and disinfection is required before the farms are repopulated.

Analysis of antibiotic resistance gene cassettes in a newly identified Salmonella enterica serovar Gallinarum strain in Korea

Antimicrobial resistant pathogens are a global health threat driven by the indiscriminate use of antimicrobials. Antimicrobial resistance can be acquired by resistance genes encoded by mobile genetic elements. In this study, we identified a strain of Salmonella enterica serovar Gallinarum (SG4021) from an infected chicken in Korea and characterized the presence of resistance genes in its plasmid by whole genome sequencing. The sequence was then compared with that of a plasmid (P2) from strain SG_07Q015, the only other strain of S. Gallinarum isolated in Korea for which a genome sequence is available. The results revealed that both strains harbored nearly identical DNA carrying antibiotic resistance gene cassettes inserted into integron In2 of the transposable element Tn21, namely an aadA1 resistance gene conferring resistance to aminoglycosides and a sul1 resistance gene conferring resistance to sulfonamide. Interestingly, despite the presence of sul1 in SG4021, an antibiotic sensitivity test revealed that it was sensitive to sulfonamides. Further analysis revealed that this disparity was due to the insertion of a ~ 5 kb ISCR16 sequence downstream of the promoter driving sul1 expression in SG4021. Using various mutants, we showed that the insertion of ISCR16 blocked the expression of the sul1 gene from the upstream promoter. Therefore, the functionality of antimicrobial resistance genes determines phenotypic antimicrobial resistance.

Genomic Characterization and Genetic Profiles of Salmonella Gallinarum Strains Isolated from Layers with Fowl Typhoid in Colombia

Salmonella Gallinarum (SG) is the causative agent of fowl typhoid (FT), a disease that is harmful to the poultry industry. Despite sanitation and prophylactic measures, this pathogen is associated with frequent disease outbreaks in developing countries, causing high morbidity and mortality. We characterized the complete genome sequence of Colombian SG strains and then performed a comparative genome analysis with other SG strains found in different regions worldwide. Eight field strains of SG plus a 9R-derived vaccine were subjected to whole-genome sequencing (WGS) and bioinformatics analysis, and the results were used for subsequent molecular typing; virulome, resistome, and mobilome characterization; and a comparative genome study. We identified 26 chromosome-located resistance genes that mostly encode efflux pumps, and point mutations were found in gyrase genes (gyrA and gyrB), with the gyrB mutation S464T frequently found in the Colombian strains. Moreover, we detected 135 virulence genes, mainly in 15 different Salmonella pathogenicity islands (SPIs). We generated an SPI profile for SG, including C63PI, CS54, ssaD, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-6, SPI-9, SPI-10, SPI-11, SPI-12, SPI-13, and SPI-14. Regarding mobile genetic elements, we found the plasmids Col(pHAD28) and IncFII(S) in most of the strains and 13 different prophage sequences, indicating a frequently obtained profile that included the complete phage Gifsy_2 and incomplete phage sequences resembling Escher_500465_2, Shigel_SfIV, Entero_mEp237, and Salmon_SJ46. This study presents, for the first time, the genomic content of Colombian SG strains and a profile of the genetic elements frequently found in SG, which can be further studied to clarify the pathogenicity and evolutionary characteristics of this serotype.

JMM Profile: Salmonella enterica serovar Gallinarum, biovars Pullorum and Gallinarum

Salmonella serovar Gallinarum has two distinct biovars, Pullorum and Gallinarum. They are host-adapted avian pathogens that infect a number of wild and domesticated species but they pose a particular threat to farmed and backyard chickens and turkeys. Both biovars cause invasive and septicaemic disease, often resulting in high mortality. Pullorum is transmitted in eggs and typically affects birds soon after hatch. Gallinarum may cause disease in any age of bird, which often progresses through mature flocks. The establishment of clean breeding stock has resulted in freedom from the pathogens in many countries although even in these territories sporadic incursions still occur.

The activity of Meniran (Phyllanthus niruri Linn.) extract on Salmonella pullorum infected broilers

Background and Aim: Pullorum is an acute and chronic disease caused by Salmonella pullorum, often infecting chicken farms. Pullorum disease treatment using antibiotics that do not follow the control dose can cause bacteria to become antibiotic-resistant. Meniran contributes to inhibiting and antagonizing bacteria and can increase the efficiency of chicken feed because of its bioactive compounds, including alkaloids, flavonoids, tannins, and saponins. This study aimed to determine the activity of Meniran extract (Phyllanthus niruri Linn.) in broilers infected with S. pullorum. Materials and Methods: In vitro study that was conducted includes phytochemical test, diffusion, and dilution methods using Meniran extract at 5%, 10%, 20%, and 40% concentrations and tylosin at 2% concentration. The data of the dilution method (minimum inhibitory concentration [MIC] and minimum bactericidal concentration [MBC]) were processed using probit analysis to determine LC50. In vivo study was conducted by randomly dividing 20 broilers into five treatment groups, four per group. The chickens (except in group P0–) were infected with S. pullorum aged 14 days. Then, the treatment was conducted according to the divided groups when the chickens were aged 21-34 days. The said treatments are P0– (uninfected S. pullorum and unadministered with Meniran extract), P0+ (infected with S. pullorum and unadministered with Meniran extract), and P1, P2, and P3 (infected with S. pullorum and administered with Meniran extract with 5%, 10%, and 20% concentrations, respectively). Data from the phytochemical test were analyzed as descriptive. The data from the diffusion method were analyzed using one-way analysis of variance (ANOVA) and Duncan's test. Then, the results of broilers' performance were analyzed using ANOVA and Duncan's test. Results: The phytochemical test showed positive for alkaloid, tannin, saponin, flavonoid, and steroid/triterpenoid. The diffusion method formed the largest zone at 40% concentration with 15.6 mm, while 20%, 10%, and 5% had average of 13.15 mm, 8.38 mm, and 5.8 mm, respectively. The dilution method (MIC and MBC) exhibited the antibacterial ability of Meniran extract against S. pullorum at 20% dose and LC50 14.118% concentration. The Meniran extract administration in broilers exhibited improved performance of chickens infected with S. pullorum, with the administration of 20% dose of Meniran extract showing the best result. Conclusion: About 20% concentration Meniran extract can serve as an antibacterial agent and showed the best results in broilers infected with S. pullorum.

SGP-C: A Broad Host Range Temperate Bacteriophage; Against Salmonella gallinarum

Salmonella gallinarum is a poultry restricted-pathogen causing fowl-typhoid disease in adult birds with mortality rates up-to 80% and exhibit resistance against commonly used antibiotics. In this current study, a temperate broad host range bacteriophage SGP-C was isolated against S. gallinarum from poultry digesta. It showed infection ability in all the 15 tested field strains of S. gallinarum. The SGP-C phage produced circular, turbid plaques with alternate rings. Its optimum activity was observed at pH 7.0 and 37-42°C, with a latent period of 45 min and burst size of 187 virions/bacterial cell. The SGP-C lysogens, SGPC-L5 and SGPC-L6 exhibited super-infection immunity against the same phage, an already reported feature of lysogens. A virulence index of 0.5 and 0.001 as MV50 of SGP-C suggests its moderate virulence. The genome of SGP-C found circular double stranded DNA of 42 Kbp with 50.04% GC content, which encodes 63 ORFs. The presence of repressor gene at ORF49, and absence of tRNA sequence in SGP-C genome indicates its lysogenic nature. Furthermore, from NGS analysis of lysogens we propose that SGP-C genome might exist either as an episome, or both as integrated and temporary episome in the host cell and warrants further studies. Phylogenetic analysis revealed its similarity with Salmonella temperate phages belonging to family Siphoviridae. The encoded proteins by SGP-C genome have not showed homology with any known toxin and virulence factor. Although plenty of lytic bacteriophages against this pathogen are already reported, to our knowledge SGP-C is the first lysogenic phage against S. gallinarum reported so far.

Antimicrobial Resistance and PFGE Molecular Typing of Salmonella enterica serovar Gallinarum Isolates from Chickens in South Korea from 2013 to 2018

Simple Summary

Salmonella enterica serovar Gallinarum (S. enterica ser. Gallinarum) is a host-specific agent of fowl typhoid (FT). This is one of the most important bacterial infections in the poultry industry in both developing and developed countries, including South Korea. The use of antimicrobial drugs is the first choice for disease control. Antimicrobials, such as β-lactams, aminoglycosides, and fluoroquinolones, are frequently used to treat FT. However, the continuous use of antimicrobial drugs has led to the emergence and persistence of antimicrobial-resistant S. enterica ser. Gallinarum. In this study, we analyzed the antimicrobial susceptibility and epidemiological relationship of thirty isolates of S. enterica ser. Gallinarum isolated from poultry farms with an FT outbreak from 2013 to 2018 in South Korea. All the isolates showed a multi-drug resistant (MDR) phenotype. This study confirmed horizontal transmission and cross-contamination between farms within the same integrated poultry company or between farms belonging to different companies. The characterization of these isolates would be helpful to develop prevention and control strategies for the MDR S. enterica ser. Gallinarum infection in South Korea.

Abstract

Antimicrobial resistance and pulsed-field gel electrophoresis (PFGE) genotypes of collected S. enterica ser. Gallinarum isolates were investigated to examine the epidemiological relationship between field outbreak isolates of S. enterica ser. Gallinarum. Thirty S. enterica ser. Gallinarum isolates collected from poultry farms with FT outbreaks from 2013 to 2018 in South Korea were analyzed. All isolates were resistant to at least 3 of the 18 antimicrobials tested and exhibited an MDR phenotype. All isolates showed resistance to streptomycin, sulfisoxazole, and colistin. One isolate was resistant to 9 antimicrobials. The antimicrobial resistance profile, streptomycin-sulfisoxazole-colistin-nalidixic acid-ciprofloxacin-gentamicin (18/30, 60.0%), was the most prevalent. PFGE types were classified into 10 groups with a 100% correlation cutoff in dendrograms for 30 field isolates. The dominant PFGE types were 1 (8/30, 26.7%), 4 (7/30, 23.3%), and 9 (5/30, 16.7%). Interestingly some isolates collected from the same and different companies had the same PFGE type. We reported a high MDR rate in S. enterica ser. Gallinarum isolates. The present study highlights the occurrence of horizontal spread and cyclic contamination of MDR S. enterica ser. Gallinarum within the same company. Furthermore, we showed cross-contamination between different companies. The characterization of these isolates would be helpful in the development of prevention and control strategies for MDR S. enterica ser. Gallinarum infection in South Korea.

A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda

There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures.

Salmonella Gallinarum in Small-Scale Commercial Layer Flocks: Occurrence, Molecular Diversity and Antibiogram

Salmonella Gallinarum is one of the most important bacterial pathogens associated with diminished egg production in poultry. The aim of this study was to understand the occurrence, molecular traits and antimicrobial resistance patterns of Salmonella Gallinarum strains isolated from small-scale commercial layer flocks with low level biosecurity standards in Bangladesh. A total of 765 samples, including cloacal swabs (535), visceral organs (50), and droppings (180), were collected from chickens of 12 layer flocks in 11 districts. Salmonella Gallinarum was isolated and characterized through culture-based method, followed by biochemical tests, sero-grouping, PCR assays, sequencing, and antibiogram. The identity of biochemically detected isolates of Salmonella Gallinarum was confirmed via genus-specific 16S rRNA gene based PCR, followed by invA and spvC genes based PCR assays. Occurrence of Salmonella Gallinarum was detected in overall 25.75% (197/765) samples, with a significantly (p < 0.05) higher incidence in visceral organs (42%) in comparison to cloacal swab (24%) and droppings (26%). Sequencing and subsequent phylogenetic analysis of invA and spvC genes in representative strains of Salmonella Gallinarum revealed a close genetic lineage, with a sequence similarity of 98.05–99.21% and 97.51–99.45%, respectively, to previously published sequences of the corresponding genes from the same serogroup strains. Remarkably, 66.5% (131/197) of the isolated strains of Salmonella Gallinarum were found to be resistant to 3 to 6 antimicrobial agents, and interpreted as multidrug resistant (MDR). The findings of this study underscore an inherent need of appropriate control measures to curb the widespread incidence of MDR Salmonella Gallinarum in small-scale commercial layer flocks, thereby, facilitating enhanced egg production and further support to the food security and safety in low resource settings.

Epidemic patterns of antimicrobial resistance of Salmonella enterica serovar Gallinarum biovar Pullorum isolates in China during the past half-century

Pullorum is a chicken-specific systemic disease caused by Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum). This study was carried out to provide basic data for understanding the trends of S. Pullorum. A total of 652 S. Pullorum isolates collected in China during 1962-2019 were examined. Overall, 525 (80.5%) isolates were resistant to at least one antibiotic; 280 (42.9%) isolates resisted 3 or more classes of antibiotics and showed an increasing trend until 2015 and then decreased significantly. The most common multidrug-resistant pattern was ampicillin-tetracycline-nalidixic acid (13.6%). After 2008, 6 classes of antibiotic-resistant strains began to appear, and they have been prevalent ever since. In 2014, a strain resistant to 7 antibiotics (ampicillin-cefazolin-streptomycin-tetracycline-sulphonamides-nalidixic acid-nitrofurantoin) was isolated. The highest antimicrobial resistance was observed for nalidixic acid (71.9%), and the lowest was found for cefotaxime, meropenem, amikacin, gentamicin, fosfomycin, and polymyxin (0%). Our findings monitored the prevalence of the resistance of S. Pullorum during the past half-century in China. Continued surveillance of antimicrobial resistance and the rational use of antimicrobials is necessary and important to control the rapid increase in antimicrobial resistance in S. Pullorum.

Effect of two lytic bacteriophages against multidrug-resistant and biofilm-forming Salmonella Gallinarum from poultry

1. Salmonella Gallinarum (SG) infections cause fowl typhoid, which leads to important economic losses. Multidrug resistance (MDR) and the capacity for bacteria to form biofilms could play an important role in the persistence of SG in poultry flocks resulting in intermittent disease outbreaks. The aim of the following study was to assess the lytic activity of two new bacteriophages (Salmonella phages UPF_BP1 and UPF_BP2) against MDR and biofilm-forming SG. 2. Forty-six strains of SG, isolated in 2015, were characterised by antimicrobial resistance, biofilm formation profiles and susceptibility to two new bacteriophages. 3. Of these strains, 24% were multidrug resistant and more than 80% formed biofilm, with no statistical difference between incubation temperatures (42°C or 22°C). With regard to the lytic activity of the phages, 85% of strains were susceptible to at least one phage. Of these, 74% were lysed by both phages, including MDR and biofilm producing strains. 4. The use of salmonella phages UPF_BP1 and UPF_BP2 were shown to be promising alternatives for the biological control of fowl typhoid.

Genetic Characterization of Fluoroquinolone Resistance in Salmonella enterica Serovar Gallinarum Isolates from Chicken in Korea

Salmonella enterica serovar Gallinarum is a nonmotile host-adapted Salmonella that causes fowl typhoid (FT), and an outbreak of FT is characterized by anorexia, greenish-yellow diarrhea, paleness, and sudden death with high mortality in poultry. To control and treat FT in commercial chickens, fluoroquinolones are widely used in Korea. This study aimed to investigate the genetic characteristics of fluoroquinolone-resistant Salmonella Gallinarum isolates from 2014-18 from chicken in Korea. A total of 35 ciprofloxacin (CIP)-resistant Salmonella Gallinarum was tested, and 22 (62.9%) isolates were observed to have multidrug resistance. All isolates had a mutation at the Ser83 or Asp87 codon in the gyrA gene, whereas three isolates had only double mutations at Ser83 → Phe and Asp87 → Asn or Ser83 → Phe and Asp87 → Gly. Minimum inhibitory concentrations of isolates with double mutations were relatively higher (≥8 mg/L for CIP and ≥16 mg/L for enrofloxacin) than those of other isolates with a single mutation in gyrA. Among 35 CIP-resistant Salmonella Gallinarum, plasmid-mediated quinolone resistance genes were detected in six (17.1%) isolates, and qnrB and qnrS were detected in four and two isolates, respectively. In the distribution of antimicrobial resistance genes in 35 CIP-resistant Salmonella Gallinarum, ant(2″)-I (54.3%) was the most prevalent gene, followed by TEM-1 (14.3%), sul1 (11.4%), and cmlA (5.7%). Fifteen (42.9%) of the 35 CIP-resistant Salmonella Gallinarum also carried class 1 integrons, which showed five types of resistance gene cassettes: aadA2 (7 isolates), aadA2 + dfrA12 (5 isolates), and aadA1 + aad A2 (3 isolates). Among plasmid replicons, 23 isolates (65.7%) carried five different plasmid replicons: Frep (9 isolates), FIB (7 isolates), FIIA (6 isolates), B/O (4 isolates), and I1 (3 isolates). These results suggest that continued monitoring of fluoroquinolone resistance is necessary to preserve the effectiveness of fluoroquinolones in poultry and to surveil the transmission to humans through the food chain.

Molecular characteristic of antimicrobial resistance of Salmonella Gallinarum isolates from chickens in Korea, 2014 to 2018

Fowl typhoid (FT), which is caused by Salmonella enterica serovar Gallinarum (S. Gallinarum), leads to high morbidity and acute or subacute mortality in chickens of all ages. Although a live S. Gallinarum 9R vaccine was introduced in 2001 for commercial layer chickens in Korea, until recently, a variety of antimicrobials were widely used to prevent or treat FT. In this study, we investigated antimicrobial resistance in S. Gallinarum strains isolated from 2014 to 2018 and characterized the multidrug-resistant (MDR) strains to better understand the resistance trends in recent isolates. A total of 130 S. Gallinarum isolates were collected from chickens with FT, and the isolates showed highest rates of resistance to nalidixic acid (78.5%), followed by gentamicin (52.3%), ciprofloxacin (26.9%), and ampicillin (14.6%). Particularly, significant increases (P < 0.05) in the frequencies of resistance to the following antimicrobials were observed: ampicillin (from 7.7 to 28.6%), amoxicillin-clavulanate (from 0.0 to 10.7%), nalidixic acid (from 69.2 to 100.0%), ciprofloxacin (from 15.4 to 50.0%), chloramphenicol (from 0.0 to 17.9%), and colistin (from 0.0 to 14.3%). The prevalence of MDR isolates also rapidly increased from 23.1% in the 2014 to 60.7% in the 2018 (P < 0.05). The distribution of antimicrobial resistance genes in the 39 MDR S. Gallinarum isolates was as follows: ant(2")-I gene (22 isolates), blaTEM-1 gene (13 isolates), sul1 (9 isolates), sul2 (3 isolates), cmlA (3 isolates), and qnrB (3 isolates). Of 39, 25 (64.1%) MDR S. Gallinarum isolates also carried class 1 integrons, and these showed 5 types of resistance gene cassettes: dfrA12+aadA2 (36.0%), aadA2 (36.0%), aadA1-aadA2 (20.0%), dfrA12+catB3+aadA2 (4.0%), and dfrA12 (4.0%). Among the plasmid replicons, B/O (33.3%) was more prevalent than the other replicon types, followed by Frep (25.0%), FIIA (19.4%), FIB (13.9%), and I1 (8.3%). Antimicrobial resistance may become a serious problem because many drugs are likely ineffective for the treatment of FT. Therefore, these data support the critical need for comprehensive surveillance of antimicrobial resistance in poultry.

Molecular characterization of antimicrobial-resistant Enterococcus faecalis and Enterococcus faecium isolated from layer parent stock

Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) are ubiquitous intestinal bacteria in humans and animals that can easily acquire antimicrobial resistance, which allows them to have roles as antimicrobial resistance indicators. In addition, layer parent stock produces thousands of eggs for the production of commercial laying hens and can transfer a variety of viral and bacterial agents to chicks. The objective of this study was to determine the prevalence and characteristics of antimicrobial-resistant E. faecalis and E. faecium isolated in the layer parent stock level of the egg-layer operating system in South Korea. A total of 129 E. faecalis and 166 E. faecium isolates from 74 flocks of 30 layer parent stock were tested for resistance in this study. The prevalence of doxycycline- (51.9%), erythromycin- (53.5%), high-level gentamicin- (13.2%), high-level kanamycin- (31.0%), high-level streptomycin- (30.2%), and tetracycline- (64.3%) resistant E. faecalis isolates were higher than those for E. faecium isolates (P < 0.05). The ermB gene was detected in 66 (95.7%) erythromycin-resistant E. faecalis isolates, which was higher than that of 32 (71.7%) erythromycin-resistant E. faecium isolates. Twenty-one high-level gentamicin-resistant Enterococcus spp. (17 E. faecalis and 4 E. faecium) carried at least one aminoglycoside-modifying enzyme gene, aac(6')Ie-aph(2')-Ia or ant(6)-Ia. Fourteen isolates that harbored both aac(6')Ie-aph(2')-Ia and ant(6)-Ia exhibited pattern A with IS256 at both ends. Ten high-level ciprofloxacin-resistant Enterococcus spp. (8 E. faecalis and 2 E. faecium) showed amino acid changes from serine to isoleucine at codons 83 in gyrA, and 80 in parC. Also, the virulence genes ace, asa1, efaA, and gelE were detected in this study. To the best of our knowledge, this is the first study to examine the prevalence and characteristics of antimicrobial-resistant E. faecalis and E. faecium isolates in the layer parent stock. Our findings support the need for a surveillance program to monitor the emergence of antimicrobial-resistant E. faecalis and E. faecium in layer operating system.

Salmonella Gallinarum field isolates and its relationship to vaccine strain SG9R

1. The aim of the present study was to determine if the 9R-strain of the Salmonella Gallinarum live vaccine was responsible for having fowl typhoid outbreaks in chicken flocks from both chicken and turkey breeders as well as to verify the antimicrobial resistance of the isolates from the outbreaks. 2. The triplex polymerase chain reaction, standard antimicrobial test, beta-lactamase genes identification and Ion Torrent PMG whole-genome sequence were used in the field isolates and in the vaccine strain of S. Gallinarum. 3. The 60 tested isolates were not from vaccine origin and manifested high resistance to drugs from macrolide and quinolone groups. Whole-genome sequencing (WGS) and single nucleotide polymorphism analysis on selected isolates for core genes from Salmonella enterica confirmed the wild origin of these isolates and showed two possible sources of S. Gallinarum in the studied outbreaks. 4. S. Gallinarum isolated from fowl typhoid outbreaks in the studied period were not caused by the use of the SG9R live vaccine. The source of strains sequenced was diverse.

Antimicrobial Resistance in Bacterial Poultry Pathogens: A Review

Antimicrobial resistance (AMR) is a global health threat, and antimicrobial usage and AMR in animal production is one of its contributing sources. Poultry is one of the most widespread types of meat consumed worldwide. Poultry flocks are often raised under intensive conditions using large amounts of antimicrobials to prevent and to treat disease, as well as for growth promotion. Antimicrobial resistant poultry pathogens may result in treatment failure, leading to economic losses, but also be a source of resistant bacteria/genes (including zoonotic bacteria) that may represent a risk to human health. Here we reviewed data on AMR in 12 poultry pathogens, including avian pathogenic Escherichia coli (APEC), Salmonella Pullorum/Gallinarum, Pasteurella multocida, Avibacterium paragallinarum, Gallibacterium anatis, Ornitobacterium rhinotracheale (ORT), Bordetella avium, Clostridium perfringens, Mycoplasma spp., Erysipelothrix rhusiopathiae, and Riemerella anatipestifer. A number of studies have demonstrated increases in resistance over time for S. Pullorum/Gallinarum, M. gallisepticum, and G. anatis. Among Enterobacteriaceae, APEC isolates displayed considerably higher levels of AMR compared with S. Pullorum/Gallinarum, with prevalence of resistance over >80% for ampicillin, amoxicillin, tetracycline across studies. Among the Gram-negative, non-Enterobacteriaceae pathogens, ORT had the highest levels of phenotypic resistance with median levels of AMR against co-trimoxazole, enrofloxacin, gentamicin, amoxicillin, and ceftiofur all exceeding 50%. In contrast, levels of resistance among P. multocida isolates were less than 20% for all antimicrobials. The study highlights considerable disparities in methodologies, as well as in criteria for phenotypic antimicrobial susceptibility testing and result interpretation. It is necessary to increase efforts to harmonize testing practices, and to promote free access to data on AMR in order to improve treatment guidelines as well as to monitor the evolution of AMR in poultry bacterial pathogens.

Further investigations on the epidemiology of fowl typhoid in Brazil

Salmonella Gallinarum (SG) causes fowl typhoid (FT), a disease responsible for economic losses to the poultry industry worldwide. FT has been considered to be under control in Brazil; nevertheless, since 2012 it has frequently been identified in poultry farming of several Brazilian states. The present study was aimed at assessing (i) the pathogenicity of a SG strain recently isolated from an FT outbreak affecting chickens of both white and brown layers; (ii) the transmission of SG through eggs and hatching; (iii) the effects of antibiotic therapy on SG persistence in poultry tissues and on its vertical transmission and (iv) the genetic profiles of strains isolated over 27 years by Pulsed Field Gel Electrophoresis. Clinical signs, mortality and gross pathologies were very marked amongst brown-egg layers. In contrast, clinical manifestation of FT and mortality were barely present amongst the white-egg layers, although bacteria could be re-isolated from their tissues up to 35 days after infection. No bacteria were re-isolated from the laid eggs, so vertical transmission was not achieved, although newly hatched uninfected chicks became infected spontaneously after hatching. Antibiotic therapy was shown to be effective at reducing mortality, but was not able to clear infection or to favour SG transmission via eggs. Our pulsed field gel electrophoresis results revealed an endemic SG clone that may have been circulating in the Brazilian poultry flocks in the south and southeast regions for more than 20 years. The results suggest that the industrial incubation of SG-contaminated eggs could be one of the factors responsible for the spread of FT in Brazil.

Amino acid substitutions in gyrA and parC associated with quinolone resistance in nalidixic acid-resistant Salmonella isolates

This study was undertaken to identify and characterize amino acid substitutions in gyrA and parC related with quinolone resistance of 27 nalidixic acid-resistant (Na^R) Salmonella isolates collected in poultry slaughterhouses in Korea. A total of 51 Salmonella isolates were detected from 44.8% (47/105) of the total samples from 15 poultry slaughterhouses examined, among which 27 (52.9%) Na^R isolates were detected while ciprofloxacin (Cip) resistance was not present in the isolates. These 27 Na^R isolates of DNA sequencing revealed that it contained three types of gyrA mutations in only D87 codon. Mutations in the D87 codon resulted in substitutions to G in most of the isolates, but D87Y and D87N exchanges were also detected. Although Cip resistance was absent, reduced susceptibility characterized by mutations in gyrA was apparent among Salmonella isolates from poultry slaughterhouses in Korea.

Comparative proteome and transcriptome analyses of wild-type and live vaccine strains of Salmonella enterica serovar Gallinarum

Salmonella enterica serovar Gallinarum causes fowl typhoid in chickens and is of economic importance to the chicken industry. A serovar Gallinarum live vaccine strain 9R (SG 9R) has been used to control fowl typhoid in many areas where the disease is endemic. Because the attenuation mechanism of SG 9R was not defined, there has been continued concern about reversion to virulence. In this study, we examined the molecular characteristics, which might provide better insight into attenuation of SG 9R, by comparing its proteome and transcriptome with those of two wild-type strains (287/91 and 06Q110). Proteins present in wild-type strains but absent in SG 9R were identified by two-dimensional gel electrophoresis and MALDI-TOF MS. Genes up- or down-regulated in SG 9R compared to wild-type strains were identified using an expression array. The proteome analysis identified nine proteins absent in SG 9R of which one protein had relevance to virulence. The transcriptome analysis revealed 24 up-regulated and 97 down-regulated genes in SG 9R. Approximately one-half of down-regulated genes (42 genes) were associated with virulence mechanisms. This finding suggests that attenuation of SG 9R may be associated with a combination of impaired virulence factors and thus reversion to virulence would not be caused by any single mutation event.