Prevalence, Serotype, Antibiotic Susceptibility, and Genotype of Salmonella in Eggs From Poultry Farms and Marketplaces in Yangling, Shaanxi Province, China

A pan-genome perspective on the evolutionary dynamics of polyphyly, virulence, and antibiotic resistance in Salmonella enterica serovar Mbandaka highlights emerging threats to public health and food safety posed by cloud gene families

Salmonella enterica serovar Mbandaka, a prevalent foodborne pathogen, poses a threat to public health but remains poorly understood. We have determined the phylogenomic tree, genetic diversity, virulence, and antimicrobial resistance (AMR) profiles on a large genomic scale to elucidate the evolutionary dynamics within the Mbandaka pan-genome. The polyphyletic nature of this serovar is characterized by two distinct phylogenetic groups and inter-serovar recombination boundaries, that potentially arising from recombination events at the H2-antigen loci. The open pan-genome exhibited a flexible gene repertoire, with numerous cloud gene families involved in virulence and AMR. Extensive gene gain and loss observed at the terminal nodes of the phylogenetic tree indicate that Mbandaka individuals have undergone frequent gene turnover. The resulting changes in virulence and AMR genes potentially pose emerging threats to public health. We explored serovar conversion due to recombination of H-antigen loci, inter-serovar divergences in gene gain and loss, prophage-mediated acquisition of virulence factors, and the role of incompatibility group plasmids in acquiring resistance determinants as key molecular mechanisms driving the pathogenicity and antibiotic resistance of Mbandaka. Our work contributes to a comprehensive understanding of the complex mechanisms of pathogenesis and the ongoing evolutionary arms race with current therapeutic approaches in serovar Mbandaka.

Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka

Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.

Multiplex PCR-based genotyping of Salmonella Enteritidis and Salmonella Typhimurium from food sources and assessment of their antimicrobial resistance profiles in Egypt

BACKGROUND

Salmonellosis is a widespread zoonotic disease that poses a significant threat to livestock and public health. This study aimed to serotype 20 Salmonella isolates obtained from sixty retail chicken meats, assess Salmonella contamination from eggs, and evaluate antibiotic resistance profiles.

METHODS AND RESULTS

Twenty eggs were randomly collected in the new Borg El Arab market. Bacterial isolation was carried out utilizing both traditional culture, biochemical, and PCR methods. Among the twenty eggs analyzed, three (15%) tested positive for Salmonella, while the remaining seventeen (85%) were confirmed as negative. Genotyping through multiplex PCR revealed the presence of two S. Enteritidis and other serovar, with the use of three specific gene sets: a random sequence for Salmonella spp., sdfI gene for S. Enteritidis, and flagellin (fliC gene) for S. Typhimurium. Out of the 20 isolates obtained from chicken meat, five (25%) were identified as S. Typhimurium, and three (15%) were classified as S. Enteritidis. All isolates sourced from chicken meat exhibited resistance to Rifampicin and Amoxicillin, with 90% displaying sensitivity to cefotaxime, gemifloxacin, and Erythromycin. Importantly, S. Blegdam, identified via serological methods, displayed resistance to all tested antibiotics. For the three isolates obtained from eggs, 66.6% showed sensitivity to cefotaxime, erythromycin, cefuraxime, and cefaclor, while displaying complete resistance (100%) to Amoxicillin, rifampicin, clarithromycin, and cefadroxil. Notably, one serovar exhibited absolute resistance to all tested drugs.

CONCLUSION

Stakeholders must implement strict control measures and rationalize antibiotic use in veterinary and human medicine due to the rise of antibiotic-resistant strains.

Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China

Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.

Prevalence and antimicrobial susceptibility of Salmonella enteritidis and Salmonella typhimurium isolated from hen eggs and quail eggs in Karaj, Iran

BACKGROUND AND AIM

Different Salmonella serotypes are considered one of the most important food pathogens in the world. Poultry meat and eggs are the primary carriers of Salmonella in human populations. This study aimed to estimate the Salmonella enteritidis and Salmonella typhimurium contamination rates of retail hen and quail eggs in Karaj, Iran. Moreover, the antimicrobial resistance patterns of the strains were evaluated, and the efficiency of the standard culture method and multiplex polymerase chain reaction (m-PCR) were compared.

MATERIALS AND METHODS

In this descriptive cross-sectional study over 1 year (Jan-Dec 2022), 150 commercial and 150 backyard hen eggs and 300 commercial quail eggs, without cracks and fractures, were collected randomly from best selling groceries in Karaj city. All samples were examined for Salmonella contamination independently by standard culture and m-PCR approaches. A standard disc diffusion method was employed to assess the antimicrobial susceptibility of the strains against 18 antimicrobial agents.

RESULTS

Out of 300 examined eggs, 2 S. enteritidis strains were isolated from the shell of backyard hen eggs. The same serotype was also detected in the contents of one of these two eggs. One S. typhimurium was isolated from the shell of a commercial hen egg. Overall, the Salmonella contamination of the shell and contents was 1% and 0.3%, respectively. Salmonella was not isolated from the eggshells or the contents of the quail eggs. There was complete agreement between the results of m-PCR and the standard culture methods. Among the 18 tested antibiotics, the highest resistance was recorded for colistin (100%), followed by nalidixic acid (75%).

CONCLUSION

As most Salmonella spp. are associated with human food poisoning, continuous surveillance is required to effectively reduce the risk posed by contaminated poultry eggs. Furthermore, mandatory monitoring of antimicrobial use on Iranian poultry farms is recommended.

Salmonella in eggs and egg-laying chickens: pathways to effective control

Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents.

Genomic Features and Phylogenetic Analysis of Antimicrobial-Resistant Salmonella Mbandaka ST413 Strains

In recent years, Salmonella enterica subsp. enterica serovar Mbandaka (S. Mbandaka) has been increasingly isolated from laying hens and shell eggs around the world. Moreover, this serovar has been identified as the causative agent of several salmonellosis outbreaks in humans. Surprisingly, little is known about the characteristics of this emerging serovar, and therefore, we investigated antimicrobial resistance, virulence, and prophage genes of six selected Brazilian strains of Salmonella Mbandaka using Whole Genome Sequencing (WGS). Multi-locus sequence typing revealed that the tested strains belong to Sequence Type 413 (ST413), which has been linked to recent multi-country salmonellosis outbreaks in Europe. A total of nine resistance genes were detected, and the most frequent ones were aac(6')-Iaa, sul1, qacE, blaOXA-129, tet(B), and aadA1. A point mutation in ParC at the 57th position (threonine → serine) associated with quinolone resistance was present in all investigated genomes. A 112,960 bp IncHI2A plasmid was mapped in 4/6 strains. This plasmid harboured tetracycline (tetACDR) and mercury (mer) resistance genes, genes contributing to conjugative transfer, and genes involved in plasmid maintenance. Most strains (four/six) carried Salmonella genomic island 1 (SGI1). All S. Mbandaka genomes carried seven pathogenicity islands (SPIs) involved in intracellular survival and virulence: SPIs 1-5, 9, and C63PI. The virulence genes csgC, fimY, tcfA, sscA, (two/six), and ssaS (one/six) were absent in some of the genomes; conversely, fimA, prgH, and mgtC were present in all of them. Five Salmonella bacteriophage sequences (with homology to Escherichia phage phiV10, Enterobacteria phage Fels-2, Enterobacteria phage HK542, Enterobacteria phage ST64T, Salmonella phage SW9) were identified, with protein counts between 31 and 54, genome lengths of 24.7 bp and 47.7 bp, and average GC content of 51.25%. In the phylogenetic analysis, the genomes of strains isolated from poultry in Brazil clustered into well-supported clades with a heterogeneous distribution, primarily associated with strains isolated from humans and food. The phylogenetic relationship of Brazilian S. Mbandaka suggests the presence of strains with high epidemiological significance and the potential to be linked to foodborne outbreaks. Overall, our results show that isolated strains of S. Mbandaka are multidrug-resistant and encode a rather conserved virulence machinery, which is an epidemiological hallmark of Salmonella strains that have successfully disseminated both regionally and globally.

Prevalence of Salmonella in Eggs from Conventional and Cage-Free Egg Production Systems and the Role of Consumers in Reducing Household Contamination

Salmonella is one of the leading causes of foodborne disease worldwide, usually related to contaminated poultry or poultry products, such as eggs. Since egg contamination with Salmonella depends on multiple factors that make it challenging to control, consumers' knowledge about food safety and the proper handling of eggs is crucial. The aims of the study were (1) to determine the prevalence of Salmonella in eggs from conventional and alternative production systems, (2) to characterize the Salmonella isolates according to phenotypic-genotypic and antimicrobial-resistant traits, and (3) to understand how consumers manage the hazards related to egg contamination in the household. A total of 426 egg samples were analyzed (conventional systems = 240; alternative systems = 186). Culture-based and molecular microbiological methods were used to identify Salmonella and bioinformatics analysis of whole genome sequences was used to determine the serotype and antimicrobial-resistant genes. Salmonella enterica serotype Enteritidis was detected only in eggs from alternative systems (1.1%, 2/186). Isolates showed resistance to nalidixic acid (100%, 2/2), and the aac(6')-Iaa gene and a mutation in the gyrA gene were identified in both isolates. Overall, consumers demonstrated knowledge regarding food safety; however, many still engage in practices that pose a risk of acquiring foodborne illnesses.

Resistance profiles, virulence and antimicrobial resistance genes of XDR S. Enteritidis and S. Typhimurium

Avian salmonellosis is concomitant with high financial crises in the poultry industry as well as food-borne illness in man. The present study is designed to investigate the emergence of Salmonella Enteritidis and Salmonella Typhimurium in diseased broilers, resistance profiles, and monitoring virulence and antibiotic resistance genes. Consequently, 450 samples (cloacal swabs, liver, and spleen) were collected from 150 diseased birds from different farms in Giza Governorate, Egypt. Subsequently, the bacteriological examination was done. Afterward, the obtained Salmonella isolates were tested for serogrouping, antibiogram, PCR monitoring of virulence (invA, stn, hilA, and pefA), and antimicrobial resistance genes (blaTEM, blaCTX-M, blaNDM, ermA, sul1, tetA, and aadA1). The total prevalence of Salmonella in the examined diseased broilers was 9.3%, and the highest prevalence was noticed in cloacal swabs. Among the recovered Salmonella isolates (n = 35), 20 serovars were recognized as S. Enteritidis and 15 serovars were identified as S. Typhimurium. Almost 60% of the retrieved S. Enteritidis serovars were extensively drug-resistant (XDR) to seven antimicrobial classes and inherited sul1, blaTEM, tetA, blaCTX-M, ereA, and aadA1 genes. Likewise, 25% of the recovered S. Enteritidis serovars were multidrug-resistant (MDR) to six classes and have sul1, blaTEM, tetA, blaCTX-M, and ereA resistance genes. Also, 66.7% of the retrieved S. Typhimurium serovars were XDR to seven classes and have sul1, blaTEM, tetA, blaCTX-M, ereA, and aadA1 genes. Succinctly, this report underlined the reemergence of XDR S. Typhimurium and S. Enteritidis in broiler chickens. Meropenem and norfloxacin exposed a hopeful antimicrobial activity toward the re-emerging XDR S. Typhimurium and S. Enteritidis in broilers. Moreover, the recurrence of these XDR Salmonella strains poses a potential public health threat.

Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China

Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.

Probiotics as a Friendly Antibiotic Alternative: Assessment of Their Effects on the Health and Productive Performance of Poultry

Antibiotics have been used to maintain the overall health of poultry by increasing production efficiency, promoting growth, and improving intestinal function for more than 50 years. However, they have a number of side effects, such as antibiotic resistance, gut dysbiosis, destruction of beneficial bacteria, and the potential to spread diseases to humans. In order to address the aforementioned issues, a lot of effort is put into the development of antibiotic alternatives. One of them is the use of probiotics that can be added to the feed in order to increase poultry performance and avoid the aforementioned problems. Probiotics are live microorganisms consumed as feed additives or supplements. They function in the poultry gastrointestinal tract to benefit the host. Probiotics improve growth performance, bone health, meat and eggshell quality. The addition of probiotics to the diet also positively affects the immune response, intestinal microflora, and disease resistance. Careful selection of probiotic strains is of utmost importance. This review focuses on the significance of probiotics as a potential antibiotic-free alternative and the way in which they can be used as supplements in poultry feed for boosting production and safeguarding health.

Prevalence and molecular detection of multidrug-resistant Salmonella spp. isolated from eggshells in the local markets of Dhaka, Bangladesh

Background and Aim: Salmonella spp. are frequently associated with various parts of the egg, including the shell, and cause foodborne outbreaks worldwide. Antibiotic-resistant Salmonella spp. pose serious threats to human and animal health; therefore, preventive measures against these pathogens are important. This study aimed to isolate and characterize Salmonella spp. from eggshell samples from different local markets in Dhaka, Bangladesh. Materials and Methods: Salmonella spp. were recovered from eggshells by enrichment culture and biochemical tests and characterized through molecular amplification of Salmonella-specific genes. Antibiotic sensitivity testing and molecular detection of isolates were performed by disk diffusion method and polymerase chain reaction (PCR), respectively. The invA, fliC, and sdfI genes were used in PCR to identify the genus Salmonella, and the species Salmonella Typhimurium and Salmonella Enteritidis, respectively. Results: The prevalence of Salmonella spp. was recorded as 40%, in which S. Typhimurium was the predominant serotype. PCR analysis revealed that 100%, 59%, and 13.6% of these isolates possessed the invA, fliC, and sdfI genes, respectively. The isolates exhibited multidrug resistance phenotypes, with resistance (95.5%) toward tetracycline, sulfamethoxazole, and clindamycin and sensitivity (86.3%) toward chloramphenicol. Conclusion: The findings of this study reflect the potential of eggs as a reservoir of multidrug-resistant Salmonella spp.; therefore, we recommend the careful handling of eggs to avoid contamination from farm to market.

Prudencio C, da Costa AC, Leal E, Chang CM, Pandey RP. Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA

Since the discovery of antibiotics in the 20th century, they have been used to fight against infections. The overuse of antibiotics in the wider environment has resulted in the emergence of multidrug-resistant bacteria. In developing countries such as China and developed countries such as the USA, there is evidence of the high pervasiveness of antibiotic-resistant infections. However, the studies on the spread of antibiotic-resistant microorganisms that inform about the consequences are limited. The aim of our study was to analyze and compare antimicrobial resistance (AMR) identified in published research papers from that found in different food sources, which were published between 2012 and December 2021, covering most retail food items. Out of 132 research papers identified, 26 papers have met our strict criteria and are included in the qualitative and quantitative analysis. The selected papers led to 13,018 food samples, out of which 5000 samples were contaminated, including 2276 and 2724 samples from China and the USA, respectively. Meat, aquatic products, milk, and eggs show high to medium potential for AMR exposure to Gram-positive bacteria such as Staphylococcus, Enterococci, etc. and Gram-negative foodborne pathogens such as Campylobacter, Salmonella, Vibrio, etc. Most of the food samples show antibiotic resistance to β-lactams, tetracycline, quinolones, and aminoglycosides. Retail food products such as meat, sea food, and some other food products, as well as AMR genetics and technically important bacteria, are proposed to be better merged with mitigation strategies and systematic One Health AMR surveillance to minimize the knowledge gaps and facilitate comprehensive AMR risk computation for the consumers.

Phenotypic and genotypic characterization of antimicrobial resistance profiles in Salmonella isolated from waterfowl in 2002–2005 and 2018–2020 in Sichuan, China

Salmonella enterica is a widespread foodborne pathogen with concerning antimicrobial resistance (AMR). Waterfowl are a major source of Salmonella transmission, but there are few systematic studies on Salmonella prevalence in waterfowl species. In this study, 126 Salmonella isolates (65 collected in 2018–2020 and 61 collected in 2002–2005) were obtained from waterfowl samples in Sichuan, China. Their serotypes, pulsed-field gel electrophoresis (PFGE) types, and phenotypic and genotypic AMR profiles were systematically examined. The isolates were distributed in 7 serotypes, including serovars Enteritidis (46.0%), Potsdam (27.8%), Montevideo (7.9%), Cerro (6.3%), Typhimurium (4.8%), Kottbus (4.0%) and Apeyeme (3.2%). Their PFGE characteristics were diverse; all isolates were distributed in four groups (cutoff value: 60.0%) and 20 clusters (cutoff value: 80.0%). Moreover, all isolates were multidrug resistant, and high rates of AMR to lincomycin (100.0%), rifampicin (100.0%), sulfadiazine (93.7%), erythromycin (89.7%), ciprofloxacin (81.0%), and gentamicin (75.4%) were observed. Finally, 49 isolates were subjected to whole-genome sequencing, and a wide variety of AMR genes were found, including multiple efflux pump genes and specific resistance genes. Interestingly, the tet(A)/tet(B) and catII resistance genes were detected in only isolates obtained in the first collection period, while the gyrA (S83F, D87N and D87G) and gyrB (E466D) mutations were detected at higher frequencies in the isolates obtained in the second collection period, supporting the findings that isolates from different periods exhibited different patterns of resistance to tetracycline, chloramphenicol and nalidixic acid. In addition, various incompatible plasmid replicon fragments were detected, including Col440I, Col440II, IncFIB, IncFII, IncX1, IncX9, IncI1-I and IncI2, which may contribute to the horizontal transmission of AMR genes and provide competitive advantages. In summary, we demonstrated that the Salmonella isolates prevalent in Sichuan waterfowl farms exhibited diverse serotypes, multiple AMR phenotypes and genotypes, and AMR changes over time, indicating their potential risks to public health.

Use of Phages to Treat Antimicrobial-Resistant Salmonella Infections in Poultry

Salmonellosis is one of the most common bacterial infections that impacts both human health and poultry production. Although antibiotics are usually recommended for treating Salmonella infections, their misuse results in the evolution and spread of multidrug-resistant (MDR) bacteria. To minimize the health and economic burdens associated with antimicrobial resistance, a novel antibacterial strategy that can obliterate pathogens without any adverse effects on humans and animals is urgently required. Therefore, therapeutic supplementation of phages has gained renewed attention because of their unique ability to lyse specific hosts, cost-effective production, environmentally-friendly properties, and other potential advantages over antibiotics. In addition, the safety and efficacy of phage therapy for controlling poultry-associated Salmonella have already been proven through experimental studies. Phages can be applied at every stage of poultry production, processing, and distribution through different modes of application. Despite having a few limitations, the optimized and regulated use of phage cocktails may prove to be an effective option to combat infections caused by MDR pathogens in the post-antibiotic era. This article mainly focuses on the occurrence of salmonellosis in poultry and its reduction with the aid of bacteriophages. We particularly discuss the prevalence of Salmonella infections in poultry and poultry products; review the trends in antibiotic resistance; and summarize the application, challenges, and prospects of phage therapy in the poultry industry.

Phylogenomic Analysis of Salmonella enterica Serovar Indiana ST17, an Emerging Multidrug-Resistant Clone in China

Salmonella enterica serovar Indiana (S. Indiana) is an extremely expanded foodborne pathogen in China in recent years. This study aimed to elucidate the national prevalence and phylogenomic characterization of this pathogen in China. Among 5, 287 serotyped Salmonella isolates collected during 2002 to 2018, 466 S. Indiana isolates were found in 15 provinces, and 407 were identified to be ST17, and the rest were ST2040. Among 407 ST17 isolates, 372 (91.4%) were multidrug resistant, and 366 (89.9%) were resistant to ciprofloxacin, 235 (57.7%) were further resistant to ceftriaxone. Phylogenomic analysis revealed that ST17 isolates were classified into four clades (I, II, III and IV), which appeared in international clonal dissemination. ST17 isolates from China fell into Clade IV with part of isolates from the United Kingdom, the United States, South Korea, and Thailand, suggesting their close genetic relationship. Mutations in quinolone resistance-determining regions (QRDR) of GyrA and ParC, and plasmid-mediated quinolone resistance (PMQR) genes aac(6′)-Ib-cr, oqxAB, and qnrS as well as extended spectrum β-lactamases (ESBL) genes bla_CTX-M, bla_OXA, and bla_TEM in isolates from Clade IV were much higher than those from other three clades. Various bla_CTX-M subtypes (bla_CTX-M-65, bla_CTX-M-55, bla_CTX-M-27, bla_CTX-M-14, and bla_CTX-M-123) with ISEcp1, IS903B, ISVsa5, and IS1R were found in ST17 isolates, especially Tn1721 containing ΔISEcp1-bla_CTX-M-27-IS903B in P1-like bacteriophage plasmids. These findings on the prevalent and genomic characterization for the S. Indiana multidrug-resistant ST17 clone in China, which have not been reported yet, provide valuable insights into the potential risk of this high-resistant clone.

IMPORTANCE Fluoroquinolones and cephalosporins are the primary choices for severe salmonellosis treatment. S. Indiana has become one of the most prevalent serovars in breeding poultry and poultry meats in China in recent years. ST17 was recognized as the leading epidemiological importance in S. Indiana because of its high-level resistance to the most of common antibiotics, including ciprofloxacin and ceftriaxone. However, the prevalence and phylogenomic characterization of ST17 isolates are unclear. Here, we did a retrospective screening on a large scale for S. Indiana in China, and performed its phylogenomic analysis. It was found that ST17 isolates had extensive spread in 15 provinces of China and became a multidrug-resistant clone. The international spread of the ST17 isolates was observed among several countries, especially China, the United Kingdom, and the United States. Our study emphasized the importance of surveillance of a high-resistant S. Indiana ST17 clone to combat its threat to public health.

Transcriptomic Analysis of the Spleen of Different Chicken Breeds Revealed the Differential Resistance of Salmonella Typhimurium

Salmonella Typhimurium (ST) is a foodborne pathogen that adversely affects the health of both animals and humans. Since poultry is a common source and carrier of the disease, controlling ST infection in chickens will have a protective impact on human health. In the current study, Beijing-You (BY) and Cobb chicks (5-day-old specific-pathogen-free) were orally challenged by 2.4 × 1012 CFU ST, spleen transcriptome was conducted 1 day post-infection (DPI) to identify gene markers and pathways related to the immune system. A total of 775 significant differentially expressed genes (DEGs) in comparisons between BY and Cobb were identified, including 498 upregulated and 277 downregulated genes (fold change ≥2.0, p < 0.05). Several immune response pathways against Salmonella were enriched, including natural killer-cell-mediated-cytotoxicity, cytokine−cytokine receptor interaction, antigen processing and presentation, phagosomes, and intestinal immune network for IgA production, for both BY and Cobb chickens. The BY chicks showed a robust response for clearance of bacterial load, immune response, and robust activation of phagosomes, resulting in ST resistance. These results confirmed that BY breed more resistance to ST challenge and will provide a better understanding of BY and Cobb chickens’ susceptibility and resistance to ST infection at the early stages of host immune response, which could expand the known intricacies of molecular mechanisms in chicken immunological responses against ST. Pathways induced by Salmonella infection may provide a novel approach to developing preventive and curative strategies for ST, and increase inherent resistance in animals through genetic selection.

Prevalence of Salmonella in Chinese Food Commodities: A Meta-Analysis

ABSTRACT

The objective of the present study was to analyze the prevalence of Salmonella in multiple food commodities in the People's Republic of China by performing a meta-analysis. Accordingly, we screened studies that examined the prevalence of Salmonella in PubMed, Embase, and Web of Science databases. Methodological quality assessment and heterogeneity analyses were performed for included studies. The prevalence rate with the 95% confidence interval (CI) was selected as the effect size. Subgroup analyses for each food type were conducted and then stratified by regions, food chain processing points, and seasons. In total, 49 studies were included in the meta-analysis, among them, 8 (16.3%) studies were deemed "high risk," 13 (26.5%) studies were "unclear risk," and 28 (57.2%) studies were "low risk." The overall prevalence rate of Salmonella was 20.0% (95% CI: 15.9 to 24.4). The prevalence rate of Salmonella in raw meat products was 23.6% (95% CI: 19.8 to 27.6), which was higher than that in aquatic products, 13.7% (95% CI: 3.1 to 29.9), milk products, 0.9% (95% CI: 0.0 to 3.9), frozen convenience foods, 6.5% (95% CI: 4.4 to 8.9), ready-to-eat foods, 2.0% (95% CI: 1.1 to 3.2), vegetables and fruits, 0.9% (95% CI: 0.0 to 5.2), and shell eggs, 4.2% (95% CI: 3.0 to 5.7). Subgroup analyses revealed that prevalence rates of Salmonella in raw meat products from abattoirs, 26.3% (95% CI: 17.4 to 36.3) and retail stores, 30.0% (95% CI: 24.6 to 35.8) were higher than those determined from farms, 10.2% (95% CI: 7.0 to 13.9); P < 0.05); however, no significant difference was observed in the prevalence of Salmonella stratified by different geographical regions or seasons (P > 0.05). On the basis of these findings, high levels of Salmonella contamination could be detected in raw meat products in China, and the prevalence rate of Salmonella in raw meat products from abattoirs and retail stores was high.

HIGHLIGHTS

Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r < 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r > −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

Characteristics of Salmonella From Chinese Native Chicken Breeds Fed on Conventional or Antibiotic-Free Diets

Salmonella is a common food-borne Gram-negative pathogen with multiple serotypes. Pullorum disease, caused by Salmonella Pullorum, seriously threatens the poultry industry. Many previous studies were focused on the epidemiological characteristics of Salmonella infections in conventional antibiotic use poultry. However, little is known about Salmonella infections in chicken flocks fed on antibiotic-free diets. Herein, we investigated and compared Salmonella infections in three Chinese native breeders fed on antibiotic-free diets, including the Luhua, Langya, and Qingjiaoma chickens, and one conventional breeder, the Bairi chicken, via analyzing 360 dead embryos in 2019. The results showed that the main Salmonella serotypes detected in a total of 155 isolates were S. Pullorum (82.6%) and S. Enteritidis (17.4%). Coinfection with two serotypes of Salmonella was specifically found in Bairi chicken. The sequence type (ST) in S. Pullorum was ST92 (n = 96) and ST2151 (n = 32), whereas only ST11 (n = 27) was found in S. Enteritidis. The Salmonella isolates from three breeder flocks fed on antibiotic-free diets exhibited phenotypic heterogeneity with a great variety of drug resistance spectrum. Most of the isolates among three chicken breeds Luhua (64.9%, 50/77), Langya (60%, 12/20) and Qingjiaoma (58.3%, 7/12) fed on antibiotic-free diets were resistant to only one antibiotic (erythromycin), whereas the rate of resistance to one antibiotic in conventional Bairi chicken isolates was only 4.3% (2/46). The multidrug-resistance rate in Salmonella isolates from layer flocks fed on antibiotic-free diets (20.2%, 22/109) was significantly (P < 0.0001) lower than that from chickens fed on conventional diets (93.5%, 43/46). However, high rate of resistance to erythromycin (97.4%~100%) and streptomycin (26%~41.7%) were also found among three breeder flocks fed on antibiotic-free diets, indicating resistance to these antibiotics likely spread before antibiotic-free feeding in poultry farms. The findings of this study supplement the epidemiological data of salmonellosis and provide an example of the characteristics of Salmonella in the chicken flocks without direct antibiotic selective pressure.

Prevalence and Antimicrobial Resistance of Salmonella Isolated From Dead-in-Shell Chicken Embryos in Shandong, China

The present study was designed to explore the Salmonella prevalence and antimicrobial resistance characteristics in the context of chick mortality at hatching in China. Between December 2015 and August 2017, 1,288 dead-in-shell chicken embryos were collected from four breeder chicken hatcheries in Tai'an, Rizhao, Jining, and Heze, China. Salmonella isolates were successfully recovered from 6.7% of these embryos (86/1,288) and were evaluated for serotype, antimicrobial susceptibility, Class 1 integron prevalence, antimicrobial resistance gene expression, and multilocus sequence typing (MLST). Salmonella Thompson (37.2%), and Salmonella Infantis (32.6%) were the two most prevalent isolates in these chicken embryos, and 66.3% of isolates exhibited robust ampicillin resistance, while 55.8% of isolates exhibited multi-drug resistance (MDR). The majority of isolates harbored the bla_TEM gene (74.4%), with the qnrS gene also being highly prevalent (50.0%). In contrast, just 27.9% of these isolates carried Class 1 integrons. These 86 isolates were separated into four sequence types (STs), whereby ST26 (32.2%) was the most prevalent. Overall, these results suggested that Salmonella infections may be an important cause of chicken embryo mortality in China, and that efforts to support the appropriate use of antibiotics in managing poultry populations are essential.