Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old

Mimicking bacterial infection in male mice changes sperm small RNA profiles and multigenerationally alters offspring behavior and physiology

Paternal pre-conceptual exposures, including stress, diet, substance abuse, parasite infection, and viral immune activation via Poly I:C, have been reported to influence the brains and behavior of offspring through sperm epigenetic changes. However, the effects of paternal (F0) pre-conceptual exposure to bacterial-induced immune activation on the behavior and physiology of F1 and F2 generations remain unexplored. We examined this using C57BL/6J mice. Eight-week-old males (F0) received a single intraperitoneal injection of the bacterial mimetic lipopolysaccharide (LPS: 5 mg/kg) or 0.9 % saline (vehicle control) before mating with naïve females at four weeks post-injection. Comprehensive behavioral assessments were conducted to investigate anxiety, social behaviors, depressive-like behaviors and cognition in both the F1 and F2 generations within the age range of 8 to 14 weeks. Results demonstrated that only female offspring of LPS-exposed fathers exhibited reduced anxiety levels in the light/dark box, large open field, and novelty-suppressed feeding test. These F1 female offspring also exhibited heightened sociability in the 3-chambered social interaction test and a reduced preference for saccharin in the saccharin preference test. Additionally, the F1 male offspring of LPS-challenged males demonstrated an increased total distance traveled in the light/dark box and a longer distance covered in the light zone. They also exhibited diminished preference for social novelty in the 3-chambered social interaction test and an elevated novel arm preference index in the Y-maze. In the F2 generation, male descendants of LPS-treated fathers showed reduced latency to feed in the novelty-suppressed feeding test. Additionally, the F2 generation of LPS-challenged fathers, but not the F1 generation, displayed enhanced immune response in both sexes after an acute LPS immune challenge (5 mg/kg). Analysis of sperm small noncoding RNA profiles from LPS-treated F0 mice revealed significant changes at 4 weeks after administration of LPS. These changes included three microRNAs, eight PIWI-interacting RNAs, and two transfer RNAs, exhibiting significant upregulation (mmu-miR-146a-5p, mmu-piR-27082 and mmu-piR-29102) or downregulation (mmu-miR-5110, mmu-miR-467e-3p, mmu-piR-22583, mmu-piR-23548, mmu-piR-36341, mmu-piR-50293, mmu-piR-16583, mmu-piR-36507, Mus_musculus_tRNA-Ile-AAT-2-1 and Mus_musculus_tRNA-Tyr-GTA-1-1). Additionally, we detected 52 upregulated small noncoding RNAs (including 9 miRNAs, 41 piRNAs, and 2 tRNAs) and 7 downregulated small noncoding RNAs (3 miRNAs, 3 piRNAs, and 1 tRNA) in the sperm of F1 offspring from LPS-treated males. These findings provide compelling evidence for the involvement of epigenetic mechanisms in the modulation of brain function and immunity, and associated behavioral and immunological traits, across generations, in response to bacterial infection.

Antimicrobial Resistance Profiles and Molecular Characteristics of Salmonella enterica Serovar Agona Isolated from Food-Producing Animals During 2010-2020 in South Korea

Multidrug-resistant (MDR) Salmonella enterica serovar Agona infections affect public health globally. This investigation aimed to ascertain the antimicrobial resistance profiles and molecular characteristics of Salmonella Agona isolates obtained from food-producing animals. A total of 209 Salmonella Agona isolates were recovered from mostly chickens (139 isolates), pigs (56 isolates), cattle (11 isolates), and ducks (3 isolates) between 2010 and 2020 in South Korea. In addition, these Salmonella Agona isolates were obtained from 25 slaughterhouses nationwide. Furthermore, this serotype suddenly increased in chickens in 2020. Salmonella Agona from chickens showed high resistance (69-83%) to ampicillin, streptomycin, tetracycline, trimethoprim/sulfamethoxazole, and chloramphenicol. Moreover, chicken/duck isolates (83.1%) showed significantly higher levels of MDR than cattle/pig isolates (1.5%). For molecular analysis by pulsed-field gel electrophoresis, infrared spectroscopy biotyping, and multilocus sequence typing in combination, a total of 23 types were observed. Especially two major types, P1-III-2-13 and P1-IV-2-13, comprised 59.3% of the total isolates spreading in most farms. Moreover, Salmonella Agona sequence type (ST)13 was predominant (96.7%) among three different STs (ST13, ST11, and ST292) widely detected in chickens (94.3%) in most farms located nationwide. Taken together, MDR Salmonella Agona in chickens might pose a potential risk to public health through direct contact or the food chain.

Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay

Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.

Whole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan

BACKGROUND

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan.

METHODOLOGY

We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation.

RESULTS

MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis.

CONCLUSION

This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.

An extremely rare serovar of Salmonella enterica (Yopougon) discovered in a Western Whip Snake (Hierophis viridiflavus) from Montecristo Island, Italy: case report and review

Reptiles, including snakes, can be asymptomatically infected with multiple pathogen microorganisms, including Salmonella spp., which is considered an important concern for public and animal health. Small and uninhabited isles are quite ecologically different from mainland and represent interesting fields of study, to discover unexpected biological and microbiological aspects of their wild inhabitants. This work reports the presence of the very rare Salmonella enterica serovar Yopougon, isolated in a carcass of a native wild snake (Hierophis viridiflavus) from an Italian uninhabited island of Mediterranean Sea, Montecristo. To our knowledge, S. enterica serovar Yopougon was previously isolated only once 34 years earlier in Ivory Coast, from a human fecal sample. In the present study, we present the genomic characterization of the new isolate, the phylogenetic comparison with the previously isolated S. enterica serovar Yopougon strain of human origin and with other sequences available in public databases. In addition, an extensive review of available data in the literature and from our case history is provided. Our finding represents an example of the ability of some pathogens to travel for very long distances within their hosts and then to infect others, even from different taxa.

An integrated nationwide genomics study reveals transmission modes of typhoid fever in China

IMPORTANCE

Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi, resulting in a significant disease burden across developing countries. Historically, China was very much close to the global epicenter of typhoid, but the role of typhoid transmission within China and among epicenter remains overlooked in previous investigations. By using newly produced genomics on a national scale, we clarify the complex local and global transmission history of such a notorious disease agent in China spanning the most recent five decades, which largely undermines the global public health network.

A therapeutic epitopes-based vaccine engineering against Salmonella enterica XDR strains for typhoid fever: a Pan-vaccinomics approach

A prevalent food-borne pathogen, Salmonella enterica serotypes Typhi, is responsible for gastrointestinal and systemic infections globally. Salmonella vaccines are the most effective, however, producing a broad-spectrum vaccine remains challenging due to Salmonella's many serotypes. Efforts are urgently required to develop a novel vaccine candidate that can tackle all S. Typhi strains because of their high resistance to multiple kinds of antibiotics (particularly the XDR H58 strain). In this work, we used a computational pangenome-based vaccine design technique on all available (n = 119) S. Typhi reference genomes and identified one TonB-dependent siderophore receptor (WP_001034967.1) as highly conserved and prospective vaccine candidates from the predicted core genome (n = 3,351). The applied pan-proteomics and Immunoinformatic approaches help in the identification of four epitopes that may trigger adequate host body immune responses. Furthermore, the proposed vaccine ensemble demonstrates a stable binding conformation with the examined immunological receptor (HLAs and TRL2/4) and has large interaction energy determined via molecular docking and molecular dynamics simulation techniques. Eventually, an expression vector for the Escherichia. coli K12 strain was constructed from the vaccine sequence. Additional analysis revealed that the vaccine may help to elicit strong immune responses for typhoid infections, however, experimental analysis is required to verify the vaccine's effectiveness based on these results. Moreover, the applied computer-assisted vaccine design may considerably decrease vaccine development costs and speed up the process. The study's findings are intriguing, but they must be evaluated in the experimental labs to confirm the developed vaccine's biological efficiency against XDR S. Typhi.Communicated by Ramaswamy H. Sarma.

Assessment of multidrug-resistant profile, multi-locus sequence typing and efflux pump activity in Salmonella Typhimurium isolated from hospital sewage

Salmonella enterica serovar Typhimurium is becoming a leading cause of gastroenteritis and mortality. The use of antibiotics has increased natural resistance of S. Typhimurium to antibiotics. This study aims to isolate and characterize multi-drug-resistant (MDR) Salmonella strains from hospital sewage samples in Bhopal City, central India. The MDR isolates were characterized by molecular identification, antimicrobial resistance patterns, multi-locus sequence typing, and efflux pump activity. Specific genes (hilA, stn, invA, typh, and iroB) were used to confirm S. Typhimurium isolates. The Kirbey-Bauer method was employed to profile antimicrobial resistance using 20 antibiotics. Multi-locus sequence typing confirmed S. Typhimurium using seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thr). Out of five strains, only four were confirmed as S. Typhimurium during MLST analysis. Efflux pump activity was determined using the ethidium bromide (EtBr) cartwheel test. Of the 160 isolates, 38 were presumptively confirmed as S. Typhimurium based on biochemical characterization, and only five MDR Salmonella strains were selected for their resistance against most antibiotics. Efflux pump activity revealed that five out of the four MDR isolates did not retain EtBr inside the cells, indicating pronounced efflux activity. Additionally, the isolated strains showed a specific correlation between the antimicrobial phenotypes and genotypes. The results of this study provide a better understanding of the characterization of S. Typhimurium serotype in Bhopal City. Future studies should focus on understanding changing antimicrobial resistance patterns, pathogenicity, and the genetic background of Salmonella serotypes. Further surveillance activities for antimicrobial-resistant Salmonella in different environmental sources should be prioritized.

Salmonella enterica Serovar Typhi on an Island: No H58, No Multidrug Resistance, but for How Long?

Little genomic data is available for typhoid fever from island nations, though the disease has a moderately high burden there. Sikorski et al. (M. J. Sikorski, T. H. Hazen, S. N. Desai, S. Nimarota-Brown, et al., mBio 13:e01920-22, 2022, https://doi.org/10.1128/mbio.01920-22) studied 306 Salmonella enterica serovar Typhi genomes from the Samoan Islands collected during 1983 to 2020 and reported dominance of a rare genotype, 2.5.4, and no H58 (genotype 4.3.1). They found pansusceptibility of all isolates to three first lines of antimicrobial agents (ampicillin, chloramphenicol, and cotrimoxazole). This commentary evaluates the importance of these findings for the Samoan Islands and how they can help the global typhoid community. The microbial community in the environment and human gut could have played a role in the lack of antimicrobial resistance (AMR). However, drug-resistant strains may arrive soon at the island, as their international spread is common. Further investigation would help the global typhoid community to better understand the evolution of an isolated pathogen community and the effect of vaccination there.

A Familiar Outbreak of Monophasic Salmonella serovar Typhimurium (ST34) Involving Three Dogs and Their Owner's Children

Salmonella is a Gram-negative enteric bacterium responsible for the foodborne and waterborne disease salmonellosis, which is the second most reported bacterial zoonosis in humans. Many animals are potential sources of salmonellosis, including dogs, cats, and other pets. We report the case of an outbreak of salmonellosis in a family in central Italy, affecting two children and involving their three dogs as carriers. One of the children needed medical care and hospitalisation. Isolation and analysis of stool samples from the sibling and the animals present in the house were carried out. Serotyping allowed the identification of S. enterica subsp. enterica serovar Typhimurium in its monophasic variant for all the isolates. The results of whole-genome sequencing confirmed that the strains were tightly related. The minimum inhibitory concentration (MIC) test documented the resistance to ampicillin, sulfamethoxazole, and tetracycline. The origin of the zoonotic outbreak could not be assessed; however, the case study showed a clear passage of the pathogen between the human and non-human members of the family. The possibility of a transmission from a dog to a human suggests the need for further studies on the potential ways of transmission of salmonellosis through standard and alternative feed.

Multi‑locus sequence and drug resistance analysis of Salmonella infection in children with diarrhea in Guangdong to identify the dominant ST and cause of antibiotic‑resistance

Multi-locus sequence typing (MLST) can be used to analyze the homology among the drug resistance gene cassettes in Salmonella and determine the prevalence. Information extracted using this technique can provide a theoretical basis for hospitals to devise protocols to control Salmonella infections. The aim of the present study was to investigate the possible association between drug resistance and integrons in clinical isolates of Salmonella from human fecal samples. Therefore, in the present study, 52 clinical fecal isolates of non-duplicate (i.e., not genome contamination) Salmonella were harvested from children with diarrhea and used for bacterial identification using biochemical tests, drug susceptibility analysis by antibiotic susceptibility testing and serotype identification using an agglutination assay. In total, seven Salmonella housekeeping genes (chorismate synthase, β sliding clamp of DNA polymerase III, uroporphyrinogen-III synthase, histidinol dehydrogenase, phosphoribosylaminoimidazole carboxylase catalytic subunit, 2-oxoglutarate dehydrogenase E1 component and homoserine dehydrogenase) were amplified and sequenced using MLST, before sequence alignment was performed against the Pub MLST database to determine the sequence-typed (ST) strains and construct genotypic evolutionary diagrams. Subsequently, the 52 Salmonella strains were subdivided into 11 serotypes and 11 sequence types. The dominant subtypes were found to be Salmonella typhimurium ST34 and ST19, which were diversely distributed. However, no new subtypes were found. Although the serotypes, including ST19, ST29, ST34, ST40, ST11, ST27, ST469, ST365, ST1499, ST413 and ST588, were closely associated with the MLST subtype, they did not correspond entirely. The detection rate of class I integrons was 38.46% (20/52), but no class II and III integrons were detected. The variable regions of three of 20 class I integrons were found to be amplified, whereas nine gene cassettes, including dihydrofolate reductase A12, open reading frame F, aminoglycoside-adenylyltransferase (aad)A2, aadA22, aadA23, aadA1, cadmium-translocating P-type ATPase 2, lincosamide and linF, were associated with drug resistance. These data suggest that Class I integrons are important factors underlying drug resistance in Salmonella, which may serve a role in the spread of drug resistance and warrant specific focus. In addition, MLST typing and serotyping should be applied cooperatively in epidemiological research.

Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa

For decades, the remote island nation of Samoa (population ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008 to 2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sublineages were identified, and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other 3.5 clade isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically cryptic plasmid, detected in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as fill a critical knowledge gap in S. Typhi genomic data from Oceania. IMPORTANCE In this study, we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rare S. Typhi population in Samoa that likely emerged around the early 1970s and evolved into sublineages that are presently dominant. The dominance of these endemic genotypes in Samoa is not readily explained by genomic content or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance of S. Typhi in Samoa for public health benefit.

Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo

Background

Invasive non-typhoidal Salmonella (iNTS–mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans.

Methodology/Principal findings

From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans—obtained from blood cultures at Kisangani University Hospital—was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible.

Conclusion

The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa.

Dadi (°1974, DR Congo) is a Medical Doctor (Kisangani University 2005) with a master in pediatrics (Kisangani University 2015) with special interest in infectious diseases and tropical medicine. He has 11 years of field research experience. He was team member of scientific expedition “Boyekoli Ebale Congo” in 2010 as medical support for the researchers. He conducted work field in a multidisciplinary framework with biologists from faculty of sciences (university of Kisangani) exploring zoonotic diseases in several places in the Congo. Currently, he is doing his PhD research at KU Leuven and Institute of Tropical Medicine Antwerp (ITM), Belgium. Passionate about transmissible diseases, Dadi is exploring the potential reservoirs of non-typhoidal Salmonella in Kisangani, DR Congo.

Dynamics of Antimicrobial Resistance and Genomic Epidemiology of Multidrug-Resistant Salmonella enterica Serovar Indiana ST17 from 2006 to 2017 in China

The genetic features of foodborne Salmonella have changed in recent years as multidrug-resistant (MDR) strains have become prevalent among various serovars. The recent expansion of MDR Salmonella enterica serovar Indiana sequence type 17 (ST17) poses an increasing threat to global public health, as 24.3% (61/251) of S. Indiana isolates in this study exhibited resistance to three clinically important antimicrobial agents: fluoroquinolones (ciprofloxacin), extended-spectrum β-lactams (cephalosporin), and macrolides (azithromycin). Both the evolutionary histories and antimicrobial resistance (AMR) profiles of this serovar remain to be described. Bioinformatic analysis revealed multiple lineages have coexisted and spread throughout China. Specifically, emergence of a predominant lineage appears to be associated with accumulated various substitutions in the chromosomal quinolone resistance-determining regions (GyrA S83F D87N and ParC T57S S80R) (141 [56.2%]), as well as acquisition of an extended-spectrum β-lactamase (ESBL)-producing IncHI2 plasmid that has subsequently undergone extensive rearrangement and an IncX1 plasmid that contains mph(A), conferring resistance to azithromycin. Several other evolutionary events influencing the trajectory of this drug-resistant serovar were also identified, including sporadic acquisitions of bla_CTX-M-carrying plasmids, along with chromosomal integration of bla_CTX-M within subclusters. Most human isolates reside in clusters containing isolates from animals, mainly from chickens, indicating the close relationship of human isolates with those from food animals. These data demonstrate that MDR S. Indiana ST17 is already widespread and capable of acquiring resistance traits against the clinical important antimicrobial agents, suggesting it should be considered a high-risk global MDR pathogen. The complexity of its evolutionary history has implications for AMR surveillance, epidemiological analysis, and control of emerging clinical lineages.

IMPORTANCE The emergence and worldwide spread of AMR Salmonella constitute great public health concerns. S. enterica serovar Indiana is a typical MDR serovar characterized by sporadic reports. However, comprehensive population genomics studies have not been performed on this serovar. This study provides a detailed and comprehensive insight into the rapid evolution of AMR in this important Salmonella serovar in the past 15 years in eight provinces of China. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, the persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance determinants that occur at all genetic levels (genes, genetic contexts, plasmids, and host strains). There are different mechanisms of antimicrobial resistance in S. enterica serovar Indiana from those of other serovars. This study sheds light on the formation of MDR S. enterica serovar Indiana with chickens as its potential reservoirs and paves the way to curb its further expansion among food animals.

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

BACKGROUND

Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji.

METHODS

Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases.

FINDINGS

Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted.

INTERPRETATION

Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries.

FUNDING

This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.

Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica

Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.

Changes in physiological states of Salmonella Typhimurium measured by qPCR with PMA and DyeTox13 Green Azide after pasteurization and UV treatment

Diarrheal diseases caused by Salmonella pose a major threat to public health, and assessment of bacterial viability is critical in determining the safety of food and drinking water after disinfection. Viability PCR could overcome the limitations of traditional culture-dependent methods for a more accurate assessment of the viability of a microbial sample. In this study, the physiological changes in Salmonella Typhimurium induced by pasteurization and UV treatment were evaluated using a culture-based method, RT-qPCR, and viability PCR. The plate count results showed no culturable S. Typhimurium after the pasteurization and UV treatments, while viability PCR with propidium monoazide (PMA) and DyeTox13-qPCR indicated that the membrane integrity of S. Typhimurium remained intact with no metabolic activity. The RT-qPCR results demonstrated that invasion protein (invA) was detectable in UV-treated cells even though the log2-fold change ranged from - 2.13 to - 5.53 for PMA treatment. However, the catalytic activity gene purE was under the detection limit after UV treatment, indicating that most Salmonella entered metabolically inactive status after UV disinfection. Also, viability PCRs were tested with artificially contaminated eggs to determine physiological status on actual food matrices. DyeTox13-qPCR methods showed that most Salmonella lost their metabolic activity but retained membrane integrity after UV disinfection. RT-qPCR may not determine the physiological status of Salmonella after UV disinfection because mRNA could be detectable in UV-treated cells depending on the choice of target gene. Viability PCR demonstrated potential for rapid and specific detection of pathogens with physiological states such as membrane integrity and metabolic activity.Key Points• Membrane integrity of Salmonella remained intact with no metabolic activity after UV.• mRNA could be detectable in UV-treated cells depending on the choice of target gene.• Viability PCR could rapidly detect specific pathogens with their physiological states.

Detection of free chlorine in water using graphene-like carbon based chemiresistive sensors

Free chlorine is the most commonly used water disinfectant. Measuring its concentration during and after water treatment is crucial to ensure its effectiveness. However, many of the existing methods do not allow for continuous on-line monitoring. Here we demonstrate a solid state chemiresistive sensor using graphene-like carbon (GLC) that overcomes that issue. GLC films that were either bare or non-covalently functionalized with the redox-active phenyl-capped aniline tetramer (PCAT) were successfully employed to quantify aqueous free chlorine, although functionalized devices showed better performance. The response of the sensors to increasing concentrations of free chlorine followed a Langmuir adsorption isotherm in the two tested ranges: 0.01–0.2 ppm and 0.2–1.4 ppm. The limit of detection was estimated to be 1 ppb, permitting the detection of breaches in chlorine filters. The devices respond to decreasing levels of free chlorine without the need for a reset, allowing for the continuous monitoring of fluctuations in the concentration. The maximum sensor response and saturation concentration were found to depend on the thickness of the GLC film. Hence, the sensitivity and dynamic range of the sensors can be tailored to different applications by adjusting the thickness of the films. Tap water samples from a residential area were tested using these sensors, which showed good agreement with standard colorimetric measurement methods. The devices did not suffer from interferences in the presence of ions commonly found in drinking water. Overall, these sensors are a cost-effective option for the continuous automated monitoring of free chlorine in drinking water.

Chemiresistive sensors based on graphene-like carbon films are very stable and sensitive. They can be used for continuous online monitoring of free chlorine.

Agar-Integrated Three-Dimensional Microelectrodes for On-Chip Impedimetric Monitoring of Bacterial Viability

Monitoring bacterial viability is critical in food safety, clinical microbiology, therapeutics, and microbial fuel cell applications. Traditional techniques for detecting and counting viable cells are slow, require expensive and bulky analytical tools and labeling agents, or are destructive to cells. Development of low-cost, portable diagnostics to enable label-free detection and in situ probing of bacterial viability can significantly advance the biomedical field (both applied and basic research). We developed a highly sensitive method for the detection of bacterial viability based on their metabolic activity using non-Faradaic impedimetric sensors comprised of three-dimensional (3D) interdigitated microelectrodes (3D-IDME). Specifically, the 3D-IDME is modified with electrolessly deposited gold (Au) nanoparticles which amplify the sensitivity by increasing the sensing area. A nutrient-rich agarose gel as the seeding layer is integrated with the sensor to enable direct culturing of bacteria and probing of their metabolic activity in situ. The proposed platform enables monitoring of bacterial viability, even in lag-phase, as they metabolize and release ionic species into the surrounding environment (nutrient agar layer). The sensor can detect down to 10⁴ CFU/mL (~2.5 CFU/mm²) of Escherichia coli K12 (a model strain) in under 1 h without the need for any labeling. By integrating these sensors with agar layers containing different types/concentrations of antibacterial agents, this work can be expanded to enable rapid, high-throughput antibacterial susceptibility testing which can in turn assist caregivers in early prescription of the right treatment to patients with clinical conditions.

Molecular Characteristics and Antimicrobial Resistance of Salmonella enterica Serovar Schwarzengrund from Chicken Meat in Japan

Our previous study revealed that Salmonella enterica serovar Schwarzengrund-contaminated areas of broiler chickens have expanded from West Japan to East Japan. The present study investigated the antimicrobial resistance and molecular characteristics of 124 S. Schwarzengrund isolates obtained from chicken meat produced in East and West Japan from 2008 to 2019. Comparing the isolates obtained in 2008 and 2015–2019, an increase in the proportion of those resistant to kanamycin [51.4–89.7% (p < 0.001)] was observed. In contrast, the proportion of isolates resistant to both streptomycin and tetracycline and those that harbored a 1.0-kb class 1 integron, aadA1, and tetA, significantly decreased from 100% in 2008 to 47.1% in 2015–2019 (p < 0.001). A 1.0-kb class 1 integron containing aadA1, harbored by 78 isolates, was different from that reported in globally distributed S. Schwarzengrund strains (1.9 kb, containing the dfrA12-aadA2 gene cassette). Twenty-five isolates from different product districts and years of isolation were typed as sequence type (ST) 241 with multilocus sequence typing. Our results suggest that S. Schwarzengrund, which contaminates chicken meat in Japan, shares a common ancestor regardless of the product district from 2008 to recent years. Moreover, S. Schwarzengrund ST241 may have spread from western to eastern Japan.

Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

Prevalence, typing and antimicrobial resistance of Salmonella isolates from commercial shellfish in the North coast of Morocco

Salmonellosis is one of the most common foodborne illnesses in the world. The irrational use of antibiotics in medicine and in animal nutrition has greatly favored the emergence and spread of resistant strains of non-typhoid Salmonella. This study aims the determination of the prevalence of Salmonella in bivalve mollusks in Northern Morocco, as well as the molecular typing and antibiotic susceptibility testing of the strains isolated from positive samples. In total, 150 samples from shellfish composed of mussels (Mytilus galloprovincialis), clams (Callista chione and Ruditapes descussatus) and oysters (Magallana gigas). Isolated Salmonella were characterized by Molecular techniques PCR, MLST and MLVA, phylogenetically grouped by MLSA, and susceptibilities were determined for 30 antimicrobial drugs using microdilution method by the BD Phoenix Automated Microbiology System. Prevalence of Salmonella enterica subsp. enterica was 12.67%, grouped in four serovars identified as Chester, Hadar, Typhimurium and Kentucky. Five different MLST STs (sequence types) were detected, ST1954 being the most common, which was mostly found in Chester isolates. Forty-two percent of the isolates showed resistance to more than one antibiotic, especially trimethoprim, sulfa drugs, quinolones and β-lactam. There was a marked change in the serovars and antimicrobial resistance profiles of the Salmonella isolates in this study compared to those in previous studies.

Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.

Prevalence, Characterization, and Pathogenicity of Salmonella enterica Subspecies enterica Serovar Derby from Yaks in the Aba Tibetan Autonomous Prefecture, China

Simple Summary

Salmonella spp. is a very important pathogen in the livestock industry and public health, which poses a major threat to global public health. Yaks and their by-products have a significant economic status in the Qinghai–Tibetan Plateau. The aim of this study was to investigate the prevalence of salmonella in yak farms and to conduct a molecular characterization and tests on its pathogenicity in mice with the use of salmonella isolated from yaks with diarrhea as well as from drinking water samples. The prevalence of salmonella was 19.75% of 162 samples collected from yak farms, and all isolates were found to belong to the serovar of Salmonella Derby and ST40. All Salmonella Derby isolates from both fecal and drinking water samples from 13 farms were clonally related based on SNP alignment. Salmonella Derby was still detected positively in the feces of model mice on day 24 post-injection. This study reports the prevalence of Salmonella Derby in yaks with diarrhea and in their drinking water. In addition, the pathogenicity of the S. Derby in mice was investigated. Findings suggest that Salmonella Derby excreted by diarrheic yaks is a source of contamination for other yaks and the environment and is highly pathogenic to mice. Seeing that Salmonella Derby has become one of the most common Salmonella serovars, this situation gives rise to further risk from the potential spread of food-borne diseases.

Abstract

Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the numerous non-typhoidal Salmonella serovars and has been recognized as a food-borne pathogen. In 2019, outbreaks of salmonellosis were reported in 13 yak farms in the Aba Tibetan Autonomous Prefecture, China. A total of 32 salmonella strains were isolated from 162 fecal samples of yaks with diarrhea as well as from drinking water samples. The isolates were subjected to serovar identification, animal experiments, and whole-genome sequencing (WGS) analyses. The serovar of all the isolates was S. Derby, and the sequence types (STs) were ST40. The analysis of the differences of single-nucleotide polymorphisms (SNPs) showed that the salmonella strains isolated from 13 farms were clonally related. Animal experiments showed that the lethal dose (LD₅₀) was 4.57 × 10⁷ CFU (colony-forming units); the shedding time of S. Derby in mice was 24 days; the bacterial loads in spleen were higher than those in other organs (ileum, liver, and cecum). Pathological analyses by hematoxylin and eosin (H&E) staining revealed obvious damage in the spleen, liver, and intestine. These results indicate that the S. Derby from yaks can cause infection in mice.

Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies

Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighboring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real data sets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.

Donnan Potential across the Outer Membrane of Gram-Negative Bacteria and Its Effect on the Permeability of Antibiotics

The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans trapped in the periplasmic space, and the displacement of cell surface charges. The focus of our discussion is the impact of Donnan potential on the cellular permeability of selected antibiotics including fluoroquinolones, tetracyclines, β-lactams, and trimethoprim.

Subtyping Salmonella isolated from pet dogs with multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs)

Salmonella, as a zoonotic pathogen, has attracted widespread attention worldwide, especially in the transmission between household pets and humans. Therefore, we investigated the epidemic distribution of dog Salmonella from pet hospitals and breeding base in Xuzhou, Jiangsu Province, China, and used multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs) to subtype Salmonella isolates. From April 2018 to November 2019, a total of 469 samples were collected from pet hospitals and breeding base, including 339 dog samples and 60 cat samples. S. Kentucky (40.74%) was the most prevalent serotype, but other, such as S. Typhimurium (18.52%) and S. Indiana (18.52%), were also widespread. Eight different sequence type (ST) patterns were identified by MLST and ST198 was the highest proportion of these isolates. CRISPRs analysis showed that 9 different Kentucky CRISPR types (KCTs) was identified from ST198. 48 spacers including 29 (6 News) for CRISPR1 and 19 (4 News) for CRISPR2 that proved the polymorphic of Salmonella genes in samples from different sources. The analysis demonstrated that the common serotypes were widely present in pet hosts in the same area. This analysis shows that CRISPR genes have better recognition ability in the same serotype, which has a positive effect on the traceability of Salmonella and the prevention and treatment of salmonellosis.

Mobile Colistin Resistance Gene mcr-1 Detected on an IncI2 Plasmid in Salmonella Typhimurium Sequence Type 19 from a Healthy Pig in South Korea

Colistin is considered the last resort for the treatment of multi-drug resistant Gram-negative bacterial infections. We studied colistin resistance and the mcr-1 gene carriage in Salmonella isolates recovered from food animals in South Korea between 2010 and 2018. Colistin resistance was found in 277 isolates, predominantly in Salmonella Enteritidis (57.1%) and Salmonella Gallinarum (41.9%). However, the mcr-1 gene was identified in only one colistin-resistant Salmonella Typhimurium (MIC = 16 µg/mL) isolated from a healthy pig. The mcr-1 carrying isolate presented additional resistance to multiple antimicrobials. The strain belonged to sequence type (ST)19 and carried various virulence factor genes that are associated with adhesion and invasion of Salmonella into intestinal epithelial cells, as well as its survival in macrophages. The mcr-1 gene was identified on an IncI2 plasmid and it was also transferred to the E. coli J53 recipient strain. The mcr-1-carrying plasmid (pK18JST013) in this study was closely related to that previously reported in S. Indiana (pCFSA664-3) from chicken in China. This is the first report of mcr-1 carrying S. Typhimurium in South Korea. The finding indicates the importance of regular screening for the presence of the mcr-1 gene in S. Typhimurium in food animals to prevent the spread to humans.

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

Can domestic pigeon be a potential carrier of zoonotic Salmonella?

Salmonellosis is one of the most important bacterial diseases in pigeons. This study aimed to estimate the prevalence of Salmonella spp. in domestic pigeons (Columba livia f. domestica) in Poland, its antimicrobial susceptibility (both phenotypic and genotypic), and its capability for biofilm formation. The presence of selected virulence genes, nucleotide homology of selected genes, and susceptibility to bacteriophages were investigated as well. From the 585 pigeons tested, 5.47% turned out positive. All isolated strains were recognized as Salmonella enterica ser. Typhimurium. The asymptomatic pigeons were carriers of 37.5% of the isolates. The dominant variants were as follows: 1,4,[5],12,:i:1,2 (53.13%) and 1,4,[5],12,:‐:‐ (31.25%). Most of the strains analysed showed the ability to produce biofilm after 24 and 48 hr of incubation (59.38% and 53.13%, respectively). Over 90% of the strains were confirmed for lpfA, agafA, invA, sivH, and avrA virulence genes. Also, of the thirteen antimicrobial susceptibility genes, the following were confirmed: sul1, tet(A), bla_TEM‐1, floR, strA, and strB. The most common were the strB (18%) and tet(A) (12%) genes that are responsible for coding resistance to aminoglycosides and tetracyclines, respectively. Most of the strains were phenotypically resistant to oxytetracycline (46.88%), neomycin (53.13%) and tylosin (100%). The susceptibility of the investigated Salmonella strains to the bacteriophages was between 33% and 100%. MLST, PCR MP and ERIC PCR analyses indicated a very high genetic similarity of the investigated strains (over 99%). Results of our study indicate that Salmonella enterica ser. Typhimurium is still an important agent in domestic pigeons and that its antimicrobial resistance increases. Alarming is also the confirmation of a single‐phase variant 1,4,[5],12:i,‐, which could have increased virulence and multi‐drug resistance encoded on the plasmid. Most importantly, however, such strains have been isolated from humans with clinical symptoms of Salmonella infection.

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby–Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.

Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018

Background

In 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Simultaneously, S. Agona was detected in animal feed samples in Bavaria.

Aim

Using next generation sequencing (NGS) and three data analysis methods, this study’s objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. Agona isolates from 1993 to 2018 and compare the analysis approaches employed, for practicality and ability to delineate outbreaks caused by the genetically monomorphic Agona serovar.

Methods

In this observational retrospective study, three 2017 Bavarian feed isolates were compared to a French outbreak isolate and 48 S. Agona isolates from our strain collections. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. All isolates were subjected to NGS and analysed by: (i) a publicly available species-specific core genome multilocus sequence typing (cgMLST) scheme, (ii) single nucleotide polymorphism phylogeny and (iii) an in-house serovar-specific cgMLST scheme. Using additional international S. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed.

Results

We could prove clonality of the feed isolates and exclude their relation to the French outbreak. All approaches confirmed former Bavarian epidemiological clusters.

Conclusion

Even for S. Agona, species-level cgMLST can produce reasonable resolution, being standardisable by public health laboratories. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations.

E. coli diversity: low in colorectal cancer

BACKGROUND

Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases.

METHODS

Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity.

RESULTS

We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions.

CONCLUSIONS

The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.

Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data

We compared the performance of four open-source in silico Salmonella typing tools (SeqSero, SeqSero2, Salmonella In Silico Typing Resource [SISTR], and Metric Oriented Sequence Typer [MOST]) to assess their potential for replacing laboratory serological testing with serovar predictions from whole-genome sequencing data. We conducted a retrospective analysis of 1,624 Salmonella isolates of 72 serovars submitted to the German National Salmonella Reference Laboratory between 1999 and 2019. All isolates are derived from animal and foodstuff origins. We conducted Illumina short-read sequencing and compared the in silico serovar prediction results with the results of routine laboratory serotyping. We found the best-performing in silico serovar prediction tool to be SISTR, with 94% correctly typed isolates, followed by SeqSero2 (87%), SeqSero (81%), and MOST (79%). Furthermore, we found that mapping-based tools like SeqSero and SeqSero2 (allele mode) were more reliable for the prediction of monophasic variants, while sequence type and cluster-based methods like MOST and SISTR (core-genome multilocus sequence type [cgMLST]), showed greater resilience when confronted with GC-biased sequencing data. We showed that the choice of library preparation kit could substantially affect O antigen detection, due to the low GC content of the wzx and wzy genes. Although the accuracy of computational serovar predictions is still not quite on par with traditional serotyping by Salmonella reference laboratories, the command-line tools investigated in this study perform a rapid, efficient, inexpensive, and reproducible analysis, which can be integrated into in-house characterization pipelines. Based on our results, we find SISTR most suitable for automated, routine serotyping for public health surveillance of Salmonella IMPORTANCE Salmonella spp. are important foodborne pathogens. To reduce the number of infected patients, it is essential to understand which subtypes of the bacteria cause disease outbreaks. Traditionally, characterization of Salmonella requires serological testing, a laboratory method by which Salmonella isolates can be classified into over 2,600 distinct subtypes, called serovars. Due to recent advances in whole-genome sequencing, many tools have been developed to replace traditional testing methods with computational analysis of genome sequences. It is crucial to validate that these tools, many already in use for routine surveillance, deliver accurate and reliable serovar information. In this study, we set out to compare which of the currently available open-source command-line tools is most suitable to replace serological testing. A thorough evaluation of the differing computational approaches is highly important to ensure the backward compatibility of serotyping data and to maintain comparability between laboratories.

Characterization of Salmonella enterica Isolates from Diseased Poultry in Northern China between 2014 and 2018

Salmonella infection not only causes acute and chronic diseases in poultry flocks, but the infected poultry are among the most important reservoirs for a variety of Salmonella serovars frequently transmitted to humans. This study aimed to investigate the occurrence of Salmonella spp. in local poultry farms in China. Samples (n = 4255), including dead-in-shell embryos, culled day-old-hatchings and 1- to 4-week-old diseased birds, were collected for Salmonella culture from broiler chicken, meat-type duck and pigeon farms in northern China between 2014 and 2018. A total of 103 Salmonella were isolated. S. enterica serovar Enteritidis and S. Typhimurium were the most prevalent serovars, representing 53.4% and 34.9% of the isolates, respectively. Serovar diversity was the highest in ducks, with the S. Apeyeme being isolated for the first time from duck tissues. All isolates were characterized by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). MLST showed that all S. Enteritidis isolates shared the same sequence type (ST11), and Typhimurium showed several rare STs in addition to ST19. In comparison, PFGE showed better discrimination for S. Enteritidis and S. Typhimurium isolates, with nine distinct pulsotypes being observed. The isolates exhibited varying degrees of resistance to 15 tested antimicrobials and identified S. Enteritidis isolates (98.18%) with multiple antimicrobial resistance were a cause for concern. Our data on invasive Salmonella infection in meat-type poultry in local farms can be used to identify sources and factors associated with Salmonella spread in poultry and the associated food chain.

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.

Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella

Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name “pBSSB1-family”.

WGS based study of the population structure of Salmonella enterica serovar Infantis

BACKGROUND

Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar.

RESULTS

We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed.

CONCLUSIONS

This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.

The speciation and hybridization history of the genus Salmonella

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.

Evaluation of a Salmonella Strain Isolated from Honeybee Gut as a Potential Live Oral Vaccine Against Lethal Infection of Salmonella Typhimurium

In this research, Salmonella species were isolated from the animal, insect and human enteric sources in Faisalabad, Punjab, Pakistan. These species were characterized by different microbiological and molecular techniques including polymerase chain reaction (PCR) by amplification of the 16S rRNA gene. Furthermore, sequencing of the amplicons confirmed all ten isolates as Salmonella strains. The antigenic cross-reactivity was found maximum between the HB1 (strain isolated from honeybee) antiserum and its antigen with an antibody titer of 1:128, while the HB1 antiserum showed a cross-reactive titer range of 1:8 to 1:64. On the basis of the highest geometric mean titer (GMT) shown by the antiserum of the HB1 antigen, it was selected as the best candidate for a cross-reactive live Salmonella oral antigen. Moreover, the HB1 antigen was used a live oral antigen (1 × 10¹⁰ CFU/ml) in a safety test in rabbits and proved to be avirulent. During the animal trial, three different oral doses of the HB1 live oral antigen were evaluated in four different rabbits' groups (R1, R2, R3, and R4). The dose number 2 of 0.5 ml (two drops orally and repeated after one week) gave the best GMT measured by indirect hemagglutination (IHA) as compared to the other two doses, while R4 group was kept as control. Results of the challenge protection test also validated the efficacy of the double dose of the HB1 live vaccine, which gave the highest survival percentage. Results of this study lay the foundation for a potential cross-reactive live oral Salmonella vaccine that has proved to be immunogenic in rabbits.

In this research, Salmonella species were isolated from the animal, insect and human enteric sources in Faisalabad, Punjab, Pakistan. These species were characterized by different microbiological and molecular techniques including polymerase chain reaction (PCR) by amplification of the 16S rRNA gene. Furthermore, sequencing of the amplicons confirmed all ten isolates as Salmonella strains. The antigenic cross-reactivity was found maximum between the HB1 (strain isolated from honeybee) antiserum and its antigen with an antibody titer of 1:128, while the HB1 antiserum showed a cross-reactive titer range of 1:8 to 1:64. On the basis of the highest geometric mean titer (GMT) shown by the antiserum of the HB1 antigen, it was selected as the best candidate for a cross-reactive live Salmonella oral antigen. Moreover, the HB1 antigen was used a live oral antigen (1 × 10¹⁰ CFU/ml) in a safety test in rabbits and proved to be avirulent. During the animal trial, three different oral doses of the HB1 live oral antigen were evaluated in four different rabbits’ groups (R1, R2, R3, and R4). The dose number 2 of 0.5 ml (two drops orally and repeated after one week) gave the best GMT measured by indirect hemagglutination (IHA) as compared to the other two doses, while R4 group was kept as control. Results of the challenge protection test also validated the efficacy of the double dose of the HB1 live vaccine, which gave the highest survival percentage. Results of this study lay the foundation for a potential cross-reactive live oral Salmonella vaccine that has proved to be immunogenic in rabbits.

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.

Evaluation of a Salmonella Strain Isolated from Honeybee Gut as a Potential Live Oral Vaccine Against Lethal Infection of Salmonella Typhimurium

In this research, Salmonella species were isolated from the animal, insect and human enteric sources in Faisalabad, Punjab, Pakistan. These species were characterized by different microbiological and molecular techniques including polymerase chain reaction (PCR) by amplification of the 16S rRNA gene. Furthermore, sequencing of the amplicons confirmed all ten isolates as Salmonella strains. The antigenic cross-reactivity was found maximum between the HB1 (strain isolated from honeybee) antiserum and its antigen with an antibody titer of 1:128, while the HB1 antiserum showed a cross-reactive titer range of 1:8 to 1:64. On the basis of the highest geometric mean titer (GMT) shown by the antiserum of the HB1 antigen, it was selected as the best candidate for a cross-reactive live Salmonella oral antigen. Moreover, the HB1 antigen was used a live oral antigen (1 × 10¹⁰ CFU/ml) in a safety test in rabbits and proved to be avirulent. During the animal trial, three different oral doses of the HB1 live oral antigen were evaluated in four different rabbits’ groups (R1, R2, R3, and R4). The dose number 2 of 0.5 ml (two drops orally and repeated after one week) gave the best GMT measured by indirect hemagglutination (IHA) as compared to the other two doses, while R4 group was kept as control. Results of the challenge protection test also validated the efficacy of the double dose of the HB1 live vaccine, which gave the highest survival percentage. Results of this study lay the foundation for a potential cross-reactive live oral Salmonella vaccine that has proved to be immunogenic in rabbits.

Non-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics

Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals–Al Farwaniya and Al Amiri–in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world. The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates.

Salmonella organisms are classified into typhoidal Salmonella (causing enteric fever) and non-typhoidal Salmonella (NTS) (causing infections other than enteric fever). Apart from causing other infections, NTS causes blood-stream infection (bacteremia and septicemia). NTS blood stream infection (NTS-BI) is considered to be an emerging and neglected tropical disease in Africa. It causes a very high morbidity and mortality in Africa. The individuals affected in Africa are children, malnourished people, patients with malaria or HIV etc. These conditions affect the immune system and make them vulnerable to infection with NTS. In these patients, diarrheal disease due to NTS is rare. The majority of infections are due to two types of NTS: Typhimurium and Enteritidis. There is a very high prevalence of multidrug-resistance in NTS making the infection difficult to treat. NTS-BI is also present in other parts of the world including developed countries albeit at a lower prevalence. Kuwait is a high-income, subtropical country in transition (from a developing to developed country), located in the Middle East. We studied NTS-BI in Al Farwaniya and Al Amiri hospitals in Kuwait during April 2013 to May 2016. Out of nearly 30,000 to more than 50,000 blood cultures done in these hospitals, NTS was present in 0. 75 to 1.33% of blood cultures, representing a very small proportion of blood cultures, unlike in Africa. This showed that 31 patients in Al Farwaniya hospital and 30 patients in Al Amari hospital had NTS-BI. Most of these patients had underlying illnesses such as diabetes, lung infection, cancer etc. that affect the immune system, as in Africa. Many patients also had diarrheal disease caused by the same NTS that caused blood stream infection, unlike in Africa. Only two patients in each hospital died, a low mortality, unlike in Africa. The majority of the isolates belonged to Typhimurium and Enteritidis as in Africa. Even though resistance to drugs was a problem, about quarter of the isolates only were multidrug-resistant, a lower prevalence compared to in Africa. In Kuwait, we performed a detailed genetic study of a selected number of Typhimurium and Enteritidis isolates by a modern technique called whole genome sequencing. This revealed genetic determinants encoding drug-resistance and virulence causing blood-stream infection. This type of study was not performed in African isolates. Thus, our study revealed similarities and differences with studies of NTS-BI in Africa.

Abortion in donkeys associated with Salmonella abortus equi infection

BACKGROUND

Salmonella enterica subspecies enterica serovar abortus equi (S. abortus equi) is well known as the aetiological agent of equine abortion. However, abortion caused by S. abortus equi has not been previously described in donkeys.

OBJECTIVES

To investigate whether S. abortus equi was correlated with an abortion outbreak consisting of 61 abortions.

STUDY DESIGN

Investigation of the clinical cases using pathoanatomical, bacteriological, serological and molecular approaches.

METHODS

Autopsies on nine aborted foetuses were performed. Tissue specimens from seven aborted foetuses and two mares were cultured and subjected to detection of equine herpesvirus 1 (EHV-1), equine herpesvirus 4 (EHV-4) and equine arteritis virus (EAV) by polymerase chain reaction. The isolates were serotyped according to the Kaufmann-White scheme and analysed by multi-locus sequence typing (MLST). Detection of EHV and EAV antibodies was performed in all pregnant mares.

RESULTS

No obvious gross lesions were observed in the foetuses. Nine Gram-negative isolates were obtained from all nine tissue samples and were identified as Salmonella spp. All of the isolates belonged to the B group, the O antigen epitope was 4, 12 and H antigen was not obtained. The isolates of Salmonella were characterised as sequence type (ST) 251. Detection of EHV-1, EHV-4 and EAV was negative.

MAIN LIMITATIONS

The mechanism that causes abortion in donkeys needs further study and the lack of histological examination.

CONCLUSION

Salmonella abortus equi was isolated as the single agent and was responsible for the abortions. Equine practitioners should be aware of S. abortus equi infection as a cause of abortion in donkeys.