Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence

Prevalence and Antimicrobial Resistance Diversity of Salmonella Isolates in Jiaxing City, China

Nontyphoidal Salmonella (NTS) is a cause of foodborne diarrheal diseases worldwide. Important emerging NTS serotypes that have spread as multidrug-resistant high-risk clones include S. Typhimurium monophasic variant and S. Kentucky. In this study, we isolated Salmonella in 5019 stool samples collected from patients with clinical diarrhea and 484 food samples. Antibiotic susceptibility testing and whole-genome sequencing were performed on positive strains. The detection rates of Salmonella among patients with diarrhea and food samples were 4.0% (200/5019) and 3.1% (15/484), respectively. These 215 Salmonella isolates comprised five main serotypes, namely S. Typhimurium monophasic variant, S. Typhimurium, S. London, S. Enteritidis, and S. Rissen, and were mainly resistant to ampicillin, tetracycline, chloramphenicol, and trimethoprim/sulfamethoxazole. The MDR rates of five major serotypes were 77.4%, 56.0%, 66.7%, 53.3%, and 80.0%, respectively. The most commonly acquired extended-spectrum β-lactamase-encoding genes were blaTEM-1B, blaOXA-10, and blaCTX-M-65. The S. Typhimurium monophasic variant strains from Jiaxing City belonged to a unique clone with broad antibiotic resistance. S. Kentucky isolates showed the highest drug resistance, and all were MDR strains. The discovery of high antibiotic resistance rates in this common foodborne pathogen is a growing concern; therefore, ongoing surveillance is crucial to effectively monitor this pathogen.

Poultry production as the main reservoir of ciprofloxacin- and tigecycline-resistant extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Kentucky ST198.2-2 causing human infections in China

Salmonella enterica serovar Kentucky (S. Kentucky) has been regarded as a common serotype causing human nontyphoidal salmonellosis, frequently associated with the consumption of contaminated poultry products. Recently, multidrug-resistant (MDR) S. Kentucky ST198 with strong resistance to cefotaxime, ciprofloxacin, and tigecycline has emerged and been frequently detected in both poultry and humans in Europe and Asia. In this study, whole-genome sequencing (WGS) analysis divided 327 S. Kentucky ST198 isolates into two clades, of which ST198.2 is more prevalent than ST198.1 worldwide. We further compared the genomic characteristics of 70 ST198 isolates from animals and humans during 2019-2022 plus previously reported 38 isolates from 2013 to 2019 in China. One hundred five of the 108 isolates were ST198.2, which could be differentiated into two subclades. ST198.2-1 was prevalent in isolates during 2013-2019, while ST198.2-2 has increased to be the predominant subclade in isolates since 2019. CRISPR typing can differentiate the clade ST198.1 isolates from clade ST198.2 ones but cannot differentiate the two subclade isolates. The acquisition of a large multi-drug resistant region in ST198.2-2 enhanced bacterial resistance to β-lactam, aminoglycoside, amphenicol, and fosfomycin. In addition, compared with the extended-spectrum β-lactamase (ESBL)-encoding gene blaCTX-M-14b in ST198.2-1, co-existence of blaCTX-M-55 and blaTEM-1B was detected in most of the ST198.2-2 isolates. The emergence of ciprofloxacin- and tigecycline-resistant ESBL-producing S. Kentucky ST198.2-2 strains highlight the necessity for Salmonella surveillance. It is imperative to implement more effective measures to prevent and control transmission of these strains from poultry to humans. IMPORTANCE Salmonella enterica serovar Kentucky (S. Kentucky) can cause human infections through consumption of contaminated food of animal origin, and the emergence of multidrug-resistant (MDR) ST198-S. Kentucky strains are of concern for human and animal health. Based on whole-genome sequencing (WGS) analysis, this study revealed that the clade ST198.2-2 S. Kentucky has increased to the predominant group in both chickens and humans in China since 2019, which is different to previous studies of the prevalent ST198.2-1 S. Kentucky before 2019. Acquirement of a multidrug resistance region (MRR) makes the ST198.2-2 S. Kentucky to be extensively drug-resistant (XDR) isolate compared with ST198.2-1 S. Kentucky. Besides, the ST198.2-2 S. Kentucky was mainly detected in chickens (chicken meat, intestinal contents, and slaughterhouse) and humans, indicating chicken is the main reservoir for these XDR S. Kentucky isolates. Therefore, it is necessary to implement continuous Salmonella surveillance and effective measures, such as the development of phages and novel antibiotics/compounds, to prevent the transmission of XDR ST198.2-2 S. Kentucky from chickens to humans across China.

Genomic characterization of Salmonella enterica serovar Kentucky and London recovered from food and human salmonellosis in Zhejiang Province, China (2016–2021)

Increasing human salmonellosis caused by Salmonella enterica serovar Kentucky and London has raised serious concerns. To better understand possible health risks, insights were provided into specific genetic traits and antimicrobial resistance of 88 representative isolates from human and food sources in Zhejiang Province, China, during 2016–2021. Phylogenomic analysis revealed consistent clustering of isolates into the respective serovar or sequence types, and identified plausible interhost transmission via distinct routes. Each serovar exhibited remarkable diversity in host range and disease-causing potential by cgMLST analyses, and approximately half (48.6%, 17/35) of the food isolates were phylogenetically indistinguishable to those of clinical isolates in the same region. S. London and S. Kentucky harbored serovar-specific virulence genes contributing to their functions in pathogenesis. The overall resistance genotypes correlated with 97.7% sensitivity and 60.2% specificity to the identified phenotypes. Resistance to ciprofloxacin, cefazolin, tetracycline, ampicillin, azithromycin, chloramphenicol, as well as multidrug resistance, was common. High-level dual resistance to ciprofloxacin and cephalosporins in S. Kentucky ST198 isolates highlights evolving threats of antibiotic resistance. These findings underscored the necessity for the development of effective strategies to mitigate the risk of food contamination by Salmonella host-restricted serovars.

Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa

Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, bla_TEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

Genomics of human and chicken Salmonella isolates in Senegal: Broilers as a source of antimicrobial resistance and potentially invasive nontyphoidal salmonellosis infections

Salmonella enterica is the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection. Salmonella gastroenteritis is caused by several serotypes and is common worldwide. In contrast, invasive salmonellosis is rare in high-income countries (HIC) while frequent in low- and middle-income countries (LMIC), especially in sub-Saharan Africa (sSA). Invasive Nontyphoidal Salmonella (iNTS), corresponding to serotypes other than Typhi and Paratyphi, have emerged in sSA and pose a significant risk to public health. We conducted a whole-genome sequence (WGS) analysis of 72 strains of Salmonella isolated from diarrheic human patients and chicken meat sold in multipurpose markets in Dakar, Senegal. Antimicrobial susceptibility testing combined with WGS data analysis revealed frequent resistance to fluoroquinolones and the sulfamethoxazole-trimethoprim combination that are among the most used treatments for invasive Salmonella. In contrast, resistance to the historical first-line drugs chloramphenicol and ampicillin, and to cephalosporins was rare. Antimicrobial resistance (AMR) was lower in clinical isolates compared to chicken strains pointing to the concern posed by the excessive use of antimicrobials in farming. Phylogenetic analysis suggested possible transmission of the emerging multidrug resistant (MDR) Kentucky ST198 and serotype Schwarzengrund from chicken to human. These results stress the need for active surveillance of Salmonella and AMR in order to address invasive salmonellosis caused by nontyphoidal Salmonella strains and other important bacterial diseases in sSA.

Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011-2017)

Salmonella Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the Salmonella genomic island (SGI-1) and in some cases (bla_SHV-12, catA1, cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.

Genomic Analysis of Ciprofloxacin-Resistant Salmonella enterica Serovar Kentucky ST198 From Spanish Hospitals

Salmonella enterica serovar Kentucky (S. Kentucky) with sequence type (ST) 198 and highly resistant to ciprofloxacin (ST198-Cip^R) has emerged as a global MDR clone, posing a threat to public health. In the present study, whole genome sequencing (WGS) was applied to characterize all Cip^RS. Kentucky detected in five Spanish hospitals during 2009–2018. All Cip^R isolates (n = 13) were ST198 and carried point mutations in the quinolone resistance-determining regions (QRDRs) of both gyrA (resulting in Ser83Phe and Asp87Gly, Asp87Asn, or Asp87Tyr substitutions in GyrA) and parC (with Thr57Ser and Ser80Ile substitutions in ParC). Resistances to other antibiotics (ampicillin, chloramphenicol, gentamicin, streptomycin, sulfonamides, and tetracycline), mediated by the bla_TEM–1B, catA1, aacA5, aadA7, strA, strB, sul1, and tet(A) genes, and arranged in different combinations, were also observed. Analysis of the genetic environment of the latter resistance genes revealed the presence of multiple variants of SGI1 (Salmonella genomic island 1)-K and SGI1-P, where all these resistance genes except catA1 were placed. IS26 elements, found at multiple locations within the SGI1 variants, have probably played a crucial role in their generation. Despite the wide diversity of SGI1-K- and SGI1-P-like structures, phylogenetic analysis revealed a close relationship between isolates from different hospitals, which were separated by a minimum of two and a maximum of 160 single nucleotide polymorphisms. Considering that S. enterica isolates resistant to fluoroquinolones belong to the high priority list of antibiotic-resistant bacteria compiled by the World Health Organization, continuous surveillance of the S. Kentucky ST198-CIP^R clone is required.

Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland

BACKGROUND

Salmonella Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical S. Kentucky strains isolated in Poland remain undescribed.

METHODS

Eighteen clinical S. Kentucky strains collected in the years 2018-2019 in Poland were investigated. All the strains were tested for susceptibility to 11 antimicrobials using the disc diffusion and E-test methods. Whole genome sequences were analysed for antimicrobial resistance genes, mutations, the presence and structure of SGI1-K (Salmonella Genomic Island and the genetic relationship of the isolates.

RESULTS

Sixteen of 18 isolates (88.9%) were assigned as ST198 and were found to be high-level resistant to ampicillin (>256 mg/L) and quinolones (nalidixic acid MIC ≥ 1024 mg/L, ciprofloxacin MIC range 6-16 mg/L). All the 16 strains revealed three mutations in QRDR of GyrA and ParC. The substitutions of Ser83 → Phe and Asp87 → Tyr of the GyrA subunit and Ser80→Ile of the ParC subunit were the most common. One S. Kentucky isolate had qnrS1 in addition to the QRDR mutations. Five of the ST198 strains, grouped in cluster A, had multiple resistant determinants like blaTEM1-B, aac(6')-Iaa, sul1 or tetA, mostly in SGI1 K. Seven strains, grouped in cluster B, had shorter SGI1-K with deletions of many regions and with few resistance genes detected.

CONCLUSION

The results of this study demonstrated that a significant part of S. Kentucky isolates from humans in Poland belonged to ST198 and were high-level resistant to ampicillin and quinolones.

Genomic epidemiology of emerging ESBL-producing Salmonella Kentucky bla CTX-M-14b in Europe

Global dissemination of ciprofloxacin-resistant Salmonella Kentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum β-lactamase (ESBL) producing S. Kentucky. Routine surveillance at the European Centre for Disease Prevention and Control (ECDC) detected cases with a ciprofloxacin-resistant S. Kentucky with the ESBL-gene bla_CTX-M-14b. Ensuing research identified 78 cases in 2013–2018 in eight European countries. Compared to other S. Kentucky and non-typhoidal Salmonella infections, reported to the European Surveillance System, these cases were more likely to be elderly and to present urinary-tract infections. Bayesian time-scaled phylogeny on whole genome sequences of isolates from these cases and supplementary isolates from public sequence databases was used to infer the origin and spread of this clone. We dated the origin of the bla_CTX-M-14b clone to approximately 2005 in Northern Africa, most likely in Egypt. The geographic origin predicted by the phylogenetic analysis is consistent with the patients’ travel history. Next to multiple introductions of the clone to Europe from Egypt, our analysis suggests that in some parts of Europe the clone might have formed a stable population, from which further spread has occurred. Comparative genomics indicated that the bla_CTX-M-14b gene is present on the bacterial chromosome, within the type VI secretion system region. The bla_CTX-M-14b gene is integrated downstream of the hcp1 gene, on a 2854 bp plasmid fragment containing also ISEcp1. This is the first report of a chromosomally integrated CTX-M gene in Salmonella spp. in Europe, previous studies having identified similar genes only on plasmids.

Characterization of the emerging multidrug-resistant Salmonella enterica serotype Kentucky ST314 in China

Salmonella enterica serotype Kentucky (S. Kentucky) is an important Salmonella serotype with multiple sequence types (ST) with a worldwide incidence. We identified 8 STs from 180 strains of S. Kentucky, and ST314 emerged as the most commonly encountered ST. Drug susceptibility testing revealed that ST314 had multiple resistance properties, and 75.5% of the strains were resistant to three or more classes of antimicrobials. The rate of resistance to chloramphenicol, florfenicol, sulfafurazole and tetracycline were greater than 60%. The rates of ST314 resistance to quinolones were as follows: ciprofloxacin, 32.1%; nalidixic acid, 16%; and ofloxacin, 7.5%. Investigating the mechanism of quinolone resistance of ST314 revealed that mutations in the quinolone resistance-determining regions were rare, and resistance mainly occurred due to the resistance genes carried by plasmids. Only 1.9% (2/106) of ST314 strains had mutations in the quinolone resistance-determining regions (QRDR). The drug resistance genes of ST314 were primarily of plasmid-mediated quinolone resistance (PMQR). The detection rate of Salmonella genomic island 1 (SGI1) in ST314 was 12.3%. XbaI-pulsed-field gel electrophoresis revealed that S. enterica Kentucky ST314 was capable of cross-regional and cross-host transmission in China. We found ST314 to be the dominant S. Kentucky ST in China, and it carried multidrug resistance. This is the first report about the emergence of quinolone-resistant S. enterica Kentucky ST314 in China, which is different from previous reports, and the findings of the present study suggest that the mechanism of quinolone resistance in these strains are plasmid-mediated. Notably, plasmids carrying resistance genes may promote the rapid spread of ciprofloxacin resistance.

Antibiotic resistance in Salmonella spp. isolated from poultry: A global overview

Salmonella enterica is the most important foodborne pathogen, and it is often associated with the contamination of poultry products. Annually, Salmonella causes around 93 million cases of gastroenteritis and 155,000 deaths worldwide. Antimicrobial therapy is the first choice of treatment for this bacterial infection; however, antimicrobial resistance has become a problem due to the misuse of antibiotics both in human medicine and animal production. It has been predicted that by 2050, antibiotic-resistant pathogens will cause around 10 million deaths worldwide, and the WHO has suggested the need to usher in the post-antibiotic era. The purpose of this review is to discuss and update the status of Salmonella antibiotic resistance, in particular, its prevalence, serotypes, and antibiotic resistance patterns in response to critical antimicrobials used in human medicine and the poultry industry. Based on our review, the median prevalence values of Salmonella in broiler chickens, raw chicken meat, and in eggs and egg-laying hens were 40.5% ( interquartile range [IQR] 11.5-58.2%), 30% (IQR 20-43.5%), and 40% (IQR 14.2-51.5%), respectively. The most common serotype was Salmonella Enteritidis, followed by Salmonella Typhimurium. The highest antibiotic resistance levels within the poultry production chain were found for nalidixic acid and ampicillin. These findings highlight the need for government entities, poultry researchers, and producers to find ways to reduce the impact of antibiotic use in poultry, focusing especially on active surveillance and finding alternatives to antibiotics.

Emergence of new variants of antibiotic resistance genomic islands among multidrug-resistant Salmonella enterica in poultry

Non-typhoidal Salmonella enterica (NTS) are diverse and important bacterial pathogens consisting of more than 2600 different serovars, with varying host-specificity. Here, we characterized the poultry-associated serovars in Israel, analysed their resistome and illuminated the molecular mechanisms underlying common multidrug resistance (MDR) patterns. We show that at least four serovars including Infantis, Muenchen, Newport and Virchow present a strong epidemiological association between their temporal trends in poultry and humans. Worrisomely, 60% from all of the poultry isolates tested (n = 188) were multidrug resistant, mediated by chromosomal SNPs and different mobile genetics elements. A novel streptomycin-azithromycin resistance island and previously uncharacterized versions of the mobilized Salmonella genomic island 1 (SGI1) were identified and characterized in S. Blockley and S. Kentucky isolates respectively. Moreover, we demonstrate that the acquisition of SGI1 does not impose fitness cost during growth under nutrient-limited conditions or in the context of Salmonella infection in the mouse model. Overall, our data emphasize the role of the poultry production as a pool of specific epidemic MDR strains and autonomous genetic elements, which confer resistance to heavy metals and medically relevant antibiotics. These are likely to disseminate to humans via the food chain and fuel the increasing global antibiotic resistance crisis.

Prevalence of Multidrug Resistant Salmonellae with Increasing Frequency of Salmonella enterica Serovars Kentucky and Virchow among Hospitalized Diarrheal Cases in and around Delhi, India

Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance (MDR). In a hospital-based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars, however, 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (NA) (73%), ciprofloxacin (CIP) (48%), ampicillin (AM) and norfloxacin (NOR) (36% each), and gentamicin (CN) (31%). The AMR profiles for CN and NA; and AM, CIP, NA and NOR, were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of the pulsed-field gel electrophoresis patterns of S. Kentucky revealed 3 clusters. S. Kentucky has clones closely related to become prominent in recent years in Delhi. The AMR appears to be consistent with the change in MDR patterns during 2014-2017. The observed prevalence of S. Kentucky and S. Virchow in large numbers of diarrheal cases is novel. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.

Occurrence and Phenotypic and Molecular Characterization of Antimicrobial Resistance of Salmonella Isolates from Food in Tunisia

HIGHLIGHTS

Multidrug-resistant Salmonella isolates have been recovered from food in Tunisia. Salmonella isolates from food are resistant to fluoroquinolones and cephalosporins. Surveillance of the antimicrobial susceptibility of foodborne bacteria is needed in Tunisia.

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

Distribution and characteristics of SGI1/PGI2 genomic island from Proteus strains in China

The emergence of multidrug-resistant Salmonella genomic island 1 (SGI1) and Proteus genomic island (PGI) bearing P. mirabilis present a serious threat to public health. In this study, we screened 288 Proteus isolates recovered from seven provinces in China. Fourteen strains (4.9%) all belonged to P. mirabilis were positive for SGI1/PGI2, including twelve from clinical samples (5.3%) and two from food (3.3%). A Blastn search against GenBank and phylogenetic analyses identified eight different SGI1 variants and one PGI2 variant from the fourteen SGI1/PGI2 variants. All SGI1 variants shared a common backbone and harbored different resistance gene(s), except the sul1 gene at its multidrug-resistant (MDR) region. Among the variants, three novel SGI1 variants, designated as SGI1-PmCA11, SGI1-PmCA14 and SGI1-PmCA46, contained different gene cassettes, which were similar to sequences in plasmids or class 1 integrons of Klebsiella pneumoniae, P. mirabilis, Escherichia coli and Salmonella. Moreover, one novel PGI2, designated as PGI2-PmCA72, had an identical gene cassette to the first class 1 integron from PGI2 (GenBank accession no. MG201402.1) in P. mirabilis, but varied due to missing, replaced, inserted and inverted gene clusters. The four novel SGI1/PGI2 variants contained the cmlA5, dfrA14, bla_OXA-10, aadA15, bla_OXA-1, catB3 and dfrA16 resistance genes, which have never been reported in SGI1/PGI2 variants. Phenotypically, all fourteen SGI1/PGI2-containing strains showed multidrug resistance. All except four strains were resistant to the first, or the second and/or-third generation cephalosporins. Considering the increasing number and the emergence of new SGI1/PGI2 variants, further surveillance is needed to prevent the spreading of the MDR genomic islands among Proteus isolates from human and food.

Identification and Characterization of New Resistance-Conferring SGI1s (Salmonella Genomic Island 1) in Proteus mirabilis

Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.

Integrons in Enterobacteriaceae: diversity, distribution and epidemiology

Integrons are versatile gene acquisition systems that allow efficient capturing of exogenous genes and ensure their expression. Various classes of integrons possessing a wide variety of gene cassettes are ubiquitously distributed in enteric bacteria worldwide. The epidemiology of integrons associated multidrug resistance in Enterobacteriaceae is rapidly evolving. In the past two decades, the incidence of integrons in enteric bacteria has increased drastically with evolution of multiple gene cassettes, novel gene arrangements and complex chromosomal integrons such as Salmonella genomic islands. This review focuses on the distribution, versatility, spread and global trends of integrons among important members of the Enterobacteriaceae, including Escherichia coli, Klebsiella, Shigella and Salmonella, which are known to cause infections globally. Such a comprehensive understanding of integron-associated antibiotic resistance, their role in the spread of such resistance traits and their clinical relevance especially with regard to each genus individually is paramount to contain the global spread of antibiotic resistance.

Multidrug Resistance Salmonella Genomic Island 1 in a Morganella morganii subsp. morganii Human Clinical Isolate from France

Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development.

Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, bla_VEB-6 and bla_NDM-1, respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15, floR, tetA(G), bla_PSE-1 (now referred to as bla_CARB-2), and sul1, conferring resistance to trimethoprim, phenicols, tetracyclines, amoxicillin, and sulfonamides, respectively. The SGI1-L variant was integrated into the usual chromosome-specific integration site at the 3′ end of the trmE gene. Beyond Salmonella enterica and Proteus mirabilis, the SGI1 integrative mobilizable element may thus also disseminate its multidrug resistance phenotype in another genus belonging to the Proteae tribe of the family Enterobacteriaceae.

IMPORTANCE Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development.

Determination and Analysis of the Putative AcaCD-Responsive Promoters of Salmonella Genomic Island 1

The integrative genomic island SGI1 and its variants confer multidrug resistance in numerous Salmonella enterica serovariants and several Proteus mirabilis and Acinetobacter strains. SGI1 is mobilized by the IncA/C family plasmids. The island exploits not only the conjugation apparatus of the plasmid, but also utilizes the plasmid-encoded master regulator AcaCD to induce the excision and formation of its transfer-competent form, which is a key step in the horizontal transfer of SGI1. Triggering of SGI1 excision occurs via the AcaCD-dependent activation of xis gene expression. AcaCD binds in P_xis to an unusually long recognition sequence. Beside the P_xis promoter, upstream regions of four additional SGI1 genes, S004, S005, S012 and S018, also contain putative AcaCD-binding sites. Furthermore, SGI1 also encodes an AcaCD-related activator, FlhDC_SGI1, which has no known function. Here, we have analysed the functionality of the putative AcaCD-dependent promoter regions and proved their activation by either AcaCD or FlhDC_SGI1. Moreover, we provide evidence that both activators act on the same binding site in P_xis and that FlhDC_SGI1 is able to complement the acaCD deletion of the IncA/C family plasmid R16a. We determined the transcription start sites for the AcaCD-responsive promoters and showed that orf S004 is expressed probably from a different start codon than predicted earlier. Additionally, expression of S003 from promoter P_S004 was ruled out. P_xis and the four SGI1 promoters examined here also lack obvious -35 promoter box and their promoter profile is consistent with the class II-type activation pathway. Although the role of the four additionally analysed AcaCD/FlhDC_SGI1-controlled genes in transfer and/or maintenance of SGI1 is not yet clear, the conservation of the whole region suggests the existence of some selection for their functionality.

Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America

Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.

A retrospective epidemiological study on the incidence of salmonellosis in the State of Qatar during 2004-2012

Background:Salmonella is a food- and water-borne pathogen that can be easily spread in a population, leading to the outbreak of salmonellosis that is caused by ingestion of mixed salads contaminated by the pathogen. Most cases occur in the late spring months and can be seen as single cases, clusters, or episodes. Objective: The aim of this study was to describe the incidence and epidemiological characteristics of salmonellosis in the State of Qatar. Methods: This was a retrospective, descriptive study carried out in laboratory-confirmed cases of salmonellosis during 2004–2012 from all Salmonella surveillance centers. Therapeutic records of patients who were clinically suspected of having Salmonella diseases were analyzed. Initially, cases with typhoid fever were investigated in the laboratory by means of Widal agglutination tests, while non-typhoidal Salmonella diseases were determined based on culture technique. Results: The annual incident of salmonellosis cases were 12.3, 23.0, 30.3, 19.4, 15.3, 18.0, 22.7, 18.5, and 18.1 per 100,000 population in 2006–2011 and 2012, respectively. The number of salmonellosis cases was high among less than 2-year-old females and 3-year-old males. In addition, one-fourth of patients (27.7%) were Qatari when compared to other nationalities. A significant difference in age was found between Qatari (6.08 ± 12.28 years) and non-Qatari (15.04 ± 19.56 years) patients. Of the reported cases, 79.8% included the onset date of the first symptoms. Contact phone numbers were available for 94% of the cases but addresses were available for only 50.4% of cases. The time difference between onset of symptoms and diagnosis was 5.4 ± 5.7 days. The most frequent serotype reported were type b (41.9%), type d (26.9%), and type c1 (12.2%). Conclusion: The present surveillance data showed a high incidence of salmonellosis in Qatar that poses a serious public health problem. Special intervention and health awareness programs are required for early screening, detection, and treatment as well as for strengthening the surveillance system of salmonellosis, with special emphasis on the laboratory study of cases.

Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry

The discovery of antibiotics heralded the start of a “Golden Age” in the history of medicine. Over the years, the use of antibiotics extended beyond medical practice into animal husbandry, aquaculture and agriculture. Now, however, we face the worldwide threat of diseases caused by pathogenic bacteria that are resistant to all existing major classes of antibiotic, reflecting the possibility of an end to the antibiotic era. The seriousness of the threat is underscored by the severely limited production of new classes of antibiotics. Evolution of bacteria resistant to multiple antibiotics results from the inherent genetic capability that bacteria have to adapt rapidly to changing environmental conditions. Consequently, under antibiotic selection pressures, bacteria have acquired resistance to all classes of antibiotics, sometimes very shortly after their introduction. Arguably, the evolution and rapid dissemination of multiple drug resistant genes en-masse across microbial pathogens is one of the most serious threats to human health. In this context, effective surveillance strategies to track the development of resistance to multiple antibiotics are vital to managing global infection control. These surveillance strategies are necessary for not only human health but also for animal health, aquaculture and plant production. Shortfalls in the present surveillance strategies need to be identified. Raising awareness of the genetic events that promote co-selection of resistance to multiple antimicrobials is an important prerequisite to the design and implementation of molecular surveillance strategies. In this review we will discuss how lateral gene transfer (LGT), driven by the use of low-dose antibiotics in animal husbandry, has likely played a significant role in the evolution of multiple drug resistance (MDR) in Gram-negative bacteria and has complicated molecular surveillance strategies adopted for predicting imminent resistance threats.

The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain

While the spread of Salmonella enterica serotype Kentucky resistant to ciprofloxacin across Africa and the Middle-East has been described recently, the presence of this strain in humans, food, various animal species (livestock, pets, and wildlife) and in environment is suspected in other countries of different continents. Here, we report results of an in-depth molecular epidemiological study on a global human and non-human collection of S. Kentucky (n = 70). We performed XbaI-pulsed field gel electrophoresis and multilocus sequence typing, assessed mutations in the quinolone resistance-determining regions, detected β-lactam resistance mechanisms, and screened the presence of the Salmonella genomic island 1 (SGI1). In this study, we highlight the rapid and extensive worldwide dissemination of the ciprofloxacin-resistant S. Kentucky ST198-X1-SGI1 strain since the mid-2000s in an increasingly large number of contaminated sources, including the environment. This strain has accumulated an increasing number of chromosomal and plasmid resistance determinants and has been identified in the Indian subcontinent, Southeast Asia and Europe since 2010. The second substitution at position 87 in GyrA (replacing the amino acid Asp) appeared helpful for epidemiological studies to track the origin of contamination. This global study provides evidence leading to the conclusion that high-level resistance to ciprofloxacin in S. Kentucky is a simple microbiological trait that facilitates the identification of the epidemic clone of interest, ST198-X1-SGI1. Taking this into account is essential in order to detect and monitor it easily and to take rapid measures in livestock to ensure control of this infection.

The first attempt of an active integrated laboratory-based Salmonella surveillance programme in the north-eastern region of Nigeria

AIM

To identify the sources of Salmonella contamination, distribution, prevalence and antimicrobial susceptibility patterns, which have significant impact on public and animal health, and international trade.

METHODS AND RESULTS

A total of 1888 samples were collected by stratified random sampling from 2009 to 2011 from cattle, camels, poultry, fish, vegetables and humans. All identified Salmonella isolates were serotyped and tested for antimicrobial susceptibility by MIC determinations. A total of 149 Salmonella isolates comprising 17 different serovars were obtained (7·9% prevalence). Salmonella Hadar (37%), S. Eko (17%), S. Enteritidis (10%), S. Kentucky (7%) and S. Uganda (7%) were isolated from different sources. The occurrence of antimicrobial resistance was generally low, but S. Enteritidis and S. Eko showed variable antimicrobial resistance patterns, while all S. Kentucky isolates were resistant to seven of 17 tested antimicrobials, including ciprofloxacin and nalidixic acid. Three S. Hadar isolates revealed reduced susceptibility to ciprofloxacin and susceptibility to nalidixic acid and harboured the plasmid-mediated quinolone resistance gene qnrS1.

CONCLUSIONS

Salmonella serovars Hadar, Enteritidis and the previously very rarely reported Eko were the major serovars associated with human infections, animal and environmental contamination in the north-eastern region of Nigeria.

SIGNIFICANCE AND IMPACT OF THE STUDY

These serovars constitute a health risk to poultry, environment and human population in the region.