Decrease in the prevalence of extended-spectrum cephalosporin-resistant Salmonella following cessation of ceftiofur use by the Japanese poultry industry

Changes in the Phenotypes of Salmonella spp. in Japanese Broiler Flocks

Salmonella infections represent a leading cause of foodborne illnesses; resistance to third-generation cephalosporins (TGCs), which are a first-choice antimicrobial for treating human Salmonella enteritis, has become a serious public health concern worldwide. Because the consumption of undercooked chicken meat products is a major cause of foodborne salmonellosis in Japan, we conducted three surveys at different periods between 2017 and 2022, with the cooperation of four abattoirs (two in Eastern and two in Western Japan). The first survey was conducted at abattoir A, which is located in Eastern Japan. Salmonella was detected in 84.4% of broiler flocks tested (27/32); among them, all the TGC-resistant isolates obtained from one farm (farm FA) were identified as S. Infantis. Salmonella was recovered from 62.5% of breast meat samples (20/32), with one case suggesting cross-contamination. The second survey was conducted at three other abattoirs to examine the prevalence of TGC-resistant Salmonella, in both Western (abattoirs B and C) and Eastern (abattoir D) Japan. Salmonella was detected in 90.6% of broiler flocks examined (29/32). TGC-resistant S. Infantis was isolated from 2 flocks until 2018 and not thereafter. Subsequently, isolates were identified as TGC-susceptible S. Schwarzengrund in both regions. The third survey was performed at abattoir A to elucidate whether there were changes in the phenotypes. Of the 11 broiler flocks introduced from farm FA, 10 were positive for Salmonella (90.9%); all the isolates were S. Schwarzengrund susceptible to TGC. This study shows that TGC-susceptible S. Schwarzengrund has replaced the resistant phenotypes among broiler flocks in both Eastern and Western Japan. Although chicken meat products could be cross-contaminated with Salmonella during the slaughtering process, reducing the prevalence of Salmonella in broiler flocks remains important to decrease Salmonella enteritis in humans.

Bioprotective potential of lactic acid bacteria for Salmonella biocontrol in vitro

Lactic acid bacteria (LAB) are an important option for Salmonella control in animal production, resulting in lower antibiotic use. The objective of this research was to isolate LAB from meat products and from commercial probiotics sold as nutritional supplements for in vitro verification of their bioprotective potential. Eleven bacteria were identified as Pediococcus acidilactici, two as Lacticaseibacillus rhamnosus, one as Lacticaseibacillus paracasei paracasei, one as Limosilactobacillus fermentum, and one as a consortium of Lactobacillus delbrueckii bulgaricus and L. fermentum. All bacteria showed inhibitory activity against Salmonella, with emphasis on the inhibition of P. acidilactici PUCPR 011 against Salmonella Enteritidis 33SUSUP, S. Enteritidis 9SUSP, S. Enteritidis 56301, S. Enteritidis CRIFS 1016, Salmonella Typhimurium ATCC™ 14,028®, and Salmonella Gallinarum AL 1138, with inhibition halos of 7.3 ± 0.5 mm, 7.7 ± 1.0 mm, 9.0 ± 1.8 mm, 7.3 ± 0.5 mm, 7.7 ± 1.0 mm, and 7.3 ± 0.5, respectively. The isolates P. acidilactici PUCPR 011, P. acidilactici PUCPR 012, P. acidilactici PUCPR 014, L. fermentum PUCPR 005, L. paracasei paracasei PUCPR 013, and L. rhamnosus PUCPR 010 showed inhibition greater than 2 mm against at least 3 Salmonella and were used for encapsulation and in vitro digestion. The encapsulation efficiency ranged from 76.89 ± 1.54 to 116.48 ± 2.23%, and the population after 12 months of storage was from 5.31 ± 0.17 to 9.46 ± 0.09 log CFU/g. When simulating swine and chicken digestion, there was a large reduction in bacterial viability, stabilizing at concentrations close to 2.5 log CFU/mL after the analyses. The analyzed bacteria showed strong in vitro bioprotective potential; further analyses are required to determine in vivo effectiveness.

Prevalence of Chromosomally Located blaCTX-M-55 in Salmonella Typhimurium ST34 Isolates Recovered from a Tertiary Hospital in Guangzhou, China

Nontyphoidal Salmonella (NTS) is one of the most prevalent bacterial causes of gastrointestinal infections worldwide. Meanwhile, the detection rate of CTX-M-55 ESBL-positive has increased gradually in China. To identify the molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying nontyphoidal Salmonella (NTS) clinical isolates, a total of 105 NTS isolates were collected from a Chinese tertiary hospital. Antimicrobial susceptibility testing was performed to determine the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were used to determine the antimicrobial resistance genes, serotypes, phylogenetic relationships, and the genetic environment of the blaCTX-M-55 gene. The results showed that among the 22 ceftriaxone resistant isolates, the blaCTX-M-55 was the most common β-Lactamase gene carried by 14 isolates, including serotypes S. Typhimurium (10/14), S. Muenster (2/14), S. Rissen (1/14), and S. Saintpaul (1/14). Phylogenetic analysis shows that 10 blaCTX-M-55-positive S. Typhimurium ST34 isolates were divided into two clusters. The genetic relationship of isolates in each cluster was very close (≤10 cgMLST loci). The blaCTX-M-55 gene was located on the chromosome in 10 isolates, on IncI1 plasmid in three isolates, and IncHI2 plasmid in one isolate. In conclusion, the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, close attention to the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings must be monitored carefully. IMPORTANCE ESCs are the first choice for treating NTS infections. However, ESBLs and AmpC β-lactamases are the most typical cause for ESCs resistance. The CTX-M-55 ESBL-positive rate has gradually increased in the clinic in recent years. At present, the research about blaCTX-M-55-positive Salmonella mainly focuses on the foodborne animals or the environment while less on clinical patients. Thus, this study was carried out for identifying molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying NTS clinical isolates. The results showed that the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates from Conghua District, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, our work highlights the importance of monitoring the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings.

First report of multidrug-resistant Salmonella Infantis in broiler litter in Tolima, Colombia

Background and Aim:

Salmonella has been identified as one of the most widely distributed zoonotic pathogens in broiler litter. Multidrug-resistant strains have been isolated from salmonellosis outbreaks, compromising the success of their treatment. This study aimed to isolate and identify Salmonella spp. serovars in healthy broiler litter in Tolima (Colombia), determine their resistance to different antimicrobials, and detect genes associated with b-lactam resistance that could be useful to control Salmonella spp. in poultry.

Materials and Methods:

In total, 45 broiler litter samples were collected. Salmonella spp. was isolated and identified using selective and differential culture media and biochemical tests. Molecular confirmation of the pathogen was performed with the invA gene and serotyping by Kauffman–White scheme. Antimicrobial susceptibility to 15 antibiotics was determined by Kirby–Bauer method. In cefotaxime-resistant strains, blaCTX-M-F, blaCTX-M-1, blaCMY, and blaTEM genes were evaluated by polymerase chain reaction (PCR).

Results:

In total, 817 presumptive strains were obtained from xylose lysine deoxycholate and SalmonellaShigella agars and subcultured on xylose-lysine-tergitol 4 and MacConkey agars, from which 150 strains were isolated; 29 of these strains were presumptive for Salmonella spp. after performing biochemical tests and 16 were confirmed by PCR as Salmonella Infantis (15) and Gallinarum (1). All strains were found to be multiresistant to antibiotics, showing three different profiles and isolates resistant to cefotaxime, and the blaCTX-M gene was detected.

Conclusion:

This is the first study to isolate S. Infantis from broiler litter in Colombia. All isolates exhibited resistance to the evaluated antimicrobials, suggesting the misuse of antimicrobials in small- and medium-sized poultry farms. The presence of Salmonella enterica serovar Infantis is a public health problem. Thus, regular monitoring of poultry litter is recommended, as these bacteria can be transmitted to humans through animal products or contaminated environments.

Decreasing trend of β-Lactam Resistance in Salmonella Isolates from Broiler Chickens due to the Cessation of Ceftiofur in ovo Administration

•

The most prevalence of S. enterica isolated in 2017 and 2018 were S. Manhattan and S. Schwarzengrund.

•

S. enterica prevalence showed a declining trend over an extended period.

•

β-lactam resistance was absent in the predominant serovars in 2018.

Ceftiofur, a third-generation cephalosporin antimicrobial, was used in Japanese hatcheries for many years before 2012. We continue to study Salmonella in broilers and their antimicrobial resistance. The current study aimed to express how the cessation of ceftiofur affects the antimicrobial resistance of Salmonella isolated from broiler chickens in Kagoshima Prefecture, Japan in 2017 and 2018. A total of 274 Salmonella isolates were recovered from 1535 cecal content samples obtained from 96 broiler flocks over years 2017 and 2018. Among the S. enterica isolates, the predominant serovars were S. Manhattan (128/274, 46.7%), S. Schwarzengrund (120/274, 43.8%), and S. Infantis (26/274, 9.5%). The isolates showed a high proportion of antimicrobial resistance for oxytetracycline, sulfamethoxazole, and streptomycin. However, the β-lactam resistance rates were significantly decreased (p < 0.01) in 2017, while no β-lactam resistant isolates detected in 2018. The highlight of this study was the complete disappearance of β-lactam resistance in Salmonella isolates from broiler chicken in Kagoshima, Japan.

A national study through a 'Farm-to-fork' Approach to determine Salmonella dissemination along with the Lebanese poultry production chain

This cross-sectional study was conducted to determine the prevalence of Salmonella at different stages of the broiler production chain and layer flocks in addition to their antibiotic resistance profile and molecular patterns. Over a period of 3 years, different sample matrices were collected from Lebanese farms, slaughterhouses and retail markets. Out of 672 Salmonella serotyped, 514 were analysed for antimicrobial resistance and 214 for clonality using Pulsed-field gel electrophoresis (PFGE). The results highlighted an important prevalence of Salmonella, 30% in farms, 35.8% in slaughterhouses and 22.4% at retail level. A large diversity of serotypes was identified with predominance among Salmonella Infantis (32.9%), Salmonella Enteritidis (28.4%) and Salmonella Kentucky (21.4%). High resistance to nalidixic acid was revealed in all the isolates. The most prominent resistance was exhibited in S. Kentucky and S. Infantis. The latter was resistant to tetracycline (99%), streptomycin (88.2%) and remarkable multi-drug resistance (MDR) (89.7%). All S. Kentucky isolates were resistant to ciprofloxacin, MDR (62.4%) and 6% were resistant to extended-spectrum cephalosporin (ESCs). One persistent clone of S. Enteritidis was found common between poultry and humans. Similar genomic profiles were detected between farms, slaughterhouses and retail suggesting the dissemination of identical clones throughout the food chain possibly due to weak barriers preventing such transmission.

Antimicrobial Resistance in Salmonella Isolated from Food Workers and Chicken Products in Japan

Salmonella is an enteric bacterial pathogen that causes foodborne illness in humans. Third-generation cephalosporin (TGC) resistance in Salmonella remains a global concern. Food workers may represent a reservoir of Salmonella, thus potentially contaminating food products. Therefore, we aimed to investigate the prevalence of Salmonella in food workers and characterize the isolates by serotyping and antimicrobial susceptibility testing. Salmonella was isolated from 583 (0.079%) of 740,635 stool samples collected from food workers between January and December 2018, and then serotyped into 76 Salmonella enterica serovars and 22 untypeable Salmonella strains. High rates of antimicrobial resistance were observed for streptomycin (51.1%), tetracycline (33.1%), and kanamycin (18.4%). Although isolates were susceptible to ciprofloxacin, 12 (2.1%) strains (one S. Infantis, one S. Manhattan, two S. Bareilly, two S. Blockley, two S. Heidelberg, two S. Minnesota, one S. Goldcoast, and one untypeable Salmonella strain) were resistant to the TGC cefotaxime, all of which harbored β-lactamase genes (bla_CMY-2, bla_CTX-M-15, bla_CTX-M-55, and bla_TEM-52B). Moreover, 1.3% (4/309) of Salmonella strains (three S. Infantis and one S. Manhattan strains) isolated from chicken products were resistant to cefotaxime and harbored bla_CMY-2 or bla_TEM-52B. Thus, food workers may acquire TGC-resistant Salmonella after the ingestion of contaminated chicken products and further contaminate food products.

Cell-free supernatants produced by lactic acid bacteria reduce Salmonella population in vitro

The genus Salmonella is closely associated with foodborne outbreaks and animal diseases, and reports of antimicrobial resistance in Salmonella species are frequent. Several alternatives have been developed to control this pathogen, such as cell-free supernatants (CFS). Our objective here was to evaluate the use of lactic acid bacteria (LAB) CFS against Salmonella in vitro. Seventeen strains of LAB were used to produce CFS, and their antimicrobial activity was screened towards six strains of Salmonella. In addition, CFS were also pH-neutralized and/or boiled. Those with the best results were lyophilized. MICs of lyophilized CFS were 11.25-22.5 g l^-1. Freeze-dried CFS were also used to supplement swine and poultry feed (11.25 g kg^-1) and in vitro simulated digestion of both species was performed, with Salmonella contamination of 5×10⁶ and 2×10⁵ c.f.u. g^-1 of swine and poultry feed, respectively. In the antimicrobial screening, all acidic CFS were able to inhibit the growth of Salmonella. After pH neutralization, Lactobacillus acidophilus Llorente, Limosilactobacillus fermentum CCT 1629, Lactiplantibacillus plantarum PUCPR44, Limosilactobacillus reuteri BioGaia, Lacticaseibacillus rhamnosus ATCC 7469 and Pediococcus pentosaceus UM116 CFS were the only strains that partially maintained their antimicrobial activity and, therefore, were chosen for lyophilization. In the simulated swine digestion, Salmonella counts were reduced ≥1.78 log c.f.u. g^-1 in the digesta containing either of the CFS. In the chicken simulation, a significant reduction was obtained with all CFS used (average reduction of 0.59±0.01 log c.f.u. ml^-1). In general, the lyophilized CFS of L. fermentum CCT 1629, L. rhamnosus ATCC 7469 and L. acidophilus Llorente presented better antimicrobial activity. In conclusion, CFS show potential as feed additives to control Salmonella in animal production and may be an alternative to the use of antibiotics, minimizing problems related to antimicrobial resistance.

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.

Antimicrobial Resistance of Non-Typhoid Salmonella in Meat and Meat Products

Salmonella enterica serovars are associated with numerous annual deaths worldwide and are responsible for a large number of foodborne diseases. Within this frame of reference, knowledge of antimicrobial susceptibility represents the fundamental approach of most Salmonella treatments. Therefore, scientific publications of antimicrobial susceptibilities and resistance must be precise, with interpretations adjusted to a particular standard. Hence, the three objectives in this study were: (i) to describe the frequency of antimicrobial-resistant isolates of Non-Typhoidal Salmonella (NTS) isolated from beef, pork, chicken meat, and other meat products; (ii) to describe the distribution of serovars and their multi-resistance to antibiotics for clinical use (veterinary and human) between 1996 and 2019; and (iii) to propose additional considerations that could improve the use and usefulness of the published results. Our results determined that the predominant isolates came from poultry. Enteritidis and Typhimurium were the most reported serovars by MIC (with both having the highest resistance to TET) while the lowest resistance was to CIP and CRO for Enteritidis and Typhimurium, respectively. The multi-resistance pattern AMP AMC CEP GEN KAN STR TET was the most frequently observed pattern by MIC in Montevideo and Seftenberg, while, for disc diffusion, the pattern AMP STR TET was the most frequent in the Bredeney serotype. In conclusion, researchers should carry out homogeneous sampling procedures, identify the types of the samples, use standard identification methods, and employ appropriate standards for antimicrobial susceptibility interpretation. Additionally, there is also a need for all WHO members to comply with the WHA 73.5 resolution. Our final recommendation is for all producers to reduce antibiotic prophylactic use.

Transmission of extended-spectrum cephalosporin-resistant Salmonella harboring a blaCMY-2-carrying IncA/C2 plasmid chromosomally integrated by ISEcp1 or IS26 in layer breeding chains in Japan

Dissemination of extended-spectrum cephalosporin (ESC)-resistant Salmonella is a public health concern in the egg production industry. ESC-resistant Salmonella often acquires the bla gene via insertion sequences (ISs). Therefore, this study aimed to assess antimicrobial resistance in Salmonella from Japanese layer breeding chains and egg processing chains, and determine the genetic profiles of IS-like elements in ESC-resistant Salmonella. Antimicrobial susceptibility testing was performed on 224 isolates from 49 facilities involving layer breeder farms, hatcheries, pullet-rearing farms, and layer farms in breeding chains along with egg processing chains. ESC-resistant Salmonella strains were whole-genome sequenced. Among them, 40 (17.9%) were resistant to at least streptomycin, tetracycline, ampicillin, chloramphenicol, cefpodoxime, nalidixic acid, ciprofloxacin, and/or kanamycin despite lacking resistance to azithromycin and meropenem. Moreover, 15 were ESC-resistant Salmonella harboring bla_CMY-2 (Salmonella enterica serovar Ohio, n=12; S. Braenderup, n=1; untypeable with O7:b:-, n=1) and bla_CTX-M-14 (S. Cerro, n=1). IncA/C₂ plasmids containing ISEcp1, IS26, and multiple antimicrobial resistance genes (including bla_CMY-2) were identified in S. Ohio isolates from pullet-rearing and layer farms belonging to the same company. Chromosomal integration of partial or whole IncA/C₂ plasmids was seen with two S. Ohio isolates via ISEcp1 or IS26, respectively. Antimicrobial resistance genes such as bla_CMY-2 might be transmitted among the upper and the lower levels of layer breeding chains via the replicon type IncA/C₂ plasmids containing ISEcp1 and IS26.

Isolation and plasmid characterisation of Salmonella enterica serovar Albany harbouring mcr-5 from retail chicken meat in Japan

The emergence of plasmid-mediated colistin resistance genes (mcr), which is occurring in numerous countries, is a worldwide concern, primarily because colistin is a last-resort antibiotic. Compared to E. coli, prevalence of mcr genes in Salmonella is unclear in Japan. Here we screened for mcr-1-5 genes in our collection of Salmonella strains isolated from retail meat products collected in Japan from 2012 through 2016. We found that Salmonella Albany strain 27A-368 encodes mcr-5 and that mcr genes were undetectable among the remaining 202 isolates. The resistance plasmid p27A-368 was transferred by conjugation to S. Infantis and was stably retained as a transconjugant. Whole-genome sequencing revealed that mcr-5 resided on a 115 kb plasmid (p27A-368). The plasmid backbone of p27A-368 is more similar to that of pCOV27, an ESBL-encoding plasmid recovered from avian pathogenic E. coli, rather than pSE13-SA01718 of S. Paratyphi B that encodes mcr-5. Further, mcr-5 is located on a transposon, and its sequence is similar to that of pSE13-SA01718. A phylogenetic tree based on single nucleotide variants implies a relationship between 27A-368 and S. Albany isolated in Southeast Asian countries.

[Salmonella Serovars Isolated from Retail Meats in Tokyo, Japan and Their Antimicrobial Susceptibility]

To identify the risk of Salmonella in meat, we investigated the prevalence of Salmonella, serovars and their antimicrobial susceptibility patterns. Salmonella was found in 353 out of 849 (41.6%) chicken, 9 out of 657 (1.4%) pork, 1 out of 517 (0.2%) Beef, 6 out of 8 (75.0%) chicken offal, 43 out of 142 (30.3%) pork offal and 4 out of 198 (2.0) beef offal samples collected from retail meats in Tokyo, Japan between 2009 and 2017. Salmonella Infantis was the most common serovar, followed by S. Schwarzengrund in the isolates from domestic chicken meats. The prevalence rate of S. Infantis decreased while that of S. Schwarzengrund increased by the year. Apart from this, the most prevalent serovars were S. Heidelberg in the imported chicken meat isolates, S. Typhimurium and Salmonella O4:i:- in pork, and S. Derby in beef isolates. Antimicrobial testing revealed high resistance to tetracycline (TC) in all meat sample isolates; however, all the isolates were sensitive to carbapenem and fluoroquinolone. Fourteen cefotaxime (CTX) resistant strains, seven extended spectrum β-lactamase (ESBL) producing strains and twenty-three AmpC producing strains were isolated from chicken meat samples. These findings indicate that the serovar and antimicrobial susceptibility varied among meat samples.

Whole-genome sequence analysis of Salmonella Infantis isolated from raw chicken meat samples and insights into pESI-like megaplasmid

There has been an increase in the number of reports on Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolated from animals and humans. Recent studies using whole genome sequencing (WGS) have provided evidence on the likely contribution of a unique conjugative megaplasmid (pESI; ~280 kb) to the dissemination of this serovar worldwide. In the present study, twenty-two unrelated Salmonella strains [S. Infantis (n = 20) and Salmonella 6,7:r:- (n = 2)] and their plasmids were investigated using next generation sequencing technologies (MiSeq and MinION) to unravel the significant expansion of this bacteria in Turkey. Multi-locus sequence typing, plasmid replicons, resistance gene contents as well as phylogenetic relations between strains were determined. According to the WGS data, all S. Infantis possessed the relevant megaplasmid backbone genes and belonged to sequence type 32 (ST32) with the exception of a single novel ST7091. Tetracycline and trimethoprim/sulfamethoxazole resistance were found to be widespread in S. Infantis strains and the resistant strains exclusively carried the tetA, sul1, sul2 and dfrA14 genes. One S. Infantis isolate was also a carrier of the plasmid-mediated ampC via bla_CMY-2, gene. Moreover, full genomes of four S. Infantis isolates were reconstructed based on hybrid assembly. All four strains contained large plasmids (240-290 kb) similar to previously published megaplasmid (pESI) and accompanied by several small plasmids. The megaplasmid backbone contained a toxin-antitoxin system, two virulence cassettes and segments associated with heavy metals resistance, while variable regions possessed several antibiotic resistance genes flanked by mobile elements. This study indicated that pESI-like megaplasmid is widely disseminated within the tested S. Infantis strains of chicken meat, warranting further genomic studies on clinical strains from humans and animals to uncover the overall emergence and spread of this serovar.

Coinfection with Human Norovirus and Escherichia coli O25:H4 Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus Outbreak in Shizuoka Prefecture, Japan

ABSTRACT

Hospital-acquired infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a global problem. Healthy people can carry ESBL-producing E. coli in the intestines; thus, E. coli from healthy people can potentially cause hospital-acquired infections. Therefore, the transmission routes of ESBL-producing E. coli from healthy persons should be determined. A foodborne outbreak of human norovirus (HuNoV) GII occurred at a restaurant in Shizuoka, Japan, in 2018. E. coli O25:H4 was isolated from some of the HuNoV-infected customers. Pulsed-field gel electrophoresis showed that these E. coli O25:H4 strains originated from one clone. Because the only epidemiological link among the customers was eating food from this restaurant, the customers were concurrently infected with E. coli O25:H4 and HuNoV GII via the restaurant food. Whole genome analysis revealed that the E. coli O25:H4 strains possessed genes for regulating intracellular iron and expressing the flagellum and flagella. Extraintestinal pathogenic E. coli often express these genes on the chromosome. Additionally, the E. coli O25:H4 strains had plasmids harboring nine antimicrobial resistance genes. These strains harbored ESBL-encoding blaCTX-M-14 genes on two loci of the chromosome and had higher ESBL activity. Multilocus sequence typing and fimH subtyping revealed that the E. coli O25:H4 strains from the outbreak belonged to the subclonal group, ST131-fimH30R, which has been driving ESBL epidemics in Japan. Because the E. coli O25:H4 strains isolated in the outbreak belonged to a subclonal group spreading in Japan, foods contaminated with ESBL-producing E. coli might contribute to spreading these strains among healthy persons. The isolated E. coli O25:H4 strains produced ESBL and contained plasmids with multiple antimicrobial resistance genes, which may make it difficult to select antimicrobials for treating extraintestinal infections caused by these strains.

HIGHLIGHTS

Food Workers as a Reservoir of Extended-Spectrum-Cephalosporin-Resistant Salmonella Strains in Japan

Dissemination of extended-spectrum-cephalosporin (ESC)-resistant Salmonella, especially extended-spectrum-β-lactamase (ESBL)-producing Salmonella, is a concern worldwide. Here, we assessed Salmonella carriage by food workers in Japan to clarify the prevalence of ESC-resistant Salmonella harboring blaCTX-M We then characterized the genetic features, such as transposable elements, of blaCTX-M-harboring plasmids using whole-genome sequencing. A total of 145,220 stool samples were collected from food workers, including cooks and servers from several restaurants, as well as food factory workers, from January to October 2017. Isolated salmonellae were subjected to antimicrobial susceptibility testing (disk diffusion method), and whole-genome sequencing was performed for Salmonella strains harboring blaCTX-M Overall, 164 Salmonella isolates (0.113%) were recovered from 164 samples, from which we estimated that at least 0.113% (95% confidence interval [CI]: 0.096 to 0.132%) of food workers may carry Salmonella Based on this estimation, 3,473 (95% CI = 2,962 to 4,047) individuals among the 3,075,330 Japanese food workers are likely to carry Salmonella Of the 158 culturable isolates, seven showed resistance to ESCs: three isolates harbored blaCMY-2 and produced AmpC β-lactamase, while four ESBL-producing isolates harbored blaCTX-M-14 (n = 1, Salmonella enterica serovar Senftenberg) or blaCTX-M-15 (n = 3, S. enterica serovar Haardt). blaCTX-M-15 was chromosomally located in the S Haardt isolates, which also contained ISEcp1, while the S Senftenberg isolate contained an IncFIA(HI1)/IncHI1A/IncHI1B(R27) hybrid plasmid carrying blaCTX-M-14 along with ISEcp1 This study indicates that food workers may be a reservoir of ESBL-producing Salmonella and associated genes. Thus, these workers may contribute to the spread of blaCTX-M via plasmids or mobile genetic elements such as ISEcp1IMPORTANCE Antimicrobial-resistant Salmonella bacteria arise in farm environments through imprudent use of antimicrobials. Subsequently, these antimicrobial-resistant strains, such as extended-spectrum-β-lactamase (ESBL)-producing Salmonella, may be transmitted to humans via food animal-derived products. Here, we examined Salmonella carriage among food handlers in Japan. Overall, 164 of 145,220 fecal samples (0.113%) were positive for Salmonella Among the 158 tested isolates, four were identified as ESBL-producing isolates carrying ESBL determinants blaCTX-M-15 or blaCTX-M-14 In all cases, the genes coexisted with ISEcp1, regardless of whether they were located on the chromosome or on a plasmid. Our findings suggest that food workers may be a reservoir of ESBL-producing strains and could contribute to the spread of resistance genes from farm-derived Salmonella to other bacterial species present in the human gut.

Increased Salmonella Schwarzengrund prevalence and antimicrobial susceptibility of Salmonella enterica isolated from broiler chickens in Kagoshima Prefecture in Japan between 2013 and 2016

This study aimed to analyze the Salmonella serovars, measure the minimum inhibitory concentration of antimicrobials, and examine the antimicrobial resistance genes of Salmonella isolated from 192 broiler flocks in Kagoshima Prefecture in Japan, from 2013 to 2016. We found that all Salmonella isolates belonged to three serovars: Salmonella Manhattan, S. Infantis, and S. Schwarzengrund. Among them, S. Schwarzengrund prevalence has recently increased annually making the main serovar. Most recovered isolates were highly resistant to streptomycin, sulfamethoxazole, and oxytetracycline. We saw the reduction of third-generation cephalosporin resistance and identified the reason of increased kanamycin resistance to be the increased number of S. Schwazengrund isolates. Among the kanamycin-resistant Salmonella isolates, aphA1 constituted the main resistance gene detected.

A farm-to-fork quantitative risk assessment model for Salmonella Heidelberg resistant to third-generation cephalosporins in broiler chickens in Canada

Salmonella Heidelberg resistant to ceftiofur (a third-generation cephalosporin antimicrobial agent) in broiler chicken products pose a risk to public health in Canada. The objective of this study was to assess the extent of that risk and to evaluate the effect of intervention measures along the agri-food chain. A stochastic farm-to-fork quantitative microbial risk assessment model was developed following the Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance. Different scenarios were analyzed to assess the individual relative effects of 18 possible interventions in comparison to a baseline scenario. The baseline scenario represented the first year of on-farm antimicrobial use surveillance in the Canadian broiler industry and the year before an industry-imposed ban on the preventive use of antimicrobials of very high importance to human health (2013), where 31.3% of broiler flocks consisted of birds to which ceftiofur was administered. The baseline scenario predicted an average probability of illness of 1.1 per 100,000 servings (SE: 0.064 per 100,000), corresponding to an average of 22,000 human infections (SE: 1900) with ceftiofur-resistant S. Heidelberg per year, which is likely an overestimation. This risk was reduced by 90% or 20% when two separate scenarios designed to capture the effect of withdrawing preventive ceftiofur use from poultry production were simulated using different approaches; data used for the former scenario were confounded by other potential concomitant control measures (e.g. Salmonella vaccination programme), so the true effect likely lies somewhere between the two estimates. A theoretical 'worst case' scenario where all flocks had birds exposed to ceftiofur increased the risk by 107%. A 50% reduction in the probability of human prior exposure to antimicrobials, which has a selective and competitive effect for Salmonella spp. following ingestion of contaminated products, reduced the risk by 65%. Other promising measures that could be considered for further risk management included improved cleaning and disinfection between broiler flocks on farm (risk reduction by 26%), exclusive use of air chilling (risk reduction by 34%), and the improvement of meat storage and preparation conditions, e.g., no temperature abuse at retail (risk reduction by 88%). These findings showed the importance of a structured approach to assessing and potentially implementing effective interventions to reduce the risk associated with ceftiofur-resistant S. Heidelberg at different steps along the agri-food chain. Major data gaps included information on concentrations of resistant bacteria, cross contamination at processing and how ceftiofur-resistant S. Heidelberg behave in comparison with susceptible ones, e.g., in terms of growth and survival ability, as well as pathogenicity and virulence.

Emergence and Evolution of High-Level Cephalosporin-Resistant Salmonella Goldcoast in Northern Taiwan

Background

Nontyphoidal Salmonella (NTS) is an important foodborne pathogen worldwide. We investigated a 2018 outbreak of highly antimicrobial-resistant Salmonella enterica serotype Goldcoast in northern Taiwan.

Methods

We collected 30 clinical isolates and 2 meat isolates from this outbreak in New Taipei and Taoyuan, Taiwan in 2018. The clinical manifestations and the treatment of the patients were reviewed. To trace the source, we examined NTS isolated from food samples collected from the markets in northern Taiwan. All of the isolates along with an additional human isolate from China were sequenced and compared with the sequences of Salmonella Goldcoast reported by other countries.

Results

The outbreak involved 14 pediatric patients (<5 years old) and 16 adults (36 to 83 years old). Nine patients with invasive or severe disease required carbapenem treatment. The MIC₉₀ of ceftriaxone and ciprofloxacin for the outbreak isolates was >256 μg/mL and 1 μg/mL, respectively, and a conjugative 278-kilobase plasmid harboring bla_CTX-M-55 and qnrS1 contributed towards the resistance. Whole-genome sequencing revealed a clonal relationship among the outbreak isolates and the 2 collected from the retail meats. The outbreak clone was phylogenetically close to that of Salmonella Goldcoast reported in the United Kingdom, Poland, and China, whereas similar resistance plasmids were found in China and Cambodia.

Conclusions

The clinical spectrum of the high-level cephalosporin-resistant Salmonella Goldcoast is similar to that of other NTS serotypes, but severe cases required carbapenem treatment. The study confirmed the emergence of a highly antimicrobial-resistant clone of Salmonella Goldcoast, highlighting the importance of surveillance for food safety.

Ceftiofur-resistant Salmonella enterica serovar Heidelberg of poultry origin - a risk profile using the Codex framework

Codex published the 'Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance' to standardise the approach for evaluating risk posed by foodborne antimicrobial-resistant bacteria. One of the first steps in the guidelines is to compile a risk profile, which provides the current state of knowledge regarding a food safety issue, describes risk management options and recommends next steps. In Canada, ceftiofur/ceftriaxone-resistant Salmonella enterica subsp. enterica serovar Heidelberg from poultry was identified as an antimicrobial resistance (AMR) food safety issue. The first objective of this article was to contextualise this food safety issue, using the risk profile format of the Codex Guidelines. A second objective was to evaluate the applicability of the Codex Guidelines. This risk profile indicated that ceftiofur/ceftriaxone-resistant S. Heidelberg (CSH) was commonly isolated from poultry and was associated with severe disease in humans. Ceftiofur use in poultry hatcheries temporally mirrored the prevalence of CSH from poultry meat at retail and from people with salmonellosis. The evidence was sufficient to indicate the need for risk management options, such as restricting the use of ceftiofur in poultry. The Codex Guidelines provided a useful approach to summarise data for decision-makers to evaluate an AMR food safety issue.

Characteristics of third-generation cephalosporin-resistant Salmonella from retail chicken meat produced by integrated broiler operations

Integrated broiler operations, which control and operate vertically through all phases of the chicken industry, have applied biosecurity and sanitation practices, housing technologies, feeding regimens, and antibiotic applications in different ways to improve food safety. The objective of this study was to compare the prevalence and antimicrobial resistance profiles of Salmonella isolates recovered from 6 different integrated broiler operations and to analyze the characteristics of extended-spectrum β-lactamase (ESBL)- and plasmid-mediated AmpC β-lactamase (pAmpC)-producing Salmonella isolates. Among 336 chicken meat samples, 57 were observed to be positive for Salmonella. However, the prevalence varied from 6.8% to 45.8% in chicken meat, indicating variations in Salmonella occurrence among the operations. Salmonella Albany was the dominant serovar, followed by Salmonella Virchow. In the antimicrobial resistance test, nalidixic acid-resistant isolates were the most prevalent (73.7%), followed by isolates resistant to ampicillin (49.1%) and tetracycline (42.1%). Among 14 third-generation cephalosporin-resistant isolates, 9 (64.3%) ESBL/pAmpC-producing isolates were only obtained from 2 operations: blaCTX-M-15 (n = 7) and blaCTX-M-79 (n = 1) for ESBL genes and blaCMY-2 (n = 1) for pAmpC. All ESBL/pAmpC-positive isolates exhibited high minimum inhibitory concentrations (≥128 μg/mL) of most cephalosporins and showed multidrug resistance. The transfer of ESBL/pAmpC genes was confirmed in transconjugants, which had the same genes and similar resistance patterns as those of the donor. Our findings suggest that Salmonella with resistance to third-generation cephalosporins can now be found in association with integrated broiler operations, providing data to support the development of monitoring and prevention programs for the development and spread of antimicrobial resistance in integrated broiler operations.

Effects of Antimicrobial Administration on the Prevalence of Antimicrobial-Resistant Escherichia coli in Broiler Flocks

The increase in antimicrobial-resistant (AMR) bacteria caused by antimicrobial usage is a public health problem. We investigated the proportion of cephalexin (LEX)-resistant bacteria in fresh feces obtained from antimicrobial-free broilers in three flocks at ＜15, 15-40, and＞ 40 days old. DHL agar plates containing 25 μg/mL LEX (DHL-L) showed LEX-resistant bacteria in all flocks at ＜15 days old and in one flock at ＞ 40 days old. The bacterial counts on DHL and DHL-L were 10⁵-10⁸ colony forming units (CFU)/g feces and ＜10²-10⁵ CFU/g feces, respectively. We also assessed the proportion of AMR bacteria in feces collected at 5, 12, 19, 26, 33, and 40 days old from two flocks treated with amoxicillin at 5-7 days old and co-trimoxazole at 24-26 days old. The proportion of ampicillin (AMP)-resistant bacteria was elevated at 12 and 26-33 days old on DHL containing 50 μg/mL AMP, while no increase in LEX-resistant bacteria was observed on DHL-L. All isolates tested exhibited AMP resistance at 12 days old, while most exhibited resistance to both AMP and trimethoprim/sulfamethoxazole at 26-33 days old. Our results suggest that antimicrobial administration influenced the selection of AMR bacteria with cross- and coresistance.