Genes and mutations conferring antimicrobial resistance in Salmonella: an update

Genomic characterization of antimicrobial-resistance and virulence factors in Salmonella isolates obtained from pig farms in Antioquia, Colombia

BACKGROUND

Occurrence of antimicrobial-resistant Salmonella strains has been reported worldwide, because of inappropriate use of antimicrobial products in either humans or animals. The presence of multidrug resistant Salmonella in pig production systems had been reported in Antioquia, Colombia.

AIM

To identify antimicrobial resistance genes (ARG) in different Salmonella spp. strains isolated from pig productions in Antioquia, Colombia. Methods: Samples were received at the Diagnostic Unit of the Faculty of Agrarian Sciences at the University of Antioquia, from January 1, 2019, to January 2021. A total of 28 isolates of Salmonella spp. were included, which presented phenotypic resistance to more than one antibiotic used in pig farms. Whole genome sequencing (WGS) was performed in the Unit of Genomic of Agrosavia using an automated pipeline from the GHRU- Sanger Institute, employing the Illumina MiSeq platform.

RESULTS

WGS revealed 34 ARGs among these isolates. In 25 isolates (89%) more than two ARGs were found. Genes encoding resistance were found for 10 different groups of antibiotics (beta-lactam, aminoglycosides, chloramphenicol, rifampicins, lincosamides, fluoroquinolones, tetracyclines, sulfonamides and trimethoprim). The most frequently observed MDR profile in Typhimurium isolates was AMP-CEX-CEP-CEF-EFT-CEQ-FLU-ENR-TE-FFC-SXT.

CONCLUSION

The presence of multi-drug resistant Salmonella strains in pigs destined for human consumption in Antioquia, Colombia was determined. This research emphasizes the utmost importance of epidemiological tools to understand the presence and spreading of antimicrobial resistance genes in pig farms. Additionally, it highlights the critical need for developing educational programs and public policies to help reduce the spread of antimicrobial resistance in production systems.

The intracellular concentrations of fluoroquinolones determined the antibiotic resistance response of Escherichia coli

The extensive consumption of antibiotics has been reported to significantly promote the generation of antibiotic resistance (ABR), however, a quantitative causal relationship between antibiotic exposure and ABR response is absent. This study aimed to pinpoint the accurate regulatory concentration of fluoroquinolones (FQs) and to understand the biochemical mechanism of the mutual action between FQ exposure and FQ resistance response. Highly sensitive analytical methods were developed by using UPLC-MS/MS to determine the total residual, extracellular residual, total intracellular, intracellular residual and intracellular degraded concentration of three representative FQs, including ciprofloxacin (CIP), ofloxacin (OFL) and norfloxacin (NOR), with detection limits in the range of 0.002-0.057 μg/L, and recoveries in the range of 80-93%. The MICs of Escherichia coli (E. coli) were 7.0-31.4-fold of the respective MIC0 after 40-day FQ exposure, and significant negative associations were discovered between the intracellular (residual, degraded or the sum) FQ concentrations and FQ resistance. Transcriptional expression and whole-genome sequencing results indicated that reduced membrane permeability and enhanced multi-drug efflux pumps contributed to the decreasing intracellular concentration. These results unveiled the pivotal role of intracellular concentration in triggering FQ resistance, providing important information to understand the dose-response relationship between FQ exposure and FQ resistance response, and ascertain the target dose metric of FQs for eliminating FQ resistance crisis.

Emergence and genomic characteristics of multi-drug-resistant Salmonella in pet turtles and children with diarrhoea

Pet turtles are a well-recognized source of human salmonellosis, posing a threat to human health, particularly children who commonly keep pet turtles. To date, the genomic characteristics of Salmonella among pet turtles and children has not been well described. We investigated the prevalence, antimicrobial resistance (AMR) and genomic characteristics of Salmonella from pet turtles in Beijing, China. In total, 9.6 % (46/480) of pet turtles were positive for Salmonella with S. Thompson being the dominant serovar (19/46) in 2019. Moreover, 80.4 % of Salmonella were multi-drug resistant (MDR) and 60.7 % were resistant to ampicillin, streptomycin, sulfonamides and tetracycline (ASSuT). We further compared the genomes of S. Thompson isolates from pet turtles (n=19) with those from children with diarrhoea (n=28) in the same region and year, most of which were sequence type (ST)26, with one novel ST7937 identified from a child-associated isolate. S. Thompson isolates from children with diarrhoea exhibited less resistance than isolates from pet turtles. Most MDR isolates possessed multiple AMR genes, including the AmpC β-lactamase-encoding genes bla DHA-15 and bla DHA-1 which co-occurred with the IncA/C and IncHI plasmid replicon types. To the best of our knowledge, this is the first time that the bla DHA-15 gene has been detected from Salmonella. Several pet turtle-associated S. Thompson isolates comprised phylogenetically close clusters with those from children with diarrhoea (<20 SNP differences). Bayesian analysis demonstrated that the Chinese ST26 S. Thompson strains had a recent evolutionary history and evolved into two major clades, with one clade acquiring various resistant plasmids. Our findings revealed the emergence of MDR Salmonella among pet turtles in China and provided evidence for the interspecies transmission of S. Thompson.

Prevalence of efflux pump and heavy metal tolerance encoding genes among Salmonella enterica serovar Infantis strains from diverse sources in Brazil

Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) is a non-typhoid, zoonotic and foodborne serovar with worldwide distribution, and often associated with increasing antimicrobial resistance. Efflux pumps are antimicrobial resistance mechanisms able to promote and increase resistance levels to multiple distinct drug classes. Heavy metal tolerance genes have been demonstrated to promote resistance against these compounds and act in the co-selection of antimicrobial resistant strains. Despite the relevance of S. Infantis in clinical and non-clinical fields, few studies worldwide have investigated the occurrence of such genes in strains from diverse sources. Therefore, the present study aimed at determining the prevalence of antimicrobial efflux pump and heavy metal tolerance genes and their genomic relatedness through core-genome multi-locus sequence typing (cgMLST) of 80 S. Infantis strains isolated from food, environmental, human and animal sources from 2013 to 2018 in Brazil. Twenty efflux pump encoding genes were detected, with 17 of these (acrA, acrB, baeR, crp, emrB, emrR, hns, kdpE, kpnF, marA, marR, mdtK, msbA, rsmA, sdiA, soxR and soxS) detected in all strains studied, golS in 98.75%, mdfA in 58.75% and tet(A) in 37.5%. Tolerance genes to arsenic (arsR) were detected in 100% of the strains, gold (golS and golT) in 98.75%, silver (silABCDEFPRS) in 36.25% and mercury (merR and merT) in 1.25%. cgMLST demonstrated a closer genetic relationship among strains harboring similar profiles of heavy metal and efflux pump encoding genes, despite their origin. In conclusion, the high prevalence of some efflux pump and heavy metal tolerance encoding genes alert us about the importance of strong surveillance measures to monitor resistance and the transmission of S. Infantis among diverse sources in Brazil.

Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection

Background

Although urinary tract infections (UTIs) are extremely common, isolation of causative uropathogens is not always routinely performed, with antibiotics frequently prescribed empirically. This study determined the susceptibility of urinary isolates from two Health and Social Care Trusts (HSCTs) in Northern Ireland to a range of antibiotics commonly used in the treatment of UTIs. Furthermore, we determined if detection of trimethoprim resistance genes (dfrA) could be used as a potential biomarker for rapid detection of phenotypic trimethoprim resistance in urinary pathogens and from urine without culture.

Methods

Susceptibility of E. coli and Klebsiella spp. isolates (n = 124) to trimethoprim, amoxicillin, ceftazidime, ciprofloxacin, co-amoxiclav and nitrofurantoin in addition to susceptibility of Proteus mirabilis (n = 61) and Staphylococcus saprophyticus (n = 17) to trimethoprim was determined by ETEST® and interpreted according to EUCAST breakpoints. PCR was used to detect dfrA genes in bacterial isolates (n = 202) and urine samples(n = 94).

Results

Resistance to trimethoprim was observed in 37/124 (29.8%) E. coli and Klebsiella spp. isolates with an MIC₉₀ > 32 mg/L. DfrA genes were detected in 29/37 (78.4%) trimethoprim-resistant isolates. Detection of dfrA was highly sensitive (93.6%) and specific (91.4%) in predicting phenotypic trimethoprim resistance among E. coli and Klebsiella spp. isolates. The dfrA genes analysed were detected using a culture-independent PCR method in 16/94 (17%) urine samples. Phenotypic trimethoprim resistance was apparent in isolates cultured from 15/16 (94%) dfrA-positive urine samples. There was a significant association (P < 0.0001) between the presence of dfrA and trimethoprim resistance in urine samples containing Gram-negative bacteria (Sensitivity = 75%; Specificity = 96.9%; PPV = 93.8%; NPV = 86.1%).

Conclusions

This study demonstrates that molecular detection of dfrA genes is a good indicator of trimethoprim resistance without the need for culture and susceptibility testing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02551-9.

Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam

Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long- and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84 % of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.

A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021

Salmonella contamination of eggs and egg shells has been identified as a public health problem worldwide. Here, we reported an outbreak of severe gastrointestinal symptoms caused by Salmonella enterica serovar Enteritidis (S. enteritidis) in China. We evaluated the outbreak by using epidemiological surveys, routine laboratory testing methods, and whole genome sequencing (WGS). This outbreak occurred in a canteen in Beijing, during March 9–11, 2021, 225 of the 324 diners who have eaten at the canteen showed gastrointestinal symptoms. The outbreak had characteristical epidemiological and clinical features. It caused a very high attack rate (69.4%) in a short incubation time. All patients developed diarrhea and high fever, accompanied by abdominal pain (62.3%), nausea (50.4%), and vomiting (62.7%). The average frequency of diarrhea was 12.4 times/day, and the highest frequency of diarrhea was as high as 50 times/day. The average fever temperature was 39.4°C, and the highest fever temperature was 42°C. Twenty strains of S. enteritidis were recovered, including 19 from the patients samples, and one from remained egg fried rice. Antibiotic susceptibility test showed that the 20 outbreak strains all had the same resistance pattern. PFGE results demonstrated that all 20 strains bore completely identical bands. Phylogenetic analysis based on WGS revealed that all 20 outbreak strains were tightly clustered together. So the pathogenic source of this food poisoning incident may was contaminated egg fried rice. Resistance gene analysis showed that the outbreak strains are all multi-drug resistant strains. Virulence gene analysis indicated that these outbreak strains carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2). Other important virulence genes were also carried by the outbreak strains, such as pefABCD, rck and shdA. And the shdA gene was not in other strains located in the same evolutionary branch as the outbreak strain. We speculated that this is a significant reason for the serious symptoms of gastroenteritis in this outbreak. This outbreak caused by S. enteritidis suggested government should strengthen monitoring of the prevalence of outbreak clone strains, and take measures to mitigate the public health threat posed by contaminated eggs.

Multidrug-Resistant and Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Heidelberg Is Widespread in a Poultry Processing Facility in Southern Brazil

ABSTRACT

This study was conducted to characterize the distribution of Salmonella isolates in a poultry processing facility and to identify their antibiotic resistance profiles. Salmonella enterica was detected in 146 samples (66.7%), and 125 isolates were identified as Salmonella Heidelberg (n = 123), Salmonella Abony (n = 1), and Salmonella O:4,5 (n = 1). Salmonella Heidelberg isolates were subjected to XbaI macrorestriction analysis and pulsed-field gel electrophoresis. The 66 pulsotypes obtained were grouped into four major clusters, indicating cross-contamination and persistence of this serotype in the processing facility. Selected S. enterica isolates were characterized by their antibiotic resistance, and most (n = 122, 97.6%) were multidrug resistant. Resistance to third-generation cephalosporins ceftazidime (84 isolates, 67.2%) and cefotaxime and ceftriaxone (91 isolates, 72.8%) was particularly prevalent. Production of extended-spectrum β-lactamases (ESBL) was identified in 24 isolates (19.2%), and ESBL-producing isolates were resistant to at least eight antibiotics. This study revealed the high prevalence of Salmonella Heidelberg in the poultry chain, providing insight into the ecology of this pathogen in this facility. The high prevalence of multidrug-resistant S. enterica is a concern due to the potential consequences for public health.

HIGHLIGHTS

Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil

The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the bla_SHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of bla_CTX–M and bla_CMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.

Molecular Characterization of Cephalosporin-Resistant Salmonella Enteritidis ST11 Isolates Carrying blaCTX-M from Children with Diarrhea

Salmonella Enteritidis is an important foodborne pathogen with high prevalence of resistance to cephalosporins, imposing a serious threat to public health. Therefore, a total of 162 Salmonella Enteritidis isolates collected from child patients in China from 2007 to 2017 were characterized for their resistance to cephalosporins and investigated the transmission characteristics of cephalosporin resistance gene. We found that 15 (9.26%) isolates were all resistant to cefalotin (minimum inhibitory concentration [MIC] ≥512 μg/mL), ceftazidime (MIC 16-128 μg/mL), ceftriaxone (MIC 64 to ≥512 μg/mL), ceftiofur (MIC 64-256 μg/mL), and cefotaxime (MIC 64 to ≥512 μg/mL) with the possession of cephalosporin resistance genes bla_CTX-M-55 (n = 13), bla_CTX-M-101 (n = 1), and bla_CTX-M-153 (n = 1). Molecular typing further revealed that these 15 isolates belonged to sequence type ST11 and shared close pulsed-field gel electrophoresis patterns, suggesting the possibility of clonal spread in Salmonella Enteritidis interspecies. Furthermore, conjugation experiments were successfully performed in 13 of 15 isolates, and bla_CTX-M-55 was present on conjugative plasmids with sizes ranging from 54.7 to 173.4 kb. Compared with recipient Escherichia coli C600, transconjugants conferred elevated MICs for cephalosporins ranging from 2- to 2048-fold. The genetic structure surrounding of bla_CTX-M-55 gene in transconjugants were ΔISEcp1-bla_CTX-M-55-orf477 (n = 8) and ISEcp1-bla_CTX-M-55-orf477 (n = 3), respectively. Taken together, bla_CTX-M on the plasmids might contribute to cephalosporin resistance in Salmonella Enteritidis, and conjugative transfer of bla_CTX-M-55 might facilitate the spread of cephalosporin resistance in Salmonella Enteritidis. Hence, effective mitigation measurements are needed to reduce the threat caused by cephalosporin-resistant Salmonella Enteritidis to public health.

A β-lactamase-producing plasmid from Neisseria gonorrhoeae carrying a unique 6 bp deletion in blaTEM-1 encoding a truncated 24 kDa TEM-1 penicillinase that hydrolyses ampicillin slowly

BACKGROUND

Seven structurally related β-lactamase-producing plasmids have been characterized in penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates. We characterized a variant (i.e. pJRD20, Canada type) of the Africa-type (pJD5) plasmid isolated from N. gonorrhoeae strain 8903.

OBJECTIVES

To compare the DNA sequence of pJRD20 with that of pJD5 and pJD4 (Asia-type) and their TEM-1 β-lactamases.

METHODS

N. gonorrhoeae 8903 was identified as part of the Gonococcal Antimicrobial Surveillance Program in Canada. β-Lactamase production was assessed using nitrocefin. MICs were determined by agar dilution and Etest methods (CLSI). The DNA sequences of pJRD20, pJD5 and pJD4 were assembled and annotated. The structure of TEM-1 and its penicillin-binding properties were determined by in silico molecular modelling and docking. TEM-1 proteins were characterized by western blot, mass spectrometry and ampicillin hydrolysis assays.

RESULTS

N. gonorrhoeae 8903 exhibited intermediate susceptibility to penicillin with slow β-lactamase activity (i.e. 35 min to hydrolyse nitrocefin). Except for a novel 6 bp deletion starting at the G of the ATG start codon of blaTEM-1, the DNA sequence of pJRD20 was identical to that of pJD5. The TEM-1 β-lactamase produced by pJRD20 is 24 kDa and hydrolyses ampicillin only after several hours.

CONCLUSIONS

This unusual PPNG isolate might have been characterized as a non-PPNG owing to its low MIC of penicillin and its very slow hydrolysis of nitrocefin. Given the unusual nature of its TEM-1 β-lactamase, laboratories might consider extending the duration of nitrocefin hydrolysis assays.

Phenotypic and Genotypic Characterization of Virulence Factors and Susceptibility to Antibiotics in Salmonella Infantis Strains Isolated from Chicken Meat: First Findings in Chile

Simple Summary

Salmonella Infantis (S. Infantis) is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. This pathogen has emerged over the last few decades in different countries, causing outbreaks in humans subsequent to foodborne transmission. It is important to be able to characterize this pathogen in order to establish control measures in the poultry industry. In this study, we investigated the presence of virulence genes, biofilm formation abilities, antibiotic resistance genes, and antibiotic susceptibility in S. Infantis. The results showed that the S. Infantis strains isolated from chicken meat for sale in supermarkets in Santiago, Chile are multidrug-resistant (MDR) and contain virulence genes, making them pathogenic. Thus, Salmonella Infantis should be under surveillance in the poultry food production chain with the aim of protecting public health.

Abstract

Salmonella Infantis is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. In Chile, there are no data to characterize S. Infantis strains in poultry production. In this study, 87 S. Infantis strains were isolated from chicken meat for sale in supermarkets in Santiago, Chile, and characterized according to their virulence genes, biofilm formation abilities, antibiotic susceptibility, and resistance genes. Through polymerase chain reaction or PCR, the strains were analyzed to detect the presence of 11 virulence genes, 12 antibiotic resistance genes, and integrase genes. Moreover, disc diffusion susceptibility to 18 antimicrobials and the ability to form biofilm in vitro were evaluated. Results demonstrated six different virulence gene profiles. Ninety-four percent of the strains were multi-resistant to antibiotics with weak biofilm formation abilities, 63.2% of the strains were broad spectrum β- lactam resistant, and the bla_CTX-M-65 gene was amplified in 13 strains. Only 3.4% of the strains were fluoroquinolone resistant, and the qnrB gene was amplified in two strains. Colistin resistance was exhibited in 28.7% of the strains, but mrc genes were not amplified in any strain under study. The isolated S. Infantis strains are pathogenic and antibiotic multi-resistant, and thus, this Salmonella serotype should be under surveillance in the poultry food production chain with the aim of protecting public health.

Phenotypic and genotypic characterization of non-typhoidal Salmonella isolated from a Brazilian pork production chain

Pork products are important sources of foodborne non-typhoidal Salmonella in Brazil where antibiotics are commonly used throughout the pork production process and this has the potential to selectively favor antibiotic-resistant strains. We characterized the genotypic and phenotypic diversity of S. enterica isolates (n = 41) that were isolated in Brazil. Isolates were collected from ten swine farms and one slaughterhouse. Whole-genome sequencing and in silico serotyping demonstrated that the S. enterica serovar Typhimurium was the most common serotype (n = 17), but eight additional servoars were identified. Isolates presented high similarity based on comparison of DNA sequences (minimum of 89.6%), and sequence variation grouped according to serotype. Eight multilocus sequence types were identified with ST19 being most common (n = 21). Several plasmids replicons were detected, with Col (RNAI) the most abundant (n = 30), followed by IncR (n = 22), IncI1 (n = 10) and IncA/C2 (n = 10). Minimum inhibitory concentration assays showed that the principle resistance phenotypes were for streptomycin (90.2%), tetracycline (87.8%), ampicillin (80.5%), chloramphenicol (70.7%) and ciprofloxacin (51.2%). Only two isolates were resistant to third-generation cephalosporins and no isolates were resistant to two tested carbapenems. Twenty-six unique antimicrobial-resistance genes were identified with bla_TEM-1A and bla_TEM-1B likely responsible for most beta-lactam resistance and floR responsible for most chloramphenicol resistance. Six strains were positive for mcr-1. At the time of collection, the sampled farms were adding ciprofloxacin to feed and this may have contributed to the high prevalence of resistance to this antibiotic. The high number of multidrug resistant Salmonella and the presence of multiple resistant genes and plasmids emphasize the diversity of Salmonella in the studied pork chain, specially from serotype Typhimurium.

Global priority pathogens: virulence, antimicrobial resistance and prospective treatment options

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Salmonella spp. are part of a group of pathogens that pose a major threat to human health due to the emergence of multidrug-resistant strains. Moreover, these bacteria have several virulence factors that allow them to successfully colonize their hosts, such as toxins and the ability to produce biofilms, resulting in an urgent need to develop new strategies to fight these pathogens. In this review, we compile the most up-to-date information on the epidemiology, virulence and resistance of these clinically important microorganisms. Additionally, we address new therapeutic alternatives, with a focus on molecules with antivirulence activity, which are considered promising to combat multidrug-resistant bacteria.

Investigation of a Salmonellosis Outbreak Caused by Multidrug Resistant Salmonella Typhimurium in China

The rapid emergence of multidrug resistant Salmonella is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8S. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the blaOXA-1 and blaTEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant S. Typhimurium highlights the need for government improved strategies for the prevention and control of Salmonella infections.

CRISPR/Cas9/sgRNA-mediated targeted gene modification confirms the cause-effect relationship between gyrA mutation and quinolone resistance in Escherichia coli

Quinolones are broad-spectrum antibiotics that have been used for decades in treating bacterial infections in humans and animals, and subsequently bacterial resistance to these agents has increased. While studies indicated the relationship between gyrA mutations and bacterial resistance to quinolones, CRISPR/Cas9 was used in this study to investigate causal role of gyrA mutation in the quinolone resistance. In this study, 818 clinical Escherichia coli isolates were analyzed for gyrA mutations and their resistance to quinolones. The CRISPR/Cas9 system was used to generate gyrA mutations in quinolone-susceptible E. coli ATCC 25922, and quinolone-resistant clinical E. coli. The antimicrobial resistance prevalence rate in E. coli against nalidixic acid, ciprofloxacin and enrofloxacin was 77.1% (631/818), 51.1% (418/818) and 49.8% (407/818), respectively. The gyrA mutations were identified in nucleotide positions 248, 255, 259, 260, 261, 273 and 300, and mutations at positions 248 and 259 resulting in amino acid changes at positions 83 and 87 were associated with quinolone resistance. Double-site amino acid mutations increase resistance to quinolones. The gyrA mutations causing changes at amino acids 83 and 87 reversed the features of quinolone resistance in ATCC and clinical strains, verifying the causal role of gyrA mutation in the quinolone resistance of E. coli.

Antibiotic Resistance in Salmonella Typhimurium Isolates Recovered From the Food Chain Through National Antimicrobial Resistance Monitoring System Between 1996 and 2016

Salmonella is a major foodborne pathogen which causes widespread contamination and infection worldwide. Salmonella Typhimurium is one of the leading serovars responsible for human and animal salmonellosis, globally. The increasing rate of antibiotic resistance in Salmonella Typhimurium poses a significant global concern, and an improved understanding of the distribution of antibiotic resistance patterns in Salmonella Typhimurium is essential for choosing the suitable antibiotic for the treatment of infections. To evaluate the roles of animal and human in antibiotic resistance dissemination, this study aims to categorize 11,447 S. Typhimurium strains obtained across the food-chain, including food animals, retail meats and humans for 21 years in the United States by analyzing minimum inhibitory concentrations (MICs) values for 27 antibiotics. Random Forest Algorithm and Hierarchical Clustering statistics were used to group the strains according to their minimum inhibitory concentration values. Classification and Regression Tree analysis was used to identify the best classifier for human- and animal-populations’ isolates. We found the persistent population or multi-drug resistant strains of S. Typhimurium across the four time periods (1996∼2000, 2001∼2005, 2006∼2010, 2011∼2016). Importantly, we also detected that there was more diversity in the MIC patterns among S. Typhimurium strains isolated between 2011 and 2016, which suggests significant emergence of diversified multi-drug resistant strains. The most frequently observed (43%) antibiotic resistance patterns found in S. Typhimurium were tetra-resistant pattern ASSuT (ampicillin, streptomycin, sulfonamides, and tetracycline) and the penta-resistant pattern ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline). Animals (mainly swine and bovine) are the major source for these two frequently found antibiotic resistance patterns. The occurrence of antibiotic resistant strains from humans and chicken is alarming. Strains were mostly susceptible to fluoroquinolones. Together, this study helped in understanding the expansion of dynamics of antibiotic resistance of S. Typhimurium and recommended fluoroquinolones as a possible treatment options against S. Typhimurium infection.

Antimicrobial resistance profiles and virulence genotyping of Salmonella enterica serovars recovered from broiler chickens and chicken carcasses in Egypt

BACKGROUND

This study aimed to survey the prevalence, antimicrobial resistance, and virulence-associated genes of Salmonella enterica recovered from broiler chickens and retail shops at El-Sharkia Province in Egypt. Salmonella virulence factors were determined using the polymerase chain reaction assays targeting the invA, csgD, hilC, bcfC, stn, avrA, mgtC, ompF, sopE1 and pefA genes.

RESULTS

One hundred tweenty out of 420- samples from broiler chickens' cloacal swabs, farm environmental samples, and freshly dressed whole chicken carcasses were positive Salmonella species. The isolates were serotyped as S. Enteritidis as the most dominant serotypes. Interestingly, none of the isolates were resistant to imipenem. The multidrug resistance was determined in 76.7% of the isolates with multidrug antibiotic resistance index of 0.2-0.6. Eight virulence genes (invA, csgD, hilC, stn, bcfC, mgtC, avrA, and ompf) were characterized among 120 S. enterica isolates with variable frequencies, while sopE1and pefA genes that were completely absent in all isolates. Based on the combination of presence and absence of virulence genes, the most common genetic profile (P7, 30%) was invA and csgD genes.

CONCLUSION

S. Enteritidis and S. Typhimurium were the most common identified serotypes in the examined sources. Circulation of such strains in broiler farms required introducing special biosecurity and biocontrol measures for control of Salmonella. Such measures might limit the adverse effects of antibiotics and ensure the safety of the environment and animal-derived food.

Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA

Background

Trimethoprim/sulfamethoxazole is a synthetic antibiotic combination recommended for the treatment of complicated non-typhoidal Salmonella infections in humans. Resistance to trimethoprim/sulfamethoxazole is mediated by the acquisition of mobile genes, requiring both a dfr gene (trimethoprim resistance) and a sul gene (sulfamethoxazole resistance) for a clinical resistance phenotype (MIC ≥4/76 mg/L). In 2017, the CDC investigated a multistate outbreak caused by a Salmonella enterica serotype Heidelberg strain with trimethoprim/sulfamethoxazole resistance, in which sul genes but no known dfr genes were detected.

Objectives

To characterize and describe the molecular mechanism of trimethoprim resistance in a Salmonella Heidelberg outbreak isolate.

Methods

Illumina sequencing data for one outbreak isolate revealed a 588 bp ORF encoding a putative dfr gene. This gene was cloned into Escherichia coli and resistance to trimethoprim was measured by broth dilution and Etest. Phylogenetic analysis of previously reported dfrA genes was performed using MEGA. Long-read sequencing was conducted to determine the context of the novel dfr gene.

Results and conclusions

The novel dfr gene, named dfrA34, conferred trimethoprim resistance (MIC ≥32 mg/L) when cloned into E. coli. Based on predicted amino acid sequences, dfrA34 shares less than 50% identity with other known dfrA genes. The dfrA34 gene is located in a class 1 integron in a multiresistance region of an IncC plasmid, adjacent to a sul gene, thus conferring clinical trimethoprim/sulfamethoxazole resistance. Additionally, dfrA34 is associated with ISCR1, enabling easy transmission between other plasmids and bacterial strains.

Antimicrobial Resistance in Nontyphoidal Salmonella

Non-typhoidal Salmonella is the most common foodborne bacterial pathogen in most countries. It is widely present in food animal species, and therefore blocking its transmission through the food supply is a prominent focus of food safety activities worldwide. Antibiotic resistance in non-typhoidal Salmonella arises in large part because of antibiotic use in animal husbandry. Tracking resistance in Salmonella is required to design targeted interventions to contain or diminish resistance and refine use practices in production. Many countries have established systems to monitor antibiotic resistance in Salmonella and other bacteria, the earliest ones appearing the Europe and the US. In this chapter, we compare recent Salmonella antibiotic susceptibility data from Europe and the US. In addition, we summarize the state of known resistance genes that have been identified in the genus. The advent of routine whole genome sequencing has made it possible to conduct genomic surveillance of resistance based on DNA sequences alone. This points to a new model of surveillance in the future that will provide more definitive information on the sources of resistant Salmonella, the specific types of resistance genes involved, and information on how resistance spreads.

Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda

Non-typhoidal Salmonella (NTS) are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE). Phenotypically resistant isolates (n = 54) were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4%) of the 54 resistant isolates carried at least one of the seven genes (blaTEM-1,cmlA, tetA, qnrS,sul1,dhfrI,dhfrVII) identified by PCR and six (11%) carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

Comparing TiO2 photocatalysis and UV-C radiation for inactivation and mutant formation of Salmonella typhimurium TA102

Salmonellosis is one of the most common causes of foodborne bacterial human disease worldwide, and the emergence of multidrug-resistant (MDR) strains of Salmonella enterica serovar Typhimurium (S. typhimurium) was associated to the incidence of invasive salmonellosis. The objective of the present work was to investigate the effects of the TiO₂ photocatalysis process in terms of both bacteria inactivation and the emergence of mutants, on S. typhimurium TA102 water suspensions. The TiO₂ photocatalysis was compared with a conventional disinfection process such as UV-C radiation. In spite of the faster bacterial inactivation obtained in UV-C disinfection experiments (45, 15, and 10 min for total inactivation for initial cell density 10⁹, 10⁸, and 10⁷ CFU mL^-1, respectively), photocatalytic disinfection (60, 30, and 15 min) was more energy efficient because of a lower energy requirement (2-20 mWs cm^-2) compared to the UV-C disinfection process (5-30 mWs cm^-2). During the photocatalytic experiments, the mutation frequency increased up to 1648-fold compared to background level for a 10⁸ CFU mL^-1 initial bacterial density, and mutants were inactivated after 1-10-min treatment, depending on initial bacterial cell density. In UV-C disinfection experiments, the mutation frequency increased up to 2181-fold for a 10⁸ CFU mL^-1 initial bacterial cell density, and UV-C doses in the range of 0.5-4.8 mWs cm^-2 were necessary to decrease mutation frequency. In conclusion, both disinfection processes were effective in the inactivation of S. typhimurium cells, and mutants released into the environment can be avoided if cells are effectively inactivated.

Antimicrobial resistance in zoonotic nontyphoidal Salmonella: an alarming trend?

Zoonotic bacteria of the genus Salmonella have acquired various antimicrobial resistance properties over the years. The corresponding resistance genes are commonly located on plasmids, transposons, gene cassettes, or variants of the Salmonella Genomic Islands SGI1 and SGI2. Human infections by nontyphoidal Salmonella isolates mainly result from ingestion of contaminated food. The two predominantly found Salmonella enterica subsp. enterica serovars in the USA and in Europe are S. Enteritidis and S. Typhimurium. Many other nontyphoidal Salmonella serovars have been implicated in foodborne Salmonella outbreaks. Summary reports of the antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates over time suggest a moderate to low level of antimicrobial resistance and multidrug-resistance. However, serovar-specific analyses showed in part a steady state, a continuous decline, or a recent increase in resistance to certain antimicrobial agents. Resistance to critically important antimicrobial agents, e.g. third-generation cephalosporins and (fluoro)quinolones is part of many monitoring programmes and the corresponding results confirm that extended-spectrum β-lactamases are still rarely found in nontyphoidal Salmonella serovars, whereas resistance to (fluoro)quinolones is prevalent at variable frequencies among different serovars from humans and animals in different countries. Although it is likely that nontyphoidal Salmonella isolates from animals represent a reservoir for resistance determinants, it is mostly unknown where and when Salmonella isolates acquired resistance properties and which exchange processes have happened since then.

Diagnosis of imported Ugandan typhoid fever based on local outbreak information: A case report

Re-emerging multidrug-resistant typhoid fever is becoming a worldwide threat, especially in East Africa. At the beginning of 2015, an outbreak of typhoid fever started in the capital city of Uganda, and 1940 suspected cases were reported by 5 March 2015. In this report, we describe a case of typhoid fever caused by a MDR strain with HIV infection and hemoglobin S-syndrome thalassemia in an Ugandan from Kampala City. It is essential to consider MDR strains of Salmonella enterica serovar Typhi infections, including fluoroquinolone-resistant strains, in patients from Africa and Southeast Asia.

Antimicrobial Resistance in Salmonella in the United States from 1948 to 1995

We conducted a retrospective study of 2,149 clinicalSalmonellastrains to help document the historical emergence of antimicrobial resistance. There were significant increases in resistance to older drugs, including ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline, which were most common inSalmonella entericaserotype Typhimurium. An increase in multidrug resistance was observed for each decade since the 1950s. These data help show howSalmonellaevolved over the past 6 decades, after the introduction of new antimicrobial agents.

Molecular level understanding of resistance to nalidixic acid in Salmonella enteric serovar typhimurium associates with the S83F sequence type

Nalidixic acid is an antibiotic drug used for treatment of Salmonellosis, a gastrointestinal infection. DNA gyrase subunit A (GyrA) of Salmonella typhimurium is the drug target for nalidixic acid. Resistance of GyrA to nalidixic acid, because of a point mutation in S. typhimurium, was recently reported. Substitution of Phe in place of Ser at locus 83 in GyrA of S. typhimurium has been experimentally associated with nalidixic acid resistance. Despite recent efforts, the mechanism of this resistance is not well understood. In this investigation we used computational techniques to address this shortcoming. Our results showed that contact with residue Arg 91 is certainly important for efficient binding of nalidixic acid to the target protein, and that mutation of this residue results in 180° rotation of the antibiotic in its binding pocket, around its own long axis. It is hoped these findings may enable development of new antibiotics against resistant forms of Salmonella.

Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco

Antimicrobial-resistant non-typhoidal Salmonella (NTS) are an important cause of infection in Africa, but there is a lack of information on their molecular mechanisms of resistance and epidemiology. This study contributes to fill this gap through the characterization by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), plasmid profiling and analysis of antibiotic-resistance determinants of 94 Salmonella enterica strains isolated from food in Morocco. PFGE revealed considerable heterogeneity among the strains, showing 32 pulsotypes. MLST of strains representative of the different serovars evidenced 13 sequence types (STs), three of which were newly identified (ST1694, ST1768 and ST1818) and nine not previously reported in Morocco. Thirty-four strains harbored from one to four plasmids, of IncI1 group in S. Mbandaka, IncFIIA in S. Typhimurium, IncL/M in S. Hadar and S. Blockley. For the first time in Morocco an intact Salmonella Genomic Island 1 (SGI1) carrying the resistance genes aadA2, floR, tetG, blaPSE-1 and sul1 was detected in S. Typhimurium DT104. In serovar Hadar resistance to ampicillin, tetracycline and streptomycin was associated to blaTEM-1, tetA and strA genes respectively, whereas one mutation in gyrA (Asp87Asn) and one in parC (Thr54Ser) genes conferred resistance to nalidixic acid. These findings improve the information on foodborne Salmonella in Morocco, evidencing the presence of MDR strains potentially dangerous to humans, and provide useful data for future studies.

Extensive amplification of GI-VII-6, a multidrug resistance genomic island of Salmonella enterica serovar Typhimurium, increases resistance to extended-spectrum cephalosporins

GI-VII-6 is a chromosomally integrated multidrug resistance genomic island harbored by a specific clone of Salmonella enterica serovar Typhimurium (S.Typhimurium). It contains a gene encoding CMY-2 β-lactamase (bla CMY-2), and therefore contributes to extended-spectrum cephalosporin resistance. To elucidate the significance of GI-VII-6 on adaptive evolution, spontaneous mutants of S. Typhimurium strain L-3553 were selected on plates containing cefotaxime (CTX). The concentrations of CTX were higher than its minimum inhibition concentration to the parent strain. The mutants appeared on the plates containing 12.5 and 25 mg/L CTX at a frequency of 10(-6) and 10(-8), respectively. No colonies were observed at higher CTX concentrations. The copy number of bla CMY-2 increased up to 85 per genome in the mutants, while the parent strain contains one copy of that in the chromosome. This elevation was accompanied by increased amount of transcription. The bla CMY-2 copy number in the mutants drastically decreased in the absence of antimicrobial selection pressure. Southern hybridization analysis and short-read mapping indicated that the entire 125 kb GI-VII-6 or parts of it were tandemly amplified. GI-VII-6 amplification occurred at its original position, although it also transposed to other locations in the genome in some mutants, including an endogenous plasmid in some of the mutants, leading to the amplification of GI-VII-6 at different loci. Insertion sequences were observed at the junction of the amplified regions in the mutants, suggesting their significant roles in the transposition and amplification. Plasmid copy number in the selected mutants was 1.4 to 4.4 times higher than that of the parent strain. These data suggest that transposition and amplification of the bla CMY-2-containing region, along with the copy number variation of the plasmid, contributed to the extensive amplification of bla CMY-2 and increased resistance to CTX.

Salmonella enterica: survival, colonization, and virulence differences among serovars

Data indicate that prevalence of specific serovars of Salmonella enterica in human foodborne illness is not correlated with their prevalence in feed. Given that feed is a suboptimal environment for S. enterica, it appears that survival in poultry feed may be an independent factor unrelated to virulence of specific serovars of Salmonella. Additionally, S. enterica serovars appear to have different host specificity and the ability to cause disease in those hosts is also serovar dependent. These differences among the serovars may be related to gene presence or absence and expression levels of those genes. With a better understanding of serovar specificity, mitigation methods can be implemented to control Salmonella at preharvest and postharvest levels.

High resolution melting analysis for rapid mutation screening in gyrase and Topoisomerase IV genes in quinolone-resistant Salmonella enterica

The increased Salmonella resistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62 Salmonella strains to identify mutations in the QRDR of gyrA, gyrB, parC, and parE genes. Mutations were detected in QRDR of gyrA (n = 52; S83F, S83Y, S83I, D87G, D87Y, and D87N) and parE (n = 1; M438I). Salmonella strains with mutations within QRDR of gyrA are generally more resistant to nalidixic acid (MIC 16 > 256 μg/mL). Mutations were uncommon within the QRDR of gyrB, parC, and parE genes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes in Salmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes.

Characterisation of blaTEM genes and types of β-lactamase plasmids in Neisseria gonorrhoeae - the prevalent and conserved blaTEM-135 has not recently evolved and existed in the Toronto plasmid from the origin

Background

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major concern worldwide. It has been recently feared that the bla_TEM-1 gene is, via bla_TEM-135, evolving into an extended-spectrum β-lactamase (ESBL), which could degrade all cephalosporins including ceftriaxone. The aims of the present study were to characterize the bla_TEM genes, types of β-lactamase plasmids, the degradation of ampicillin by TEM-135 compared to TEM-1, and to perform molecular epidemiological typing of β-lactamase-producing N. gonorrhoeae strains internationally.

Methods

β-lactamase producing N. gonorrhoeae isolates (n = 139) cultured from 2000 to 2011 in 15 countries were examined using antibiograms, bla_TEM gene sequencing, β-lactamase plasmid typing, and N. gonorrhoeae multiantigen sequence typing (NG-MAST). Furthermore, the bla_TEM gene was sequenced in the first described Toronto plasmid (pJD7), one of the first Asian plasmids (pJD4) and African plasmids (pJD5) isolated in Canada. The degradation of ampicillin by TEM-135 compared to TEM-1 was examined using a MALDI-TOF MS hydrolysis assay.

Results

Six different bla_TEM sequences were identified (among isolates with 125 different NG-MAST STs), i.e. bla_TEM-1 (in 104 isolates), bla_TEM-135 (in 30 isolates), and four novel bla_TEM sequences (in 5 isolates). The bla_TEM-1 allele was only found in the African and Asian plasmids, while all Rio/Toronto plasmids possessed the bla_TEM-135 allele. Most interesting, the first described gonococcal Toronto plasmid (pJD7), identified in 1984, also possessed the highly conserved bla_TEM-135 allele. The degradation of ampicillin by TEM-135 compared to TEM-1 was indistinguishable in the MALDI-TOF MS hydrolysis assay.

Conclusions

bla_TEM-135, encoding TEM-135, is predominantly and originally associated with the Rio/Toronto plasmid and prevalent among the β-lactamase producing gonococcal strains circulating globally. bla_TEM-135 does not appear, as previously hypothesized, to have recently evolved due to some evolutionary selective pressure, for example, by the extensive use of extended-spectrum cephalosporins worldwide. On the contrary, the present study shows that bla_TEM-135 existed in the Toronto plasmid from its discovery and that bla_TEM-135 is highly conserved (not further evolved in the past >30 years). Nevertheless, international studies for monitoring the presence of different bla_TEM alleles, the possible evolution of the bla_TEM-135 allele, and the types of β-lactamase producing plasmids, remain imperative.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2334-14-454) contains supplementary material, which is available to authorized users.

Prevalence and molecular epidemiological typing of penicillinase-producing Neisseria gonorrhoeae and their bla(TEM-135) gene variants in Nanjing, China

BACKGROUND

This study aimed to investigate the prevalence of penicillinase-producing Neisseria gonorrhoeae (PPNG) and their blaTEM-135 gene variant in 2007 and 2012 in Nanjing, China. In addition, molecular epidemiological typing of all isolates was performed to elucidate the genetic relationships of the PPNG strains.

METHODS

A total of 199 and 77 N. gonorrhoeae isolates were collected at the National Center for STD Control in 2007 and 2012, respectively. Nitrocefin tests were performed to identify PPNG. Mismatch amplification mutation assay was used to identify blaTEM-135. All isolates were genotyped using N. gonorrhoeae multiantigen sequence typing (NG-MAST), and additionally, porB-based phylogenetic analysis was performed for the PPNG isolates.

RESULTS

The total prevalence of PPNG isolates was 41% (114/276) and 58% (66/114) of these PPNG isolates possessed bla(TEM-135). In 2007, 45% (90/199) produced β-lactamase, and of those PPNG, 58% (52/90) possessed bla(TEM-135). In 2012, 31% (24/77) were PPNG, and 58% (14/24) of those isolates contained bla(TEM-135). There were 162 NG-MAST STs among the 276 isolates, and 89 of those were novel STs. A strong association between specific NG-MAST STs and bla(TEM-135) was found, and the porB-based phylogenetic analysis showed a distant evolutionary relationship between isolates in 2007 and isolates in 2012.

CONCLUSIONS

A high prevalence of PPNG and blaTEM-135 was found in Nanjing, China. bla(TEM-135) might be a precursor in the evolution into an extended-spectrum β-lactamase that can degrade ceftriaxone, which stresses the need to continuously monitor PPNG, blaTEM-135, and additional evolving blaTEM gene variants.

Antimicrobial drug resistance patterns among cattle- and human-associated Salmonella strains

During the year 2004, 178 human and 158 bovine clinical Salmonella isolates were collected across New York State to better understand the transmission dynamics and genetic determinants of antimicrobial resistance among human and bovine hosts. Serotyping, sequence typing, and pulsed-field gel electrophoresis typing results have been reported previously. Here we tested all isolates for phenotypic susceptibility to 15 antimicrobial drugs that are part of the National Antimicrobial Monitoring System bovine susceptibility panel. PCR was performed on a representative subset of unique isolates (n = 53) to screen for the presence of 21 known antimicrobial resistance genes (i.e., ampC, blaTEM-1, blaCMY-2, blaPSE-1, cat1, cat2, cmlA, flo, aadA1, aadA2, aacC2, strA, strB, aphA1-IAB, dhrfI, dhrfXII, sulI, sulII, tetA, tetB, and tetG); selected fluoroquinolone- and nalidixic acid-resistant (n = 3) and -sensitive (n = 6) isolates were also tested for known resistance-conferring mutations in gyrA and parC. Genes responsible for antimicrobial resistance were shared among isolates of human and bovine origin. However, bovine isolates were significantly more likely than human isolates to be multidrug resistant (P < 0.0001; Fisher's exact test). Our analyses showed perfect categorical agreement between phenotypic and genotypic resistance for beta-lactam and chloramphenicol. Our data confirm that resistance profiles of amoxicillin-clavulanic acid, chloramphenicol, kanamycin, and tetracycline were strongly associated with the presence of blaCMY or ampC, flo, aphA1-IAB, and tetA, respectively. Our findings provide evidence for the clinical value of genotypic resistance typing if incorporating multiple known genes that can confer a phenotypic resistance profile.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

Resistance genes, phage types and pulsed field gel electrophoresis pulsotypes in Salmonella enterica strains from laying hen farms in southern Italy

Twenty-four Salmonella enterica isolates (13 serovar Enteritidis and 11 Typhimurium) isolated from 5,600 samples from intensive laying hen farms in Italy in 1998-2007 were characterized for antimicrobial resistance genes, pulsotype and phage type. Most of S. Typhimurium strains were pulsotype STYMXB.0147 (81.8%), phage type DT143 and resistant to sulfamethoxazole encoded by sul2. Two multidrug resistant (MDR) strains were identified. One strain, STYMXB.0061, was resistant to ampicillin (A), chloramphenicol (C), streptomycin (S), sulfamethoxazole (Su) and tetracycline (T) encoded by the Salmonella Genomic Island SGI1. The second MDR strain, STYMXB.0110, was resistant to SSuT encoded by sul1 and sul2, aadA1 and tet(C)-flanked by an IS26 element, respectively. The tet(C) gene has been reported to confer low levels of resistance and it has very rarely been detected in S. Typhimurium from poultry. In the current study, the MIC value (32 µg/mL) was consistent with the breakpoint (≥16 µg/mL) reported for Enterobacteriaceae. Most of the S. Enteritidis strains were resistant to Su (encoded by sul2). One MDR strain (ANxSSuT) was identified. With the exception of nalidixic acid (Nx), the resistances were respectively encoded by bla(TEM), strAB, sul2 and tet(A) harbored by an IncN conjugative plasmid. All isolates were pulsotype SENTXB.0001 with PT14b being the most prevalent identified phage type (57.1%). In Europe, SENTXB.0001 is the predominant PFGE profile from clinical cases and the identification of PT14b has steadily been on the increase since 2001. The findings presented in this study highlight the potential spread of S. Enteritidis phage types PT14b and S. Typhimurium DT143 in a field of particular relevance for zoonoses. Additional, the presence of resistance genes and genetic elements (conjugative plasmid and IS element) underlines the need to assess routinely studies in field, such as poultry farms, relevant fot the public health and suitable for the storage and diffusion of antimicrobial resistance.

Unique class 1 integron and multiple resistance genes co-located on IncHI2 plasmid is associated with the emerging multidrug resistance of Salmonella Indiana isolated from chicken in China

The objective of this study was to clarify the molecular antimicrobial resistance mechanisms of Salmonella enterica serovar Indiana isolated from chickens in China. A total of 327 chicken intestinal content and feces were collected in Shandong, China in 2009. Isolates were serotyped and antimicrobial susceptibility testing was performed. Thirty-five (10.7%) Salmonella isolates were recovered, and 16 (45.7%) were Salmonella enterica serovar Indiana, which were resistant to at least 14 of 15 antimicrobial agents. The 16 Salmonella enterica serovar Indiana detected and other 13 Salmonella enterica serovar Indiana that were selected from 133 Salmonella enterica serovar Indiana isolated in 2008 were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Then class 1 integron and drug resistance genes were detected by polymerase chain reaction. Linkage between plasmids and resistance components was determined by conjugation, electrotransformation, S1 nuclease-PFGE, polymerase chain reaction-based replicon typing and Southern blot assays. Regions flanking integrons were sequenced by modified random primer walking strategy. PFGE and MLST suggested that all the 29 Salmonella enterica serovar Indiana isolates that shared >78% similarity in PFGE patterns were of the same MLST type, ST17. Two kinds of class 1 integrons had different integrase genes and the same variable region (dfrA7/aadA4/IS26/aac(6')-Ib/blaOXA-1/catB3/arr-3), and additional antimicrobial resistance genes such as blaCTX-M-24, floR, and so on were detected on IncHI2 plasmids in 29 Salmonella enterica serovar Indiana, and seven plasmids were conjugative. Analysis of the genetic environment of the integrons suggested that these integrons might have been formed by the help of IS26. To our knowledge, the variable region in class 1 integrons is the longest reported in Salmonella to date. The unique integrons and multiple resistance genes co-located on the IncHI2 plasmid contributed to the dissemination of multidrug resistance.

Antimicrobial resistance in Salmonella serovars isolated from meat shops at the markets in North Vietnam

A total of 97 out of 245 carcass, sewage effluent, and table surface samples in meat shops at the retail markets in North Vietnam showed Salmonella positive. Eleven Salmonella serovars, including Infantis, Anatum, Rissen, Reading, London, Typhimurium, Enteritidis, Agona, Newport, Emek, and Derby, were identified. The Salmonella isolates were tested for antimicrobial susceptibility and further investigated for antimicrobial resistance genes. Resistance to kanamycin, gentamicin, neomycin, nalidixic acid, chloramphenicol, trimethoprim, streptomycin, tetracycline, ampicillin, and sulphonamides was found in 28.9-56.7%. The isolates were neither resistant to ceftazidime nor norfloxacin. Sixty-four (66.0%) out of 97 isolates were resistant to at least one of 14 antimicrobials, and 55 (85.9%) out of the 64 isolates showed multidrug resistance. Thirteen resistance genes (bla(TEM), bla(OXA-1), aadA1, sul1, tetA, tetB, tetG, cmlA1, floR, dfrA1, dfrA12, aac(3)-IV, and aphA1-1AB) were detected in the resistant isolates. This study indicates that Salmonella isolated from meat shops were resistant to multiple antimicrobials, and the resistance genes were widespread among the serovars isolated.

Increasing quinolone resistance and multidrug resistant isolates among Salmonella enterica in Hong Kong

OBJECTIVES

To study the antimicrobial susceptibility and molecular epidemiology of Salmonella enterica isolates from 2005 to 2010 in Hong Kong.

METHODS

S. enterica isolates from 2005 to 2010 in one of the hospital clusters were serotyped and studied their antimicrobial susceptibility by determining the minimal inhibitory concentration of 17 antimicrobial agents and their relatedness by pulsed-field gel electrophoresis (PFGE).

RESULTS

A total of 60 S. enterica serovars were identified among the 963 strains of Salmonella from 2005 to 2010. Enteritidis (47.3%) and Typhimurium (17.2%) were the two most common serovars. Ciprofloxacin non-susceptibility increased significantly from 39.3% in 2005 to 63% in 2010 (p < 0.05) and the percentage of multidrug resistant strains increased from 17.8% in 2005 to 36.2% in 2010 (p < 0.05). However, resistance to the third generation cephalosporins (1.4%) remained low. More strains of S. Typhimurium than other Salmonella serovars were resistant to the antimicrobial agents tested than S. Enteritidis. PFGE analysis showed there were predominant clones of S. Enteritidis, S. Typhimurium and S. Stanley circulating in the community, and two outbreaks caused by S. Enteritidis and S. Virchow during the study period.

CONCLUSIONS

The study showed both a worrying percentage of Salmonella strains resistant to quinolone and of multidrug resistant strains. PFGE identified two outbreaks in the study period.