High prevalence of plasmid-mediated quinolone resistance determinant aac(6')-Ib-cr amongst Salmonella enterica serotype Typhimurium isolates from hospitalised paediatric patients with diarrhoea in China

Characterization of quinolone resistance in Salmonella enterica serovar Typhimurium and its monophasic variants from food and patients in China

OBJECTIVES

The study aimed to characterize the quinolone resistance of Salmonella enterica serovar Typhimurium and its monophasic variant (Salmonella enterica serovar 1,4,[5],12:i:-) isolated from food and patients in China.

METHODS

All of the isolates were assessed for quinolone susceptibility via the broth microdilution method. Then, the isolates were checked for mutations within quinolone resistance-determining regions of gyrA, gyrB, parC, and parE and were examined for plasmid-mediated quinolone resistance genes.

RESULTS

High rates of resistance to nalidixic acid in the S. Typhimurium (70.7%) and S. 1,4,[5],12:i:- (41.9%) isolates were observed, and a considerable proportion of isolates with reduced susceptibility to ciprofloxacin and levofloxacin were also detected. The high frequency of mutations in GyrA (60.8%) and a variety of genes (aac[6']-Ib-cr [23.2%], oqxAB [19.2%], qnrS [13.6%], and qnrA [3.2%]) conferring quinolone resistance in these Salmonella isolates were noteworthy. Lastly, the isolates carrying qnrS for transferability and transmission of the quinolone resistance were analysed by conjugation. Multiple locus variable-number tandem repeat analysis profiles indicated that some qnrS-positive isolates were clonally related, whilst the other isolates were genetically divergent. This suggested that both clonal spread of resistant strains and horizontal transmission of the plasmid-mediated resistance genes contributed to the dissemination of qnrS-positive Salmonella isolates.

CONCLUSION

This study highlights the prevalence of quinolone-resistant S. Typhimurium and S. 1,4,[5],12:i:- in China, posing a threat to public health.

Biochemical and molecular mechanisms of antibiotic resistance in Salmonella spp

Salmonella is a diverse Gram-negative bacterium that represents the major disease burden worldwide. According to WHO, Salmonella is one of the fourth global causes of diarrhoeal disease. Antibiotic resistance is a worldwide health concern, and Salmonella spp. is one of the microorganisms that can evade the toxicity of antimicrobials via antibiotic resistance. This review aims to deliver in-depth knowledge of the molecular mechanisms and the underlying biochemical alterations perceived in antibiotic resistance in Salmonella. This information will help understand and mitigate the impact of antibiotic-resistant bacteria on humans and contribute to the state-of-the-art research developing newer and more potent antibiotics.

Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization

The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.

Spectrum of enteropathogens in cases of traveler's diarrhea that were detected using the FilmArray GI panel: New epidemiology in Japan

INTRODUCTION

Traveler's diarrhea (TD) is the most common illness among people traveling from resource-rich regions to resource-limited regions, although the precise microbial etiology is unclear in many cases.

METHODS

Stool specimens were prospectively collected from 106 consecutive patients with TD and 16 healthy controls without TD, and were tested using both the FilmArray gastrointestinal panel (BioFire Diagnostics) and conventional stool cultures.

RESULTS

The 106 patients had traveled to Southeast Asia (55 cases), South Asia (22 cases), Africa (11 cases), and East Asia (7 cases). Among the 106 specimens, 95 specimens (89.6%) were positive for pathogens during the FilmArray testing. The FilmArray testing also identified multiple pathogens in 75.8% of the specimens from positive cases. Conventional stool cultures only detected pathogens in 23.6% of the specimens.

CONCLUSION

The FilmArray gastrointestinal panel significantly improved the detection of enteropathogens and allowed for a rapid assessment of the TD's etiology. In addition, conventional stool cultures are likely to underestimate co-infections with multiple infectious pathogens.

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.

Salmonella Typhimurium and Salmonella Enteritidis Infections in Sporadic Diarrhea in Children: Source Tracing and Resistance to Third-Generation Cephalosporins and Ciprofloxacin

OBJECTIVES

This study aimed to trace the transmission source of Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis strains associated with enteric infections in Shanghainese children, and understand the molecular mechanism of resistance to third-generation cephalosporins and ciprofloxacin.

MATERIALS AND METHODS

The profiles of pulsed-field gel electrophoresis (PFGE) were compared among the isolates from children, animal, and environment. Antimicrobial susceptibility was determined using the minimal inhibitory concentrations and Kirby-Bauer disk diffusion method. Extended-spectrum β-lactamase (ESBL) producing isolates mediated by resistance genes were identified using polymerase chain reaction and sequencing.

RESULTS

Based on PFGE patterns, 49 (33.1%) of 148 human Salmonella Typhimurium isolates located in the dominant PFGE clusters were genetically related to the isolates from poultry source, environment water, aquatic products, and reptiles, whereas 97 (97.0%) of 100 human Salmonella Enteritidis isolates were genetically related to isolates from poultry and water. The rates of resistance to ceftriaxone among clinical Salmonella Typhimurium and Salmonella Enteritidis isolates were 42.0% and 14.2%, respectively. Besides, 35.1% of Salmonella Typhimurium isolates displayed resistance to ciprofloxacin; 64.9% of Salmonella Typhimurium isolates and 97.0% of Salmonella Enteritidis isolates displayed reduced susceptibility to ciprofloxacin. Of 64 ESBL/AmpC-producing strains, CTX-M, TEM, DHA, and CMY were detected at frequencies of 86.0%, 62.5%, 7.8%, 3.1%, and 3.1%, respectively.

CONCLUSIONS

The transmission sources of Salmonella Typhimurium and Salmonella Enteritidis infections in Shanghainese children were diverse. The high prevalence of resistance to third-generation cephalosporins and ciprofloxacin mediated by multiple molecular mechanisms needs continuous monitoring and intervention.

Characterization of Quinolone Resistance in Salmonella enterica from Farm Animals in China

This study was focused on the prevalence and antimicrobial susceptibilities of Salmonella directly isolated at animal clinics in Guangdong, People's Republic of China. The isolation rates from chickens, ducks, and pigs were 11.3% (11 of 97 samples), 15.4% (53 of 344 samples), and 3.0% (13 of 434 samples), respectively. Among the 77 Salmonella enterica isolates, the most predominant serovar was Typhimurium (81.8%, 63 isolates), followed by serovars Meleagridis (2.6%, 2 isolates) and Abaetetuba (1.3%, 1 isolate). Salmonella isolates were resistant to ciprofloxacin (16.9% of isolates) and nalidixic acid (66.2% of isolates), and 68 isolates (88.3%) were multidrug resistant, displaying resistance to three or more classes of antimicrobial agents. Eighteen isolates (23.4%) had at least one plasmid-mediated quinolone resistance gene, which was identified using PCR and DNA sequencing. The most prevalent plasmid-mediated quinolone resistance gene was aac(6')-Ib-cr, found in 14 isolates (18.2%), followed by oqxAB (9.1%) and qnrS (7.8%). Alterations in the gyrA gene were detected in 24 (57.1%) of 42 strains with a ciprofloxacin MIC of ≥0.25 μg/mL; the same level of susceptibility was found for enrofloxacin. Six types of mutations were found in the quinolone resistance determining regions of gyrA, and the predominant one (S83Y) was found singly in 15 (62.5%) of 24 isolates. We also found 22 different pulsed-field gel electrophoresis types among the Salmonella isolates. The Salmonella serovars and MICs of ciprofloxacin were similar within clusters, although individual differences were noted. This finding suggests that resistance plasmids were horizontally transmitted but also clonally spread.

Using In Vitro Dynamic Models To Evaluate Fluoroquinolone Activity against Emergence of Resistant Salmonella enterica Serovar Typhimurium

The objectives of this study were to determine pharmacokinetic/pharmacodynamic (PK/PD) indices of fluoroquinolones that minimize the emergence of resistant Salmonella enterica serovar Typhimurium (S Typhimurium) using in vitro dynamic models and to establish mechanisms of resistance. Three fluoroquinolones, difloxacin (DIF), enrofloxacin (ENR), and marbofloxacin (MAR), at five dose levels and 3 days of treatment were simulated. Bacterial killing-regrowth kinetics and emergence of resistant bacteria after antibacterial drug exposure were quantified. PK/PD indices associated with different levels of antibacterial activity were computed. Mechanisms of fluoroquinolone resistance were determined by analyzing target mutations in the quinolone resistance-determining regions (QRDRs) and by analyzing overexpression of efflux pumps. Maximum losses in susceptibility of fluoroquinolone-exposed S Typhimurium occurred at a simulated AUC/MIC ratio (area under the concentration-time curve over 24 h in the steady state divided by the MIC) of 47 to 71. Target mutations in gyrA (S83F) and overexpression of acrAB-tolC contributed to decreased susceptibility in fluoroquinolone-exposed S Typhimurium. The current data suggest AUC/MIC (AUC/mutant prevention concentration [MPC])-dependent selection of resistant mutants of S Typhimurium, with AUC/MPC ratios of 69 (DIF), 62 (ENR), and 39 (MAR) being protective against selection of resistant mutants. These values could not be achieved in veterinary clinical areas under the current recommended therapeutic doses of the fluoroquinolones, suggesting the need to reassess the current dosing regimen to include both clinical efficacy and minimization of emergence of resistant bacteria.

Fluoroquinolone Resistance in Salmonella and the Utility of Pefloxacin Disk Diffusion [corrected]

Fluoroquinolone resistance is a serious and increasingly common problem in Salmonella. Two companion studies in this issue of the Journal of Clinical Microbiology (E. Deak, R. Skov, J. A. Hindler, and R. M. Humphries, J Clin Microbiol 53:3405-3410, 2015, http://dx.doi.org/10.1128/JCM.01393-15; R. Skov, E. Matuschek, M. Sjölund-Karlsson, J. Åhman, A. Petersen, M. Stegger, M. Torpdahl, and G. Kahlmeter, J Clin Microbiol 53:3411-3417, 2015, http://dx.doi.org/10.1128/JCM.01287-15) provide data to support the use of pefloxacin disk diffusion as a convenient and inexpensive surrogate laboratory method to detect fluoroquinolone resistance in Salmonella when the direct measurement of fluoroquinolone MICs is not feasible [corrected]. Recently updated CLSI and EUCAST susceptibility breakpoints will help to optimize clinical outcomes and reduce the likelihood of emergent resistance.

Study of aminoglycoside resistance genes in enterococcus and salmonella strains isolated from ilam and milad hospitals, iran

Background:

Aminoglycosides are a group of antibiotics that have been widely used in the treatment of life-threatening infections of Gram-negative bacteria.

Objectives:

This study aimed to evaluate the frequency of aminoglycoside resistance genes in Enterococcus and Salmonella strains isolated from clinical samples by PCR.

Materials and Methods:

In this study, 140 and 79 isolates of Enterococcus and Salmonella were collected, respectively. After phenotypic biochemical confirmation, 117 and 77 isolates were identified as Enterococcus and Salmonella, respectively. After the biochemical identification of the isolates, antibiotic susceptibility for screening of resistance was done using the Kirby-Bauer method for gentamicin, amikacin, kanamycin, tobramycin and netilmycin. DNA was extracted from resistant strains and the presence of acc (3)-Ia, aac (3′)-Ib, acc (6)-IIa ,16SrRNA methylase genes (armA and rat) was detected by PCR amplification using special primers and positive controls.

Results:

Enterococcus isolates have the highest prevalence of resistance to both kanamycin and amikacin (68.4%), and Salmonella isolates have the highest prevalence of resistance against kanamycin (6.9%). Ninety-three and 26 isolates of Enterococcus and Salmonella at least were resistant against one of the aminoglycosides, respectively. Moreover, 72.04%, 66.7%, and 36.6% of the resistant strains of Enterococcus had the aac (3′)-Ia, aac (3′)-IIa, and acc (6′)-Ib genes, respectively. None of the Salmonella isolates have the studied aminoglycoside genes.

Conclusions:

Our results indicate that acetylation genes have an important role in aminoglycoside resistance of the Enterococcus isolates from clinical samples. Moreover, Salmonella strains indicate very low level of aminoglycoside resistance, and aminoglycoside resistance genes were not found in Salmonella isolates. These results indicate that other resistance mechanisms, including efflux pumps have an important role in aminoglycoside resistance of Salmonella.

Plasmid-mediated quinolone resistance in Salmonella serotypes isolated from chicken carcasses in Turkey

Quinolones have been extensively used for treatment of a variety of invasive and systemic infections of salmonellosis. Widespread use of these agents has been associated with the emergence and dissemination of quinolone-resistant pathogens. The quinolone resistance and plasmid-mediated quinolone resistance determinants (qnrA, qnrB, qnrS and aac(6’)-Ib-cr) of 85 Salmonella isolates from chicken carcasses were investigated in this study. Isolates were serotyped according to the Kauffman-White-Le Minor scheme, and broth microdilution method was used to determine quinolone resistance. Plasmid-mediated quinolone resistance genes were investigated by real-time PCR and positive results were confirmed by sequencing. Among the Salmonella isolates, 30/85 (35%) and 18/85 (21%) were found to be resistant to enrofloxacin (MIC ≥ 2 mg/ml), and danofloxacin (MIC ≥ 2 mg/ml), respectively. All the isolates were negative for qnrA, qnrB and aac(6’)-Ib-cr genes, nevertheless 2% (S. Brandenburg and S. Dabou) were positive for qnrS (qnrS1 determinant). This study is the first and unique investigating the plasmid- mediated quinolone resistance determinants of Salmonella isolated from chicken carcasses in Turkey.

Performance of Etest and disk diffusion for detection of ciprofloxacin and levofloxacin resistance in Salmonella enterica

We compared Etest and disk diffusion to broth microdilution for the detection of fluoroquinolone resistance in 135 typhoidal and nontyphoidal serovars of Salmonella. Categorical agreements for the ciprofloxacin and levofloxacin Etests were 89.6 and 83.7%, respectively. Disk diffusion categorical agreements were 88.2 and 93.3%, respectively. Only minor errors were observed.

Incidence, clinical presentation, and antimicrobial resistance trends in Salmonella and Shigella infections from children in Yucatan, Mexico

BACKGROUND

Salmonella and Shigella cause significant morbidity and mortality among children worldwide. Increased antimicrobial resistance results in greater burden of disease.

MATERIALS AND METHODS

From 2005 to 2011, Salmonella and Shigella isolates collected from ill children at a major hospital in Yucatan, Mexico, were subjected to serotyping and antimicrobial susceptibility testing by disk diffusion and agar dilution. The identification of bla CTX, bla CMY, bla SHV, bla TEM, and bla OXA and qnr resistance genes was conducted by PCR and sequencing.

RESULTS

Among 2344 children with acute gastroenteritis, salmonellosis decreased from 17.7% in 2005 to 11.2% in 2011 (p < 0.001). In contrast, shigellosis increased from 8.3% in 2010 to 12.1% in 2011. Compared to children with Salmonella, those with Shigella had significantly more bloody stools (59 vs 36%, p < 0.001), dehydration (27 vs 15%, p = 0.031), and seizures (11 vs 3%, p = 0.03). In Salmonella (n = 365), there was a significant decrease in resistance to ampicillin (43 to 16%, p < 0.001), trimethoprim-sulfamethoxazole (44 to 26%, p = 0.014), and extended-spectrum cephalosporins (27 to 10%, p = 0.009). Reduced susceptibility to ciprofloxacin in Salmonella rose from 30 to 41% (p < 0.001). All ceftriaxone-resistant isolates harbored the bla CMY-2 gene. qnr genes were found in 42 (36%) of the 117 Salmonella isolates with a ciprofloxacin MIC ≥ 0.125 μg/ml. Four were qnrA1 and 38 were qnrB19. Resistance to ampicillin (40%) and trimethoprim-sulfamethoxazole (58%) was common in Shigella (n = 218), but isolates remained fully susceptible to ceftriaxone and ciprofloxacin.

CONCLUSION

Illness from Salmonella has decreased while severe Shigella infections have increased among children with gastroenteritis in the Yucatan Peninsula. While Shigella resistance to clinically important antibiotics remained unchanged, resistance to most of these, except ciprofloxacin, declined in Salmonella. bla CMY-2 and qnr genes are common in Salmonella isolates.

In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards

Fluoroquinolone (FQ) resistance in Salmonella enterica is a significant clinical concern. Recognition of resistance by the clinical laboratory is complicated by the multiple FQ resistance mechanisms found in Salmonella. The Clinical Laboratory Standards Institute (CLSI) recently addressed this issue by revising the ciprofloxacin break points for Salmonella species. It is critical for clinicians and laboratory workers to be aware of the multiple technical issues surrounding these revised break points. In this article, we review FQ resistance mechanisms in Salmonella, their clinical significance, and data supporting the revised ciprofloxacin break points. We encourage clinical laboratories to adopt the revised CLSI ciprofloxacin break points for all Salmonella isolates in which susceptibility testing is indicated and discuss the technical issues for laboratories using commercial antimicrobial susceptibility systems.