Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid

Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.

Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient

In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of β-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2″)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.

Isolation and antimicrobial resistance of motile Salmonella enterica from the poultry hatchery environment

Salmonella is a globally distributed major food-borne pathogen and poultry is one of the predominant sources of salmonellosis in humans. To investigate the presence of motile Salmonella in the poultry hatchery environment, we collected 97 fluff samples from four selected broiler breeder chicken hatcheries from Chattogram, Bangladesh during July-December 2015. To isolate motile Salmonella enterica, we used conventional bacteriological techniques followed by serological verification using anti-Salmonella Poly A-E serum and species confirmation by conventional PCR assay. Antimicrobial susceptibility testing by Kirby-Bauer disc diffusion method for 10 commonly used antibiotics was performed on all isolates. Isolates displaying phenotypic resistance to ampicillin were tested by PCR for bla_TEM gene, whereas those resistant to tetracycline were tested for the presence of tetA, tetB and tetC genes. A total of 24 samples (24.7%; 95% CI: 16.5-34.5, N = 97) from 3 hatcheries were positive for motile Salmonella. Of them, 21 (87.5%) and 12 (50.0%) were resistant to ampicillin and tetracycline, respectively, 9 (37.5%) to nalidixic acid and sulphamethoxazole/trimethoprim. No resistance was detected to ceftriaxone, cefoxitin, gentamicin, neomycin, ciprofloxacin and colistin. Ten (42%) of 24 isolates from 2 hatcheries were multi-drug resistant (i.e. resistant to ≥ 3 antimicrobial classes). Six of 21 ampicillin resistant isolates contained bla_TEM gene and 10 of 12 tetracycline resistant isolates contained tetA gene. This study highlights the circulation of multi-drug resistant motile Salmonella in the hatchery environment for the first time in Bangladesh. Further epidemiological and molecular studies are therefore needed to identify the serotypes and source of the bacteria in hatcheries.

Contamination Status of Salmonella spp., Shigella spp. and Campylobacter spp. in Surface and Groundwater of the Kelani River Basin, Sri Lanka

Waterborne diseases are a global problem that causes more than 2.2 million deaths annually. Therefore, the present study was focused on microbiological contamination of both ground and surface water by means of total coliform, Escherichia coli (E. coli), Salmonella spp., Shigella spp. and Campylobacter spp. Seventy two groundwater and 45 surface water sampling locations were selected to collect water from the head, transitional and meandering regions of the Kelani River Basin for a period of one year (both dry and wet seasons). The results of the study revealed that the entire Kelani River basin was contaminated with total coliform and E. coli bacteria and almost all the sampling locations exceed Sri Lanka Standards Institute (SLSI) guideline value given for drinking water (0 CFU/100 mL). Further, in groundwater, 17 locations were positive for Salmonella spp., whereas only 2 locations were positive for Campylobacter spp. In surface water, 26 and three sampling locations were positive for Salmonella spp. and Campylobacter spp., respectively. In this study, 23 different human pathogenic serovars were isolated and the Salmonella enterica serovar Kentucky was identified as the commonest type. Thus, the result of the study revealed that the consumption of raw water from the Kelani River Basin is unsafe and possible to cause gastrointestinal diseases.

Variability in the Adaptive Response of Antibiotic-Resistant Salmonella Typhimurium to Environmental Stresses

This study was designed to evaluate the resistance phenotype and genotype of wild type (WT)-, cefotaxime (CET)-, and ciprofloxacin (CIP)-induced Salmonella Typhimurium ATCC 19585, CIP-resistant Salmonella Typhimurium ATCC 19585, Salmonella Typhimurium CCARM 8009, and Salmonella Typhimurium KCCM 40253 before and after exposure to pH 4.5, 4% NaCl, and heat at 42°C. The susceptibilities of WT Salmonella Typhimurium ATCC 19585 and WT Salmonella Typhimurium KCCM 40253 to all antibiotics tested in this study were decreased after CET and CIP induction with the exception with kanamycin, meropenem, and polymyxin B. The highest β-lactamase activities were 2.8 and 3.3 nmol/(min·mL), respectively, at the WT- and CET-induced Salmonella Typhimurium CCARM 8009. FT-IR spectra were found to be dominant at the region from 1,700 to 1,500 cm^-1 corresponding to proteins such as amides I, II, and III. The relative expression levels of efflux pump-related genes (acrA, acrB, and TolC), porin-related gene (ompC), virulence-related gene (stn), adhesion-related gene (fimA), and stress-induced alternative sigma factor (rpoS) varied in the antibiotic resistance and stress exposure. This study provides useful information for understanding the antibiotic resistance profile, physicochemical property, and gene expression pattern in Salmonella Typhimurium in association with the induction of antibiotic resistance and exposure to environmental stresses.

Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans, Animals and Food

Non-typhoidal serovars of Salmonella enterica (NTS) are a leading cause of food-borne disease in animals and humans worldwide. Like other zoonotic bacteria, NTS have the potential to act as reservoirs and vehicles for the transmission of antimicrobial drug resistance in different settings. Of particular concern is the resistance to critical "last resort" antimicrobials, such as carbapenems. In contrast to other Enterobacteriaceae (e.g., Klebsiella pneumoniae, Escherichia coli, and Enterobacter, which are major nosocomial pathogens affecting debilitated and immunocompromised patients), carbapenem resistance is still very rare in NTS. Nevertheless, it has already been detected in isolates recovered from humans, companion animals, livestock, wild animals, and food. Five carbapenemases with major clinical importance-namely KPC (Klebsiella pneumoniae carbapenemase) (class A), IMP (imipenemase), NDM (New Delhi metallo-β-lactamase), VIM (Verona integron-encoded metallo-β-lactamase) (class B), and OXA-48 (oxacillinase, class D)-have been reported in NTS. Carbapenem resistance due to the production of extended spectrum- or AmpC β-lactamases combined with porin loss has also been detected in NTS. Horizontal gene transfer of carbapenemase-encoding genes (which are frequently located on self-transferable plasmids), together with co- and cross-selective adaptations, could have been involved in the development of carbapenem resistance by NTS. Once acquired by a zoonotic bacterium, resistance can be transmitted from humans to animals and from animals to humans through the food chain. Continuous surveillance of resistance to these "last resort" antibiotics is required to establish possible links between reservoirs and to limit the bidirectional transfer of the encoding genes between S. enterica and other commensal or pathogenic bacteria.

Characterization and horizontal transfer of qacH-associated class 1 integrons in Escherichia coli isolated from retail meats

The aim of this study was to examine the presence of genes responsible for resistance to quaternary ammonium compounds (QACs) and the association of qac genes with class 1 integrons in Escherichia coli isolated from retail meats. Among the 179 E. coli isolates tested, the minimum inhibitory concentrations (MICs) of benzalkonium chloride (BC) ranged from 4 to 64μg/mL. PCR assays indicated that QAC-resistance genes sugE(c), ydgE/ydgF, mdfA, emrE and qacEΔ1 were commonly present (40.2%-88.3%) in these isolates, but qacE, qacF, qacH and sugE(p) were less prevalent (2.2%-28.5%). Seven different gene cassette arrangements were identified in 31 intI1-positive isolates. Three types of qacH-sul3-associated non-classic integrons were observed in four isolates: dfrA12-orfF-aadA2-cmlA1-aadA1-qacH-IS440-sul3, aadA2-cmlA1-aadA1-qacH-IS440-sul3 and dfrA1-aadA1-qacH-IS440-sul3. Non-classic class 1 integrons were located on plasmids of 100-150kb in these four isolates. Our results demonstrated that the qacH-associated integrons located on 100 kb plasmids in two isolates could be transferred to an E. coli recipient, indicating the co-existence and co-dissemination of disinfectant and antimicrobial resistance genes among bacterial species.

Characterization of Clinically Isolated Antibiotic-Resistant Salmonella Typhimurium Exposed to Subinhibitory Concentrations of Ceftriaxone and Ciprofloxacin

This study was designed mainly to assess the phenotypic properties of clinically isolated Salmonella Typhimurium exposed to ceftriaxone and ciprofloxacin. The antibiotic susceptibility, β-lactamase activity, efflux activity, bacterial motility, biofilm-forming ability, and gene expression were determined in S. Typhimurium ATCC 19585 and S. Typhimurium CCARM 8009 when exposed to subinhibitory concentrations of ceftriaxone and ciprofloxacin. S. Typhimurium CCARM 8009 was highly resistant to ampicillin, kanamycin, penicillin G, and streptomycin, showing minimum inhibitory concentration values of more than 512 μg/ml, while S. Typhimurium ATCC 19585 showed resistance to erythromycin alone (64 μg/ml). The highest β-lactamase activity was observed in S. Typhimurium CCARM 8009 when exposed to ceftriaxone (8.2 μmol/min/ml), while the least β-lactamase activity was observed in S. Typhimurium ATCC 19585. Compared to S. Typhimurium CCARM 8009, the ethidium bromide (EtBr) accumulation was considerably increased in S. Typhimurium ATCC 19585 when treated with efflux pump inhibitors. S. Typhimurium ATCC 19585 and S. Typhimurium CCARM 8009 were highly susceptible to ciprofloxacin, erythromycin, levofloxacin, and sparfloxacin in the presence of phenylalanine-arginine-β-naphthylamide. The swimming motility of S. Typhimurium ATCC 19585 exposed to ceftriaxone was significantly reduced to 54% when compared to S. Typhimurium CCARM 8009 (93%). The numbers of attached S. Typhimurium CCARM 8009 cells were significantly increased by more than 1 log cfu/ml when exposed to ceftriaxone and ciprofloxacin. The relative gene expression was stable in S. Typhimurium CCARM 8009 in the presence of ceftriaxone and ciprofloxacin compared to the absence of antibiotics. These results suggest that the antibiotic susceptibility of S. Typhimurium having different antibiotic resistance profiles varied depending on the presence of ceftriaxone and ciprofloxacin.

Plasmid-mediated quinolone resistance

Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC code for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. The qnr genes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6')-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.

Clinical isolates of Salmonella enterica serovar Agona producing NDM-1 metallo-β-lactamase: first report from Pakistan

We report two cases of infantile diarrhea due to multidrug-resistant, NDM-1 metallo-β-lactamase-producing Salmonella enterica serovar Agona from Pakistan. This study alerts toward possible risk of NDM-1 transmission to enteric fever pathogens and encourages microbiologists to consider active screening of carbapenem resistance in nontyphoidal Salmonella isolates.

Antimicrobial susceptibility to azithromycin among Salmonella enterica isolates from the United States

Due to emerging resistance to traditional antimicrobial agents, such as ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol, azithromycin is increasingly used for the treatment of invasive Salmonella infections. In the present study, 696 isolates of non-Typhi Salmonella collected from humans, food animals, and retail meats in the United States were investigated for antimicrobial susceptibility to azithromycin. Seventy-two Salmonella enterica serotype Typhi isolates from humans were also tested. For each isolate, MICs of azithromycin and 15 other antimicrobial agents were determined by broth microdilution. Among the non-Typhi Salmonella isolates, azithromycin MICs among human isolates ranged from 1 to 32 μg/ml, whereas the MICs among the animal and retail meat isolates ranged from 2 to 16 μg/ml and 4 to 16 μg/ml, respectively. Among Salmonella serotype Typhi isolates, the azithromycin MICs ranged from 4 to 16 μg/ml. The highest MIC observed in the present study was 32 μg/ml, and it was detected in three human isolates belonging to serotypes Kentucky, Montevideo, and Paratyphi A. Based on our findings, we propose an epidemiological cutoff value (ECOFF) for wild-type Salmonella of ≤16 μg/ml of azithromycin. The susceptibility data provided could be used in combination with clinical outcome data to determine tentative clinical breakpoints for azithromycin and Salmonella enterica.

Infectious agents of food- and water-borne illnesses

Food- and water-borne infections have afflicted mankind since the earliest days of human development and preceded the emergence of civilization. Despite current knowledge of microbial pathogenicity, modern methods of food production and rigorous industrial hygiene, these infections are still commonplace and exact significant health and economic tolls on human populations in all parts of the globe. This review uses data derived from new surveillance networks to survey the current epidemiology of bacterial, protozoan and viral pathogens transmitted by food and water. In addition, we will discuss clinical features of human disease caused by pathogens of current and emerging relevance.

Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica

A microarray was developed to simultaneously screen Escherichia coli and Salmonella enterica for multiple genetic traits. The final array included 203 60-mer oligonucleotide probes, including 117 for resistance genes, 16 for virulence genes, 25 for replicon markers, and 45 other markers. Validity of the array was tested by assessing inter-laboratory agreement among four collaborating groups using a blinded study design. Internal validation indicated that the assay was reliable (area under the receiver-operator characteristic curve=0.97). Inter-laboratory agreement, however, was poor when estimated using the intraclass correlation coefficient, which ranged from 0.27 (95% confidence interval 0.24, 0.29) to 0.29 (0.23, 0.34). These findings suggest that extensive testing and procedure standardization will be needed before bacterial genotyping arrays can be readily shared between laboratories.

Global trends in typhoid and paratyphoid Fever

Typhoid and paratyphoid fever continue to be important causes of illness and death, particularly among children and adolescents in south-central and Southeast Asia, where enteric fever is associated with poor sanitation and unsafe food and water. High-quality incidence data from Asia are underpinning efforts to expand access to typhoid vaccines. Efforts are underway to develop vaccines that are immunogenic in infants after a single dose and that can be produced locally in countries of endemicity. The growing importance of Salmonella enterica serotype Paratyphi A in Asia is concerning. Antimicrobial resistance has sequentially emerged to traditional first-line drugs, fluoroquinolones, and third-generation cephalosporins, posing patient treatment challenges. Azithromycin has proven to be an effective alternative for treatment of uncomplicated typhoid fever. The availability of full genome sequences for S. enterica serotype Typhi and S. enterica serotype Paratyphi A confirms their place as monomorphic, human-adapted pathogens vulnerable to control measures if international efforts can be redoubled.

Efflux-mediated drug resistance in bacteria: an update

Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.