Antibiotic Resistance and Plasmid Profile Analysis of Salmonella Enteritidis Isolated in Siberia and the Far East of Russia between 1990 and 2017

Salmonella is one of the major causes of foodborne disease outbreaks globally. Specifically, Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the major causes of zoonotic Salmonella infection in humans worldwide. In this study, we present data on antimicrobial resistance (AMR) and plasmid profiles of S. Enteritidis strains isolated from patients, food, and the environment in Siberia and the Far East of Russia obtained during Salmonella monitoring between 1990 and 2017. A total of 345 S. Enteritidis isolates were tested by the disk diffusion method with a set of 15 antibiotics using EUCAST breakpoints v. 10 and by plasmid profile analysis using the alkaline lysis method. The results have shown a substantial decrease in susceptibility to aminoglycosides and quinolones during the study period. No significant differences were found in the susceptibility of strains between regions as well as in the its correlation with different plasmid types of the pathogen. Several S. Enteritidis strains were found to be resistant to ampicillin, kanamycin, tetracycline, chloramphenicol, and cephalosporins. All tested S. Enteritidis strains were susceptible only to imipenem. In this study, we observed a relatively low level of AMR in S. Enteritidis strains isolated in Siberia and the Far East of Russia. Nevertheless, it is important to continue the molecular genetic monitoring and AMR surveillance of S. Enteritidis to track further increases in AMR using conventional phenotypic susceptibility testing and by introducing whole-genome sequencing to identify AMR mechanisms.

Multi-drug resistant Aeromonas species in Annelida: An evidence of pathogen harbouring leech in recreation water nexus of Oghara Nigeria environs

Aeromonas infections have shown diverse complications in management due to the multiple antibiotic resistance observed amongst its members. The origin and habitat of its resistance development yet remain vague. The present study depicts Leech and its infested recreational water as a reservoir of multidrug-resistant Aeromonas hydrophila. Skin swabs of recreational water bathers before (Bb)/after bathing (Ab) (250 each) and 250 leeches (Hirudomedicinalis) were collected from recreational water sites. Standard Microbiological and Molecular biology methods were applied for isolation and characterization. Two hundred and forty-five (98%)Bb specimen, showed a negative growth oforganisms, 84% (210) of the Ab specimen harboured presumptive Aeromonas species, while 100% (250) Leeches specimen harboured Aeromonas species. The Polymerase Chain Reaction (PCR) of 16SrRNA gene detection confirmed all (465/100%) isolates as Aeromonas species while 13.6% (63) were further delineated as Aeromonas hydrophila. The antibiogram showed 45(97.82%) resistance to the β-lactam antibiotic and other antibiotic groups. The PCR detection of resistant markers, virulent and plasmid profile of isolates reveals conjugative plasmid mediation, lip (123/97.6%), act (104/82%), hhly (93/73%) genes and BlaampC gene, BlaTEM, gene and BlaSHV gene. Observation of pathogens with similar multiple antibiotic-resistant gene-profile both in the bathers'skin swab and gut of leeches indicates origin/habitat, association and suggests the gut of leeches as breeding habitat for the pathogen. This is an emerging public health concern that associates specifically the environment and human superficial infections.

Antibiotic Resistance Pattern and Plasmid Profile of Bacteria Isolates from Household Water Distribution Tanks in Ado-Ekiti

Water is essential to life. The existence of all forms of life is dependent on an adequate water supply. The exigent need for water supply in homes prompted the construction of water sources and water storage devices in the homes. This however does not guarantee that the water is safe to drink. If the water is safe at the source, it may be contaminated during transportation storage and drawing at home. This study was carried out to determine the microbial counts, antibiotics susceptibility and plasmid profile of bacteria isolates from household water distribution tanks in the Ado-Ekiti metropolis. The total bacteria and coliform counts were determined using the pour plating technique. The antibiotic susceptibility pattern of the isolates was determined using the disc diffusion technique while the plasmid profile of the isolates was determined using the alkaline lysis method and agar gel electrophoresis. The mean total bacteria count of the water sample was 6.96 log10 CFU/ml, while the mean total of coliform count is 5.50 log10CFU/ml. The isolates with multiple antibiotics resistance belonged to five bacteria genera namely: Escherichia, Pseudomonas, Klebsiella, Enterobacter and Proteus. The plasmid analysis showed that four of the resistant strains had multiple plasmids, Enterobacter aerogens had 3 plasmids (1kb, 1.5kb and 2kb), Pseudomonas aeruginosa and Klebsiella aerogens had two plasmids (1kb, 1.5kb) respectively while Proteus vulgaris and Escherichia coli had no plasmid.

Antibiotic Sensitivity Pattern and Plasmid Profile of Bacteria Isolated from Diabetic Ulcers in Mbano Metropolis, Imo State, Southeastern Nigeria

The study was undertaken to evaluate the bacteriology and antibiogram of isolates from diabetic patients with chronic foot ulcers in Nigeria. A total of 150 pus samples were collected and processed according to standard aerobic and anaerobic microbiological methods. Antibiogram was done using Kirby-Bauer method. Biofilm tests, ESBL & AmpC production was conducted using Congo red agar, Double disc synergy test and Cefoxitin disc test respectively. Total number of isolates obtained was 210. The Plasmid profiles of some of the Multi-Drug Resistance (MDR) isolates were carried out using the alkaline lysis method for plasmid extraction and electrophoresis on agarose gel with standard markers. The most frequently isolated aerobic organism in the study was Escherichia coli (32.1%) while the least occurring was Enterobacter spp (1.57%). For the anaerobes, Peptostreptococcus spp (40%) was the highest isolated bacterium. Percentage of Extended Spectrum -lactamase ( ESBL) producers among E. coli isolates was 44%. Percentages of biofilm formation potential among the isolates were: E. coli (36.8%), S. aureus (23.1%) and Proteus vulgaris (4.2%). Escherichia coli and S. aureus showed considerable levels of resistance to some common antibiotics. No methicilin resistant S. aureus was encountered. AmpC producers encountered were Klebsiella pneumonia (10%) and E. coli (8.1%). Post-curring antibiogram tests revealed that nine isolates carried plasmids, suggesting that the mode of resistance may be plasmid mediated. Keywords: Diabetic ulcers, Bacteria, Antibiogram, Plasmid profile

Main Results of the Research on the Far Eastern Scarlet-Like Fever as a Specific Clinical and Epidemic Manifestation of Pseudotuberculosis: A Review of Comprehensive Studies

Introduction: Until 1950s, pseudotuberculosis in humans was known in the world as a sporadic disease with appendicular syndrome. In 1959, the first outbreak of a previously unknown disease called Far Eastern scarlet-like fever (FESLF) was registered in Vladivostok. The purpose of this article is to review priority achievements of the Research Institute of Epidemiology and Microbiology named after G.P. Somov in the field of studying FESLF as a specific clinical and epidemic manifestation of pseudotuberculosis in Russia. Materials and methods: The priority data were obtained based on microbiological, epidemiological, molecular genetic, as well as pathomorphological and electron microscopic studies of biological samples from human FESLF cases and experimental animals infected with Yersinia pseudotuberculosis strains with different plasmid characteristics. Results: It has been proven that the FESLF pathogen is a specific clone of Yersinia pseudotuberculosis having a certain plasmid profile pVM82, pYV 48 MDa, sequence type (2ST) and the first allele of the yadA gene. The causative agent of FESLF is characterized by the phenomenon of psychrophilicity, which consists in its ability to multiply in the environment with its biologically low and changing temperature (4–12 °C), at which the pathogen multiplies and accumulates while preserving or increasing its virulence, thus inducing the epidemic process. The article describes the main genetic and biochemical mechanisms of Y. pseudotuberculosis adaptation to changing environmental conditions, reveals morphological manifestations of the adaptive variability of these bacteria under different conditions of their habitat, and presents the main features of the pathogenesis and morphogenesis of FESLF, including those associated with plasmid characteristics and toxigenicity of Y. pseudotuberculosis. Conclusion: Currently, the epidemic process of pseudotuberculosis/FESLF is characterized by a decrease in the proportion of outbreaks and predominance of sporadic cases. The relevance of further research is associated with the study of the dormant forms of Y. pseudotuberculosis and the formation of ideas about pseudotuberculosis as a persistent infectious disease.

Zymomonas diversity and potential for biofuel production

Background Zymomonas mobilis is an aerotolerant α-proteobacterium, which has been genetically engineered for industrial purposes for decades. However, a comprehensive comparison of existing strains on the genomic level in conjunction with phenotype analysis has yet to be carried out. We here performed whole-genome comparison of 17 strains including nine that were sequenced in this study. We then compared 15 available Zymomonas strains for their natural abilities to perform under conditions relevant to biofuel synthesis. We tested their growth in anaerobic rich media, as well as growth, ethanol production and xylose utilization in lignocellulosic hydrolysate. We additionally compared their tolerance to isobutanol, flocculation characteristics, and ability to uptake foreign DNA by electroporation and conjugation. Results Using clustering based on 99% average nucleotide identity (ANI), we classified 12 strains into four clusters based on sequence similarity, while five strains did not cluster with any other strain. Strains belonging to the same 99% ANI cluster showed similar performance while significant variation was observed between the clusters. Overall, conjugation and electroporation efficiencies were poor across all strains, which was consistent with our finding of coding potential for several DNA defense mechanisms, such as CRISPR and restriction–modification systems, across all genomes. We found that strain ATCC31821 (ZM4) had a more diverse plasmid profile than other strains, possibly leading to the unique phenotypes observed for this strain. ZM4 also showed the highest growth of any strain in both laboratory media and lignocellulosic hydrolysate and was among the top 3 strains for isobutanol tolerance and electroporation and conjugation efficiency. Conclusions Our findings suggest that strain ZM4 has a unique combination of genetic and phenotypic traits that are beneficial for biofuel production and propose investing future efforts in further engineering of ZM4 for industrial purposes rather than exploring new Zymomonas isolates.

Antibiotic susceptibility pattern and plasmid profiles of nasal staphylococci from apparently healthy Nigerians

A total of 480 nasal samples from apparently healthy Nigerian students were collected aseptically and analyzed bacteriologically. Staphylococci were recovered from 432 (90%) of the subjects, constituting 288 (66.7%) and 144 (33.3%) of S. aureus and S. epidermidis respectively. The in-vitro antibiotic susceptibility testing using the disc diffusion technique showed high multiple resistance to the most commonly used antibiotics by Staphylococcus aureus such as penicillin (98.6%), ampicillin (97.2%), tetracycline (95.8%) and streptomycin (84.7%), but less resistance to erythromycin (9.7%), rocephin (8.3%), peflacin (4.2%) respectively. The S. epidermis showed less resistance to all the antibiotics tested. Sixty percent of S. aureus harbored plasmids which molecular sizes ranged from 0.1 to 12.0 kilobases. The high prevalence of multiple antibiotic resistance appear to be plasmid mediated as plasmid profile analysis showed that about 90% of S. aureus harbored plasmids

Cultural, serotyping and plasmid profile of Salmonellae in Lagos, Nigeria

Problems associated with typhoid fever epidemic about its diagnosis in developing countries like Nigeria is a perennial healthcare challenge the healthcare sector grapples with. Improper diagnosis of clinical cases have also led to treatment failure and errors as diseases caused by other microorganisms are treated as typhoid fever especially as a result of inadequate reliable diagnostic laboratories. A total of 3,000 stool specimens from patients were analyzed using standard microbiological techniques. Of this, 1,391 Salmonella spp. were recovered, constituting 233 (88.14%) S. typhi while 158 (11.36%) were non-typhoidal Salmonella. S. typhi was recovered from more females, 685(55.6%), than males, 548 (44.4%). The 41 and above age group had the highest incidence of S. typhi of 220(17.8%) in females as against 280 (22.7%) in males within the 21-30 age group. Antibiotic susceptibility testing using the disc diffusion method by Kirby Bauer showed high multiple resistance to most of the 15 different antibiotics tested but susceptible to the first line typhoid fever drugs (chloramphenicol 85%, cotrimoxazole 86.7%, ampicillin 88.3% and amoxicillin 90%) and highly susceptible to third generation cephalosporins and fourth generation fluoroquinolones. The S. typhi tested showed four different resistance patterns. Plasmid profile analysis of 200 multiple antibiotic resistant Salmonella isolates identified culturally and biochemically as S. typhi but by serotyping showed Salmonella other than S. typhi were erroneously classified as S. typhi. Majority of the S. typhi harbored mostly small sized plasmids which ranged from 2.2 Kb to 55.5 Kb. It can be deduced from this study that multiple drug resistance in S. typhi is likely to be plasmid mediated. The eleven antibiotic resistance patterns were reduced to eight plasmid clones indicating the diagnostic efficacy of plasmid profiling over the former method.

Genomic Characterization and Plasmid Profile of Listeria and Salmonella Species Isolated from Oreochromis niloticus Sold in Port Harcourt, Rivers State, Nigeria

Fish are generally regarded as safe, nutritious and beneficial but aquaculture products have sometimes been associated with certain food safety issues. Consumption of fish may also cause diseases due to infection or intoxication, Hence, the aim of this study is to characterize using genomic analysis and plasmid profile of Listeria and Salmonella species isolated from Oreochromis niloticus sold in Port Harcourt. A total of one hundred and eighty samples (180) were collected from three different markets namely; Creek road, Mile one and Rumuokoro markets over a period of six months. The samples were labelled and transported in an ice packed coolers to the laboratory for analyses. Standard analytical protocols were employed to determine the bacteriological characteristics of the various parts such as Intestine, Gill, flesh of the sample. Statistical analyses were carried out using ANOVA and All pairs tukey-kramer. Results obtained from the study showed that the total heterotrophic bacteria count ranged from 5.1 to 5.9 x10 x106cfu/g across the markets for the flesh part, 6.0 to 7.7 x106 cfu/g (Gill) and 7.1 to 7.6 x106 cfu/g for the intestinal samples. Total coliform count ranged from 4.2 to 5.4 x104cfu/g (flesh), 5.2 to 5.4 x104 cfu/g ((Gill) and 6.1 to 8.0 x104 cfu/g (Intestine). Listeria count range from 2.7 to 2.9 x104 cfu/g (Fresh), 3.3 to 3.7 cfu/g (Gill)), and 3.8 to 4.3 cfu/g (Intestine), and Salmonella count ranged from 1.0 x103 - 1 .1 x103 cfu/g (Flesh) 1.0 to 1.6 x103 cfu/g (Gill) and 1.2 to 2.0 x103 cfu/g (intestine). This results shows that the intestines harbours more bacterial load than the gill and flesh. Mean values for all the microbial counts were significantly different (P<0.05) in the three samples across the sampled markets The result of the conventional and genomics identification confirms the following species of Listeria and Salmonella: L. grayi VD-Sfg with accession number MW020239 having a closest gene bank match with Listeria grayi CIP 100% identified, L. monocytogenes VD-Sfg with accession number MW020240 closest to L. monocytogenes NCTC 10357 with 99.73% identified, L. seeligeri VD-SFF accession number MW020241 closet to L. seeligeri ATCC 35967 with 98.95%, L. welshimeri VD-SF MW020242 closest to L. welshimeri ATCC 35897 with 99.9%, L. monocytogenes VD-Fg MW020243 closet to L. monocytogenes NCTC 10357 eith 99.73% identity, S. bongori VD-SwfiA MW020245 closest to S. bongori NCTC 12419 and S. enterica VD-SwfiD MW20244 closest with S. entrica LT2 both with 100% identity. Gel electrophoresis of the plasmid DNA showed that all the isolates possess plasmid. This finding is of public health concern as these organisms are the known causes of food-borne diseases and also serve as reservoirs for resistance plasmids that may be transferred to otherwise susceptible bacteria making them resistant, thus increasing the occurrence of antibiotic resistance among microorganisms.

Extensively Drug-Resistant Hypervirulent Klebsiella pneumoniae From a Series of Neonatal Sepsis in a Tertiary Care Hospital, India

The recent emergence of multidrug-resistant (MDR) Klebsiella pneumoniae with hypervirulent traits causing severe infections and considerable mortality is a global cause for concern. The challenges posed by these hypermucoviscous strains of K. pneumoniae with regard to their optimal treatment, management, and control policies are yet to be answered. We studied a series of extensively drug-resistant (XDR) and hypervirulent K. pneumoniae ST5235 isolates with resistance to carbapenems and polymyxins causing neonatal sepsis in a tertiary care hospital in India. A total of 9 K. pneumoniae isolates from 9 cases of neonatal sepsis were studied with respect to their clinical relevance, antimicrobial susceptibility profile, presence of extended spectrum β lactamase (ESBL) production, and responsible genes, carbapenemases (classes A, B, and D), and aminoglycoside-resistant genes. Hypervirulence genes encoding hypermucoid nature, iron uptake, and siderophores were detected by multiplex PCR. The plasmid profile was studied by replicon typing. Isolates were typed by multilocus sequence typing (MLST) and enterobacterial repetitive intergenic consensus (ERIC) PCR to study the sequence types (STs) and clonal relation, respectively. The neonates in the studied cases had history of pre-maturity or low birth weight with maternal complications. All the cases were empirically treated with piperacillin–tazobactam and amikacin followed by imipenem/meropenem and vancomycin and polymyxin B as a last resort. However, all the neonates finally succumbed to the condition (100%). The studied isolates were XDR including resistance to polymyxins harboring multiple ESBL genes and carbapenemase genes (blaNDM and blaOXA−48). Hypervirulence genes were present in various combinations with rmpA/A2 genes present in all the isolates. IncFI plasmids were detected in these isolates. All belonged to ST5235. In ERIC PCR, 6 different clusters were seen. The study highlighted the emergence and burden of XDR hypervirulent isolates of K. pneumoniae causing neonatal sepsis in a tertiary care hospital.