Molecular epidemiology of fluoroquinolone resistant Salmonella in Africa: A systematic review and meta-analysis

Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar

BACKGROUND

Typhoid fever is a common cause of febrile illness in low- and middle-income countries. While multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) has spread globally, fluoroquinolone resistance has mainly affected Asia.

METHODS

Consecutively, 1038 blood cultures were obtained from patients of all age groups with fever and/or suspicion of serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar in 2015-2016. S. Typhi were analyzed with antimicrobial susceptibility testing and with short read (61 strains) and long read (9 strains) whole genome sequencing, including three S. Typhi strains isolated in a pilot study 2012-2013.

RESULTS

Sixty-three S. Typhi isolates (98%) were MDR carrying blaTEM-1B, sul1 and sul2, dfrA7 and catA1 genes. Low-level ciprofloxacin resistance was detected in 69% (43/62), with a single gyrase mutation gyrA-D87G in 41 strains, and a single gyrA-S83F mutation in the non-MDR strain. All isolates were susceptible to ceftriaxone and azithromycin. All MDR isolates belonged to genotype 4.3.1 lineage I (4.3.1.1), with the antimicrobial resistance determinants located on a composite transposon integrated into the chromosome. Phylogenetically, the MDR subgroup with ciprofloxacin resistance clusters together with two external isolates.

CONCLUSIONS

We report a high rate of MDR and low-level ciprofloxacin resistant S. Typhi circulating in Zanzibar, belonging to genotype 4.3.1.1, which is widespread in Southeast Asia and African countries and associated with low-level ciprofloxacin resistance. Few therapeutic options are available for treatment of typhoid fever in the study setting. Surveillance of the prevalence, spread and antimicrobial susceptibility of S. Typhi can guide treatment and control efforts.

Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria

Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby-Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included blaCTX-M, blaSHV, and blaTEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either blaCTX-M-15 or blaCTX-M-1 4 and phenotypically produced ESBLs. The blaNDM-7 and blaVIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained blaNDM-7, while blaNDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6')-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL blaCTX-M-15, the serine carbapenemase, blaOXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance.

Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland

Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIP^R) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIP^R. High- and low-level ciprofloxacin resistance among CIP^R isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.

Prevalence of Antimicrobial Resistance Genes in Salmonella Typhi: A Systematic Review and Meta-Analysis

Salmonella enterica serovar Typhi (S. Typhi) that has developed resistance to many antimicrobials poses a serious challenge to public health. Hence, this study aimed to systematically determine the prevalence of antimicrobial resistance (AMR) in S. Typhi isolated from the environment and humans as well as to ascertain the spread of the selected AMR genes in S. Typhi. This systematic review and meta-analysis were performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines, and the study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO). A total of 2353 studies were retrieved from three databases, of which 42 studies fulfilled the selection criteria. The pooled prevalence of AMR S. Typhi (using a random-effect model) was estimated at 84.8% (95% CI; 77.3−90.2), with high heterogeneity (I2: 95.35%, p-value < 0.001). The high estimated prevalence indicates that control methods should be improved immediately to prevent the spread of AMR among S. Typhi internationally.

Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa

Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatics analysis. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and faeces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.

One Health Perspective of Salmonella Serovars in South Africa Using Pooled Prevalence: Systematic Review and Meta-Analysis

Salmonella is a bacterium that is commonly associated with food-borne infections and is regarded as one of the most important pathogens in public health. Salmonella serovars, particularly Typhimurium and Enteritidis, which are widely distributed globally, mainly result in outbreaks commonly linked to the consumption of animal products. This study is a systematic review and meta-analysis of studies reporting the prevalence of Salmonella serovars from one health perspective that included human, environmental, and animal samples in South Africa. PubMed, ScienceDirect, African Journals Online, and Scopus databases were used to conduct extensive searches of articles which were ultimately included or excluded following the Systematic Reviews and Meta-Analysis (PRISMA) guidelines. According to the data obtained in this review, the overall pooled prevalence estimates (PPE) of Salmonella serovars detection were 79.6%, 61.6%, 56.5%, and 43.2% for human, environment, animal, and environment/animal samples in South Africa, respectively. The majority of the studies (50%) used the polymerase chain reaction (PCR) technique for the detection of Salmonella serovars, followed by culture methods (26.7%), while 20% used serotyping. The PPE for nontyphoidal Salmonellae (NTS) was 65.6% and 34.4% for Salmonella Typhimurium and Salmonella Enteritidis, respectively. Our data further shows that 3 serovars, namely, Salmonella Typhimurium, Salmonella Enteriditis, and Salmonella Hadar, have been isolated from animals, humans, and the environment in South Africa. Our results highlight the ongoing spread of Salmonella spp. especially on animals which might end up infecting humans via direct contact with infected animals or eating infected animal products. This calls for deliberate “One Health” epidemiological studies in order to document information on the transmission between humans, animals, and the environment. This will ultimately result in the formulation of a consolidated salmonellosis control policy by the environmental, human, and veterinary health sectors.

Molecular Epidemiology of Salmonella enterica in Poultry in South Africa Using the Farm-to-Fork Approach

The presence of the zoonotic pathogen Salmonella in the food supply chain poses a serious public health threat. This study describes the prevalence, susceptibility profiles, virulence patterns, and clonality of Salmonella from a poultry flock monitored over six weeks, using the farm-to-fork approach. Salmonella was isolated using selective media and confirmed to the genus and species level by real-time polymerase chain reaction (RT-PCR) of the invA and iroB genes, respectively. Antimicrobial susceptibility profiles were determined using Vitek-2 and the Kirby–Bauer disk diffusion method against a panel of 21 antibiotics recommended by the World Health Organisation Advisory Group on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR). Selected virulence genes were identified by conventional PCR, and clonality was determined using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Salmonella was present in 32.1% of the samples: on the farm (30.9%), at the abattoir (0.6%), and during house decontamination (0.6%). A total of 210 isolates contained the invA and iroB genes. Litter, faeces, and carcass rinsate isolates were classified as resistant to cefuroxime (45.2%), cefoxitin (1.9%), chloramphenicol (1.9%), nitrofurantoin (0.4%), pefloxacin (11.4%), and azithromycin (11%). Multidrug resistance (MDR) was observed among 3.8% of the isolates. All wastewater and 72.4% of carcass rinsate isolates were fully susceptible. All isolates harboured the misL, orfL, pipD, stn, spiC, hilA, and sopB virulence genes, while pefA, spvA, spvB, and spvC were absent. In addition, fliC was only present among the wastewater isolates. Various ERIC-PCR patterns were observed throughout the continuum with different subtypes, indicating the unrelated spread of Salmonella. This study concluded that poultry and the poultry environment serve as reservoirs for resistant and pathogenic Salmonella. However, there was no evidence of transmission along the farm-to-fork continuum.

Genotypic Diversity of Ciprofloxacin Nonsusceptibility and Its Relationship with Minimum Inhibitory Concentrations in Nontyphoidal Salmonella Clinical Isolates in Taiwan

This study analyzed the genetic diversity of ciprofloxacin (CIP) nonsusceptibility and the relationship between two major mechanisms and minimum inhibitory concentrations (MICs) of CIP in nontyphoidal Salmonella (NTS). Chromosomal mutations in quinolone resistance-determining regions (QRDRs) and plasmid-mediated quinolone resistance (PMQR) genes were searched from ResFinder, ARG-ANNOT, and PubMed for designing the sequencing regions in gyrA, gyrB, parC, and parE, and the 13 polymerase chain reactions for PMQR genes. We found that QRDR mutations were detected in gyrA (82.1%), parC (59.0%), and parE (20.5%) but not in gyrB among the 39 isolates. Five of the 13 PMQR genes were identified, including oqxA (28.2%), oqxB (28.2%), qnrS (18.0%), aac(6′)-Ib-cr (10.3%), and qnrB (5.1%), which correlated with the MICs of CIP within 0.25–2 μg/mL, and it was found that oxqAB contributed more than qnr genes to increase the MICs. All the isolates contained either QRDR mutations (53.8%), PMQR genes (15.4%), or both (30.8%). QRDR mutations (84.6%) were more commonly detected than PMQR genes (46.2%). QRDR mutation numbers were significantly associated with MICs (p < 0.001). Double mutations in gyrA and parC determined high CIP resistance (MICs ≥ 4 μg/mL). PMQR genes contributed to intermediate to low CIP resistance (MICs 0.25–2 μg/mL), thus providing insights into mechanisms underlying CIP resistance.

Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland

BACKGROUND

Salmonella Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical S. Kentucky strains isolated in Poland remain undescribed.

METHODS

Eighteen clinical S. Kentucky strains collected in the years 2018-2019 in Poland were investigated. All the strains were tested for susceptibility to 11 antimicrobials using the disc diffusion and E-test methods. Whole genome sequences were analysed for antimicrobial resistance genes, mutations, the presence and structure of SGI1-K (Salmonella Genomic Island and the genetic relationship of the isolates.

RESULTS

Sixteen of 18 isolates (88.9%) were assigned as ST198 and were found to be high-level resistant to ampicillin (>256 mg/L) and quinolones (nalidixic acid MIC ≥ 1024 mg/L, ciprofloxacin MIC range 6-16 mg/L). All the 16 strains revealed three mutations in QRDR of GyrA and ParC. The substitutions of Ser83 → Phe and Asp87 → Tyr of the GyrA subunit and Ser80→Ile of the ParC subunit were the most common. One S. Kentucky isolate had qnrS1 in addition to the QRDR mutations. Five of the ST198 strains, grouped in cluster A, had multiple resistant determinants like blaTEM1-B, aac(6')-Iaa, sul1 or tetA, mostly in SGI1 K. Seven strains, grouped in cluster B, had shorter SGI1-K with deletions of many regions and with few resistance genes detected.

CONCLUSION

The results of this study demonstrated that a significant part of S. Kentucky isolates from humans in Poland belonged to ST198 and were high-level resistant to ampicillin and quinolones.

Molecular mechanisms associated with quinolone resistance in Enterobacteriaceae: review and update

BACKGROUND

Quinolones are broad-spectrum antibiotics, which are used for the treatment of different infectious diseases associated with Enterobacteriaceae. During recent decades, the wide use as well as overuse of quinolones against diverse infections has led to the emergence of quinolone-resistant bacterial strains. Herein, we present the development of quinolone antibiotics, their function and also the different quinolone resistance mechanisms in Enterobacteriaceae by reviewing recent literature.

METHODS

All data were extracted from Google Scholar search engine and PubMed site, using keywords; quinolone resistance, Enterobacteriaceae, plasmid-mediated quinolone resistance, etc.

RESULTS AND CONCLUSION

The acquisition of resistance to quinolones is a complex and multifactorial process. The main resistance mechanisms consist of one or a combination of target-site gene mutations altering the drug-binding affinity of target enzymes. Other mechanisms of quinolone resistance are overexpression of AcrAB-tolC multidrug-resistant efflux pumps and downexpression of porins as well as plasmid-encoded resistance proteins including Qnr protection proteins, aminoglycoside acetyltransferase (AAC(6')-Ib-cr) and plasmid-encoded active efflux pumps such as OqxAB and QepA. The elucidation of resistance mechanisms will help researchers to explore new drugs against the resistant strains.

Ciprofloxacin interferes with Salmonella Typhimurium intracellular survival and host virulence through repression of Salmonella pathogenicity island-2 (SPI-2) genes expression

Current study aims to characterize the influence of sub-minimum inhibitory concentration (sub-MIC) of ciprofloxacin on Salmonella intracellular survival and host virulence. Herein, Salmonella resistance patterns to various antibiotics were in agreement with those reported in previous studies. Moreover, intracellular survival of both ciprofloxacin-sensitive and -resistant Salmonella was markedly reduced upon treatment with sub-MIC of ciprofloxacin as determined by gentamicin protection assay. These findings were further confirmed using immunostaining indicating an inhibitory effect of sub-MIC of ciprofloxacin on Salmonella intracellular survival. RT-qPCR revealed that expression of genes encoding Salmonella type three secretion system (TTSS) decreased upon bacterial exposure to sub-MIC of ciprofloxacin. Furthermore, bacterial exposure to sub-MIC of ciprofloxacin significantly reduced expression of both sifA and sifB, which are important for Salmonella filaments formation within the host. Treatment of Salmonella with sub-MIC of ciprofloxacin reduced bacterial capacity to kill mice infection models. A lower mortality rate was observed in mice injected with Salmonella treated with sub-MIC of ciprofloxacin as compared with mice inoculated with untreated bacteria. Collectively, current findings indicate that, in addition to its bactericidal potential, sub-MIC of ciprofloxacin could inhibit Salmonella intracellular survival, virulence genes expression as well as host pathogenesis, providing another mechanism for ciprofloxacin in limiting Salmonella host infection.

Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development

Invasive non-typhoidal Salmonella (iNTS) infections are a leading cause of bacteremia in Sub-Saharan Africa (sSA), thereby representing a major public health threat. Salmonella Typhimurium clade ST313 and Salmonella Enteriditis lineages associated with Western and Central/Eastern Africa are among the iNTS serovars which are of the greatest concern due to their case-fatality rate, especially in children and in the immunocompromised population. Identification of pathogen-associated features and host susceptibility factors that increase the risk for invasive non-typhoidal salmonellosis would be instrumental for the design of targeted prevention strategies, which are urgently needed given the increasing spread of multidrug-resistant iNTS in Africa. This review summarizes current knowledge of bacterial traits and host immune responses associated with iNTS infections in sSA, then discusses how this knowledge can guide vaccine development while providing a summary of vaccine candidates in preclinical and early clinical development.

Invasive non-typhoidal Salmonella infections in sub-Saharan Africa: a systematic review on antimicrobial resistance and treatment

BACKGROUND

Non-typhoidal Salmonella (NTS) are a frequent cause of invasive infections in sub-Saharan Africa. They are frequently multidrug resistant (co-resistant to ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol), and resistance to third-generation cephalosporin and fluoroquinolone non-susceptibility have been reported. Third-generation cephalosporins and fluoroquinolones are often used to treat invasive NTS infections, but azithromycin might be an alternative. However, data on antibiotic treatment efficacy in invasive NTS infections are lacking. In this study, we aimed to assess the spatiotemporal distribution of antimicrobial resistance in invasive NTS infections in sub-Saharan Africa and to describe the available evidence and recommendations on antimicrobial treatment.

METHODS

We conducted a systematic review of all available literature on antimicrobial resistance and treatment in invasive NTS infections. We performed a random effects meta-analysis to assess the temporal distribution of multidrug resistance, third-generation cephalosporin resistance, and fluoroquinolone non-susceptibility. We mapped these data to assess the spatial distribution. We provided a narrative synthesis of the available evidence and recommendations on antimicrobial treatment.

RESULTS

Since 2001, multidrug resistance was observed in 75% of NTS isolates from all sub-Saharan African regions (95% confidence interval, 70-80% and 65-84%). Third-generation cephalosporin resistance emerged in all sub-Saharan African regions and was present in 5% (95% confidence interval, 1-10%) after 2010. Fluoroquinolone non-susceptibility emerged in all sub-Saharan African regions but did not increase over time. Azithromycin resistance was reported in DR Congo. There were no reports on carbapenem resistance. We did not find high-quality evidence on the efficacy of antimicrobial treatment. There were no supranational guidelines. The "Access group" antibiotics ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol and "Watch group" antibiotics ceftriaxone, cefotaxime, and ciprofloxacin were recommended as the first-choice antibiotics in national guidelines or reviews. These also recommended (a switch to) oral fluoroquinolones or azithromycin.

CONCLUSIONS

In addition to the widespread multidrug resistance in invasive NTS infections in sub-Saharan Africa, resistance to third-generation cephalosporins and fluoroquinolone non-susceptibility was present in all regions. There was a lack of data on the efficacy of antimicrobial treatment in these infections, and supranational evidence-based guidelines were absent.

Plasmid profile and role in virulence of salmonella enterica serovars isolated from food animals and humans in Lagos Nigeria

Infections caused by non-typhoidal Salmonella (NTS) are common around the world, with high morbidity and mortality rates recorded annually. Salmonella serovars harbor plasmids of various sizes which may play roles in antibiotic resistance and virulence. The aim of this study was to profile and determine the role of plasmids in ciprofloxacin resistance and virulence of Salmonella serovars. Using alkaline lysis method 25 NTS serovars from food animals and humans were assayed for plasmids. Isolates ability to resist healthy human serum, bind congo red, produce hemolysin and susceptibility to ciprofloxacin before and after plasmid curing were evaluated. Mobility of plasmids was determined by conjugation. Fifteen (60%) of the 25 Salmonella serovars harbored plasmids with sizes ranging from 0.4 to 38.4 kb. S. Budapest serovars harbored 5-9 plasmids, while S. Essen and S. Mura had six plasmids each. S. Chomedey and a S. Budapest serovar were sensitive to ciprofloxacin after plasmid curing while other serovars remained resistant to ciprofloxacin after plasmid curing. All Salmonella isolates had the ability to withstand human serum before and after plasmid curing, however, some serovars lost their ability to bind congo red after plasmid curing. All Salmonella isolates that initially displayed hemolysin activity retained their ability after curing. Thirteen (86.7%) of the 15 serovars that harbored plasmids conjugatively transferred their plasmids to E. coli K-12 (DH5α). Having Salmonella serovars that harbor transferrable plasmids in the food chain can drive antibiotic resistance and enhanced virulence of otherwise less virulence strains.

[Current trends in the development of resistance to clinically significant antibiotics in Salmonella (review of literature).]

Salmonella is one of the leading bacterial pathogens of acute diarrhea as well as foodborne outbreaks. Salmonellosis can occur as gastroenteritis with the development of complications and generalization of infection, also the extra intestinal diseases that require antibiotic therapy are often registered. Currently, the effectiveness of many antibiotics is reduced due to the development of resistance in Salmonella. National Salmonella surveillance systems monitor Salmonella resistance to «critically important for medicine» antibiotics (extended-spectrum cephalosporins and fluoroquinolones), as well as multidrug resistance. Quinoloneresistant Salmonella is considered as a high-priority resitant pathogen by the World Health Organization. The article describes the current situation on salmonellosis in the world. Foreign and Russian current data about the leading Salmonella serotypes in different regions of the world are presented. The prevalence of clinically significant resistance depending of the Salmonella serotypes in countries with state monitoring systems is shown. The authors described the leading molecular resistance mechanisms (chromosomal and plasmid mediated) and showed their prevalence in different Salmonella serotypes. The article gives the information about Salmonella successful international multidrug resistant clones with specific resistance phenotypes and genotypes. The authors describe the molecular methods for detection of resistance mechanisms, and show the necessity and significance of antimicrobial susceptibility monitoring in the epidemiological Salmonella surveillance.

A systematic review of antimicrobial resistance of typhoidal Salmonella in India

Background & objectives:

The temporal trends in the development of antimicrobial resistance (AMR) among Salmonella Typhi and Salmonella Paratyphi in India have not been systematically reported. We aimed to systematically review the temporal AMR trends (phenotypic and molecular mechanisms) in bacterial isolates from patients with enteric fever over two decades in India.

Methods:

To identify trends in AMR in India, resistance patterns among 4611 individual S. Typhi isolates and 800 S. Paratyphi A isolates, reported from 1992 to 2017 in 40 publications, were analysed. Molecular resistance determinants were extracted from 22 publications and also reviewed in accordance with the PRISMA guidelines. Articles were sourced using a predefined search strategy from different databases.

Results:

The analyses suggested that multidrug-resistant (MDR) enteric fever was declining in India and being replaced by fluoroquinolone (FQ) resistance. Mutations in gyrA and parC were key mechanisms responsible for FQ resistance, whereas MDR was largely driven by resistance determinants encoded on mobile genetic elements (plasmids, transposons).

Interpretation & conclusions:

The results reflect the effect of antimicrobial pressure which has been driving AMR in typhoidal Salmonella in India. Understanding these trends is important in planning future approaches to therapy, which serve as a baseline for assessment of the impact of new typhoid conjugate vaccines against these resistant organisms.

Molecular diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals in Lagos, Nigeria

Outbreaks of Salmonellosis remain a major public health problem globally. This study determined the diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals. Using standard methods, Salmonella spp. were isolated from fecal samples, profiled for antimicrobial susceptibility and resistance genes. Seventy-one Salmonella isolates were recovered from both humans and food animals comprising cattle, sheep, and chicken. Forty-four serovars were identified, with dominant Salmonella Budapest (31.8%). Rare serovars were present in chicken (S. Alfort, S. Wichita, S. Linton, S. Ealing, and S. Ebrie) and humans (S. Mowanjum, S. Huettwillen, S. Limete, and S. Chagoua). Sixty-eight percent of isolates were sensitive to all test antibiotics, while the highest rate of resistance was to nalidixic acid (16.9%; n = 12), followed by ciprofloxacin (11.3%; n = 8) and tetracycline (9.9%; n = 8). Five isolates (7%) were multidrug-resistant and antimicrobial resistance genes coding resistance to tetracycline (tetA), beta-lactam (bla_TEM), and quinolone/fluoroquinolone (qnrB and qnrS) were detected. Evolutionary analysis of gyrA gene sequences of human and food animal Salmonella isolates revealed variations but are evolutionarily interconnected. Isolates were grouped into four clades with S. Budapest isolate from cattle clustering with S. Budapest isolated from chicken, whereas S. Essen isolated from sheep and chicken was grouped into a clade. Diverse S. enterica serovars with high antibiotic resistance profile are ubiquitous in food animals; hence, there is a need for surveillance and prudent use of antibiotics in human and veterinary medicine.

[Antimicrobial resistance and clinical significant resistance mechanisms of Salmonella isolated in 2014-2018 in St.Petersburg, Russia.]

The article presents the results of antimicrobial resistance monitoring of Salmonella isolated from children and adults with diarrhea in St. Petersburg in 2014-2018. In 746 isolates of 42 serovars more than 90,0% belonged to three: S. enteritidis (79,6%), S. typhimurium (6,8%) and S. infantis (3,8%). The antimicrobial susceptibility testing (according the EUCAST) to 7 classes of antimicrobials revealed the resistance in 78,6% of Salmonella. Low-level quinolone resistance (MIC of ciprofloxacin 0,12-0,5 mg/l) was detected in 63,3% isolates (S. enteritidis -71,0%, S. typhimurium - 15,7%, S. infantis - 89,3%) and was due to five kinds of single nucleotide substitutions in gyrA: Asp87Tyr - 36,1% of studied isolates (only S. infantis); Ser83Phe - 22,2% (only S. enteritidis); Asp87Asn - 19,4% (S. enteritidis, S. typhimurium, S. hadar, S. newport); Ser83Tyr -11,1% (S. enteritidis and S. infantis) and Asp87Gly - 8,3% (only S. enteritidis). Only in one S. kentucky isolate with high-level fluoroquinolone resistance (MIC of ciprofloxacin > 8,0 mg/l) two substitutions (Ser83Phe and Asp87Asn) were detected. Two Salmonella isolates (S. typhimurium and S. corvallis) had plasmid-mediated quinolone resistance (qnrS). Extended-spectrum cephalosporin resistance was found in 6 Salmonella serovars (1,6%). The bla-genes were detected: of genetic group CTX-M1 - in 10 isolates (serovars S. typhimurium, S. enteritidis, S. abony, S. coeln and S. virchow), CTX-M2 - in 2 S. typhimurium isolates, CTX-M9 - in three S. enteritidis isolates. In one S. typhimurium CTX-M1 and CTX-M2 were detected. The gene of CMY-2 (molecular class C cephalosporinase) was revealed in two isolates (S. newport and S. enteritidis). Our study showed that Salmonella (the main bacterial pathogen of acute diarrhea in children and adults) isolated in Saint-Petersburg had antimicrobial resistance to drugs of choice for salmonellosis treatment.

Chromosomal and plasmid-mediated fluoroquinolone resistance in human Salmonella enterica infection in Ghana

Background

Salmonella infection poses significant public health threat globally, especially in resource-limited countries. Emergence and spread of antibiotic resistant strains to fluoroquinolones have led to treatment failures and increased mortality in Salmonella infection. However, there is dearth of information regarding mechanisms of resistance to fluoroquinolones in Ghana. This study therefore sought to identify chromosomal mutations and plasmid-mediated resistance as possible mechanisms of fluoroquinolone resistance from clinical isolates in Ghana.

Methods

This was a retrospective study of archived isolates biobanked at Kumasi Centre for Collaborative Research in Tropical Medicine, Ghana. Isolates were obtained from blood, stool and oropharynx samples at two hospitals, between May, 2016 and January, 2018. Salmonella identification was done using standard microbiological protocols and antibiotic susceptibility testing performed by Kirby-Bauer disc diffusion method. Isolates with intermediate susceptibility and/or resistance to nalidixic acid and/or ciprofloxacin were selected and examined for chromosomal mutations by Sanger sequencing and plasmid-mediated resistance by PCR.

Results

Of 133 biobanked isolates cultured, 68 (51.1%) and 16 (12%) were identified as Salmonella Typhi and non-typhoidal Salmonella (NTS), respectively. Sequence analysis of gyrA gene revealed the presence of 5 different nonsynonymous mutations, with the most frequent mutation (Ile203Ser) occurring in 12 out of 13 isolates tested. Gyrase B (gyrB) gene had 1 nonsynonymous mutation in 3 out of 13 isolates, substituting phenylalanine with leucine at codon 601 (Phe601Leu). No mutation was observed in parC and parE genes. Two NTS isolates were found to harbour qnrS plasmid-mediated resistant gene of molecular size 550 bp with high ciprofloxacin MIC of 0.5 μg/ml.

Conclusion

This study reports for the first time in Ghana plasmid-mediated fluoroquinolone resistant gene qnrS in Salmonella clinical isolates. Nonsynonymous mutations of gyrA and gyrB genes likely to confer Salmonella reduced susceptibility to ciprofloxacin were also reported.

Epidemiology and Antimicrobial Susceptibility of Salmonella enterica Bloodstream Isolates Among Febrile Children in a Rural District in Northeastern Tanzania: A Cross-sectional Study

BACKGROUND

Salmonella enterica including Salmonella Typhi and nontyphoidal Salmonella (NTS) are the predominant cause of community-acquired bloodstream infections in sub-Saharan Africa (sSA). Multiple-drug resistance and emerging fluoroquinolone resistance are of concern. Data on the age distribution of typhoid fever in sSA are scarce but essential for typhoid conjugate vaccine policy. We sought to describe Salmonella bloodstream infections, antimicrobial resistance, and age distribution at a rural district hospital in northeastern Tanzania.

METHODS

From 2008 to 2016, febrile children or children with a history of fever aged 1 month to 5 years admitted to Korogwe District Hospital were enrolled. Demographic, clinical data and blood cultures were collected. Organisms were identified by conventional microbiological methods, and antimicrobial susceptibility test was done by disc diffusion.

RESULTS

Of 4176 participants receiving blood cultures, 383 (9.2 %) yielded pathogens. Of pathogens, 171 (44.6%) were Salmonella enterica of which 129 (75.4%) were Salmonella Typhi, and 42 (24.6%) were NTS. The median (interquartile range age of participants was 13.1 (6.3-28.0) months for those with Salmonella Typhi and 11.5 (8.5-23.4) months for NTS. Of 129 Salmonella Typhi, 89 (89.9%) were resistant to amoxicillin, 85 (81.0%) to chloramphenicol, and 93 (92.1%) to trimethoprim-sulfamethoxazole compared with 22 (62.9%), 15 (39.4%), and 27 (79.4%), respectively, for NTS. Multidrug resistance was present in 68 (81.0%) of Salmonella Typhi and 12 (41.4%) of NTS.

CONCLUSION

Salmonella Typhi was the leading cause of bloodstream infection among infants and young children <2 years of age admitted to Korogwe District Hospital. Multidrug resistance was common, highlighting a role for typhoid conjugate vaccine into routine infant vaccine schedules.

Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide

In the last few decades, peptides have been victorious over small molecules as therapeutics due to their broad range of applications, high biological activity, and high specificity. However, the main challenges to overcome if peptides are to become effective drugs is their low oral bioavailability and instability under physiological conditions. Cyclic peptides play a vital role in this context because they show higher stability under physiological conditions, higher membrane permeability, and greater oral bioavailability than that of their corresponding linear analogues. In this regard, cyclic antimicrobial peptides (AMPs) have gained considerable attention in the field of novel antibiotic development. Bacterial strains produce cyclic AMPs through two pathways: ribosomal and nonribosomal. This review provides an overview of the chemical classification of cyclic AMPs isolated from bacteria, and provides a description of their biological activity and mode of action.

Epidemiology of common resistant bacterial pathogens in the countries of the Arab League

No uniformly organised collection of data regarding antimicrobial resistance has occurred in the countries of the Arab League. 19 countries of the Arab League have published data for antimicrobial susceptibility for the WHO priority organisms, and seven of 14 of these organisms are included in this Review (Escherichia coli, Klebsiella spp, Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella spp, Staphylococcus aureus, and Streptococcus pneumoniae). Although E coli and Klebsiella spp resistance to third-generation cephalosporins is common in all countries, with prevalence reaching more than 50% in Egypt and Syria, carbapenem resistance is emerging, albeit with a prevalence of less than 10%. Conversely, a large amount of carbapenem resistance has been reported for P aeruginosa and A baumannii across the Arab League, reaching 50% and 88% of isolates in some countries. As for Salmonella spp, the prevalence of fluoroquinolone resistance has exceeded 30% in several areas. With regards to the Gram-positive pathogens, the prevalence of meticillin resistance in S aureus is reported to be between 20% and 30% in most countries, but exceeds 60% in Egypt and Iraq. The prevalence of penicillin non-susceptibility among pneumococci has reached more than 20% in Algeria, Egypt, Morocco, Saudi Arabia, and Tunisia. These findings highlight the need for structured national plans in the region to target infection prevention and antimicrobial stewardship.

A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid

BACKGROUND

The temporal and spatial change in trends of antimicrobial resistance (AMR) in typhoid have not been systematically studied, and such information will be critical for defining intervention, as well as planning sustainable prevention strategies.

METHODOLOGY AND FINDINGS

To identify the phenotypic trends in AMR, 13,833 individual S. Typhi isolates, reported from 1973 to 2018 in 62 publications, were analysed to determine the AMR preponderance over time. Separate analyses of molecular resistance determinants present in over 4,000 isolates reported in 61 publications were also conducted. Multi-drug resistant (MDR) typhoid is in decline in Asia in a setting of high fluoroquinolone resistance while it is on the increase in Africa. Mutations in QRDRs in gyrA (S83F, D87N) and parC (S80I) are the most common mechanisms responsible for fluoroquinolone resistance. Cephalosporin resistant S. Typhi, dubbed extensively drug-resistant (XDR) is a real threat and underscores the urgency in deploying the Vi-conjugate vaccines.

CONCLUSION

From these observations, it appears that AMR in S. Typhi will continue to emerge leading to treatment failure, changes in antimicrobial policy and further resistance developing in S. Typhi isolates and other Gram-negative bacteria in endemic regions. The deployment of typhoid conjugate vaccines to control the disease in endemic regions may be the best defence.

Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing

Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.