Salmonella strains resistant to multiple antibiotics: therapeutic implications

A Retrospective Analysis of Salmonella Isolates across 11 Animal Species (1982-1999) Led to the First Identification of Chromosomally Encoded blaSCO-1 in the USA

Antimicrobial resistance (AMR) in non-typhoidal Salmonella is a pressing public health concern in the United States, necessitating continuous surveillance. We conducted a retrospective analysis of 251 Salmonella isolates from 11 animal species recovered between 1982 and 1999, utilizing serotyping, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Phenotypic resistance was observed in 101 isolates, with S. Typhimurium, S. Dublin, S. Agona, and S. Muenster prevailing among 36 identified serovars. Notably, resistance to 12 of 17 antibiotics was detected, with ampicillin being most prevalent (79/251). We identified 38 resistance genes, primarily mediating aminoglycoside (n = 13) and β-lactamase (n = 6) resistance. Plasmid analysis unveiled nine distinct plasmids associated with AMR genes in these isolates. Chromosomally encoded blaSCO-1 was present in three S. Typhimurium and two S. Muenster isolates from equine samples, conferring resistance to amoxicillin/clavulanic acid. Phylogenetic analysis revealed three distinct clusters for these five isolates, indicating evolutionary divergence. This study represents the first report of blaSCO-1 in the USA, and our recovered isolates harboring this gene as early as 1989 precede those of all other reports. The enigmatic nature of blaSCO-1 prompts further research into its function. Our findings highlight the urgency of addressing antimicrobial resistance in Salmonella for effective public health interventions.

Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya

A high burden of Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the region. Understanding regional differences in the predominant strains of S. Typhi can provide insight into the genomic epidemiology. We genetically characterized 310 S. Typhi isolates from typhoid fever surveillance conducted over a 12-year period (2007–2019) in Kibera, an urban informal settlement in Nairobi, Kenya, to assess the circulating strains, their antimicrobial resistance attributes, and how they relate to global S. Typhi isolates. Whole genome multi-locus sequence typing (wgMLST) identified 4 clades, with up to 303 pairwise allelic differences. The identified genotypes correlated with wgMLST clades. The predominant clade contained 290 (93.5%) isolates with a median of 14 allele differences (range 0–52) and consisted entirely of genotypes 4.3.1.1 and 4.3.1.2. Resistance determinants were identified exclusively in the predominant clade. Determinants associated with resistance to aminoglycosides were observed in 245 isolates (79.0%), sulphonamide in 243 isolates (78.4%), trimethoprim in 247 isolates (79.7%), tetracycline in 224 isolates (72.3%), chloramphenicol in 247 isolates (79.6%), β-lactams in 239 isolates (77.1%) and quinolones in 62 isolates (20.0%). Multidrug resistance (MDR) determinants (defined as determinants conferring resistance to ampicillin, chloramphenicol and cotrimoxazole) were found in 235 (75.8%) isolates. The prevalence of MDR associated genes was similar throughout the study period (2007–2012: 203, 76.3% vs 2013–2019: 32, 72.7%; Fisher’s Exact Test: P = 0.5478, while the proportion of isolates harboring quinolone resistance determinants increased (2007–2012: 42, 15.8% and 2013–2019: 20, 45.5%; Fisher’s Exact Test: P<0.0001) following a decline in S. Typhi in Kibera. Some isolates (49, 15.8%) harbored both MDR and quinolone resistance determinants. There were no determinants associated with resistance to cephalosporins or azithromycin detected among the isolates sequenced in this study. Plasmid markers were only identified in the main clade including IncHI1A and IncHI1B(R27) in 226 (72.9%) isolates, and IncQ1 in 238 (76.8%) isolates. Molecular clock analysis of global typhoid isolates and isolates from Kibera suggests that genotype 4.3.1 has been introduced multiple times in Kibera. Several genomes from Kibera formed a clade with genomes from Kenya, Malawi, South Africa, and Tanzania. The most recent common ancestor (MRCA) for these isolates was from around 1997. Another isolate from Kibera grouped with several isolates from Uganda, sharing a common ancestor from around 2009. In summary, S. Typhi in Kibera belong to four wgMLST clades one of which is frequently associated with MDR genes and this poses a challenge in treatment and control.

Typhoid fever is a major public health concern in endemic regions. Understanding the circulating strains of S. Typhi, could provide insight into the genomic epidemiology and guide in the choice of appropriate antibiotics. In this paper, our aim was to characterize S. Typhi strains causing invasive disease in Kibera, where a high typhoid burden has been described. We also aim to understand the evolutionary history of these strains and how antimicrobial resistance determinants have changed over time. We found that there was low diversity of S. Typhi observed in Kibera isolates with isolates grouping into 4 wgMLST clades and five genotypes. The majority (93.5%) of the isolates belonged to genotype 4.3.1; phylodynamic analysis suggest isolates of this genotype from Kibera are related to other 4.3.1 isolates from Africa and this genotype has been introduced multiple times in Kibera. This genotype in particular warrants close monitoring to inform antibiotic strategy in this population. Furthermore, concurrent detection of gene markers for MDR and quinolone resistance in some isolates raise concern about the potential emergence of extensive drug resistant (XDR) strains. Additional surveillance is needed in Kibera to monitor changing trends in resistance that may require altering clinical treatment, and to inform other preventive measures such as typhoid-conjugate vaccine introduction.

Curcumin Analogues as a Potential Drug against Antibiotic Resistant Protein, β-Lactamases and L, D-Transpeptidases Involved in Toxin Secretion in Salmonella typhi: A Computational Approach

Typhoid fever caused by the bacteria Salmonella typhi gained resistance through multidrug-resistant S. typhi strains. One of the reasons behind β-lactam antibiotic resistance is -lactamase. L, D-Transpeptidases is responsible for typhoid fever as it is involved in toxin release that results in typhoid fever in humans. A molecular modeling study of these targeted proteins was carried out by various methods, such as homology modeling, active site prediction, prediction of disease-causing regions, and by analyzing the potential inhibitory activities of curcumin analogs by targeting these proteins to overcome the antibiotic resistance. The five potent drug candidate compounds were identified to be natural ligands that can inhibit those enzymes compared to controls in our research. The binding affinity of both the Go-Y032 and NSC-43319 were found against β-lactamase was −7.8 Kcal/mol in AutoDock, whereas, in SwissDock, the binding energy was −8.15 and −8.04 Kcal/mol, respectively. On the other hand, the Cyclovalone and NSC-43319 had an equal energy of −7.60 Kcal/mol in AutoDock, whereas −7.90 and −8.01 Kcal/mol in SwissDock against L, D-Transpeptidases. After the identification of proteins, the determination of primary and secondary structures, as well as the gene producing area and homology modeling, was accomplished. The screened drug candidates were further evaluated in ADMET, and pharmacological properties along with positive drug-likeness properties were observed for these ligand molecules. However, further in vitro and in vivo experiments are required to validate these in silico data to develop novel therapeutics against antibiotic resistance.

Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a global public health concern due to increasing antimicrobial resistance (AMR). Characterization of S Typhi genomes for AMR and the evolution of different lineages, especially in countries where typhoid fever is endemic such as Bangladesh, will help public health professionals to better design and implement appropriate preventive measures. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh during 1999 to 2013 and compared those sequences with data from a recent outbreak in Pakistan reported previously by E. J. Klemm, S. Shakoor, A. J. Page, F. N. Qamar, et al. (mBio 9:e00105-18, 2018, https://doi.org/10.1128/mBio.00105-18), and a laboratory surveillance in Nepal reported previously by C. D. Britto, Z. A. Dyson, S. Duchene, M. J. Carter, et al. [PLoS Negl. Trop. Dis. 12(4):e0006408, 2018, https://doi.org/10.1371/journal.pntd.0006408]. WGS had high sensitivity and specificity for prediction of ampicillin, chloramphenicol, co-trimoxazole, and ceftriaxone AMR phenotypes but needs further improvement for prediction of ciprofloxacin resistance. We detected a new local lineage of genotype 4.3.1 (named lineage Bd) which recently diverged into a sublineage (named Bdq) containing qnr genes associated with high-level ciprofloxacin resistance. We found a ceftriaxone-resistant isolate with the bla _CTX-M-15 gene and a genotype distinct from the genotypes of extensively drug-resistant (XDR) isolates from Pakistan. This result suggests a different source and geographical origin of AMR. Genotype 4.3.1 was dominant in all three countries but formed country-specific clusters in the maximum likelihood phylogenetic tree. Thus, multiple independent genetic events leading to ciprofloxacin and ceftriaxone resistance took place in these neighboring regions of Pakistan, Nepal, and Bangladesh. These independent mutational events may enhance the risk of global spread of these highly resistant clones. A short-term global intervention plan is urgently needed.IMPORTANCE Typhoid fever, caused by Salmonella enterica serovar Typhi, is responsible for an estimated burden of approximately 17 million new episodes per year worldwide. Adequate and timely antimicrobial treatment invariably cures typhoid fever. The increasing antimicrobial resistance (AMR) of S Typhi severely limits the treatment options. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh between 1999 and 2013 and compared those sequences with data from a recent outbreak in Pakistan and a laboratory surveillance in Nepal. The analysis suggests that multiple ancestral origins of resistance against ciprofloxacin and ceftriaxone are present in three countries. Such independent genetic events and subsequent dissemination could enhance the risk of a rapid global spread of these highly resistant clones. Given the current treatment challenges, vaccination seems to be the most appropriate short-term intervention to reduce the disease burden of typhoid fever at a time of increasing AMR.

Case Fatality Rate of Enteric Fever in Endemic Countries: A Systematic Review and Meta-analysis

Enteric fever is a febrile illness, occurring mostly in Asia and Africa, which can present as a severe and possibly fatal disease. Currently, a case fatality rate (CFR) of 1% is assumed when evaluating the global burden of enteric fever. Until now, no meta-analysis has been conducted to summarize mortality from enteric fever. Therefore, we conducted a systematic review and meta-analysis to aggregate all available evidence. We estimated an overall CFR of 2.49% (95% confidence interval, 1.65%-3.75%; n = 44), and a CFR in hospitalized patients of 4.45% (2.85%-6.88%; n = 21 of 44). There was considerably heterogeneity in estimates of the CFR from individual studies. Neither age nor antimicrobial resistance were significant prognostic factors, but limited data were available for these analyses. The combined estimate of the CFR for enteric fever is higher than previously estimated, and the evaluation of prognostic factors, including antimicrobial resistance, urgently requires more data.

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

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

Salmonella typhimurium harboring plasmid expressing interleukin-12 induced attenuation of infection and protective immune responses

IL-12 is known to be an essential cytokine which appears to provide protective immunity against intracellular bacteria, such as Salmonella. In this study, we investigated the possibility of developing a vaccine using IL-12 against virulent Salmonella. We used the host defense system activated by cytokine IL-12. The highly virulent Salmonella strain (Salmonella typhimurium UK-1) was transformed with cytokine-expressing plasmids. These live, wild-type pathogens were used as vaccine strains without undergoing any other biological or genetic attenuating processes. The newly developed strains induced partial protection from infections (30-40%). Of note, the interleukin-12-transformed pathogen was safe upon immunization with low doses (10(3) cfu), induced IgG responses, and stimulated protective immune responses against Salmonella typhimurium in mice (80-100%). These results suggest that IL-12 induced attenuation of wild-type Salmonella in the host infection stage and vaccine development using the wild-type strain harboring plasmid-secreting IL-12 may be considered as an alternative process for intracellular bacterial vaccine development without the inconvenience of time-consuming attenuation processes.

Isolation and antibiotic susceptibility of Salmonella and Shigella strains isolated from children in Gaza, Palestine from 1999 to 2006

BACKGROUND AND AIM

Diarrhea and acute gastroenteritis are among the leading causes of illnesses and death in infants and children throughout the world, especially in developing countries, Globally, Salmonella and Shigella remain the major contributors to acute enteric infections and diarrhea.

METHODS

In the present study, Shigella- and Salmonella-related diarrhea was studied among 3570 children in Gaza, Palestine from January 1999 to September 2006 to determine the prevalence and the antimicrobial susceptibility of the isolates.

RESULTS

The frequency of isolation was 1.8% (65/3570) for Salmonella spp. and 0.8% (28/3570) for Shigella spp. Shigella flexneri (16/28) was the most frequently isolated Shigella species. Most of the Shigella isolates were resistant to trimethoprim-sulfamethoxazole (89%), ampicillin (79%) and chloramphenicol (46%) and most of the Salmonella isolates showed resistance to ampicillin (62%), trimethoprim-sulfamethoxazole (35%), chloramphenicol (35%) and cephalexin (26%).

CONCLUSION

These data reinforce the need for continuous monitoring of microbiological and antimicrobial surveillance and the necessity to regulate the use of antimicrobials. According to the current study, ampicillin, trimethoprim-sulfamethoxazole and chloramphenicol should not be used as empiric treatment of diarrhea in children.

Risk factors for mortality caused by nontyphoidal Salmonella sp. in children

OBJECTIVE

To identify the risk factors for mortality in extraintestinal nontyphoidal Salmonella (NTS) infections in infants and children.

METHODS

We performed a retrospective analysis of 107 patients with at least one nonfecal culture for NTS seen from January 1988 to December 1995.

RESULTS

The median age was 12 (range 1-216) months. Malnutrition was found in 55 patients (51%), and 22 (20%) displayed severe features (weight loss >40%). Seventy-two patients (67%) had previously been hospitalized, and 59 (55%) had received antibiotics during the month before admission. Fever (85%) and diarrhea (56%) were the most frequent clinical manifestations. Nineteen children (18%) had leukopenia. Forty-nine patients (46%) had only bacteremia, 33 (31%) bacteremia with focal infections, and 25 (23%) focal infections with negative blood cultures. Forty-seven strains (44%) were multiresistant, and 40 of them were nosocomially acquired. Eight patients (7%) had received inappropriate antibiotic treatment, and two of them died. Thirteen (12%) children died. Age, underlying disease, previous admission, previous antibiotic therapy, type of infection, susceptibility of the strains and inappropriate antibiotic treatment were not statistically significant risk factors for mortality. A logistic regression analysis selected the following variables as independently influencing outcome: malnutrition (P<0.01), leukopenia (P<0.002) and presence of diarrhea (P<0.02).

CONCLUSIONS

Children with extraintestinal infections by NTS with leukopenia, malnutrition and presence of diarrhea have a higher risk of death.

Use of commercially available rapid chloramphenicol acetyltransferase test to detect resistance in Salmonella species

Chloramphenicol resistance among Salmonella spp. has important public health and clinical implications, especially in areas of the world where these strains are endemic. The availability of rapid and sensitive screening methods for detection of antibiotic resistance is important. Therefore, we tested 33 strains of Salmonella for chloramphenicol acetyltransferase (CAT) activity using two rapid techniques. Evaluation of a 1-h tube method and a 30-min commercial disk procedure demonstrated that they are as accurate as standardized susceptibility techniques. Both the 1-h tube and 30-min disk methods detected CAT enzymatic activity produced by one CAT gene copy per cell.

Third-generation cephalosporins. A plea to save them for specific infections

Third-generation cephalosporins are indicated for treatment of sexually transmitted diseases, resistant salmonellosis, and infections in the febrile leukopenic host. The practicing physician must weigh the expanding role of these agents against their limitations. Some potential problems include bleeding (confined to the use of moxalactam [Moxam] or cefoperazone [Cefobid]), a reaction like that to disulfiram (Antabuse) when combined with alcohol (also confined to the use of moxalactam or cefoperazone), and superinfection. A prolonged course of treatment entails significant expense. Further evaluation and clinical experience is necessary before use of third-generation cephalosporins for some of the newer indications (eg, late stages of Lyme disease, neurosyphilis) becomes routine medical practice.

Chloramphenicol and tetracyclines

Tetracyclines have a broad range of clinical usefulness because of their broad antimicrobial spectrum of activity. For most routine gram positive and gram negative infections, alternative agents are available, but for Chlamydiae, Rickettsiae, Brucella, and Borrelia they still remain agents of choice. To some extent, gastrointestinal intolerance and inability to use these agents in patients with renal dysfunction have been overcome by the availability of doxycycline. Phototoxicity is a problem with this agent, however. Tetracycline is still useful as a sclerogenic agent for malignant effusions, and demeclocycline often is an agent of choice in therapy of inappropriate antidiuretic hormone secretion.

Ceftriaxone treatment of multidrug-resistant Salmonella osteomyelitis

Empiric treatment of serious Salmonella infections has been complicated by the emergence of strains resistant to multiple antimicrobial agents, including ampicillin, chloramphenicol, and trimethoprim/sulfamethoxazole. Recent reports suggest that the third-generation cephalosporins may be effective therapy for Salmonella infections. This report describes a case of antibiotic-resistant Salmonella heidelberg prosthetic hip infection successfully treated with prosthesis removal and once-daily ceftriaxone. Tube dilution sensitivity testing of the organism demonstrated minimal inhibitory and minimal bactericidal concentrations of 0.12 microgram/ml. Serum bactericidal activity, 30 minutes after infusion, was inhibitory and bactericidal at 1:512. It is concluded that the favorable preliminary results reported in the literature and the outcome in this patient suggest that the third-generation cephalosporins may be effective therapy for Salmonella infections and should undergo clinical trials.